From 4d88687ba7f1244ef1b8e9703ce190708c599efc Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Thu, 5 May 2016 17:09:01 +0100 Subject: [PATCH 01/13] Removes needless typechecks. --- ga4gh/datamodel/references.py | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/ga4gh/datamodel/references.py b/ga4gh/datamodel/references.py index e16ee216d..7be8e296c 100644 --- a/ga4gh/datamodel/references.py +++ b/ga4gh/datamodel/references.py @@ -184,10 +184,7 @@ def getNcbiTaxonId(self): which do not belong to the modeled species, e.g. EBV in a human reference genome. """ - if self._ncbiTaxonId is not None: - return int(self._ncbiTaxonId) - else: - return None + return self._ncbiTaxonId def toProtocolElement(self): """ @@ -308,10 +305,7 @@ def getNcbiTaxonId(self): which do not belong to the modeled species, e.g. EBV in a human reference genome. """ - if self._ncbiTaxonId is not None: - return int(self._ncbiTaxonId) - else: - return None + return self._ncbiTaxonId def getMd5Checksum(self): """ @@ -460,7 +454,7 @@ def populateFromRow(self, row): self._assemblyId = row[b'assemblyId'] self._isDerived = bool(row[b'isDerived']) self._md5checksum = row[b'md5checksum'] - self.setNcbiTaxonId(row[b'ncbiTaxonId']) + self._ncbiTaxonId = row[b'ncbiTaxonId'] self._sourceAccessions = json.loads(row[b'sourceAccessions']) self._sourceUri = row[b'sourceUri'] From d51774a41cc55ab1e6141398989671e5fec02d2c Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Fri, 6 May 2016 16:33:01 +0100 Subject: [PATCH 02/13] Added sphinx-argparse based repo manager docs. --- docs/conf.py | 1 + docs/configuration.rst | 127 ++++++++++++++++++++++++++++++++++++++--- ga4gh/cli.py | 7 +++ requirements.txt | 3 + 4 files changed, 131 insertions(+), 7 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index e9faced93..5293f27b7 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -35,6 +35,7 @@ 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', + 'sphinxarg.ext', ] # Add any paths that contain templates here, relative to this directory. diff --git a/docs/configuration.rst b/docs/configuration.rst index 6f40be9c7..a4b414e86 100644 --- a/docs/configuration.rst +++ b/docs/configuration.rst @@ -20,22 +20,29 @@ to the administrator. The repository manager provides an administration interface to the the data repository. It can be accessed via ``ga4gh_repo`` (or ``python repo_dev.py`` if -developing). Following are descriptions of the commands that the repo manager -exposes. +developing). The ``ga4gh_repo`` commands provides a suite of commands to +help administer a GA4GH data repository. +++++++ init +++++++ -Initializes a data repository at the path provided. All of the other -commands require a data repository file as an argument, so this will likely be -the first command you run. +.. todo:: Description of init. + +.. argparse:: + :module: ga4gh.cli + :func: getRepoManagerParser + :prog: ga4gh_repo + :path: init + :nodefault: + + +**Examples:** .. code-block:: bash $ ga4gh_repo init path/to/repo.db - +++++++ verify +++++++ @@ -43,6 +50,15 @@ verify Performs some consistency checks on the given data repository to ensure it is well-formed. +.. argparse:: + :module: ga4gh.cli + :func: getRepoManagerParser + :prog: ga4gh_repo + :path: verify + :nodefault: + +**Examples:** + .. code-block:: bash $ ga4gh_repo verify path/to/repo.db @@ -53,6 +69,15 @@ list Lists the contents of the given data repository. +.. argparse:: + :module: ga4gh.cli + :func: getRepoManagerParser + :prog: ga4gh_repo + :path: list + :nodefault: + +**Examples:** + .. code-block:: bash $ ga4gh_repo list path/to/repo.db @@ -63,6 +88,15 @@ add-dataset Creates a dataset in the given repository with a given name. +.. argparse:: + :module: ga4gh.cli + :func: getRepoManagerParser + :prog: ga4gh_repo + :path: add-dataset + :nodefault: + +**Examples:** + .. code-block:: bash $ ga4gh_repo add-dataset path/to/repo.db aDataset @@ -73,6 +107,15 @@ remove-dataset Destroys a dataset in the given repository with a given name. +.. argparse:: + :module: ga4gh.cli + :func: getRepoManagerParser + :prog: ga4gh_repo + :path: remove-dataset + :nodefault: + +**Examples:** + .. code-block:: bash $ ga4gh_repo remove-dataset path/to/repo.db aDataset @@ -83,6 +126,15 @@ add-referenceset Adds a given reference set file to a given data repository. +.. argparse:: + :module: ga4gh.cli + :func: getRepoManagerParser + :prog: ga4gh_repo + :path: add-referenceset + :nodefault: + +**Examples:** + .. code-block:: bash $ ga4gh_repo add-referenceset path/to/repo.db path/to/aReferenceSet.fa.gz @@ -93,6 +145,15 @@ remove-referenceset Removes a given reference set from a given data repository. +.. argparse:: + :module: ga4gh.cli + :func: getRepoManagerParser + :prog: ga4gh_repo + :path: remove-referenceset + :nodefault: + +**Examples:** + .. code-block:: bash $ ga4gh_repo remove-referenceset path/to/repo.db aReferenceSet @@ -105,6 +166,14 @@ Adds an Ontology Map, which maps identifiers to ontology terms, to the repository. Ontology maps are tab delimited files with an identifier/term pair per row. +.. argparse:: + :module: ga4gh.cli + :func: getRepoManagerParser + :prog: ga4gh_repo + :path: add-ontology + :nodefault: + +**Examples:** .. code-block:: bash @@ -116,11 +185,19 @@ remove-ontology Removes a given Ontology Map from a given data repository. +.. argparse:: + :module: ga4gh.cli + :func: getRepoManagerParser + :prog: ga4gh_repo + :path: remove-ontology + :nodefault: + +**Examples:** + .. code-block:: bash $ ga4gh_repo remove-ontology path/to/repo.db aOntoMap - +++++++++++++++++ add-readgroupset +++++++++++++++++ @@ -128,6 +205,15 @@ add-readgroupset Adds a given read group set file to a given data repository and dataset. The file must have the extension ``.bam``. +.. argparse:: + :module: ga4gh.cli + :func: getRepoManagerParser + :prog: ga4gh_repo + :path: add-readgroupset + :nodefault: + +**Examples:** + .. code-block:: bash $ ga4gh_repo add-readgroupset path/to/repo.db aDataset path/to/aReadGroupSet.bam @@ -138,6 +224,15 @@ remove-readgroupset Removes a read group set from a given data repository and dataset. +.. argparse:: + :module: ga4gh.cli + :func: getRepoManagerParser + :prog: ga4gh_repo + :path: remove-readgroupset + :nodefault: + +**Examples:** + .. code-block:: bash $ ga4gh_repo remove-readgroupset path/to/repo.db aDataset aReadGroupSet @@ -150,6 +245,15 @@ Adds a variant set directory to a given data repository and dataset. The directory should contain file(s) with extension ``.vcf.gz``. If a variant set is annotated it will be added as both a variant set and a variant annotation set. +.. argparse:: + :module: ga4gh.cli + :func: getRepoManagerParser + :prog: ga4gh_repo + :path: add-variantset + :nodefault: + +**Examples:** + .. code-block:: bash $ ga4gh_repo add-variantset path/to/repo.db aDataset path/to/aVariantSet @@ -160,6 +264,15 @@ remove-variantset Removes a variant set from a given data repository and dataset. +.. argparse:: + :module: ga4gh.cli + :func: getRepoManagerParser + :prog: ga4gh_repo + :path: remove-variantset + :nodefault: + +**Examples:** + .. code-block:: bash $ ga4gh_repo remove-variantset path/to/repo.db aDataset aVariantSet diff --git a/ga4gh/cli.py b/ga4gh/cli.py index f3a675efa..4a8454f00 100644 --- a/ga4gh/cli.py +++ b/ga4gh/cli.py @@ -2110,6 +2110,13 @@ def runCommand(cls, args): runMethod() +def getRepoManagerParser(): + """ + Used by sphinx.argparse. + """ + return RepoManager.getParser() + + def repoExitError(message): """ Exits the repo manager with error status. diff --git a/requirements.txt b/requirements.txt index 7a2262a10..92dc0d32c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -43,3 +43,6 @@ requests==2.7.0 oic==0.7.6 pyOpenSSL==0.15.1 lxml==3.4.4 + +# We need sphinx-argparse to build on readthedocs. +sphinx-argparse==0.1.15 From b5d7824b1c652421394a95ac5cc8b6e18304086a Mon Sep 17 00:00:00 2001 From: Danny Colligan Date: Tue, 3 May 2016 10:20:11 -0400 Subject: [PATCH 03/13] Test for incorrect data file indexes Issue #1180 --- ga4gh/datamodel/reads.py | 9 +++- tests/paths.py | 20 +++++++-- tests/unit/test_repo_manager.py | 78 +++++++++++++++++++++++++++++++++ 3 files changed, 101 insertions(+), 6 deletions(-) diff --git a/ga4gh/datamodel/reads.py b/ga4gh/datamodel/reads.py index 3883601e8..bd126ff52 100644 --- a/ga4gh/datamodel/reads.py +++ b/ga4gh/datamodel/reads.py @@ -211,8 +211,13 @@ def openFile(self, dataFile): # not throw an error if the index is missing. if not os.path.exists(self._indexFile): raise exceptions.FileOpenFailedException(self._indexFile) - return pysam.AlignmentFile( - self._dataUrl, filepath_index=self._indexFile) + try: + return pysam.AlignmentFile( + self._dataUrl, filepath_index=self._indexFile) + except IOError as exception: + # IOError thrown when the index file passed in is not actually + # an index file... may also happen in other cases? + raise exceptions.DataException(exception.message) class AbstractReadGroupSet(datamodel.DatamodelObject): diff --git a/tests/paths.py b/tests/paths.py index 55988ce60..11e3e54c1 100644 --- a/tests/paths.py +++ b/tests/paths.py @@ -25,6 +25,14 @@ testDataDir, 'datasets/dataset1/variants/1kgPhase1') vcfDirPath2 = os.path.join( testDataDir, 'datasets/dataset1/variants/1kgPhase3') +vcfPath1 = os.path.join( + vcfDirPath, 'chr1.vcf.gz') +vcfPath2 = os.path.join( + vcfDirPath, 'chr2.vcf.gz') +vcfIndexPath1 = os.path.join( + vcfDirPath, 'chr1.vcf.gz.tbi') +vcfIndexPath2 = os.path.join( + vcfDirPath, 'chr2.vcf.gz.tbi') ontologyName = "sequence_ontology" @@ -33,12 +41,16 @@ # reads readGroupSetName = 'chr17.1-250' +bamDir = os.path.join( + testDataDir, 'datasets/dataset1/reads') bamPath = os.path.join( - testDataDir, 'datasets/dataset1/reads/chr17.1-250.bam') + bamDir, 'chr17.1-250.bam') bamPath2 = os.path.join( - testDataDir, - 'datasets/dataset1/reads/' - 'wgEncodeUwRepliSeqBg02esG1bAlnRep1_sample.bam') + bamDir, 'wgEncodeUwRepliSeqBg02esG1bAlnRep1_sample.bam') +bamIndexPath = os.path.join( + bamDir, 'chr17.1-250.bam.bai') +bamIndexPath2 = os.path.join( + bamDir, 'wgEncodeUwRepliSeqBg02esG1bAlnRep1_sample.bam.bai') # sequence annotations featureSetName = 'gencodeV21Set1' diff --git a/tests/unit/test_repo_manager.py b/tests/unit/test_repo_manager.py index 7dbdf83ef..adb2c0b04 100644 --- a/tests/unit/test_repo_manager.py +++ b/tests/unit/test_repo_manager.py @@ -14,6 +14,7 @@ import ga4gh.exceptions as exceptions import ga4gh.datarepo as datarepo import ga4gh.cli as cli +import ga4gh.datamodel as datamodel import tests.paths as paths @@ -681,3 +682,80 @@ def testFeatureSetDelete(self): self.readDatasets() self.assertEqual(len(self.dataset1.getFeatureSets()), 0) self.assertEqual(len(self.dataset2.getFeatureSets()), 1) + + +class TestInvalidVariantIndexFile(AbstractRepoManagerTest): + """ + Test that the repo manager throws exceptions when invalid index + files are provided for vcf files. + """ + def setUp(self): + super(TestInvalidVariantIndexFile, self).setUp() + self.init() + self.addDataset() + self.addReferenceSet() + + def _testWithIndexPath(self, indexPath): + cmd = ( + "add-variantset {} {} {} --referenceSetName={} -I {}").format( + self._repoPath, self._datasetName, paths.vcfPath1, + self._referenceSetName, indexPath) + with self.assertRaises(exceptions.NotIndexedException): + self.runCommand(cmd) + + def testNonexistentIndexFile(self): + indexPath = '/path/does/not/exist' + self._testWithIndexPath(indexPath) + + def testIndexFileNotAnIndexFile(self): + indexPath = paths.vcfPath2 # not an index file + self._testWithIndexPath(indexPath) + + @unittest.skip("Skipping until we can detect incorrect indexes") + def testWrongIndexFile(self): + indexPath = paths.vcfIndexPath2 # incorrect index + self._testWithIndexPath(indexPath) + + +class TestInvalidReadGroupSetIndexFile(AbstractRepoManagerTest): + """ + Test that the repo manager throws exceptions when invalid index + files are provided for bam files. + """ + @classmethod + def setUpClass(cls): + # clear the file handle cache because if the data file we are + # testing with an invalid index is already in the cache, the + # index will not be opened during the test; without this line + # the below tests will succeed when the test class is run but + # fail when the file's tests are run + datamodel.fileHandleCache = datamodel.PysamFileHandleCache() + + def setUp(self): + super(TestInvalidReadGroupSetIndexFile, self).setUp() + self.init() + self.addDataset() + self.addReferenceSet() + + def _testWithIndexPath(self, indexPath): + cmd = ( + "add-readgroupset {} {} {} --referenceSetName={} " + "-I {}").format( + self._repoPath, self._datasetName, paths.bamPath, + self._referenceSetName, indexPath) + self.runCommand(cmd) + + def testNonexistentIndexFile(self): + indexPath = '/path/does/not/exist' + with self.assertRaises(exceptions.FileOpenFailedException): + self._testWithIndexPath(indexPath) + + def testIndexFileNotAnIndexFile(self): + indexPath = paths.bamPath2 # not an index file + with self.assertRaises(exceptions.DataException): + self._testWithIndexPath(indexPath) + + @unittest.skip("Skipping until we can detect incorrect indexes") + def testWrongIndexFile(self): + indexPath = paths.bamIndexPath2 # incorrect index + self._testWithIndexPath(indexPath) From 0482b1f572f4cbb18fcd05573d17dff8e10af0a5 Mon Sep 17 00:00:00 2001 From: Maciek Smuga-Otto Date: Thu, 5 May 2016 09:03:25 -0700 Subject: [PATCH 04/13] Docker container deployment redo. --- .dockerignore | 2 +- Dockerfile | 66 +++++++++++++++---- deploy/001-ga4gh.conf | 14 ++++ deploy/application.wsgi | 2 +- deploy/config.py | 13 +--- .../variants/centos-demo-noapache/Dockerfile | 52 --------------- deploy/variants/demo/Dockerfile | 22 ------- deploy/variants/ubuntu-demo-apache/Dockerfile | 49 -------------- 8 files changed, 70 insertions(+), 150 deletions(-) create mode 100644 deploy/001-ga4gh.conf delete mode 100644 deploy/variants/centos-demo-noapache/Dockerfile delete mode 100644 deploy/variants/demo/Dockerfile delete mode 100644 deploy/variants/ubuntu-demo-apache/Dockerfile diff --git a/.dockerignore b/.dockerignore index 8d6a40cd3..e876a5324 100644 --- a/.dockerignore +++ b/.dockerignore @@ -1,4 +1,4 @@ Dockerfile -.git .dockerignore +./build *.swp diff --git a/Dockerfile b/Dockerfile index 1f78e58e4..032dec3af 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,21 +1,61 @@ ############################################################ ## Dockerfile to build the ga4gh server on mod_wsgi-express ## Configurable to use a local dataset -## Based on mod_wsgi-docker -## Results of this build are available from Dockerhub as afirth/ga4gh_server_apache:prod ############################################################ -FROM grahamdumpleton/mod-wsgi-docker:python-2.7-onbuild +FROM ubuntu -# File Author / Maintainer -MAINTAINER Alastair Firth +# Originally created by Steve Hershman GitHub @hershman +# previously maintained by Alastair Firth +# currently maintained by Maciek Smuga-Otto at UCSC Genomics Institute +MAINTAINER Maciek Smuga-Otto -# Place the config, if an existing config is not in place -ADD deploy/config.py /app/ga4gh/docker_config.py -RUN cp --no-clobber /app/ga4gh/docker_config.py /app/ga4gh/config.py +# Update the sources list +RUN apt-get update -# Pass '-e GA4GH_DATA_SOURCE=/container/data/path' and '-v /host/data/path:/container/data/path:ro' to docker run to mount local data -# See docs for more info +# Install packages +RUN apt-get install -y tar git curl wget dialog net-tools build-essential \ + python python-dev python-distribute python-pip zlib1g-dev \ + apache2 libapache2-mod-wsgi libxslt1-dev libffi-dev libssl-dev -CMD [ "--working-directory", "ga4gh", \ - "--log-to-terminal", \ - "ga4gh/application.wsgi" ] +# Enable wsgi module +RUN a2enmod wsgi + +# Create cache directories +RUN mkdir /var/cache/apache2/python-egg-cache && \ + chown www-data:www-data /var/cache/apache2/python-egg-cache/ + +# build the GA4GH server +RUN mkdir -p /srv/ga4gh/server +WORKDIR /srv/ga4gh/server + +# Configure the python requirements +# Do this as a separate step prior to the build so that changes +# to the GA4GH Server codebase do not trigger a full rebuild of the +# pip requirements. +COPY requirements.txt /srv/ga4gh/server/ +RUN pip install -r requirements.txt + +# Install the code +COPY . /srv/ga4gh/server/ +RUN python setup.py install + +# Write new apache config +COPY deploy/001-ga4gh.conf /etc/apache2/sites-available/001-ga4gh.conf + +# Write application.wsgi +COPY deploy/application.wsgi /srv/ga4gh/application.wsgi +COPY deploy/config.py /srv/ga4gh/config.py + +# Configure apache to serve GA4GH site +WORKDIR /etc/apache2/sites-enabled +RUN rm -f 000-default.conf && ln -s /etc/apache2/sites-available/001-ga4gh.conf 001-ga4gh.conf + +# Open port 80 for HTTP +EXPOSE 80 + +# Prepare container for deployment +# The directory that the user will land in when executing an interactive shell +WORKDIR /srv/ga4gh/server + +# Default action: Bring up a webserver instance to run as a daemon +CMD ["/usr/sbin/apache2ctl", "-D", "FOREGROUND"] diff --git a/deploy/001-ga4gh.conf b/deploy/001-ga4gh.conf new file mode 100644 index 000000000..bde337d20 --- /dev/null +++ b/deploy/001-ga4gh.conf @@ -0,0 +1,14 @@ + + ServerAdmin webmaster@localhost + DocumentRoot /var/www/html + ErrorLog ${APACHE_LOG_DIR}/error.log + CustomLog ${APACHE_LOG_DIR}/access.log combined + WSGIDaemonProcess ga4gh python-eggs=/var/cache/apache2/python-egg-cache \ + processes=10 threads=1 + WSGIScriptAlias /ga4gh /srv/ga4gh/application.wsgi + + WSGIProcessGroup ga4gh + WSGIApplicationGroup %{GLOBAL} + Require all granted + + \ No newline at end of file diff --git a/deploy/application.wsgi b/deploy/application.wsgi index 71e006671..f834f546c 100644 --- a/deploy/application.wsgi +++ b/deploy/application.wsgi @@ -2,4 +2,4 @@ from ga4gh.frontend import app as application import ga4gh.frontend as frontend -frontend.configure("/app/ga4gh/config.py") +frontend.configure("/srv/ga4gh/config.py") diff --git a/deploy/config.py b/deploy/config.py index ca836217e..335320a65 100644 --- a/deploy/config.py +++ b/deploy/config.py @@ -1,14 +1,3 @@ -# Configuration file for server, including Flask, see configuration documentation -# for details -# This file needs to be copied to /app/ga4gh/config.py by default import os - -#TODO this logic could move to frontend.configure() or BaseConfig -# For docker, if/when a default is set in serverconfig.py, run -v /localdata:/default-path -# If the env variable GA4GH_DATA_SOURCE is set, use that path. Otherwise, use the default path -DATA_SOURCE = os.getenv('GA4GH_DATA_SOURCE', "/ga4gh-example-data") - -# If the env variable GA4GH_DEBUG is set, use that. Otherwise, use the empty string (False) -# Enable with True. -# WARNING: this enables Flask debugging and is insecure. +DATA_SOURCE = os.getenv('GA4GH_DATA_SOURCE', "/data/repo.db") DEBUG = os.getenv('GA4GH_DEBUG', "") diff --git a/deploy/variants/centos-demo-noapache/Dockerfile b/deploy/variants/centos-demo-noapache/Dockerfile deleted file mode 100644 index 327c3904e..000000000 --- a/deploy/variants/centos-demo-noapache/Dockerfile +++ /dev/null @@ -1,52 +0,0 @@ -############################################################ -# Dockerfile to build the ga4gh demo -# Based on CentOS7 -############################################################ -FROM centos:7 - -# File Author / Maintainer -MAINTAINER Alastair Firth - - -################## BEGIN INSTALLATION ###################### -# Install ga4gh demo (non-apache) -# NOT for production use -# Ref: http://ga4gh-reference-implementation.readthedocs.org/en/stable/demo.html#demo - -#TODO add yum key - -# Install prereqs -RUN yum -y update && yum -y install \ - curl \ - git \ - python-backports \ - python-backports-ssl_match_hostname \ - python-devel \ - python-setuptools \ - tar \ - wget \ - zlib-devel -RUN yum -y groupinstall "Development Tools" -RUN yum clean all - -# Create the default data directory -RUN mkdir -p /data/ -WORKDIR /data/ - -#wget the example data -RUN wget https://github.com/ga4gh/server/releases/download/data/ga4gh-example-data-v3.2.tar -nv -O - | tar -x - -# Install setuptools and pip -RUN easy_install setuptools -RUN easy_install pip - -# Install ga4gh with pip -RUN pip install ga4gh --pre - -##################### INSTALLATION END ##################### - -# Expose the default port -EXPOSE 8000 - -ENTRYPOINT ["ga4gh_server"] - diff --git a/deploy/variants/demo/Dockerfile b/deploy/variants/demo/Dockerfile deleted file mode 100644 index 468e2cbd4..000000000 --- a/deploy/variants/demo/Dockerfile +++ /dev/null @@ -1,22 +0,0 @@ -############################################################ -## Dockerfile to build the ga4gh server on mod_wsgi-express -## Downloads and uses the demo dataset -## Based on the prod build -## Results of this build are available from Dockerhub as afirth/ga4gh_server_apache:demo -############################################################ -FROM afirth/ga4gh_server_apache:prod - -# File Author / Maintainer -MAINTAINER Alastair Firth - -# Create the data directory -RUN mkdir -p /data/ - -# Fetch the example data and extract -# On some terminals the progress bar freezes during build -WORKDIR /data/ -RUN curl https://github.com/ga4gh/server/releases/download/data/ga4gh-example-data-v3.2.tar | tar -x -WORKDIR / - -# Set the dataset location explicitly -ENV GA4GH_DATA_SOURCE=/data/ga4gh-example-data diff --git a/deploy/variants/ubuntu-demo-apache/Dockerfile b/deploy/variants/ubuntu-demo-apache/Dockerfile deleted file mode 100644 index 9bd260bab..000000000 --- a/deploy/variants/ubuntu-demo-apache/Dockerfile +++ /dev/null @@ -1,49 +0,0 @@ -# Base image -FROM ubuntu - -# Originally created by Steve Hershman GitHub @hershman -MAINTAINER Steve Hershman - -# Update the sources list -RUN apt-get update - -# Install packages -RUN apt-get install -y tar git curl nano wget dialog net-tools build-essential python python-dev python-distribute python-pip zlib1g-dev python-virtualenv apache2 libapache2-mod-wsgi - -# Enable wsgi module -RUN a2enmod wsgi - -# Create cache directories -RUN mkdir /var/cache/apache2/python-egg-cache && \ - chown www-data:www-data /var/cache/apache2/python-egg-cache/ - -# Set up GA4GH server -RUN mkdir /srv/ga4gh -WORKDIR /srv/ga4gh -RUN virtualenv ga4gh-server-env -RUN /bin/bash -c "source ga4gh-server-env/bin/activate" -RUN pip install --pre ga4gh - -# Install relevant sample data -RUN wget https://github.com/ga4gh/server/releases/download/data/ga4gh-example-data-v3.2.tar && \ - tar -xvf ga4gh-example-data-v3.2.tar - -# Write application.wsgi -RUN echo "from ga4gh.frontend import app as application\nimport ga4gh.frontend as frontend\nfrontend.configure(\"/srv/ga4gh/config.py\")" > application.wsgi - -# Write config.py -RUN echo "DATA_SOURCE = \"/srv/ga4gh/ga4gh-example-data\"" > config.py - -# Write new apache config -WORKDIR /etc/apache2/sites-available -RUN echo "\n ServerAdmin webmaster@localhost\n DocumentRoot /var/www/html\n ErrorLog ${APACHE_LOG_DIR}/error.log\n CustomLog ${APACHE_LOG_DIR}/access.log combined\n WSGIDaemonProcess ga4gh python-path=/srv/ga4gh/ga4gh-server-env/lib/python2.7/site-packages python-eggs=/var/cache/apache2/python-egg-cache\n WSGIScriptAlias /ga4gh /srv/ga4gh/application.wsgi\n \n WSGIProcessGroup ga4gh\n WSGIApplicationGroup %{GLOBAL}\n Require all granted\n \n" > 001-ga4gh.conf - -# Configure apache to serve GA4GH site -WORKDIR /etc/apache2/sites-enabled -RUN rm -f 000-default.conf && ln -s /etc/apache2/sites-available/001-ga4gh.conf 001-ga4gh.conf - -# Open port 80 -EXPOSE 80 - -# Start server when container starts -CMD ["/usr/sbin/apache2ctl", "-D", "FOREGROUND"] From 6c9ed552389a641fb0c62a67b2e05b41a57d61e3 Mon Sep 17 00:00:00 2001 From: Kevin Osborn Date: Wed, 18 May 2016 15:10:14 -0700 Subject: [PATCH 05/13] basic instructions for profiling the ref server --- docs/development.rst | 4 ++- docs/ref_server_profiling.rst | 49 +++++++++++++++++++++++++++++++++++ 2 files changed, 52 insertions(+), 1 deletion(-) create mode 100644 docs/ref_server_profiling.rst diff --git a/docs/development.rst b/docs/development.rst index 15fd74c71..8aa2c8c9a 100644 --- a/docs/development.rst +++ b/docs/development.rst @@ -303,8 +303,10 @@ server against this using:: $ python server_dev.py -c LocalOidConfig +For tips on how to profile the performance of the server see :ref:`ref_server_profiling` + ************ -Organisation +Organization ************ The code for the project is held in the ``ga4gh`` package, which corresponds to diff --git a/docs/ref_server_profiling.rst b/docs/ref_server_profiling.rst new file mode 100644 index 000000000..af77c1b17 --- /dev/null +++ b/docs/ref_server_profiling.rst @@ -0,0 +1,49 @@ +:orphan: + +.. _ref_server_profiling: + +------------------------------ +Profiling the Reference Server +------------------------------ + +We have learned a lot about profiling the code of the reference server, +but there are some tricks to getting meaningful output. This section spells out +a configuration that seems to work. As one can imagine, profiling a python program +running under Apache is very difficult. It is better to run the server from the command +line when using the python profiler. The other barrier to profiling +that we found was caused by the reloader, so we had to tell python to not use the +reloader. Finally, we found it best to disable the flask debugger (which is on +by default if you run the server from the command line) because the debugger +will cause every error message to be printed to the screen, which is in addition +to the printout we already get from our exception handler. Leaving the debugger on +will result in all exceptions print out twice. + +******************** +Running the profile: +******************** + +.. code-block:: bash + + python -m cProfile -s cumulative -o profile.out ko-server/server_dev.py -H 100.70.26.73 --dont-use-reloader --config-file /srv/ga4gh/config.py + +****************************** +Evaluating the profile output: +****************************** + +If you don't use teh -o {output file} option then all output from the profiler +runs to stdout and will be sorted with the function that takes the most +cumulative time at the top of the list. You can review the text output +manually, but a beet method is to use the -o option and then review the +output using a nifty little program we found that interactively browses +the function list. It provides a way to change the sorting and it also links +the functions together so that you can follow the called and caller stacks. +This is pretty handy. You can install and run it like this: + +.. code-block:: bash + + sudo pip install cprofilev + cprofilev -f profile.out -a 100.70.26.73 + +Note that it takes the '''profile.out''' file that was generated by the cProfile +run. To review the output simply point your browser to http://localhost:4000 + From 00d6b7962019a86d77e549f4be6d49436e602446 Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Tue, 17 May 2016 17:39:24 +0100 Subject: [PATCH 06/13] Expands repository admin docs with details and egs. --- docs/configuration.rst | 317 ++++++++++++++++++++++++++++++----------- ga4gh/cli.py | 26 ++-- tests/unit/test_cli.py | 63 ++++---- 3 files changed, 279 insertions(+), 127 deletions(-) diff --git a/docs/configuration.rst b/docs/configuration.rst index a4b414e86..7302908c5 100644 --- a/docs/configuration.rst +++ b/docs/configuration.rst @@ -11,23 +11,36 @@ the `Data repository`_ and the `Configuration file`_. Data repository --------------- -The repository in the GA4GH reference server defines how your data is organised. The -repository itself is a SQLite database, which contains information about your -datasets, reference sets and so on. Bulk data (such as variants and reads) -is not stored in database, but instead accessed directly from the primary -data files at run time. The locations of these data files is entirely up -to the administrator. - -The repository manager provides an administration interface to the the data -repository. It can be accessed via ``ga4gh_repo`` (or ``python repo_dev.py`` if -developing). The ``ga4gh_repo`` commands provides a suite of commands to -help administer a GA4GH data repository. +Each GA4GH server represents a repository of information. This repository +consists of the reference sets, datasets, readgroup sets, variant sets etc. in +the server's data model and may contain data from many different unrelated +projects. The server administrator defines and manages this repository using +the ``ga4gh_repo`` command line interface, which provides commands to manage +all of the objects represented by a GA4GH server. + +The information about the objects in the GA4GH data model is stored in an SQL +database, called the "registry DB" or "registry". The registry DB does not +contain the raw bulk data but rather "registers" the information about where +the server can find this information and some metadata about the object in +question. For example, if we have a variant set that is backed by a single VCF +file, the registry DB will contain the path to this file as well as the name of +the variant set, the reference set it is defined by, and other information +necessary to implement the GA4GH protocol. This registry architecture allows us +a lot of flexibility in the sources of data that we can use. + +.. todo:: Architecture diagram showing the registry DB, the server, the + data container objects (like HtslibVariantSet, etc), etc. + +.. todo:: Explain how the datamodel is structured and how names are + used as local identifiers. +++++++ init +++++++ -.. todo:: Description of init. +The ``init`` command initialises a new registry DB at a given +file path. This is the first command that must be issued +when creating a new GA4GH repository. .. argparse:: :module: ga4gh.cli @@ -41,14 +54,23 @@ init .. code-block:: bash - $ ga4gh_repo init path/to/repo.db + $ ga4gh_repo init registry.db +++++++ verify +++++++ -Performs some consistency checks on the given data repository to ensure it is -well-formed. +The ``verify`` command is used to check that the integrity of the +data in a repository. The command checks each container object in turn +and ensures that it can read data from it. Read errors can occur for +any number of reasons (for example, a VCF file may have been moved +to another location since it was added to the registry), and the +``verify`` command allows an administrator to check that all is +well in their repository. + +.. note:: The ``verify`` command is under development and will + be much more sophisticated in the future. In particular, the output + of this command should improve considerably in the near future. .. argparse:: :module: ga4gh.cli @@ -61,13 +83,19 @@ well-formed. .. code-block:: bash - $ ga4gh_repo verify path/to/repo.db + $ ga4gh_repo verify registry.db +++++++ list +++++++ -Lists the contents of the given data repository. +The ``list`` command is used to print the contents of a repository +to the screen. It is an essential tool for administrators to +understand the structure of the repository that they are managing. + +.. note:: The ``list`` command is under development and will + be much more sophisticated in the future. In particular, the output + of this command should improve considerably in the near future. .. argparse:: :module: ga4gh.cli @@ -80,13 +108,15 @@ Lists the contents of the given data repository. .. code-block:: bash - $ ga4gh_repo list path/to/repo.db + $ ga4gh_repo list registry.db +++++++++++ add-dataset +++++++++++ -Creates a dataset in the given repository with a given name. +Creates a new dataset in a repository. A dataset is an arbitrary collection +of ReadGroupSets, VariantSets, VariantAnnotationSets and FeatureSets. Each +dataset has a name, which is used to identify it in the repository manager. .. argparse:: :module: ga4gh.cli @@ -99,183 +129,302 @@ Creates a dataset in the given repository with a given name. .. code-block:: bash - $ ga4gh_repo add-dataset path/to/repo.db aDataset + $ ga4gh_repo add-dataset registry.db 1kg -d 'Example dataset using 1000 genomes data' -+++++++++++++++ -remove-dataset -+++++++++++++++ +Adds the dataset with the name ``1kg`` and description +``'Example dataset using 1000 genomes data'`` to the +registry database ``registry.db``. + +++++++++++++++++ +add-referenceset +++++++++++++++++ -Destroys a dataset in the given repository with a given name. +Adds a reference set derived from a FASTA file to a repository. Each +record in the FASTA file will correspond to a Reference in the new +ReferenceSet. The input FASTA file must be compressed with ``bgzip`` +and indexed using ``samtools faidx``. Each ReferenceSet contains a +number of metadata values (.e.g. ``ncbiTaxonId``) which can be set +using command line options. .. argparse:: :module: ga4gh.cli :func: getRepoManagerParser :prog: ga4gh_repo - :path: remove-dataset + :path: add-referenceset :nodefault: **Examples:** .. code-block:: bash - $ ga4gh_repo remove-dataset path/to/repo.db aDataset + $ ga4gh_repo add-referenceset registry.db hs37d5.fa.gz \ + --description "NCBI37 assembly of the human genome" \ + --ncbiTaxonId 9606 --name NCBI37 \ + --sourceUri ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz + +Adds a reference set used in the 1000 Genomes project using the name +``NCBI37``, also setting the ``ncbiTaxonId`` to 9606 (human). ++++++++++++++++ -add-referenceset +add-ontology ++++++++++++++++ -Adds a given reference set file to a given data repository. +.. todo:: add docs for adding ontologies. .. argparse:: :module: ga4gh.cli :func: getRepoManagerParser :prog: ga4gh_repo - :path: add-referenceset + :path: add-ontology :nodefault: **Examples:** .. code-block:: bash - $ ga4gh_repo add-referenceset path/to/repo.db path/to/aReferenceSet.fa.gz + $ ga4gh_repo add-ontology registry.db path/to/so-xp.obo -++++++++++++++++++++ -remove-referenceset -++++++++++++++++++++ ++++++++++++++++ +add-variantset ++++++++++++++++ + +Adds a variant set to a named dataset in a repository. Variant sets are +currently derived from one or more non-overlapping VCF/BCF files which +may be either stored locally or come from a remote URL. Multiple VCF +files can be specified either directly on the command line or by +providing a single directory argument that contains indexed VCF files. +If remote URLs are used then index files in the local file system must be +provided using the ``-I`` option. -Removes a given reference set from a given data repository. +.. todo:: Document adding VariantAnnotationSets using the -a option. .. argparse:: - :module: ga4gh.cli - :func: getRepoManagerParser - :prog: ga4gh_repo - :path: remove-referenceset - :nodefault: + :module: ga4gh.cli + :func: getRepoManagerParser + :prog: ga4gh_repo + :path: add-variantset + :nodefault: **Examples:** .. code-block:: bash - $ ga4gh_repo remove-referenceset path/to/repo.db aReferenceSet + $ ga4gh_repo add-variantset registry.db 1kg 1kgPhase1/ -R NCBI37 -++++++++++++++++ -add-ontology -++++++++++++++++ +Adds a new variant set to the dataset named ``1kg`` in the repository defined +by the registry database ``registry.db`` using the VCF files contained in the +directory ``1kgPhase1``. Note that this directory must also contain the +corresponding indexes for these files. We associate the reference set named +``NCBI37`` with this new variant set. Because we do not provide a ``--name`` +argument, a name is automatically generated using the default name generation +rules. + +.. todo:: Add a paragraph to the section where we discuss names above + where we can define the default name generation rules, and link to + that from here. + +.. code-block:: bash -Adds an Ontology Map, which maps identifiers to ontology terms, to -the repository. Ontology maps are tab delimited files with an -identifier/term pair per row. + $ ga4gh_repo add-variantset registry.db 1kg \ + 1kgPhase1/chr1.vcf.gz 1kg/chr2.vcf.gz -n phase1-subset -R NCBI37 + +Like the last example, we add a new variant set to the dataset ``1kg``, +but here we only use the VCFs for chromosomes 1 and 2. We also specify the +name for this new variant set to be ``phase1-subset``. + +.. code-block:: bash + + $ ga4gh_repo add-variantset registry.db 1kg \ + --name phase1-subset-remote -R NCBI37 \ + --indexFiles ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz.tbi ALL.chr2.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz.tbi \ + ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/release/20110521/ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz \ + ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/release/20110521/ALL.chr2.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz + +This example performs the same task of creating a subset of the phase1 +VCFs, but this time we use the remote URL directly and do not keep a +local copy of the VCF file. Because we are using remote URLs to define +the variant set, we have to download a local copy of the corresponding +index files and provide them on the command line using the ``--indexFiles`` +option. + ++++++++++++++++++ +add-readgroupset ++++++++++++++++++ + +Adds a readgroup set to a named dataset in a repository. Readgroup sets are +currently derived from a single indexed BAM file, which can be either +stored locally or based on a remote URL. If the readgroup set is based on +a remote URL, then the index file must be stored locally and specified using +the ``--indexFile`` option. + +Each readgroup set must be associated with the reference set that it is aligned +to. The ``add-readgroupset`` command first examines the headers of the BAM file +to see if it contains information about references, and then looks for a +reference set with name equal to the genome assembly identifer defined in the +header. (Specifically, we read the ``@SQ`` header line and use the value of the +``AS`` tag as the default reference set name.) If this reference set exists, +then the readgroup set will be associated with it automatically. If it does not +(or we cannot find the appropriate information in the header), then the +``add-readgroupset`` command will fail. In this case, the user must provide the +name of the reference set using the ``--referenceSetName`` option. .. argparse:: :module: ga4gh.cli :func: getRepoManagerParser :prog: ga4gh_repo - :path: add-ontology + :path: add-readgroupset :nodefault: **Examples:** .. code-block:: bash - $ ga4gh_repo add-ontology path/to/repo.db path/to/aOntoMap.txt + $ ga4gh_repo add-readgroupset registry.db 1kg \ + path/to/HG00114.chrom11.ILLUMINA.bwa.GBR.low_coverage.20120522.bam -++++++++++++++++++++ -remove-ontology -++++++++++++++++++++ +Adds a new readgroup set for an indexed 1000 Genomes BAM file stored on the +local file system. The index file follows the usual convention and is stored in +the same directory as the BAM file and has an extra ``.bai`` extension. The +name of the readgroup set is automatically derived from the file name, and the +reference set automatically set from the BAM header. -Removes a given Ontology Map from a given data repository. +.. code-block:: bash + + $ ga4gh_repo add-readgroupset registry.db 1kg ga4gh-example-data/HG00096.bam \ + -R GRCh37-subset -n HG0096-subset + +Adds a new readgroup set based on a subset of the 1000 genomes reads for the +HG00096 sample from the example data used in the reference server. In this case +we specify that the reference set name ``GRCh37-subset`` be associated with the +readgroup set. We also override the default name generation rules and specify +the name ``HG00096-subset`` for the new readgroup set. + +.. code-block:: bash + + $ ga4gh_repo add-readgroupset registry.db 1kg \ + -n HG00114-remote + -I /path/to/HG00114.chrom11.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.bai + ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/phase3/data/HG00114/alignment/HG00114.chrom11.ILLUMINA.bwa.GBR.low_coverage.20120522.bam + +Adds a new readgroups set based on a 1000 genomes BAM directly from the NCBI +FTP server. Because this readgroup set uses a remote FTP URL, we must specify +the location of the ``.bai`` index file on the local file system. + ++++++++++++++++ +remove-dataset ++++++++++++++++ + +Removes a dataset from the repository and recursively removes all +objects (ReadGroupSets, VariantSets, etc) within this dataset. .. argparse:: :module: ga4gh.cli :func: getRepoManagerParser :prog: ga4gh_repo - :path: remove-ontology + :path: remove-dataset :nodefault: **Examples:** .. code-block:: bash - $ ga4gh_repo remove-ontology path/to/repo.db aOntoMap + $ ga4gh_repo remove-dataset registry.db dataset1 -+++++++++++++++++ -add-readgroupset -+++++++++++++++++ +Deletes the dataset with name ``dataset1`` from the repository +represented by ``registry.db`` -Adds a given read group set file to a given data repository and dataset. The -file must have the extension ``.bam``. +++++++++++++++++++++ +remove-referenceset +++++++++++++++++++++ + +Removes a reference set from the repository. Attempting +to remove a reference set that is referenced by other objects in the +repository will result in an error. .. argparse:: :module: ga4gh.cli :func: getRepoManagerParser :prog: ga4gh_repo - :path: add-readgroupset + :path: remove-referenceset :nodefault: **Examples:** .. code-block:: bash - $ ga4gh_repo add-readgroupset path/to/repo.db aDataset path/to/aReadGroupSet.bam + $ ga4gh_repo remove-referenceset registry.db NCBI37 + +Deletes the reference set with name ``NCBI37`` from the repository +represented by ``registry.db`` ++++++++++++++++++++ -remove-readgroupset +remove-ontology ++++++++++++++++++++ -Removes a read group set from a given data repository and dataset. +Removes an ontology from the repository. Attempting +to remove an ontology that is referenced by other objects in the +repository will result in an error. .. argparse:: :module: ga4gh.cli :func: getRepoManagerParser :prog: ga4gh_repo - :path: remove-readgroupset + :path: remove-ontology :nodefault: **Examples:** .. code-block:: bash - $ ga4gh_repo remove-readgroupset path/to/repo.db aDataset aReadGroupSet + $ ga4gh_repo remove-ontology registry.db so-xp -+++++++++++++++ -add-variantset -+++++++++++++++ +Deletes the ontology with name ``so-xp`` from the repository +represented by ``registry.db`` + ++++++++++++++++++ +remove-variantset ++++++++++++++++++ -Adds a variant set directory to a given data repository and dataset. The -directory should contain file(s) with extension ``.vcf.gz``. If a variant set -is annotated it will be added as both a variant set and a variant annotation set. +Removes a variant set from the repository. This also deletes all +associated call sets and variant annotation sets from the repository. .. argparse:: :module: ga4gh.cli :func: getRepoManagerParser :prog: ga4gh_repo - :path: add-variantset + :path: remove-variantset :nodefault: **Examples:** .. code-block:: bash - $ ga4gh_repo add-variantset path/to/repo.db aDataset path/to/aVariantSet + $ ga4gh_repo remove-variantset registry.db dataset1 phase3-release -+++++++++++++++++ -remove-variantset -+++++++++++++++++ +Deletes the variant set named ``phase3-release`` from the dataset +named ``dataset1`` from the repository represented by ``registry.db``. -Removes a variant set from a given data repository and dataset. +++++++++++++++++++++ +remove-readgroupset +++++++++++++++++++++ + +Removes a read group set from the repository. .. argparse:: - :module: ga4gh.cli - :func: getRepoManagerParser - :prog: ga4gh_repo - :path: remove-variantset - :nodefault: + :module: ga4gh.cli + :func: getRepoManagerParser + :prog: ga4gh_repo + :path: remove-readgroupset + :nodefault: **Examples:** .. code-block:: bash - $ ga4gh_repo remove-variantset path/to/repo.db aDataset aVariantSet + $ ga4gh_repo remove-readgroupset registry.db dataset1 HG00114 + +Deletes the readgroup set named ``HG00114`` from the dataset named +``dataset1`` from the repository represented by ``registry.db``. ------------------ Configuration file @@ -290,7 +439,7 @@ example, we might have .. code-block:: python - DATA_SOURCE = "/path/to/repo.db" + DATA_SOURCE = "/path/to/registry.db" For production deployments, we shouldn't need to add any more configuration than this, as the other keys have sensible defaults. However, diff --git a/ga4gh/cli.py b/ga4gh/cli.py index 4a8454f00..b67ea400d 100644 --- a/ga4gh/cli.py +++ b/ga4gh/cli.py @@ -181,8 +181,8 @@ def __init__(self, args): # depending on the prefix. filePrefix = "file://" if args.baseUrl.startswith(filePrefix): - repoPath = args.baseUrl[len(filePrefix):] - repo = datarepo.SqlDataRepository(repoPath) + registryPath = args.baseUrl[len(filePrefix):] + repo = datarepo.SqlDataRepository(registryPath) repo.open(datarepo.MODE_READ) theBackend = backend.Backend(repo) self._client = client.LocalClient(theBackend) @@ -1552,8 +1552,8 @@ class RepoManager(object): """ def __init__(self, args): self._args = args - self._repoPath = args.repoPath - self._repo = datarepo.SqlDataRepository(self._repoPath) + self._registryPath = args.registryPath + self._repo = datarepo.SqlDataRepository(self._registryPath) def _confirmDelete(self, objectType, name, func): if self._args.force: @@ -1587,7 +1587,7 @@ def _openRepo(self): if not self._repo.exists(): raise exceptions.RepoManagerException( "Repo '{}' does not exist. Please create a new repo " - "using the 'init' command.".format(self._repoPath)) + "using the 'init' command.".format(self._registryPath)) self._repo.open(datarepo.MODE_READ) def init(self): @@ -1598,7 +1598,7 @@ def init(self): self._repo.delete() else: raise exceptions.RepoManagerException( - forceMessage.format(self._repoPath)) + forceMessage.format(self._registryPath)) self._updateRepo(self._repo.initialise) def list(self): @@ -1849,7 +1849,8 @@ def func(): @classmethod def addRepoArgument(cls, subparser): subparser.add_argument( - "repoPath", help="the file path of the data repository") + "registryPath", + help="the location of the registry database") @classmethod def addForceOption(cls, subparser): @@ -1858,10 +1859,11 @@ def addForceOption(cls, subparser): default=False, help="do not prompt for confirmation") @classmethod - def addDescriptionOption(cls, subparser): + def addDescriptionOption(cls, subparser, objectType): subparser.add_argument( "-d", "--description", default="", - help="The human-readable description of an object.") + help="The human-readable description of the {}.".format( + objectType)) @classmethod def addDatasetNameArgument(cls, subparser): @@ -1939,7 +1941,7 @@ def getParser(cls): addDatasetParser.set_defaults(runner="addDataset") cls.addRepoArgument(addDatasetParser) cls.addDatasetNameArgument(addDatasetParser) - cls.addDescriptionOption(addDatasetParser) + cls.addDescriptionOption(addDatasetParser, "dataset") removeDatasetParser = addSubparser( subparsers, "remove-dataset", @@ -1960,12 +1962,12 @@ def getParser(cls): "The path of the FASTA file to use as a reference set. This " "file must be bgzipped and indexed.") cls.addNameOption(addReferenceSetParser, objectType) - cls.addDescriptionOption(addReferenceSetParser) + cls.addDescriptionOption(addReferenceSetParser, objectType) addReferenceSetParser.add_argument( "--ncbiTaxonId", default=None, help="The NCBI Taxon Id") addReferenceSetParser.add_argument( "--isDerived", default=False, type=bool, - help="Indicates if this is a derived object") + help="Indicates if this reference set is derived from another") addReferenceSetParser.add_argument( "--assemblyId", default=None, help="The assembly id") diff --git a/tests/unit/test_cli.py b/tests/unit/test_cli.py index 40a1f373e..768df2117 100644 --- a/tests/unit/test_cli.py +++ b/tests/unit/test_cli.py @@ -276,41 +276,41 @@ class TestRepoManagerCli(unittest.TestCase): def setUp(self): self.parser = cli.RepoManager.getParser() - self.repoPath = 'a/repo/path' + self.registryPath = 'a/repo/path' self.datasetName = "datasetName" self.filePath = 'a/file/path' def testInit(self): - cliInput = "init {}".format(self.repoPath) + cliInput = "init {}".format(self.registryPath) args = self.parser.parse_args(cliInput.split()) - self.assertEquals(args.repoPath, self.repoPath) + self.assertEquals(args.registryPath, self.registryPath) self.assertEquals(args.runner, "init") def testVerify(self): - cliInput = "verify {}".format(self.repoPath) + cliInput = "verify {}".format(self.registryPath) args = self.parser.parse_args(cliInput.split()) - self.assertEquals(args.repoPath, self.repoPath) + self.assertEquals(args.registryPath, self.registryPath) self.assertEquals(args.runner, "verify") def testList(self): - cliInput = "list {}".format(self.repoPath) + cliInput = "list {}".format(self.registryPath) args = self.parser.parse_args(cliInput.split()) - self.assertEquals(args.repoPath, self.repoPath) + self.assertEquals(args.registryPath, self.registryPath) self.assertEquals(args.runner, "list") def testAddDataset(self): cliInput = "add-dataset {} {}".format( - self.repoPath, self.datasetName) + self.registryPath, self.datasetName) args = self.parser.parse_args(cliInput.split()) - self.assertEquals(args.repoPath, self.repoPath) + self.assertEquals(args.registryPath, self.registryPath) self.assertEquals(args.datasetName, self.datasetName) self.assertEquals(args.runner, "addDataset") def testRemoveDataset(self): cliInput = "remove-dataset {} {} -f".format( - self.repoPath, self.datasetName) + self.registryPath, self.datasetName) args = self.parser.parse_args(cliInput.split()) - self.assertEquals(args.repoPath, self.repoPath) + self.assertEquals(args.registryPath, self.registryPath) self.assertEquals(args.datasetName, self.datasetName) self.assertEquals(args.runner, "removeDataset") self.assertEquals(args.force, True) @@ -324,9 +324,9 @@ def testAddReferenceSet(self): "--assemblyId ASSEMBLYID " "--sourceAccessions SOURCEACCESSIONS " "--sourceUri SOURCEURI ").format( - self.repoPath, self.filePath, description) + self.registryPath, self.filePath, description) args = self.parser.parse_args(cliInput.split()) - self.assertEquals(args.repoPath, self.repoPath) + self.assertEquals(args.registryPath, self.registryPath) self.assertEquals(args.filePath, self.filePath) self.assertEquals(args.description, description) self.assertEquals(args.ncbiTaxonId, "NCBITAXONID") @@ -339,18 +339,18 @@ def testAddReferenceSet(self): def testRemoveReferenceSet(self): referenceSetName = "referenceSetName" cliInput = "remove-referenceset {} {} -f".format( - self.repoPath, referenceSetName) + self.registryPath, referenceSetName) args = self.parser.parse_args(cliInput.split()) - self.assertEquals(args.repoPath, self.repoPath) + self.assertEquals(args.registryPath, self.registryPath) self.assertEquals(args.referenceSetName, referenceSetName) self.assertEquals(args.runner, "removeReferenceSet") self.assertEquals(args.force, True) def testAddReadGroupSet(self): cliInput = "add-readgroupset {} {} {} ".format( - self.repoPath, self.datasetName, self.filePath) + self.registryPath, self.datasetName, self.filePath) args = self.parser.parse_args(cliInput.split()) - self.assertEquals(args.repoPath, self.repoPath) + self.assertEquals(args.registryPath, self.registryPath) self.assertEquals(args.datasetName, self.datasetName) self.assertEquals(args.dataFile, self.filePath) self.assertEquals(args.indexFile, None) @@ -359,10 +359,10 @@ def testAddReadGroupSet(self): def testAddReadGroupSetWithIndexFile(self): indexPath = self.filePath + ".bai" cliInput = "add-readgroupset {} {} {} -I {}".format( - self.repoPath, self.datasetName, self.filePath, + self.registryPath, self.datasetName, self.filePath, indexPath) args = self.parser.parse_args(cliInput.split()) - self.assertEquals(args.repoPath, self.repoPath) + self.assertEquals(args.registryPath, self.registryPath) self.assertEquals(args.datasetName, self.datasetName) self.assertEquals(args.dataFile, self.filePath) self.assertEquals(args.indexFile, indexPath) @@ -371,9 +371,9 @@ def testAddReadGroupSetWithIndexFile(self): def testRemoveReadGroupSet(self): readGroupSetName = "readGroupSetName" cliInput = "remove-readgroupset {} {} {} -f".format( - self.repoPath, self.datasetName, readGroupSetName) + self.registryPath, self.datasetName, readGroupSetName) args = self.parser.parse_args(cliInput.split()) - self.assertEquals(args.repoPath, self.repoPath) + self.assertEquals(args.registryPath, self.registryPath) self.assertEquals(args.datasetName, self.datasetName) self.assertEquals(args.readGroupSetName, readGroupSetName) self.assertEquals(args.runner, "removeReadGroupSet") @@ -381,9 +381,9 @@ def testRemoveReadGroupSet(self): def testAddVariantSet(self): cliInput = "add-variantset {} {} {} ".format( - self.repoPath, self.datasetName, self.filePath) + self.registryPath, self.datasetName, self.filePath) args = self.parser.parse_args(cliInput.split()) - self.assertEquals(args.repoPath, self.repoPath) + self.assertEquals(args.registryPath, self.registryPath) self.assertEquals(args.datasetName, self.datasetName) self.assertEquals(args.dataFiles, [self.filePath]) self.assertEquals(args.indexFiles, None) @@ -395,10 +395,10 @@ def testAddVariantSetWithIndexFiles(self): indexFile1 = file1 + ".tbi" indexFile2 = file2 + ".tbi" cliInput = "add-variantset {} {} {} {} -I {} {}".format( - self.repoPath, self.datasetName, file1, file2, + self.registryPath, self.datasetName, file1, file2, indexFile1, indexFile2) args = self.parser.parse_args(cliInput.split()) - self.assertEquals(args.repoPath, self.repoPath) + self.assertEquals(args.registryPath, self.registryPath) self.assertEquals(args.datasetName, self.datasetName) self.assertEquals(args.dataFiles, [file1, file2]) self.assertEquals(args.indexFiles, [indexFile1, indexFile2]) @@ -407,9 +407,9 @@ def testAddVariantSetWithIndexFiles(self): def testRemoveVariantSet(self): variantSetName = "variantSetName" cliInput = "remove-variantset {} {} {}".format( - self.repoPath, self.datasetName, variantSetName) + self.registryPath, self.datasetName, variantSetName) args = self.parser.parse_args(cliInput.split()) - self.assertEquals(args.repoPath, self.repoPath) + self.assertEquals(args.registryPath, self.registryPath) self.assertEquals(args.datasetName, self.datasetName) self.assertEquals(args.variantSetName, variantSetName) self.assertEquals(args.runner, "removeVariantSet") @@ -417,17 +417,18 @@ def testRemoveVariantSet(self): def testAddOntology(self): cliInput = "add-ontology {} {}".format( - self.repoPath, self.filePath) + self.registryPath, self.filePath) args = self.parser.parse_args(cliInput.split()) - self.assertEquals(args.repoPath, self.repoPath) + self.assertEquals(args.registryPath, self.registryPath) self.assertEquals(args.filePath, self.filePath) self.assertEquals(args.runner, "addOntology") def testRemoveOntology(self): ontologyName = "the_ontology_name" - cliInput = "remove-ontology {} {}".format(self.repoPath, ontologyName) + cliInput = "remove-ontology {} {}".format( + self.registryPath, ontologyName) args = self.parser.parse_args(cliInput.split()) - self.assertEquals(args.repoPath, self.repoPath) + self.assertEquals(args.registryPath, self.registryPath) self.assertEquals(args.ontologyName, ontologyName) self.assertEquals(args.runner, "removeOntology") self.assertEquals(args.force, False) From ae0904812fa0e2e666126153060e2d12cc132fe8 Mon Sep 17 00:00:00 2001 From: David Steinberg Date: Mon, 16 May 2016 18:39:14 -0700 Subject: [PATCH 07/13] Thousand genomes repo demo Typos thousand -> 1000 --- docs/demo.rst | 143 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 143 insertions(+) diff --git a/docs/demo.rst b/docs/demo.rst index a591792a4..72fa73456 100644 --- a/docs/demo.rst +++ b/docs/demo.rst @@ -217,6 +217,149 @@ using: variant, and drill down into the reads in question programatically. values as parameters which have sensible defaults. +Host the 1000 Genomes VCF +============================= + +The GA4GH reference server uses a registry of files and URLs to +populate its data repository. In this tutorial we will use the +command-line client to create a registry similar to that used by +1kgenomes.ga4gh.org. Your system should have samtools installed, and at +least 30GB to host the VCF and reference sets. + +Repo administrator CLI +---------------------- + +The CLI has methods for adding and removing Feature Sets, Read Group +Sets, Variant Sets, etc. Before we can begin adding files we must first +initialize an empty registry database. The directory that this database +is in should be readable and writable by the current user, as well as the +user running the server. + +.. code-block:: bash + + ga4gh_repo init registry.db + +This command will create a file ``registry.db`` in the current working +directory. This file should stay relatively small (a few MB for +thousands of files). + +Now we will add a dataset to the registry, which is a logical container +for the genomics data we will later add. You can optionally provide a +description using the ``--description`` flag. + +.. code-block:: bash + + ga4gh_repo add-dataset registry.db 1kgenomes --description "Variants from the 1000 Genomes project and GENCODE genes annotations" + +Add a Reference Set +------------------- + +It is possible for a server to host multiple reference assemblies. Here +we will go through all the steps of downloading and adding the FASTA +used for the 1000 Genomes VCF. + +.. code-block:: bash + + wget ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz + +This file is provided in ``.gz`` format, which we will decompress, and +then with samtools installed on the system, recompress it using +``bgzip``. + +.. code-block:: bash + + gunzip hs37d5.fa.gz + bgzip hs37d5.fa + +This may take a few minutes depending on your system as this file is +around 3GB. Next, we will add the reference set. + +.. code-block:: bash + + ga4gh_repo add-referenceset registry.db /full/path/to/hs37d5.fa.gz \ + -d “NCBI37 assembly of the human genome” --ncbiTaxonId 9606 --name NCBI37 \ + --sourceUri "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz" + +A number of optional command line flags have been added. We will be +referring to the name of this reference set ``NCBI37`` when we later add +the variant set. + +Add an ontology TODO +-------------------- + +Ontologies provide a source for parsing variant annotations, as well as +organizing feature types into ontology terms. This is a custom format +created for this server. + +.. code-block:: bash + + ga4gh_repo add-ontology registry.db /full/path/to/sequence_ontology.txt + +Add sequence annotations +------------------------ + +The GENCODE Genes dataset provides annotations for features on the +reference assembly. The server uses a custom storage format for sequence +annotations, you can download a prepared set +`here `__. +It can be added to the registry using the following command. Notice +we have told the registry to associate the reference set added above +with these annotations. + +.. code-block:: bash + + ga4gh_repo add-featureset registry.db 1kgenomes /full/path/to/gencode.v24lift37.annotation.db --referenceSetName NCBI37 + +.. todo:: Demonstrate how to generate your own sequence annotations database. + +Add the 1000 Genomes VCFs +-------------------------- + +The 1000 Genomes are publicly available on the EBI server. This +command uses ``wget`` to download the "release" VCFs to a directory named +release. + +.. code-block:: bash + + wget -m ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ -nd -P release -l 1 + rm release/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz + +These files are already compressed and indexed. For the server to make use +of the files in this directory we must move the `wgs` file, since it covers +chromosomes that are represented elsewhere and overlapping VCF are not +currently supported. This file could be added as a separate variant set. + +We can now add the directory to the registry using the following command. +Again, notice we have referred to the reference set by name. + +.. code-block:: bash + + ga4gh_repo add-variantset registry.db 1kgenomes /full/path/to/release/ --name phase3-release --referenceSetName NCBI37 + +Add a BAM as a Read Group Set +----------------------------- + +Read Group Sets are the logical equivalent to BAM files within the +server. We will add a BAM hosting by the 1000 Genomes S3 bucket. +We will first download the index and then add it to the registry. + +.. code-block:: bash + + wget http://s3.amazonaws.com/1000genomes/phase3/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.bai + ga4gh_repo add-readgroupset registry.db 1kgenomes "http://s3.amazonaws.com/1000genomes/phase3/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam" -I "HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.bai" --referenceSetName NCBI37 + +This might take a moment as some metadata about the file will be +retrieved from S3. + +Start the server +---------------- + +Assuming you have set up your server to run using the registry file just +created, you can now start or restart the server to see the newly added +data. If the server is running via apache issue +``sudo service apache2 restart``. You can then visit the landing page of +the running server to see the newly added data. + --------- With OIDC --------- From 31b6ee2d7c77efd7653d49c28e3b57ce2507a791 Mon Sep 17 00:00:00 2001 From: Kevin Osborn Date: Thu, 19 May 2016 09:33:31 -0700 Subject: [PATCH 08/13] basic instructions for profiling the ref server --- docs/ref_server_profiling.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/ref_server_profiling.rst b/docs/ref_server_profiling.rst index af77c1b17..d93b93a56 100644 --- a/docs/ref_server_profiling.rst +++ b/docs/ref_server_profiling.rst @@ -30,10 +30,10 @@ Running the profile: Evaluating the profile output: ****************************** -If you don't use teh -o {output file} option then all output from the profiler +If you don't use the -o {output file} option then all output from the profiler runs to stdout and will be sorted with the function that takes the most cumulative time at the top of the list. You can review the text output -manually, but a beet method is to use the -o option and then review the +manually, but a beter method is to use the -o option and then review the output using a nifty little program we found that interactively browses the function list. It provides a way to change the sorting and it also links the functions together so that you can follow the called and caller stacks. From 6b43828a6091a265afbb737906135137f88a6d3a Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Wed, 11 May 2016 18:04:09 +0100 Subject: [PATCH 09/13] Ontology handling update; issue #1147. This update makes significant changes to ontology handling: 1. Change to using an OBO file as input, and using an Ontology object internally rather than a OntologyTermMap. Refactored ontology handling code in general. 2. Add a ontologyId field to the FeatureSet and AnnotationSet tables with a foreign key constraint on the Ontology table. 3. Add a -O 'option' to the add-featureset command which allows an admin choose the ontology they wish to associate with a given FeatureSet. 4. Changed the semantics of adding variant annotations sets so that it is now optional we want to add a VAS when annotations are detected. Now an annotation set will only be created if the -a option is provided. Also added the -O option to add-variantsets so the ontology can be specified. 5. Added the scripts/build_test_data.py scipt to build test data db. --- ga4gh/cli.py | 65 +- ga4gh/datamodel/datasets.py | 6 +- ga4gh/datamodel/ontologies.py | 147 +- ga4gh/datamodel/sequenceAnnotations.py | 18 +- ga4gh/datamodel/variants.py | 36 +- ga4gh/datarepo.py | 141 +- ga4gh/exceptions.py | 34 +- requirements.txt | 1 + scripts/build_test_data.py | 57 + tests/data/ontologies/goslim_generic.obo | 4015 +++ tests/data/ontologies/so-xp-simple.obo | 21087 ++++++++++++++++ .../sequence_ontology/sequence_ontology.txt | 2284 -- tests/data/repo.db | Bin 154624 -> 151552 bytes tests/datadriven/test_ontologies.py | 62 + tests/datadriven/test_sequenceAnnotations.py | 5 +- tests/datadriven/test_variant_annotations.py | 7 +- tests/end_to_end/test_repo_manager.py | 12 +- tests/paths.py | 12 +- tests/unit/test_repo_manager.py | 145 +- tests/unit/test_variant_annotations.py | 4 +- 20 files changed, 25638 insertions(+), 2500 deletions(-) create mode 100644 scripts/build_test_data.py create mode 100644 tests/data/ontologies/goslim_generic.obo create mode 100644 tests/data/ontologies/so-xp-simple.obo delete mode 100644 tests/data/ontologymaps/sequence_ontology/sequence_ontology.txt create mode 100644 tests/datadriven/test_ontologies.py diff --git a/ga4gh/cli.py b/ga4gh/cli.py index b67ea400d..39f0b47ae 100644 --- a/ga4gh/cli.py +++ b/ga4gh/cli.py @@ -1590,6 +1590,13 @@ def _openRepo(self): "using the 'init' command.".format(self._registryPath)) self._repo.open(datarepo.MODE_READ) + def _checkSequenceOntology(self, ontology): + so = ontologies.SEQUENCE_ONTOLOGY_PREFIX + if ontology.getOntologyPrefix() != so: + raise exceptions.RepoManagerException( + "Ontology '{}' does not have ontology prefix '{}'".format( + ontology.getName(), so)) + def init(self): forceMessage = ( "Respository '{}' already exists. Use --force to overwrite") @@ -1625,9 +1632,9 @@ def addOntology(self): name = self._args.name if name is None: name = getNameFromPath(self._args.filePath) - ontologyTermMap = ontologies.OntologyTermMap(name) - ontologyTermMap.populateFromFile(self._args.filePath) - self._updateRepo(self._repo.insertOntologyTermMap, ontologyTermMap) + ontology = ontologies.Ontology(name) + ontology.populateFromFile(self._args.filePath) + self._updateRepo(self._repo.insertOntology, ontology) def addDataset(self): """ @@ -1749,7 +1756,26 @@ def addVariantSet(self): "VariantSet using the --referenceSetName option") referenceSet = self._repo.getReferenceSetByName(referenceSetName) variantSet.setReferenceSet(referenceSet) - self._updateRepo(self._repo.insertVariantSet, variantSet) + + # Now check for annotations + annotationSets = [] + if variantSet.isAnnotated() and self._args.addAnnotationSets: + ontologyName = self._args.ontologyName + if ontologyName is None: + raise exceptions.RepoManagerException( + "A sequence ontology name must be provided") + ontology = self._repo.getOntologyByName(ontologyName) + self._checkSequenceOntology(ontology) + for annotationSet in variantSet.getVariantAnnotationSets(): + annotationSet.setOntology(ontology) + annotationSets.append(annotationSet) + + # Add the annotation sets and the variant set as an atomic update + def updateRepo(): + self._repo.insertVariantSet(variantSet) + for annotationSet in annotationSets: + self._repo.insertVariantAnnotationSet(annotationSet) + self._updateRepo(updateRepo) def removeReferenceSet(self): """ @@ -1814,6 +1840,13 @@ def addFeatureSet(self): "A reference set name must be provided") referenceSet = self._repo.getReferenceSetByName(referenceSetName) featureSet.setReferenceSet(referenceSet) + ontologyName = self._args.ontologyName + if ontologyName is None: + raise exceptions.RepoManagerException( + "A sequence ontology name must be provided") + ontology = self._repo.getOntologyByName(ontologyName) + self._checkSequenceOntology(ontology) + featureSet.setOntology(ontology) featureSet.populateFromFile(self._args.filePath) self._updateRepo(self._repo.insertFeatureSet, featureSet) @@ -1834,13 +1867,11 @@ def removeOntology(self): Removes an ontology from the repo. """ self._openRepo() - ontologyTermMap = self._repo.getOntologyTermMapByName( - self._args.ontologyName) + ontology = self._repo.getOntologyByName(self._args.ontologyName) def func(): - self._updateRepo( - self._repo.removeOntologyTermMap, ontologyTermMap) - self._confirmDelete("Ontology", ontologyTermMap.getLocalId(), func) + self._updateRepo(self._repo.removeOntology, ontology) + self._confirmDelete("Ontology", ontology.getName(), func) # # Methods to simplify adding common arguments to the parser. @@ -1878,6 +1909,15 @@ def addReferenceSetNameOption(cls, subparser, objectType): subparser.add_argument( "-R", "--referenceSetName", default=None, help=helpText) + @classmethod + def addSequenceOntologyNameOption(cls, subparser, objectType): + helpText = ( + "the name of the sequence ontology instance used to " + "translate ontology term names to IDs in this {}" + ).format(objectType) + subparser.add_argument( + "-O", "--ontologyName", default=None, help=helpText) + @classmethod def addOntologyNameArgument(cls, subparser): subparser.add_argument( @@ -2069,6 +2109,12 @@ def getParser(cls): "same order as the data files.")) cls.addNameOption(addVariantSetParser, objectType) cls.addReferenceSetNameOption(addVariantSetParser, objectType) + cls.addSequenceOntologyNameOption(addVariantSetParser, objectType) + addVariantSetParser.add_argument( + "-a", "--addAnnotationSets", action="store_true", + help=( + "If the supplied VCF file contains annotations, create the " + "corresponding VariantAnnotationSet.")) removeVariantSetParser = addSubparser( subparsers, "remove-variantset", @@ -2089,6 +2135,7 @@ def getParser(cls): "The path to the converted SQLite database containing Feature " "data") cls.addReferenceSetNameOption(addFeatureSetParser, "feature set") + cls.addSequenceOntologyNameOption(addFeatureSetParser, "feature set") removeFeatureSetParser = addSubparser( subparsers, "remove-featureset", diff --git a/ga4gh/datamodel/datasets.py b/ga4gh/datamodel/datasets.py index 4a307a360..21c8931d2 100644 --- a/ga4gh/datamodel/datasets.py +++ b/ga4gh/datamodel/datasets.py @@ -9,7 +9,6 @@ import ga4gh.datamodel.reads as reads import ga4gh.datamodel.sequenceAnnotations as sequenceAnnotations import ga4gh.datamodel.variants as variants -import ga4gh.datamodel.ontologies as ontologies import ga4gh.exceptions as exceptions import ga4gh.protocol as protocol @@ -207,9 +206,7 @@ def __init__( numAlignments=1, numFeatureSets=1): super(SimulatedDataset, self).__init__(localId) self._description = "Simulated dataset {}".format(localId) - # TODO create a simulated OntologyTermMap - sequenceOntology = ontologies.OntologyTermMap("sequence_ontology") - # TODO add some terms into the simulated sequence ontology + # TODO create a simulated Ontology # Variants for i in range(numVariantSets): localId = "simVs{}".format(i) @@ -219,7 +216,6 @@ def __init__( self.addVariantSet(variantSet) variantAnnotationSet = variants.SimulatedVariantAnnotationSet( variantSet, "simVas{}".format(i), seed) - variantAnnotationSet.setSequenceOntologyTermMap(sequenceOntology) variantSet.addVariantAnnotationSet(variantAnnotationSet) # Reads for i in range(numReadGroupSets): diff --git a/ga4gh/datamodel/ontologies.py b/ga4gh/datamodel/ontologies.py index 99ba36c49..38494859a 100644 --- a/ga4gh/datamodel/ontologies.py +++ b/ga4gh/datamodel/ontologies.py @@ -5,25 +5,63 @@ from __future__ import print_function from __future__ import unicode_literals +import collections +import os.path + import ga4gh.protocol as protocol +import ga4gh.exceptions as exceptions + +import goatools.obo_parser as obo_parser +SEQUENCE_ONTOLOGY_PREFIX = "SO" -class OntologyTermMap(object): + +class OboReader(obo_parser.OBOReader): """ - A bidectional map between ontology names and IDs (e.g. in Sequence - Ontology we would have "SO:0001583 <-> missense_variant"). This - implementation uses a tab separated TXT file: "id\tname" + We extend the OBOReader class to allow us throw a custom exception + so that it will be handled correctly. The default implementation + throws an Exception instance on error, which cannot be caught + without masking pretty much any kind of error. + """ + def _die(self, message, line): + raise exceptions.OntologyFileFormatException( + self.obo_file, "Error at line {}: {}".format(line, message)) + - This is a temporary solution and must be replaced by more comprehensive - ontology object. +class Ontology(object): + """ + A bidectional map between ontology names and IDs (e.g. in Sequence + Ontology we would have "SO:0001583 <-> missense_variant") derived + from an OBO file. """ - def __init__(self, localId): - # TODO The instance variables need to be refactored here. - self._localId = localId - self._sourceName = localId + def __init__(self, name): + self._id = None + self._name = name + self._sourceName = name + self._sourceVersion = None + self._ontologyPrefix = None self._dataUrl = None - self._nameIdMap = dict() - self._idNameMap = dict() + # There can be duplicate names, so we need to store a list of IDs. + self._nameIdMap = collections.defaultdict(list) + + def _readFile(self): + if not os.path.exists(self._dataUrl): + raise exceptions.FileOpenFailedException(self._dataUrl) + reader = OboReader(obo_file=self._dataUrl) + ids = set() + for record in reader: + if record.id in ids: + raise exceptions.OntologyFileFormatException( + self._dataUrl, "Duplicate ID {}".format(record.id)) + ids.add(record.id) + self._nameIdMap[record.name].append(record.id) + self._sourceVersion = reader.format_version + if len(ids) == 0: + raise exceptions.OntologyFileFormatException( + self._dataUrl, "No valid records found.") + # To get prefix, pull out an ID and parse it. + self._ontologyPrefix = record.id.split(":")[0] + self._sourceVersion = reader.data_version def populateFromFile(self, dataUrl): """ @@ -38,36 +76,46 @@ def populateFromRow(self, row): """ Populates this Ontology using values in the specified DB row. """ + self._id = row[b'id'] self._dataUrl = row[b'dataUrl'] self._readFile() + # TODO sanity check the stored values against what we have just read. + + def getId(self): + """ + Returns the ID of this Ontology. This is an internal + identifier. + """ + return self._id - def _add(self, id_, name): + def getOntologyPrefix(self): + """ + Returns the ontology prefix string, i.e. "SO" for a sequence + ontology and "GO" for gene a ontology. """ - Adds an ontology term (id, name pair) + return self._ontologyPrefix - :param id_: ontology term ID (ex "SO:0000704") - :param name: corresponding ontology term name (ex "gene") + def getSourceVersion(self): """ - self._nameIdMap[id_] = name - self._idNameMap[name] = id_ + The version of the ontology derived from the OBO file. + """ + return self._sourceVersion def getDataUrl(self): return self._dataUrl - def getLocalId(self): - return self._localId - - def getId(self, name, default=""): - return self._idNameMap.get(name, default) - - def hasId(self, id_): - return id_ in self._nameIdMap - - def hasName(self, name): - return name in self._idNameIdMap + def getName(self): + """ + Returns the name of this ontology. + """ + return self._name - def getName(self, id_, default=""): - return self._nameIdMap.get(id_, default) + def getTermIds(self, termName): + """ + Returns the list of ontology IDs scorresponding to the specified term + name. If the term name is not found, return the empty list. + """ + return self._nameIdMap[termName] def getGaTermByName(self, name): """ @@ -76,33 +124,18 @@ def getGaTermByName(self, name): :param name: name of the ontology term, ex. "gene". :return: GA4GH OntologyTerm object. """ + # TODO what is the correct value when we have no mapping?? + termIds = self.getTermIds(name) + if len(termIds) == 0: + termId = "" + # TODO add logging for missed term translation. + else: + # TODO what is the correct behaviour here when we have multiple + # IDs matching a given name? + termId = termIds[0] term = protocol.OntologyTerm() term.term = name - term.id = self.getId(name) - term.sourceName = self._sourceName - # TODO how do we get the right version? - term.sourceVersion = None - return term - - def getGaTermById(self, id_): - """ - Returns a GA4GH OntologyTerm object by its ontology ID. - - :param name: name of the ontology term, ex. "SO:0000704" - is the ID for "gene" in the Sequence ontology. - :return: GA4GH OntologyTerm object. - """ - term = protocol.OntologyTerm() - term.term = self.getName(id_) - term.id = id_ + term.id = termId term.sourceName = self._sourceName - # TODO how do we get the right version? - term.sourceVersion = None + term.sourceVersion = self._sourceVersion return term - - def _readFile(self): - with open(self._dataUrl) as f: - for line in f: - # File format: id \t name - fields = line.rstrip().split("\t") - self._add(fields[0], fields[1]) diff --git a/ga4gh/datamodel/sequenceAnnotations.py b/ga4gh/datamodel/sequenceAnnotations.py index 2cf4e057a..0712f6ab5 100644 --- a/ga4gh/datamodel/sequenceAnnotations.py +++ b/ga4gh/datamodel/sequenceAnnotations.py @@ -316,16 +316,23 @@ class Gff3DbFeatureSet(AbstractFeatureSet): """ def __init__(self, parentContainer, localId): super(Gff3DbFeatureSet, self).__init__(parentContainer, localId) - self._sequenceOntologyTermMap = None + self._ontology = None self._dbFilePath = None self._db = None - def setSequenceOntologyTermMap(self, sequenceOntologyTermMap): + def setOntology(self, ontology): """ - Sets the OntologyTermMap instance used by this FeatureSet to the + Sets the Ontology instance used by this FeatureSet to the specified value. """ - self._sequenceOntologyTermMap = sequenceOntologyTermMap + self._ontology = ontology + + def getOntology(self): + """ + Returns the ontology term map used to translate ontology term names + to IDs. + """ + return self._ontology def populateFromFile(self, dataUrl): """ @@ -391,8 +398,7 @@ def _gaFeatureForFeatureDbRecord(self, feature): gaFeature.childIds = map( self.getCompoundIdForFeatureId, json.loads(feature['child_ids'])) - gaFeature.featureType = self._sequenceOntologyTermMap.getGaTermByName( - feature['type']) + gaFeature.featureType = self._ontology.getGaTermByName(feature['type']) gaFeature.attributes = protocol.Attributes() gaFeature.attributes.vals = json.loads(feature['attributes']) return gaFeature diff --git a/ga4gh/datamodel/variants.py b/ga4gh/datamodel/variants.py index 4c458928b..1afbac2b3 100644 --- a/ga4gh/datamodel/variants.py +++ b/ga4gh/datamodel/variants.py @@ -740,20 +740,26 @@ class AbstractVariantAnnotationSet(datamodel.DatamodelObject): def __init__(self, variantSet, localId): super(AbstractVariantAnnotationSet, self).__init__(variantSet, localId) self._variantSet = variantSet - self._sequenceOntologyTermMap = None + self._ontology = None self._analysis = None # TODO these should be set from the DB, not created on # instantiation. self._creationTime = datetime.datetime.now().isoformat() + "Z" self._updatedTime = datetime.datetime.now().isoformat() + "Z" - def setSequenceOntologyTermMap(self, sequenceOntologyTermMap): + def setOntology(self, ontology): """ - Sets the OntologyTermMap used in this VariantAnnotationSet to + Sets the Ontology used in this VariantAnnotationSet to translate sequence ontology term names into IDs to the specified value. """ - self._sequenceOntologyTermMap = sequenceOntologyTermMap + self._ontology = ontology + + def getOntology(self): + """ + Returns the ontology term map used in this VariantAnnotationSet. + """ + return self._ontology def getAnalysis(self): """ @@ -788,15 +794,6 @@ def _createGaTranscriptEffect(self): ret.updated = self._updatedTime return ret - def _createGaOntologyTermSo(self): - """ - Convenience method to set the common fields in a GA OntologyTerm - object for Sequence Ontology. - """ - ret = protocol.OntologyTerm() - ret.ontologySource = "Sequence Ontology" - return ret - def _createGaAlleleLocation(self): """ Convenience method to set the common fields in a AlleleLocation @@ -938,7 +935,7 @@ def _getRandomOntologyTerm(self, randomNumberGenerator): term = protocol.OntologyTerm() ontologyTuple = randomNumberGenerator.choice(ontologyTuples) term.term, term.id = ontologyTuple[0], ontologyTuple[1] - term.sourceName = "sequenceOntology" + term.sourceName = "ontology" term.sourceVersion = "0" return term @@ -1267,14 +1264,9 @@ def convertSeqOntology(self, seqOntStr): :param seqOntStr: :return: [protocol.OntologyTerm] """ - seqOntTerms = seqOntStr.split('&') - soTerms = [] - for soName in seqOntTerms: - so = self._createGaOntologyTermSo() - so.term = soName - so.id = self._sequenceOntologyTermMap.getId(soName, "") - soTerms.append(so) - return soTerms + return [ + self._ontology.getGaTermByName(soName) + for soName in seqOntStr.split('&')] def convertVariantAnnotation(self, record, transcriptConverter): """ diff --git a/ga4gh/datarepo.py b/ga4gh/datarepo.py index d8dc25342..eaefe2154 100644 --- a/ga4gh/datarepo.py +++ b/ga4gh/datarepo.py @@ -34,7 +34,8 @@ def __init__(self): self._referenceSetNameMap = {} self._referenceSetIds = [] self._ontologyNameMap = {} - self._ontologyNames = [] + self._ontologyIdMap = {} + self._ontologyIds = [] def addDataset(self, dataset): """ @@ -54,13 +55,13 @@ def addReferenceSet(self, referenceSet): self._referenceSetNameMap[referenceSet.getLocalId()] = referenceSet self._referenceSetIds.append(id_) - def addOntologyTermMap(self, ontologyTermMap): + def addOntology(self, ontology): """ - Add an ontologyTermMap map to this data repository. + Add an ontology map to this data repository. """ - name = ontologyTermMap.getLocalId() - self._ontologyNameMap[name] = ontologyTermMap - self._ontologyNames.append(name) + self._ontologyNameMap[ontology.getName()] = ontology + self._ontologyIdMap[ontology.getId()] = ontology + self._ontologyIds.append(ontology.getId()) def getDatasets(self): """ @@ -109,19 +110,27 @@ def getNumReferenceSets(self): """ return len(self._referenceSetIds) - def getOntologyTermMapByName(self, name): + def getOntology(self, id_): """ - Returns an ontologyTermMap by name + Returns the ontology with the specified ID. + """ + if id_ not in self._ontologyIdMap: + raise exceptions.OntologyNotFoundException(id_) + return self._ontologyIdMap[id_] + + def getOntologyByName(self, name): + """ + Returns an ontology by name """ if name not in self._ontologyNameMap: raise exceptions.OntologyNameNotFoundException(name) return self._ontologyNameMap[name] - def getOntologyTermMaps(self): + def getOntologys(self): """ - Returns all ontologyTermMaps in the repo + Returns all ontologys in the repo """ - return [self._ontologyNameMap[name] for name in self._ontologyNames] + return [self._ontologyIdMap[id_] for id_ in self._ontologyIds] def getReferenceSet(self, id_): """ @@ -167,9 +176,12 @@ def printSummary(self): Prints a summary of this data repository to stdout. """ print("Ontologies:") - for ontologyTermMap in self.getOntologyTermMaps(): + for ontology in self.getOntologys(): print( - "", ontologyTermMap.getLocalId(), ontologyTermMap.getDataUrl(), + "", + ontology.getOntologyPrefix(), + ontology.getName(), + ontology.getDataUrl(), sep="\t") print("ReferenceSets:") for referenceSet in self.getReferenceSets(): @@ -209,12 +221,14 @@ def printSummary(self): for vas in variantSet.getVariantAnnotationSets(): print( "\t\t", vas.getLocalId(), - vas.getVariantSet().getLocalId(), sep="\t") + vas.getAnnotationType(), + vas.getOntology().getName(), sep="\t") print("\tFeatureSets:") for featureSet in dataset.getFeatureSets(): print( "\t", featureSet.getLocalId(), featureSet.getReferenceSet().getLocalId(), + featureSet.getOntology().getName(), featureSet.getId(), sep="\t") @@ -279,7 +293,7 @@ def __init__(self, versionString): def __str__(self): return "{}.{}".format(self.major, self.minor) - version = SchemaVersion("0.1") + version = SchemaVersion("1.0") systemKeySchemaVersion = "schemaVersion" systemKeyCreationTimeStamp = "creationTimeStamp" @@ -357,10 +371,10 @@ def verify(self): # have verbosity levels. We should provide a way to configure # where we look at various chromosomes and so on. This will be # an important debug tool for administrators. - for ontologyTermMap in self.getOntologyTermMaps(): + for ontology in self.getOntologys(): print( - "Verifying OntologyTermMap", ontologyTermMap.getLocalId(), - "@", ontologyTermMap.getDataUrl()) + "Verifying Ontology", ontology.getName(), + "@", ontology.getDataUrl()) # TODO how do we verify this? Check some well-know SO terms? for referenceSet in self.getReferenceSets(): print( @@ -471,50 +485,52 @@ def _readSystemTable(self, cursor): schemaVersion, self.version) def _createOntologyTable(self, cursor): - # Right now we support a crude ontology term name-ID bidirectional - # map. However, in the future we will want to have better ontology - # support. Therefore we're not making the SQL schema too specific - # so that we can make this transition without needing backwards - # incompatible schema changes. sql = """ CREATE TABLE Ontology( - name TEXT NOT NULL PRIMARY KEY, - dataUrl TEXT NOT NULL + id TEXT NOT NULL PRIMARY KEY, + name TEXT NOT NULL, + dataUrl TEXT NOT NULL, + ontologyPrefix TEXT NOT NULL, + UNIQUE (name) ); """ cursor.execute(sql) - def insertOntologyTermMap(self, ontologyTermMap): + def insertOntology(self, ontology): """ - Inserts the specified ontologyTermMap into this repository. + Inserts the specified ontology into this repository. """ sql = """ - INSERT INTO Ontology(name, dataUrl) - VALUES (?, ?); + INSERT INTO Ontology(id, name, dataUrl, ontologyPrefix) + VALUES (?, ?, ?, ?); """ cursor = self._dbConnection.cursor() + # TODO we need to create a proper ID when we're doing ID generation + # for the rest of the container objects. try: cursor.execute(sql, ( - ontologyTermMap.getLocalId(), ontologyTermMap.getDataUrl())) + ontology.getName(), + ontology.getName(), + ontology.getDataUrl(), + ontology.getOntologyPrefix())) except sqlite3.IntegrityError: - raise exceptions.DuplicateNameException( - ontologyTermMap.getLocalId()) + raise exceptions.DuplicateNameException(ontology.getName()) - def _readOntologyTermMapTable(self, cursor): + def _readOntologyTable(self, cursor): cursor.row_factory = sqlite3.Row cursor.execute("SELECT * FROM Ontology;") for row in cursor: - ontologyTermMap = ontologies.OntologyTermMap(row[b'name']) - ontologyTermMap.populateFromRow(row) - self.addOntologyTermMap(ontologyTermMap) + ontology = ontologies.Ontology(row[b'name']) + ontology.populateFromRow(row) + self.addOntology(ontology) - def removeOntologyTermMap(self, ontologyTermMap): + def removeOntology(self, ontology): """ Removes the specified ontology term map from this repository. """ sql = "DELETE FROM Ontology WHERE name=?" cursor = self._dbConnection.cursor() - cursor.execute(sql, (ontologyTermMap.getLocalId(),)) + cursor.execute(sql, (ontology.getName(),)) def _createReferenceTable(self, cursor): sql = """ @@ -824,11 +840,13 @@ def _createVariantAnnotationSetTable(self, cursor): id TEXT NOT NULL PRIMARY KEY, name TEXT NOT NULL, variantSetId TEXT NOT NULL, + ontologyId TEXT NOT NULL, analysis TEXT, annotationType TEXT, UNIQUE (variantSetId, name), FOREIGN KEY(variantSetId) REFERENCES VariantSet(id) - ON DELETE CASCADE + ON DELETE CASCADE, + FOREIGN KEY(ontologyId) REFERENCES Ontology(id) ); """ cursor.execute(sql) @@ -839,8 +857,8 @@ def insertVariantAnnotationSet(self, variantAnnotationSet): """ sql = """ INSERT INTO VariantAnnotationSet ( - id, variantSetId, name, analysis, annotationType) - VALUES (?, ?, ?, ?, ?); + id, variantSetId, ontologyId, name, analysis, annotationType) + VALUES (?, ?, ?, ?, ?, ?); """ analysisJson = json.dumps( variantAnnotationSet.getAnalysis().toJsonDict()) @@ -848,7 +866,9 @@ def insertVariantAnnotationSet(self, variantAnnotationSet): cursor.execute(sql, ( variantAnnotationSet.getId(), variantAnnotationSet.getParentContainer().getId(), - variantAnnotationSet.getLocalId(), analysisJson, + variantAnnotationSet.getOntology().getId(), + variantAnnotationSet.getLocalId(), + analysisJson, variantAnnotationSet.getAnnotationType())) def _readVariantAnnotationSetTable(self, cursor): @@ -856,14 +876,11 @@ def _readVariantAnnotationSetTable(self, cursor): cursor.execute("SELECT * FROM VariantAnnotationSet;") for row in cursor: variantSet = self.getVariantSet(row[b'variantSetId']) + ontology = self.getOntology(row[b'ontologyId']) variantAnnotationSet = variants.HtslibVariantAnnotationSet( variantSet, row[b'name']) + variantAnnotationSet.setOntology(ontology) variantAnnotationSet.populateFromRow(row) - # TODO can we make this relationship more explicit?? - sequenceOntologyTermMap = self.getOntologyTermMapByName( - "sequence_ontology") - variantAnnotationSet.setSequenceOntologyTermMap( - sequenceOntologyTermMap) assert variantAnnotationSet.getId() == row[b'id'] # Insert the variantAnnotationSet into the memory-based model. variantSet.addVariantAnnotationSet(variantAnnotationSet) @@ -953,14 +970,6 @@ def insertVariantSet(self, variantSet): variantSet.getParentContainer().getLocalId()) for callSet in variantSet.getCallSets(): self.insertCallSet(callSet) - if variantSet.isAnnotated(): - # Make sure that we have the Sequence Ontology that we - # require. TODO we should make this requirement explicit. - # This is a very ugly way of doing this, we need a better - # approach. - self.getOntologyTermMapByName("sequence_ontology") - for annotationSet in variantSet.getVariantAnnotationSets(): - self.insertVariantAnnotationSet(annotationSet) def _readVariantSetTable(self, cursor): cursor.row_factory = sqlite3.Row @@ -982,6 +991,7 @@ def _createFeatureSetTable(self, cursor): name TEXT NOT NULL, datasetId TEXT NOT NULL, referenceSetId TEXT NOT NULL, + ontologyId TEXT NOT NULL, info TEXT, sourceUri TEXT, dataUrl TEXT NOT NULL, @@ -989,6 +999,7 @@ def _createFeatureSetTable(self, cursor): FOREIGN KEY(datasetId) REFERENCES Dataset(id) ON DELETE CASCADE, FOREIGN KEY(referenceSetId) REFERENCES ReferenceSet(id) + FOREIGN KEY(ontologyId) REFERENCES Ontology(id) ); """ cursor.execute(sql) @@ -1000,13 +1011,16 @@ def insertFeatureSet(self, featureSet): # TODO add support for info and sourceUri fields. sql = """ INSERT INTO FeatureSet ( - id, datasetId, referenceSetId, name, dataUrl) - VALUES (?, ?, ?, ?, ?) + id, datasetId, referenceSetId, ontologyId, name, dataUrl) + VALUES (?, ?, ?, ?, ?, ?) """ cursor = self._dbConnection.cursor() cursor.execute(sql, ( - featureSet.getId(), featureSet.getParentContainer().getId(), - featureSet.getReferenceSet().getId(), featureSet.getLocalId(), + featureSet.getId(), + featureSet.getParentContainer().getId(), + featureSet.getReferenceSet().getId(), + featureSet.getOntology().getId(), + featureSet.getLocalId(), featureSet.getDataUrl())) def _readFeatureSetTable(self, cursor): @@ -1014,12 +1028,11 @@ def _readFeatureSetTable(self, cursor): cursor.execute("SELECT * FROM FeatureSet;") for row in cursor: dataset = self.getDataset(row[b'datasetId']) - referenceSet = self.getReferenceSet(row[b'referenceSetId']) featureSet = sequenceAnnotations.Gff3DbFeatureSet( dataset, row[b'name']) - featureSet.setReferenceSet(referenceSet) - featureSet.setSequenceOntologyTermMap( - self.getOntologyTermMapByName('sequence_ontology')) + featureSet.setReferenceSet( + self.getReferenceSet(row[b'referenceSetId'])) + featureSet.setOntology(self.getOntology(row[b'ontologyId'])) featureSet.populateFromRow(row) assert featureSet.getId() == row[b'id'] dataset.addFeatureSet(featureSet) @@ -1074,7 +1087,7 @@ def load(self): except (sqlite3.OperationalError, sqlite3.DatabaseError): raise exceptions.RepoInvalidDatabaseException( self._dbFilename) - self._readOntologyTermMapTable(cursor) + self._readOntologyTable(cursor) self._readReferenceSetTable(cursor) self._readReferenceTable(cursor) self._readDatasetTable(cursor) diff --git a/ga4gh/exceptions.py b/ga4gh/exceptions.py index 1671e3802..a9f90aaf3 100644 --- a/ga4gh/exceptions.py +++ b/ga4gh/exceptions.py @@ -237,6 +237,11 @@ def __init__(self, referenceId): self.message = "referenceId '{}' not found".format(referenceId) +class OntologyNotFoundException(ObjectNotFoundException): + def __init__(self, ontologyId): + self.message = "ontologyId '{}' not found".format(ontologyId) + + class ObjectWithIdNotFoundException(ObjectNotFoundException): def __init__(self, objectId): self.message = "No object of this type exists with id '{}'".format( @@ -405,9 +410,9 @@ def __init__(self, name): class DataException(BaseServerException): """ - Exceptions thrown during the server startup, and processing faulty VCFs + Exceptions thrown during data ingestion. """ - message = "Faulty data found or data file is missing." + message = "xs" class RepoNotFoundException(DataException): @@ -445,9 +450,18 @@ def __init__(self, filename): class EmptyDirException(DataException): def __init__(self, dirname, filetype): - msg = "Directory '{}' empty, no {} file was found".format( + self.message = "Directory '{}' empty, no {} file was found".format( dirname, filetype) - super(EmptyDirException, self).__init__(msg) + + +class OntologyFileFormatException(DataException): + """ + Exception thrown when an error occurs processing an OBO ontology + file. + """ + def __init__(self, filename, message): + self.message = "Error processing ontology OBO file '{}': {}".format( + filename, message) class MalformedException(DataException): @@ -541,18 +555,6 @@ def __init__(self, fileName, referenceSetName, otherReferenceSetName): fileName, referenceSetName, otherReferenceSetName)) -class MissingDatasetMetadataException(MalformedException): - """ - A directory containing datasets is missing some metadata - in the corresponding JSON file - """ - def __init__(self, fileName, key): - self.message = ( - "JSON dataset metadata for file {} " - "is missing key {}".format( - fileName, key)) - - ############################################################### # # Internal errors. These are exceptions that we regard as bugs. diff --git a/requirements.txt b/requirements.txt index 92dc0d32c..ac979ea55 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,6 +16,7 @@ pycrypto==2.6.1 Mako==1.0.4 Beaker==1.8.0 funcsigs==0.4 +goatools==0.6.4 alabaster==0.7.7 cryptography==1.3.1 idna==2.1 diff --git a/scripts/build_test_data.py b/scripts/build_test_data.py new file mode 100644 index 000000000..f89d76343 --- /dev/null +++ b/scripts/build_test_data.py @@ -0,0 +1,57 @@ +""" +Builds the test data repo DB. +""" +from __future__ import division +from __future__ import print_function +from __future__ import unicode_literals + +import glob +import os.path + +import utils + + +def run(*args): + cmd = "python repo_dev.py {}".format(" ".join(args)) + print("running:", cmd) + utils.runCommand(cmd) + + +def main(): + prefix = "tests/data" + repoFile = os.path.join(prefix, "repo.db") + sequenceOntologyName = "so-xp-simple" + run("init", "-f", repoFile) + + pattern = os.path.join(prefix, "referenceSets", "*.fa.gz") + for dataFile in glob.glob(pattern): + run("add-referenceset", repoFile, dataFile) + + pattern = os.path.join(prefix, "ontologies", "*.obo") + for dataFile in glob.glob(pattern): + run("add-ontology", repoFile, dataFile) + + datasetName = "dataset1" + run("add-dataset", repoFile, datasetName) + + pattern = os.path.join(prefix, "datasets/dataset1/reads", "*.bam") + for dataFile in glob.glob(pattern): + run("add-readgroupset", repoFile, datasetName, dataFile) + + pattern = os.path.join(prefix, "datasets/dataset1/variants", "*") + for j, dataFile in enumerate(glob.glob(pattern)): + name = "vs_{}".format(j) + run( + "add-variantset", repoFile, datasetName, dataFile, "-R NCBI37", + "-n ", name, "-aO", sequenceOntologyName) + + pattern = os.path.join( + prefix, "datasets/dataset1/sequenceAnnotations", "*.db") + for j, dataFile in enumerate(glob.glob(pattern)): + run( + "add-featureset", repoFile, datasetName, dataFile, "-R NCBI37", + "-O", sequenceOntologyName) + + +if __name__ == "__main__": + main() diff --git a/tests/data/ontologies/goslim_generic.obo b/tests/data/ontologies/goslim_generic.obo new file mode 100644 index 000000000..c9baf6b20 --- /dev/null +++ b/tests/data/ontologies/goslim_generic.obo @@ -0,0 +1,4015 @@ +format-version: 1.2 +subsetdef: goantislim_grouping "Grouping classes that can be excluded" +subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation" +subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation" +subsetdef: goslim_aspergillus "Aspergillus GO slim" +subsetdef: goslim_candida "Candida GO slim" +subsetdef: goslim_chembl "ChEMBL protein targets summary" +subsetdef: goslim_generic "Generic GO slim" +subsetdef: goslim_goa "GOA and proteome slim" +subsetdef: goslim_metagenomics "Metagenomics GO slim" +subsetdef: goslim_pir "PIR GO slim" +subsetdef: goslim_plant "Plant GO slim" +subsetdef: goslim_pombe "Fission yeast GO slim" +subsetdef: goslim_synapse "synapse GO slim" +subsetdef: goslim_virus "Viral GO slim" +subsetdef: goslim_yeast "Yeast GO slim" +subsetdef: gosubset_prok "Prokaryotic GO subset" +subsetdef: mf_needs_review "Catalytic activity terms in need of attention" +subsetdef: termgenie_unvetted "Terms created by TermGenie that do not follow a template and require additional vetting by editors" +subsetdef: virus_checked "Viral overhaul terms" +synonymtypedef: systematic_synonym "Systematic synonym" EXACT +ontology: go/subsets/goslim_generic + +[Term] +id: GO:0000003 +name: reproduction +namespace: biological_process +alt_id: GO:0019952 +alt_id: GO:0050876 +def: "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." [GOC:go_curators, GOC:isa_complete, GOC:jl, ISBN:0198506732] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "reproductive physiological process" EXACT [] +xref: Wikipedia:Reproduction +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0000228 +name: nuclear chromosome +namespace: cellular_component +def: "A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact." [GOC:dph, GOC:mah] +subset: goslim_chembl +subset: goslim_generic +synonym: "nuclear interphase chromosome" NARROW [] +is_a: GO:0005694 ! chromosome +intersection_of: GO:0005694 ! chromosome +intersection_of: part_of GO:0005634 ! nucleus +relationship: part_of GO:0005634 ! nucleus + +[Term] +id: GO:0000229 +name: cytoplasmic chromosome +namespace: cellular_component +def: "A chromosome found in the cytoplasm." [GOC:mah] +subset: goslim_chembl +subset: goslim_generic +subset: gosubset_prok +synonym: "cytoplasmic interphase chromosome" NARROW [] +is_a: GO:0005694 ! chromosome +intersection_of: GO:0005694 ! chromosome +intersection_of: part_of GO:0005737 ! cytoplasm +relationship: part_of GO:0005737 ! cytoplasm + +[Term] +id: GO:0000902 +name: cell morphogenesis +namespace: biological_process +alt_id: GO:0007148 +alt_id: GO:0045790 +alt_id: GO:0045791 +def: "The developmental process in which the size or shape of a cell is generated and organized." [GOC:clt, GOC:dph, GOC:go_curators, GOC:tb] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_yeast +subset: gosubset_prok +synonym: "cellular morphogenesis" EXACT [] +is_a: GO:0008150 ! biological_process +relationship: part_of GO:0048856 ! anatomical structure development + +[Term] +id: GO:0000988 +name: transcription factor activity, protein binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. This term does not provide specificity with respect to the type of protein binding, e.g. transcription factor binding or RNA polymerase binding. Please use a child term that provides that specificity or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_yeast +synonym: "protein binding transcription factor activity" EXACT [] +synonym: "transcription factor activity" BROAD [] +is_a: GO:0003674 ! molecular_function +relationship: has_part GO:0003674 ! molecular_function +relationship: part_of GO:0008150 ! biological_process +created_by: kchris +creation_date: 2010-08-10T04:03:22Z + +[Term] +id: GO:0001071 +name: nucleic acid binding transcription factor activity +namespace: molecular_function +def: "Interacting selectively and non-covalently with a DNA or RNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. This term does not provide specificity with respect to the type of nucleic acid binding, e.g. RNA or DNA. Please use a child term that provides that specificity or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_yeast +synonym: "transcription factor activity" BROAD [] +is_a: GO:0003674 ! molecular_function +relationship: has_part GO:0003674 ! molecular_function +relationship: part_of GO:0008150 ! biological_process +created_by: kchris +creation_date: 2010-10-21T04:37:54Z + +[Term] +id: GO:0002376 +name: immune system process +namespace: biological_process +def: "Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05] +comment: Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501). This term was added by GO_REF:0000022. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +xref: Wikipedia:Immune_system +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0003013 +name: circulatory system process +namespace: biological_process +def: "A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism." [GOC:mtg_cardio] +subset: goslim_chembl +subset: goslim_generic +xref: Wikipedia:Circulatory_system +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0003674 +name: molecular_function +namespace: molecular_function +alt_id: GO:0005554 +def: "Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions." [GOC:go_curators] +comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. Note that when this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "molecular function" EXACT [] + +[Term] +id: GO:0003677 +name: DNA binding +namespace: molecular_function +def: "Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid)." [GOC:dph, GOC:jl, GOC:tb, GOC:vw] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "microtubule/chromatin interaction" RELATED [] +synonym: "plasmid binding" NARROW [] +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0003723 +name: RNA binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with an RNA molecule or a portion thereof." [GOC:mah] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +xref: Reactome:REACT_101703 "Exportin-5 recognizes 3' overhang of pre-miRNA, Xenopus tropicalis" +xref: Reactome:REACT_103323 "Exportin-5 recognizes 3' overhang of pre-miRNA, Dictyostelium discoideum" +xref: Reactome:REACT_106430 "Exportin-5 recognizes 3' overhang of pre-miRNA, Mus musculus" +xref: Reactome:REACT_107757 "Exportin-5 recognizes 3' overhang of pre-miRNA, Drosophila melanogaster" +xref: Reactome:REACT_108232 "Exportin-5 recognizes 3' overhang of pre-miRNA, Oryza sativa" +xref: Reactome:REACT_108368 "Exportin-5 recognizes 3' overhang of pre-miRNA, Saccharomyces cerevisiae" +xref: Reactome:REACT_109723 "Exportin-5 recognizes 3' overhang of pre-miRNA, Arabidopsis thaliana" +xref: Reactome:REACT_12458 "Exportin-5 recognizes 3' overhang of pre-miRNA, Homo sapiens" +xref: Reactome:REACT_29965 "Exportin-5 recognizes 3' overhang of pre-miRNA, Canis familiaris" +xref: Reactome:REACT_77167 "Exportin-5 recognizes 3' overhang of pre-miRNA, Gallus gallus" +xref: Reactome:REACT_78197 "Exportin-5 recognizes 3' overhang of pre-miRNA, Sus scrofa" +xref: Reactome:REACT_87164 "Exportin-5 recognizes 3' overhang of pre-miRNA, Schizosaccharomyces pombe" +xref: Reactome:REACT_89329 "Exportin-5 recognizes 3' overhang of pre-miRNA, Rattus norvegicus" +xref: Reactome:REACT_90531 "Exportin-5 recognizes 3' overhang of pre-miRNA, Danio rerio" +xref: Reactome:REACT_98683 "Exportin-5 recognizes 3' overhang of pre-miRNA, Taeniopygia guttata" +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0003729 +name: mRNA binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns." [GOC:kmv, SO:0000234] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_yeast +subset: gosubset_prok +is_a: GO:0003723 ! RNA binding + +[Term] +id: GO:0003735 +name: structural constituent of ribosome +namespace: molecular_function +alt_id: GO:0003736 +alt_id: GO:0003737 +alt_id: GO:0003738 +alt_id: GO:0003739 +alt_id: GO:0003740 +alt_id: GO:0003741 +alt_id: GO:0003742 +def: "The action of a molecule that contributes to the structural integrity of the ribosome." [GOC:mah] +comment: Note that this term may be used to annotate ribosomal RNAs as well as ribosomal proteins. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_yeast +subset: gosubset_prok +synonym: "ribosomal protein" BROAD [] +synonym: "ribosomal RNA" RELATED [] +is_a: GO:0005198 ! structural molecule activity + +[Term] +id: GO:0003924 +name: GTPase activity +namespace: molecular_function +def: "Catalysis of the reaction: GTP + H2O = GDP + phosphate." [ISBN:0198547684] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_yeast +subset: gosubset_prok +synonym: "ARF small monomeric GTPase activity" NARROW [] +synonym: "dynamin GTPase activity" NARROW [] +synonym: "heterotrimeric G-protein GTPase activity" NARROW [] +synonym: "heterotrimeric G-protein GTPase, alpha-subunit" RELATED [] +synonym: "heterotrimeric G-protein GTPase, beta-subunit" RELATED [] +synonym: "heterotrimeric G-protein GTPase, gamma-subunit" RELATED [] +synonym: "hydrolase activity, acting on acid anhydrides, acting on GTP, involved in cellular and subcellular movement" BROAD [] +synonym: "protein-synthesizing GTPase activity" NARROW [] +synonym: "protein-synthesizing GTPase activity, elongation" NARROW [] +synonym: "protein-synthesizing GTPase activity, initiation" NARROW [] +synonym: "protein-synthesizing GTPase activity, termination" NARROW [] +synonym: "Rab small monomeric GTPase activity" NARROW [] +synonym: "Ran small monomeric GTPase activity" NARROW [] +synonym: "Ras small monomeric GTPase activity" NARROW [] +synonym: "RHEB small monomeric GTPase activity" NARROW [] +synonym: "Rho small monomeric GTPase activity" NARROW [] +synonym: "Sar small monomeric GTPase activity" NARROW [] +synonym: "signal-recognition-particle GTPase activity" NARROW [] +synonym: "small monomeric GTPase activity" NARROW [] +synonym: "tubulin GTPase activity" NARROW [] +xref: Reactome:REACT_100432 "trans-Golgi Network Vesicle Scission, Mus musculus" +xref: Reactome:REACT_100708 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Bos taurus" +xref: Reactome:REACT_101121 "trans-Golgi Network Vesicle Scission, Rattus norvegicus" +xref: Reactome:REACT_101520 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Drosophila melanogaster" +xref: Reactome:REACT_101563 "Loss of Sar1b GTPase, Arabidopsis thaliana" +xref: Reactome:REACT_101678 "G-protein alpha subunit is inactivated, Gallus gallus" +xref: Reactome:REACT_102040 "Adenylate cyclase increases the GTPase activity of G alpha-olf, Xenopus tropicalis" +xref: Reactome:REACT_102208 "Adenylate cyclase increases the GTPase activity of G alpha-olf, Danio rerio" +xref: Reactome:REACT_102307 "Adenylate cyclase increases the GTPase activity of Gi alpha, Gallus gallus" +xref: Reactome:REACT_102371 "Vesicle Uncoating, Oryza sativa" +xref: Reactome:REACT_102510 "trans-Golgi Network Vesicle Scission, Bos taurus" +xref: Reactome:REACT_102532 "Loss of Sar1b GTPase, Danio rerio" +xref: Reactome:REACT_103518 "trans-Golgi Network Lysosomal Vesicle Scission, Sus scrofa" +xref: Reactome:REACT_104081 "G alpha (i) auto-inactivates by hydrolysing GTP to GDP, Mus musculus" +xref: Reactome:REACT_104477 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Canis familiaris" +xref: Reactome:REACT_104739 "Loss of Sar1b GTPase, Dictyostelium discoideum" +xref: Reactome:REACT_105323 "trans-Golgi Network Vesicle Scission, Canis familiaris" +xref: Reactome:REACT_105697 "G-protein alpha subunit is inactivated, Saccharomyces cerevisiae" +xref: Reactome:REACT_105708 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Xenopus tropicalis" +xref: Reactome:REACT_105854 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Taeniopygia guttata" +xref: Reactome:REACT_106121 "Vesicle Uncoating, Saccharomyces cerevisiae" +xref: Reactome:REACT_106217 "Hydrolysis of eEF1A:GTP, Dictyostelium discoideum" +xref: Reactome:REACT_106301 "Adenylate cyclase increases the GTPase activity of G alpha-olf, Mus musculus" +xref: Reactome:REACT_106528 "trans-Golgi Network Lysosomal Vesicle Scission, Canis familiaris" +xref: Reactome:REACT_107176 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Taeniopygia guttata" +xref: Reactome:REACT_107306 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Rattus norvegicus" +xref: Reactome:REACT_107730 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Saccharomyces cerevisiae" +xref: Reactome:REACT_107820 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Canis familiaris" +xref: Reactome:REACT_108363 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Drosophila melanogaster" +xref: Reactome:REACT_108653 "G-protein alpha subunit is inactivated, Bos taurus" +xref: Reactome:REACT_108825 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Drosophila melanogaster" +xref: Reactome:REACT_108837 "trans-Golgi Network Vesicle Scission, Xenopus tropicalis" +xref: Reactome:REACT_109360 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Sus scrofa" +xref: Reactome:REACT_109897 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Danio rerio" +xref: Reactome:REACT_110131 "G alpha (i) auto-inactivates by hydrolysing GTP to GDP, Gallus gallus" +xref: Reactome:REACT_110443 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Xenopus tropicalis" +xref: Reactome:REACT_110557 "trans-Golgi Network Vesicle Scission, Danio rerio" +xref: Reactome:REACT_110859 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Caenorhabditis elegans" +xref: Reactome:REACT_110879 "G-protein alpha subunit is inactivated, Canis familiaris" +xref: Reactome:REACT_110931 "G-protein alpha subunit is inactivated, Sus scrofa" +xref: Reactome:REACT_111994 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Xenopus tropicalis" +xref: Reactome:REACT_112104 "Endocytosis (internalization) of clathrin-coated vesicle, Sus scrofa" +xref: Reactome:REACT_112254 "Endocytosis (internalization) of clathrin-coated vesicle, Xenopus tropicalis" +xref: Reactome:REACT_112389 "Disassembly of COPII coated vesicle, Gallus gallus" +xref: Reactome:REACT_112587 "trans-Golgi Network Vesicle Scission, Schizosaccharomyces pombe" +xref: Reactome:REACT_112651 "Vesicle Uncoating, Xenopus tropicalis" +xref: Reactome:REACT_112671 "Vesicle Uncoating, Plasmodium falciparum" +xref: Reactome:REACT_113058 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Saccharomyces cerevisiae" +xref: Reactome:REACT_113209 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Schizosaccharomyces pombe" +xref: Reactome:REACT_113727 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Saccharomyces cerevisiae" +xref: Reactome:REACT_113832 "Formation of clathrin coated vesicle, Bos taurus" +xref: Reactome:REACT_113952 "Formation of clathrin coated vesicle, Schizosaccharomyces pombe" +xref: Reactome:REACT_113954 "Endocytosis (internalization) of clathrin-coated vesicle, Schizosaccharomyces pombe" +xref: Reactome:REACT_114148 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Schizosaccharomyces pombe" +xref: Reactome:REACT_114153 "Loss of Sar1b GTPase, Xenopus tropicalis" +xref: Reactome:REACT_114188 "Formation of clathrin coated vesicle, Sus scrofa" +xref: Reactome:REACT_114210 "G-protein alpha subunit is inactivated, Schizosaccharomyces pombe" +xref: Reactome:REACT_114331 "trans-Golgi Network Vesicle Scission, Taeniopygia guttata" +xref: Reactome:REACT_114379 "Formation of clathrin coated vesicle, Taeniopygia guttata" +xref: Reactome:REACT_114384 "Hydrolysis of eEF1A:GTP, Gallus gallus" +xref: Reactome:REACT_114532 "Formation of clathrin coated vesicle, Xenopus tropicalis" +xref: Reactome:REACT_114620 "Endocytosis (internalization) of clathrin-coated vesicle, Taeniopygia guttata" +xref: Reactome:REACT_114824 "trans-Golgi Network Lysosomal Vesicle Scission, Taeniopygia guttata" +xref: Reactome:REACT_115229 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Schizosaccharomyces pombe" +xref: Reactome:REACT_115324 "Endocytosis (internalization) of clathrin-coated vesicle, Bos taurus" +xref: Reactome:REACT_12396 "Loss of Sar1b GTPase, Homo sapiens" +xref: Reactome:REACT_12397 "Endocytosis (internalization) of clathrin-coated vesicle, Homo sapiens" +xref: Reactome:REACT_12456 "Vesicle Uncoating, Homo sapiens" +xref: Reactome:REACT_12612 "Endocytosis of clathrin-coated vesicle, Rattus norvegicus" +xref: Reactome:REACT_15316 "G-protein alpha subunit is inactivated, Homo sapiens" +xref: Reactome:REACT_15335 "Adenylate cyclase increases the GTPase activity of G alpha-olf, Homo sapiens" +xref: Reactome:REACT_15449 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Homo sapiens" +xref: Reactome:REACT_15495 "Adenylate cyclase increases the GTPase activity of Gi alpha, Homo sapiens" +xref: Reactome:REACT_19123 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Homo sapiens" +xref: Reactome:REACT_19178 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Homo sapiens" +xref: Reactome:REACT_19186 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Homo sapiens" +xref: Reactome:REACT_19194 "trans-Golgi Network Lysosomal Vesicle Scission, Homo sapiens" +xref: Reactome:REACT_19219 "G alpha (i) auto-inactivates by hydrolysing GTP to GDP, Homo sapiens" +xref: Reactome:REACT_19255 "trans-Golgi Network Vesicle Scission, Homo sapiens" +xref: Reactome:REACT_19317 "G alpha (i)1 auto-inactivates by hydrolysing GTP to GDP, Rattus norvegicus" +xref: Reactome:REACT_22359 "Formation of clathrin coated vesicle, Homo sapiens" +xref: Reactome:REACT_28065 "Vesicle Uncoating, Sus scrofa" +xref: Reactome:REACT_28251 "Hydrolysis of eEF1A:GTP, Danio rerio" +xref: Reactome:REACT_28269 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Gallus gallus" +xref: Reactome:REACT_29162 "trans-Golgi Network Lysosomal Vesicle Scission, Mus musculus" +xref: Reactome:REACT_30456 "Hydrolysis of eEF1A:GTP, Plasmodium falciparum" +xref: Reactome:REACT_30463 "Adenylate cyclase increases the GTPase activity of G alpha-olf, Bos taurus" +xref: Reactome:REACT_30562 "Endocytosis (internalization) of clathrin-coated vesicle, Caenorhabditis elegans" +xref: Reactome:REACT_30687 "G-protein alpha subunit is inactivated, Xenopus tropicalis" +xref: Reactome:REACT_30707 "trans-Golgi Network Vesicle Scission, Caenorhabditis elegans" +xref: Reactome:REACT_30942 "Vesicle Uncoating, Rattus norvegicus" +xref: Reactome:REACT_31226 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Mus musculus" +xref: Reactome:REACT_31474 "Formation of clathrin coated vesicle, Danio rerio" +xref: Reactome:REACT_31530 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Caenorhabditis elegans" +xref: Reactome:REACT_31599 "trans-Golgi Network Lysosomal Vesicle Scission, Danio rerio" +xref: Reactome:REACT_31709 "Hydrolysis of eEF1A:GTP, Drosophila melanogaster" +xref: Reactome:REACT_31727 "Adenylate cyclase increases the GTPase activity of G alpha-olf, Taeniopygia guttata" +xref: Reactome:REACT_31850 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Gallus gallus" +xref: Reactome:REACT_32006 "Loss of Sar1b GTPase, Canis familiaris" +xref: Reactome:REACT_32028 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Danio rerio" +xref: Reactome:REACT_32914 "Vesicle Uncoating, Dictyostelium discoideum" +xref: Reactome:REACT_33948 "trans-Golgi Network Lysosomal Vesicle Scission, Rattus norvegicus" +xref: Reactome:REACT_34113 "Vesicle Uncoating, Schizosaccharomyces pombe" +xref: Reactome:REACT_34480 "G-protein alpha subunit is inactivated, Caenorhabditis elegans" +xref: Reactome:REACT_34592 "G alpha (i) auto-inactivates by hydrolysing GTP to GDP, Xenopus tropicalis" +xref: Reactome:REACT_34735 "Adenylate cyclase increases the GTPase activity of Gi alpha, Taeniopygia guttata" +xref: Reactome:REACT_348 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Homo sapiens" +xref: Reactome:REACT_36834 "trans-Golgi Network Lysosomal Vesicle Scission, Bos taurus" +xref: Reactome:REACT_37542 "G alpha (i) auto-inactivates by hydrolysing GTP to GDP, Sus scrofa" +xref: Reactome:REACT_552 "Hydrolysis of eEF1A:GTP, Homo sapiens" +xref: Reactome:REACT_6171 "Hydrolysis of Ran:GTP to Ran:GDP, Homo sapiens" +xref: Reactome:REACT_712 "Hydrolysis of reEF1A:GTP, Oryctolagus cuniculus" +xref: Reactome:REACT_75799 "Disassembly of COPII coated vesicle, Homo sapiens" +xref: Reactome:REACT_77032 "Hydrolysis of eEF1A:GTP, Canis familiaris" +xref: Reactome:REACT_77303 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Danio rerio" +xref: Reactome:REACT_78069 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Caenorhabditis elegans" +xref: Reactome:REACT_78231 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Taeniopygia guttata" +xref: Reactome:REACT_78653 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Bos taurus" +xref: Reactome:REACT_78945 "G-protein alpha subunit is inactivated, Rattus norvegicus" +xref: Reactome:REACT_79558 "G alpha (i) auto-inactivates by hydrolysing GTP to GDP, Taeniopygia guttata" +xref: Reactome:REACT_79620 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Mus musculus" +xref: Reactome:REACT_80275 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Bos taurus" +xref: Reactome:REACT_80612 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Canis familiaris" +xref: Reactome:REACT_81304 "Loss of Sar1b GTPase, Taeniopygia guttata" +xref: Reactome:REACT_81448 "Endocytosis (internalization) of clathrin-coated vesicle, Canis familiaris" +xref: Reactome:REACT_81580 "Disassembly of COPII coated vesicle, Mus musculus" +xref: Reactome:REACT_81664 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Caenorhabditis elegans" +xref: Reactome:REACT_81879 "Vesicle Uncoating, Drosophila melanogaster" +xref: Reactome:REACT_82203 "Formation of clathrin coated vesicle, Canis familiaris" +xref: Reactome:REACT_82263 "G-protein alpha subunit is inactivated, Taeniopygia guttata" +xref: Reactome:REACT_82457 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Taeniopygia guttata" +xref: Reactome:REACT_82603 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Canis familiaris" +xref: Reactome:REACT_82704 "Loss of Sar1b GTPase, Rattus norvegicus" +xref: Reactome:REACT_83308 "Adenylate cyclase increases the GTPase activity of G alpha-olf, Rattus norvegicus" +xref: Reactome:REACT_83403 "G-protein alpha subunit is inactivated, Drosophila melanogaster" +xref: Reactome:REACT_83440 "Hydrolysis of eEF1A:GTP, Schizosaccharomyces pombe" +xref: Reactome:REACT_83730 "Loss of Sar1b GTPase, Plasmodium falciparum" +xref: Reactome:REACT_84204 "Endocytosis (internalization) of clathrin-coated vesicle, Danio rerio" +xref: Reactome:REACT_84553 "Vesicle Uncoating, Canis familiaris" +xref: Reactome:REACT_84696 "G-protein alpha subunit is inactivated, Danio rerio" +xref: Reactome:REACT_84712 "Hydrolysis of eEF1A:GTP, Saccharomyces cerevisiae" +xref: Reactome:REACT_84735 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Rattus norvegicus" +xref: Reactome:REACT_85008 "Vesicle Uncoating, Danio rerio" +xref: Reactome:REACT_85418 "Loss of Sar1b GTPase, Gallus gallus" +xref: Reactome:REACT_85769 "Disassembly of COPII coated vesicle, Danio rerio" +xref: Reactome:REACT_85972 "Adenylate cyclase increases the GTPase activity of G alpha-olf, Canis familiaris" +xref: Reactome:REACT_86227 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Dictyostelium discoideum" +xref: Reactome:REACT_86358 "trans-Golgi Network Lysosomal Vesicle Scission, Caenorhabditis elegans" +xref: Reactome:REACT_86400 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Dictyostelium discoideum" +xref: Reactome:REACT_86630 "Vesicle Uncoating, Mus musculus" +xref: Reactome:REACT_86760 "Adenylate cyclase increases the GTPase activity of G alpha-olf, Gallus gallus" +xref: Reactome:REACT_86972 "Loss of Sar1b GTPase, Mus musculus" +xref: Reactome:REACT_87409 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Dictyostelium discoideum" +xref: Reactome:REACT_87506 "Formation of clathrin coated vesicle, Rattus norvegicus" +xref: Reactome:REACT_87558 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Mus musculus" +xref: Reactome:REACT_87653 "Endocytosis (internalization) of clathrin-coated vesicle, Mus musculus" +xref: Reactome:REACT_87661 "Formation of clathrin coated vesicle, Drosophila melanogaster" +xref: Reactome:REACT_88045 "Vesicle Uncoating, Gallus gallus" +xref: Reactome:REACT_88357 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Canis familiaris" +xref: Reactome:REACT_89231 "Loss of Sar1b GTPase, Bos taurus" +xref: Reactome:REACT_89292 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Gallus gallus" +xref: Reactome:REACT_89416 "G alpha (i) auto-inactivates by hydrolysing GTP to GDP, Bos taurus" +xref: Reactome:REACT_89668 "trans-Golgi Network Lysosomal Vesicle Scission, Xenopus tropicalis" +xref: Reactome:REACT_89763 "Vesicle Uncoating, Taeniopygia guttata" +xref: Reactome:REACT_90050 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Mus musculus" +xref: Reactome:REACT_90064 "Hydrolysis of eEF1A:GTP, Mus musculus" +xref: Reactome:REACT_90517 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Xenopus tropicalis" +xref: Reactome:REACT_90703 "G-protein alpha subunit is inactivated, Dictyostelium discoideum" +xref: Reactome:REACT_91199 "Adenylate cyclase increases the GTPase activity of Gi alpha, Bos taurus" +xref: Reactome:REACT_91588 "trans-Golgi Network Vesicle Scission, Drosophila melanogaster" +xref: Reactome:REACT_92176 "Endocytosis (internalization) of clathrin-coated vesicle, Drosophila melanogaster" +xref: Reactome:REACT_92197 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Bos taurus" +xref: Reactome:REACT_92198 "Loss of Sar1b GTPase, Oryza sativa" +xref: Reactome:REACT_92450 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Danio rerio" +xref: Reactome:REACT_93249 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Dictyostelium discoideum" +xref: Reactome:REACT_93305 "Loss of Sar1b GTPase, Sus scrofa" +xref: Reactome:REACT_93641 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Gallus gallus" +xref: Reactome:REACT_93742 "G-protein alpha subunit is inactivated, Mus musculus" +xref: Reactome:REACT_93772 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Gallus gallus" +xref: Reactome:REACT_94019 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Sus scrofa" +xref: Reactome:REACT_94095 "trans-Golgi Network Vesicle Scission, Sus scrofa" +xref: Reactome:REACT_94305 "Adenylate cyclase increases the GTPase activity of Gi alpha, Xenopus tropicalis" +xref: Reactome:REACT_94760 "Adenylate cyclase increases the GTPase activity of Gi alpha, Danio rerio" +xref: Reactome:REACT_95238 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Rattus norvegicus" +xref: Reactome:REACT_95563 "Adenylate cyclase increases the GTPase activity of Gi alpha, Canis familiaris" +xref: Reactome:REACT_96019 "Loss of Sar1b GTPase, Drosophila melanogaster" +xref: Reactome:REACT_96132 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Drosophila melanogaster" +xref: Reactome:REACT_96223 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Sus scrofa" +xref: Reactome:REACT_96612 "Adenylate cyclase increases the GTPase activity of Gi alpha, Rattus norvegicus" +xref: Reactome:REACT_96881 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Xenopus tropicalis" +xref: Reactome:REACT_97284 "Loss of Sar1b GTPase, Saccharomyces cerevisiae" +xref: Reactome:REACT_97405 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Taeniopygia guttata" +xref: Reactome:REACT_97595 "G alpha (i) auto-inactivates by hydrolysing GTP to GDP, Danio rerio" +xref: Reactome:REACT_97794 "Loss of Sar1b GTPase, Schizosaccharomyces pombe" +xref: Reactome:REACT_98431 "Formation of clathrin coated vesicle, Caenorhabditis elegans" +xref: Reactome:REACT_98556 "Vesicle Uncoating, Bos taurus" +xref: Reactome:REACT_98837 "G alpha (i) auto-inactivates by hydrolysing GTP to GDP, Canis familiaris" +xref: Reactome:REACT_98859 "Adenylate cyclase increases the GTPase activity of Gi alpha, Mus musculus" +xref: Reactome:REACT_99479 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Mus musculus" +xref: Reactome:REACT_99533 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Sus scrofa" +xref: Reactome:REACT_99616 "Formation of clathrin coated vesicle, Mus musculus" +xref: RHEA:19672 +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0004386 +name: helicase activity +namespace: molecular_function +def: "Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix." [GOC:mah, ISBN:0198506732] +comment: Note that most helicases catalyze processive duplex unwinding. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_yeast +subset: gosubset_prok +xref: Reactome:REACT_101111 "Addition of the third nucleotide on the nascent transcript, Saccharomyces cerevisiae" +xref: Reactome:REACT_101247 "Formation of open bubble structure in DNA by helicases, Bos taurus" +xref: Reactome:REACT_101622 "MCM8 mediated fork unwinding, Danio rerio" +xref: Reactome:REACT_101644 "Formation of open bubble structure in DNA by helicases, Oryza sativa" +xref: Reactome:REACT_101823 "MCM2-7 mediated fork unwinding, Plasmodium falciparum" +xref: Reactome:REACT_101994 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Xenopus tropicalis" +xref: Reactome:REACT_102121 "Addition of the third nucleotide on the nascent transcript, Rattus norvegicus" +xref: Reactome:REACT_102441 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Gallus gallus" +xref: Reactome:REACT_102560 "MCM2-7 mediated fork unwinding, Oryza sativa" +xref: Reactome:REACT_1033 "Formation of open bubble structure in DNA by helicases, Homo sapiens" +xref: Reactome:REACT_103861 "MCM8 mediated fork unwinding, Bos taurus" +xref: Reactome:REACT_103881 "RNA Polymerase II Promoter Opening: First Transition, Dictyostelium discoideum" +xref: Reactome:REACT_103897 "MCM8 mediated fork unwinding, Mus musculus" +xref: Reactome:REACT_103959 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Rattus norvegicus" +xref: Reactome:REACT_104221 "MCM2-7 mediated fork unwinding, Rattus norvegicus" +xref: Reactome:REACT_105950 "MCM2-7 mediated fork unwinding, Xenopus tropicalis" +xref: Reactome:REACT_106346 "Formation of open bubble structure in DNA by helicases, Taeniopygia guttata" +xref: Reactome:REACT_107072 "Formation of open bubble structure in DNA by helicases, Mus musculus" +xref: Reactome:REACT_107495 "RNA Polymerase II Promoter Opening: First Transition, Taeniopygia guttata" +xref: Reactome:REACT_108159 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Dictyostelium discoideum" +xref: Reactome:REACT_108648 "Addition of the third nucleotide on the nascent transcript, Arabidopsis thaliana" +xref: Reactome:REACT_108654 "MCM2-7 mediated fork unwinding, Schizosaccharomyces pombe" +xref: Reactome:REACT_109035 "RNA Polymerase II Promoter Opening: First Transition, Schizosaccharomyces pombe" +xref: Reactome:REACT_109161 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Arabidopsis thaliana" +xref: Reactome:REACT_110588 "MCM8 mediated fork unwinding, Xenopus tropicalis" +xref: Reactome:REACT_110827 "Formation of open bubble structure in DNA by helicases, Danio rerio" +xref: Reactome:REACT_110845 "Cap-bound mRNA is activated by helicases, Mus musculus" +xref: Reactome:REACT_112208 "MCM8 mediated fork unwinding, Drosophila melanogaster" +xref: Reactome:REACT_112817 "Cap-bound mRNA is activated by helicases, Schizosaccharomyces pombe" +xref: Reactome:REACT_113177 "Formation of open bubble structure in DNA by helicases, Caenorhabditis elegans" +xref: Reactome:REACT_1521 "Cap-bound mRNA is activated by helicases, Homo sapiens" +xref: Reactome:REACT_1817 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Homo sapiens" +xref: Reactome:REACT_1844 "RNA Polymerase II Promoter Opening: First Transition, Homo sapiens" +xref: Reactome:REACT_28131 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Drosophila melanogaster" +xref: Reactome:REACT_28343 "MCM2-7 mediated fork unwinding, Danio rerio" +xref: Reactome:REACT_28810 "Addition of the third nucleotide on the nascent transcript, Oryza sativa" +xref: Reactome:REACT_28880 "MCM2-7 mediated fork unwinding, Drosophila melanogaster" +xref: Reactome:REACT_29155 "Addition of the third nucleotide on the nascent transcript, Drosophila melanogaster" +xref: Reactome:REACT_29217 "Formation of open bubble structure in DNA by helicases, Xenopus tropicalis" +xref: Reactome:REACT_29818 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Oryza sativa" +xref: Reactome:REACT_29850 "RNA Polymerase II Promoter Opening: First Transition, Saccharomyces cerevisiae" +xref: Reactome:REACT_30013 "MCM8 mediated fork unwinding, Rattus norvegicus" +xref: Reactome:REACT_30989 "MCM8 mediated fork unwinding, Arabidopsis thaliana" +xref: Reactome:REACT_31034 "Cap-bound mRNA is activated by helicases, Danio rerio" +xref: Reactome:REACT_31090 "MCM2-7 mediated fork unwinding, Gallus gallus" +xref: Reactome:REACT_31554 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Schizosaccharomyces pombe" +xref: Reactome:REACT_32533 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Caenorhabditis elegans" +xref: Reactome:REACT_33205 "MCM8 mediated fork unwinding, Canis familiaris" +xref: Reactome:REACT_34016 "Formation of open bubble structure in DNA by helicases, Rattus norvegicus" +xref: Reactome:REACT_34089 "MCM2-7 mediated fork unwinding, Dictyostelium discoideum" +xref: Reactome:REACT_34560 "MCM8 mediated fork unwinding, Sus scrofa" +xref: Reactome:REACT_40 "Addition of the third nucleotide on the nascent transcript, Homo sapiens" +xref: Reactome:REACT_6134 "HIV-1 Promoter Opening: First Transition, Homo sapiens" +xref: Reactome:REACT_6184 "Addition of the fourth nucleotide on the nascent HIV-1 transcript: Second Transition, Homo sapiens" +xref: Reactome:REACT_6325 "Addition of the third nucleotide on the nascent HIV-1 transcript, Homo sapiens" +xref: Reactome:REACT_6758 "Xenopus Mcm8 mediated fork unwinding, Xenopus laevis" +xref: Reactome:REACT_6768 "MCM8 mediated fork unwinding, Homo sapiens" +xref: Reactome:REACT_6853 "Yeast Mcm2-7 mediated fork unwinding, Saccharomyces cerevisiae" +xref: Reactome:REACT_6922 "MCM2-7 mediated fork unwinding, Homo sapiens" +xref: Reactome:REACT_78086 "RNA Polymerase II Promoter Opening: First Transition, Rattus norvegicus" +xref: Reactome:REACT_78462 "Formation of open bubble structure in DNA by helicases, Drosophila melanogaster" +xref: Reactome:REACT_78667 "MCM2-7 mediated fork unwinding, Canis familiaris" +xref: Reactome:REACT_78771 "MCM8 mediated fork unwinding, Dictyostelium discoideum" +xref: Reactome:REACT_79759 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Mus musculus" +xref: Reactome:REACT_80107 "RNA Polymerase II Promoter Opening: First Transition, Arabidopsis thaliana" +xref: Reactome:REACT_80325 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Danio rerio" +xref: Reactome:REACT_80500 "MCM8 mediated fork unwinding, Gallus gallus" +xref: Reactome:REACT_80532 "Addition of the third nucleotide on the nascent transcript, Gallus gallus" +xref: Reactome:REACT_80605 "Addition of the third nucleotide on the nascent transcript, Mus musculus" +xref: Reactome:REACT_81126 "Addition of the third nucleotide on the nascent transcript, Schizosaccharomyces pombe" +xref: Reactome:REACT_81335 "RNA Polymerase II Promoter Opening: First Transition, Gallus gallus" +xref: Reactome:REACT_81427 "MCM8 mediated fork unwinding, Taeniopygia guttata" +xref: Reactome:REACT_81441 "MCM8 mediated fork unwinding, Oryza sativa" +xref: Reactome:REACT_81682 "Formation of open bubble structure in DNA by helicases, Canis familiaris" +xref: Reactome:REACT_82776 "RNA Polymerase II Promoter Opening: First Transition, Danio rerio" +xref: Reactome:REACT_83794 "Formation of open bubble structure in DNA by helicases, Gallus gallus" +xref: Reactome:REACT_84565 "Formation of open bubble structure in DNA by helicases, Schizosaccharomyces pombe" +xref: Reactome:REACT_84574 "Cap-bound mRNA is activated by helicases, Canis familiaris" +xref: Reactome:REACT_84809 "MCM2-7 mediated fork unwinding, Mus musculus" +xref: Reactome:REACT_84907 "MCM2-7 mediated fork unwinding, Taeniopygia guttata" +xref: Reactome:REACT_85111 "Cap-bound mRNA is activated by helicases, Drosophila melanogaster" +xref: Reactome:REACT_85172 "MCM2-7 mediated fork unwinding, Arabidopsis thaliana" +xref: Reactome:REACT_86220 "MCM2-7 mediated fork unwinding, Caenorhabditis elegans" +xref: Reactome:REACT_88362 "Addition of the third nucleotide on the nascent transcript, Caenorhabditis elegans" +xref: Reactome:REACT_89000 "MCM2-7 mediated fork unwinding, Bos taurus" +xref: Reactome:REACT_89030 "Formation of open bubble structure in DNA by helicases, Saccharomyces cerevisiae" +xref: Reactome:REACT_89363 "Addition of the third nucleotide on the nascent transcript, Xenopus tropicalis" +xref: Reactome:REACT_89694 "RNA Polymerase II Promoter Opening: First Transition, Drosophila melanogaster" +xref: Reactome:REACT_91822 "MCM8 mediated fork unwinding, Plasmodium falciparum" +xref: Reactome:REACT_93391 "RNA Polymerase II Promoter Opening: First Transition, Oryza sativa" +xref: Reactome:REACT_93711 "RNA Polymerase II Promoter Opening: First Transition, Mus musculus" +xref: Reactome:REACT_94645 "RNA Polymerase II Promoter Opening: First Transition, Xenopus tropicalis" +xref: Reactome:REACT_94679 "RNA Polymerase II Promoter Opening: First Transition, Caenorhabditis elegans" +xref: Reactome:REACT_95942 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Saccharomyces cerevisiae" +xref: Reactome:REACT_95993 "Formation of open bubble structure in DNA by helicases, Arabidopsis thaliana" +xref: Reactome:REACT_98273 "Addition of the third nucleotide on the nascent transcript, Dictyostelium discoideum" +xref: Reactome:REACT_98302 "Formation of open bubble structure in DNA by helicases, Sus scrofa" +xref: Reactome:REACT_98745 "Cap-bound mRNA is activated by helicases, Xenopus tropicalis" +xref: Reactome:REACT_99120 "Addition of the third nucleotide on the nascent transcript, Danio rerio" +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0004518 +name: nuclease activity +namespace: molecular_function +def: "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN:0198547684] +comment: Note that 'tRNA nucleotidyltransferase activity ; GO:0009022', also known as 'ribonuclease PH', does not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +xref: EC:3.1.-.- +is_a: GO:0003674 ! molecular_function +relationship: part_of GO:0034641 ! cellular nitrogen compound metabolic process + +[Term] +id: GO:0004871 +name: signal transducer activity +namespace: molecular_function +alt_id: GO:0005062 +alt_id: GO:0009369 +alt_id: GO:0009370 +def: "Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response." [GOC:go_curators] +comment: Ligands do NOT have the molecular function 'signal transducer activity'. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "hematopoietin/interferon-class (D200-domain) cytokine receptor signal transducer activity" NARROW [] +synonym: "quorum sensing response regulator activity" NARROW [] +synonym: "quorum sensing signal generator activity" NARROW [] +is_a: GO:0003674 ! molecular_function +intersection_of: GO:0003674 ! molecular_function +intersection_of: part_of GO:0007165 ! signal transduction +relationship: part_of GO:0007165 ! signal transduction + +[Term] +id: GO:0005198 +name: structural molecule activity +namespace: molecular_function +def: "The action of a molecule that contributes to the structural integrity of a complex or assembly within or outside a cell." [GOC:mah] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0005575 +name: cellular_component +namespace: cellular_component +alt_id: GO:0008372 +def: "The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together." [GOC:go_curators, NIF_Subcellular:sao-1337158144] +comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "cell or subcellular entity" EXACT [] +synonym: "cellular component" EXACT [] +synonym: "subcellular entity" RELATED [NIF_Subcellular:nlx_subcell_100315] +xref: NIF_Subcellular:sao-1337158144 +xref: NIF_Subcellular:sao1337158144 + +[Term] +id: GO:0005576 +name: extracellular region +namespace: cellular_component +def: "The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite." [GOC:go_curators] +comment: Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "extracellular" EXACT [] +xref: Wikipedia:Extracellular +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0005578 +name: proteinaceous extracellular matrix +namespace: cellular_component +def: "A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus." [GOC:mtg_sensu, ISBN:0198547684] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_plant +is_a: GO:0005575 ! cellular_component +relationship: part_of GO:0005576 ! extracellular region + +[Term] +id: GO:0005615 +name: extracellular space +namespace: cellular_component +def: "That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid." [ISBN:0198547684] +comment: Note that for multicellular organisms, the extracellular space refers to everything outside a cell, but still within the organism (excluding the extracellular matrix). Gene products from a multi-cellular organism that are secreted from a cell into the interstitial fluid or blood can therefore be annotated to this term. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_plant +synonym: "intercellular space" RELATED [] +xref: NIF_Subcellular:sao1425028079 +is_a: GO:0005575 ! cellular_component +relationship: part_of GO:0005576 ! extracellular region + +[Term] +id: GO:0005618 +name: cell wall +namespace: cellular_component +def: "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins." [GOC:giardia, http://en.wikipedia.org/wiki/Microbial_cyst, ISBN:0198547684, PMID:15134259] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +xref: Wikipedia:Cell_wall +is_a: GO:0030312 ! external encapsulating structure + +[Term] +id: GO:0005622 +name: intracellular +namespace: cellular_component +def: "The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm." [ISBN:0198506732] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "internal to cell" EXACT [] +synonym: "nucleocytoplasm" RELATED [GOC:mah] +synonym: "protoplasm" EXACT [] +synonym: "protoplast" RELATED [GOC:mah] +xref: Wikipedia:Intracellular +is_a: GO:0005575 ! cellular_component +relationship: part_of GO:0005623 ! cell + +[Term] +id: GO:0005623 +name: cell +namespace: cellular_component +def: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:go_curators] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_plant +subset: gosubset_prok +xref: NIF_Subcellular:sao1813327414 +xref: Wikipedia:Cell_(biology) +is_a: GO:0005575 ! cellular_component +property_value: IAO:0000589 "cell and encapsulating structures" xsd:string + +[Term] +id: GO:0005634 +name: nucleus +namespace: cellular_component +def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +synonym: "cell nucleus" EXACT [] +xref: NIF_Subcellular:sao1702920020 +xref: Wikipedia:Cell_nucleus +is_a: GO:0043226 ! organelle +relationship: part_of GO:0005622 ! intracellular + +[Term] +id: GO:0005635 +name: nuclear envelope +namespace: cellular_component +alt_id: GO:0005636 +def: "The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space)." [ISBN:0198547684] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_plant +xref: Wikipedia:Nuclear_envelope +is_a: GO:0005575 ! cellular_component +relationship: part_of GO:0005634 ! nucleus + +[Term] +id: GO:0005654 +name: nucleoplasm +namespace: cellular_component +def: "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC:ma, ISBN:0124325653] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_plant +xref: NIF_Subcellular:sao661522542 +xref: Wikipedia:Nucleoplasm +is_a: GO:0005575 ! cellular_component +relationship: part_of GO:0005634 ! nucleus + +[Term] +id: GO:0005694 +name: chromosome +namespace: cellular_component +def: "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." [ISBN:0198547684] +comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_yeast +subset: gosubset_prok +synonym: "chromatid" RELATED [] +synonym: "interphase chromosome" NARROW [] +synonym: "prophase chromosome" NARROW [] +xref: Wikipedia:Chromosome +is_a: GO:0043226 ! organelle +relationship: part_of GO:0005622 ! intracellular + +[Term] +id: GO:0005730 +name: nucleolus +namespace: cellular_component +def: "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN:0198506732] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +xref: NIF_Subcellular:sao1820400233 +xref: Wikipedia:Nucleolus +is_a: GO:0043226 ! organelle +relationship: part_of GO:0005634 ! nucleus + +[Term] +id: GO:0005737 +name: cytoplasm +namespace: cellular_component +def: "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684] +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +xref: Wikipedia:Cytoplasm +is_a: GO:0005575 ! cellular_component +relationship: part_of GO:0005622 ! intracellular + +[Term] +id: GO:0005739 +name: mitochondrion +namespace: cellular_component +def: "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [GOC:giardia, ISBN:0198506732] +comment: Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.) +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +synonym: "mitochondria" EXACT [] +xref: NIF_Subcellular:sao1860313010 +xref: Wikipedia:Mitochondrion +is_a: GO:0043226 ! organelle +relationship: part_of GO:0005737 ! cytoplasm + +[Term] +id: GO:0005764 +name: lysosome +namespace: cellular_component +def: "A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions." [GOC:mah, ISBN:0198506732] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_plant +xref: NIF_Subcellular:sao585356902 +xref: Wikipedia:Lysosome +is_a: GO:0005773 ! vacuole + +[Term] +id: GO:0005768 +name: endosome +namespace: cellular_component +def: "A vacuole to which materials ingested by endocytosis are delivered." [ISBN:0198506732, PMID:19696797] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +xref: NIF_Subcellular:sao1720343330 +xref: Wikipedia:Endosome +is_a: GO:0005773 ! vacuole + +[Term] +id: GO:0005773 +name: vacuole +namespace: cellular_component +def: "A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol." [GOC:mtg_sensu, ISBN:0198506732] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "vacuolar carboxypeptidase Y" RELATED [] +xref: Wikipedia:Vacuole +is_a: GO:0043226 ! organelle +relationship: part_of GO:0005737 ! cytoplasm + +[Term] +id: GO:0005777 +name: peroxisome +namespace: cellular_component +alt_id: GO:0019818 +def: "A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism." [GOC:pm, PMID:9302272, UniProtKB-KW:KW-0576] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_plant +subset: goslim_yeast +synonym: "peroxisomal" RELATED [GOC:curators] +synonym: "peroxisome vesicle" BROAD [] +xref: NIF_Subcellular:sao499555322 +xref: Wikipedia:Peroxisome +is_a: GO:0043226 ! organelle +relationship: part_of GO:0005737 ! cytoplasm + +[Term] +id: GO:0005783 +name: endoplasmic reticulum +namespace: cellular_component +def: "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [ISBN:0198506732] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +synonym: "ER" EXACT [] +xref: NIF_Subcellular:sao1036339110 +xref: Wikipedia:Endoplasmic_reticulum +is_a: GO:0043226 ! organelle + +[Term] +id: GO:0005794 +name: Golgi apparatus +namespace: cellular_component +def: "A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions." [ISBN:0198506732] +comment: Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +synonym: "Golgi" BROAD [] +synonym: "Golgi complex" EXACT [] +synonym: "Golgi ribbon" NARROW [] +xref: NIF_Subcellular:sao451912436 +xref: Wikipedia:Golgi_apparatus +is_a: GO:0043226 ! organelle +relationship: part_of GO:0005737 ! cytoplasm + +[Term] +id: GO:0005811 +name: lipid particle +namespace: cellular_component +def: "An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins." [GOC:mah, GOC:tb] +comment: Note that this term does not refer to vesicles, but instead to structures in which lipids do not necessarily form bilayers. +subset: goslim_chembl +subset: goslim_generic +synonym: "adiposome" EXACT [] +synonym: "lipid body" EXACT [] +synonym: "lipid droplet" EXACT [] +is_a: GO:0043226 ! organelle +relationship: part_of GO:0005622 ! intracellular + +[Term] +id: GO:0005815 +name: microtubule organizing center +namespace: cellular_component +def: "An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides." [GOC:vw, http://en.wikipedia.org/wiki/Microtubule_organizing_center, ISBN:0815316194, PMID:17072892, PMID:17245416] +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_yeast +synonym: "microtubule organising centre" EXACT [] +synonym: "MTOC" EXACT [] +xref: Wikipedia:Microtubule_organizing_center +is_a: GO:0005575 ! cellular_component +relationship: part_of GO:0005856 ! cytoskeleton + +[Term] +id: GO:0005829 +name: cytosol +namespace: cellular_component +def: "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC:hjd, GOC:jl] +subset: goslim_aspergillus +subset: goslim_chembl +subset: goslim_generic +subset: goslim_plant +subset: gosubset_prok +xref: NIF_Subcellular:sao101633890 +xref: Wikipedia:Cytosol +is_a: GO:0005575 ! cellular_component +relationship: part_of GO:0005737 ! cytoplasm + +[Term] +id: GO:0005840 +name: ribosome +namespace: cellular_component +alt_id: GO:0033279 +def: "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins." [ISBN:0198506732] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "free ribosome" NARROW [NIF_Subcellular:sao1139385046] +synonym: "membrane bound ribosome" NARROW [NIF_Subcellular:sao1291545653] +synonym: "ribosomal RNA" RELATED [] +xref: NIF_Subcellular:sao1429207766 +xref: Wikipedia:Ribosome +is_a: GO:0043226 ! organelle +relationship: part_of GO:0005737 ! cytoplasm + +[Term] +id: GO:0005856 +name: cytoskeleton +namespace: cellular_component +def: "Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles." [GOC:mah, ISBN:0198547684, PMID:16959967] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +xref: Wikipedia:Cytoskeleton +is_a: GO:0043226 ! organelle +relationship: part_of GO:0005622 ! intracellular + +[Term] +id: GO:0005886 +name: plasma membrane +namespace: cellular_component +alt_id: GO:0005904 +def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "bacterial inner membrane" NARROW [] +synonym: "cell membrane" EXACT [] +synonym: "cellular membrane" EXACT [NIF_Subcellular:sao6433132645] +synonym: "cytoplasmic membrane" EXACT [] +synonym: "inner endospore membrane" NARROW [] +synonym: "juxtamembrane" BROAD [] +synonym: "plasma membrane lipid bilayer" NARROW [GOC:mah] +synonym: "plasmalemma" EXACT [] +xref: NIF_Subcellular:sao1663586795 +xref: Wikipedia:Cell_membrane +is_a: GO:0005575 ! cellular_component +relationship: part_of GO:0005623 ! cell + +[Term] +id: GO:0005929 +name: cilium +namespace: cellular_component +def: "A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body." [GOC:cilia, GOC:kmv, GOC:vw, ISBN:0198547684] +comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +synonym: "eukaryotic flagellum" EXACT [] +synonym: "flagellum" RELATED [] +synonym: "microtubule-based flagellum" EXACT [] +xref: FMA:67181 +xref: NIF_Subcellular:sao787716553 +xref: Wikipedia:Cilium +is_a: GO:0043226 ! organelle +relationship: has_part GO:0043234 ! protein complex +relationship: part_of GO:0005623 ! cell + +[Term] +id: GO:0005975 +name: carbohydrate metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule." [GOC:mah, ISBN:0198506732] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +synonym: "carbohydrate metabolism" EXACT [] +xref: Reactome:REACT_102834 "Metabolism of carbohydrates, Mus musculus" +xref: Reactome:REACT_103806 "Metabolism of carbohydrates, Mycobacterium tuberculosis" +xref: Reactome:REACT_104502 "Metabolism of carbohydrates, Gallus gallus" +xref: Reactome:REACT_105321 "Metabolism of carbohydrates, Escherichia coli" +xref: Reactome:REACT_106046 "Metabolism of carbohydrates, Drosophila melanogaster" +xref: Reactome:REACT_107409 "Metabolism of carbohydrates, Caenorhabditis elegans" +xref: Reactome:REACT_115733 "Carbohydrate metabolism, Gallus gallus" +xref: Reactome:REACT_28218 "Metabolism of carbohydrates, Xenopus tropicalis" +xref: Reactome:REACT_32291 "Metabolism of carbohydrates, Staphylococcus aureus N315" +xref: Reactome:REACT_33141 "Metabolism of carbohydrates, Taeniopygia guttata" +xref: Reactome:REACT_33953 "Metabolism of carbohydrates, Rattus norvegicus" +xref: Reactome:REACT_34800 "Metabolism of carbohydrates, Danio rerio" +xref: Reactome:REACT_474 "Metabolism of carbohydrates, Homo sapiens" +xref: Reactome:REACT_77669 "Metabolism of carbohydrates, Plasmodium falciparum" +xref: Reactome:REACT_81945 "Metabolism of carbohydrates, Schizosaccharomyces pombe" +xref: Reactome:REACT_83038 "Metabolism of carbohydrates, Arabidopsis thaliana" +xref: Reactome:REACT_83329 "Metabolism of carbohydrates, Saccharomyces cerevisiae" +xref: Reactome:REACT_88330 "Metabolism of carbohydrates, Bos taurus" +xref: Reactome:REACT_88558 "Metabolism of carbohydrates, Canis familiaris" +xref: Reactome:REACT_90099 "Metabolism of carbohydrates, Sus scrofa" +xref: Reactome:REACT_96375 "Metabolism of carbohydrates, Dictyostelium discoideum" +xref: Reactome:REACT_98394 "Metabolism of carbohydrates, Oryza sativa" +xref: Wikipedia:Carbohydrate_metabolism +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0006091 +name: generation of precursor metabolites and energy +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances." [GOC:jl] +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +synonym: "energy pathways" BROAD [] +synonym: "intermediary metabolism" RELATED [GOC:mah] +synonym: "metabolic energy generation" RELATED [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0006259 +name: DNA metabolic process +namespace: biological_process +alt_id: GO:0055132 +def: "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "cellular DNA metabolism" EXACT [] +synonym: "DNA metabolism" EXACT [] +is_a: GO:0034641 ! cellular nitrogen compound metabolic process + +[Term] +id: GO:0006397 +name: mRNA processing +namespace: biological_process +def: "Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide." [GOC:mah] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_yeast +subset: gosubset_prok +synonym: "mRNA maturation" RELATED [] +xref: Reactome:REACT_100203 "Processing of Capped Intronless Pre-mRNA, Dictyostelium discoideum" +xref: Reactome:REACT_107308 "Processing of Capped Intronless Pre-mRNA, Xenopus tropicalis" +xref: Reactome:REACT_109953 "Processing of Capped Intronless Pre-mRNA, Canis familiaris" +xref: Reactome:REACT_113864 "Processing of Capped Intronless Pre-mRNA, Saccharomyces cerevisiae" +xref: Reactome:REACT_114358 "Processing of Capped Intronless Pre-mRNA, Schizosaccharomyces pombe" +xref: Reactome:REACT_115262 "Processing of Capped Intronless Pre-mRNA, Arabidopsis thaliana" +xref: Reactome:REACT_1768 "Processing of Capped Intronless Pre-mRNA, Homo sapiens" +xref: Reactome:REACT_32742 "Processing of Capped Intronless Pre-mRNA, Bos taurus" +xref: Reactome:REACT_33642 "Processing of Capped Intronless Pre-mRNA, Caenorhabditis elegans" +xref: Reactome:REACT_82691 "Processing of Capped Intronless Pre-mRNA, Gallus gallus" +xref: Reactome:REACT_90366 "Processing of Capped Intronless Pre-mRNA, Drosophila melanogaster" +xref: Reactome:REACT_91511 "Processing of Capped Intronless Pre-mRNA, Danio rerio" +xref: Reactome:REACT_93186 "Processing of Capped Intronless Pre-mRNA, Sus scrofa" +xref: Reactome:REACT_94083 "Processing of Capped Intronless Pre-mRNA, Taeniopygia guttata" +xref: Reactome:REACT_96661 "Processing of Capped Intronless Pre-mRNA, Oryza sativa" +xref: Reactome:REACT_97412 "Processing of Capped Intronless Pre-mRNA, Rattus norvegicus" +xref: Reactome:REACT_97436 "Processing of Capped Intronless Pre-mRNA, Mus musculus" +is_a: GO:0034641 ! cellular nitrogen compound metabolic process +relationship: part_of GO:0008150 ! biological_process + +[Term] +id: GO:0006399 +name: tRNA metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. Transfer RNA is characterized by the presence of many unusual minor bases, the function of which has not been completely established." [ISBN:0198506732] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pombe +subset: gosubset_prok +synonym: "tRNA metabolism" EXACT [] +is_a: GO:0034641 ! cellular nitrogen compound metabolic process + +[Term] +id: GO:0006412 +name: translation +namespace: biological_process +alt_id: GO:0006416 +alt_id: GO:0006453 +alt_id: GO:0043037 +def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "protein anabolism" EXACT [] +synonym: "protein biosynthesis" EXACT [] +synonym: "protein biosynthetic process" EXACT [GOC:curators] +synonym: "protein formation" EXACT [] +synonym: "protein synthesis" EXACT [] +synonym: "protein translation" EXACT [] +xref: Reactome:REACT_100338 "Translation, Sus scrofa" +xref: Reactome:REACT_100851 "Translation, Saccharomyces cerevisiae" +xref: Reactome:REACT_101045 "Translation, Dictyostelium discoideum" +xref: Reactome:REACT_101324 "Translation, Canis familiaris" +xref: Reactome:REACT_1014 "Translation, Homo sapiens" +xref: Reactome:REACT_103420 "Translation, Plasmodium falciparum" +xref: Reactome:REACT_105544 "Translation, Arabidopsis thaliana" +xref: Reactome:REACT_29980 "Translation, Bos taurus" +xref: Reactome:REACT_33559 "Translation, Rattus norvegicus" +xref: Reactome:REACT_77710 "Translation, Drosophila melanogaster" +xref: Reactome:REACT_79784 "Translation, Danio rerio" +xref: Reactome:REACT_81734 "Translation, Schizosaccharomyces pombe" +xref: Reactome:REACT_81833 "Translation, Caenorhabditis elegans" +xref: Reactome:REACT_82171 "Translation, Xenopus tropicalis" +xref: Reactome:REACT_83429 "Translation, Taeniopygia guttata" +xref: Reactome:REACT_83530 "Translation, Gallus gallus" +xref: Reactome:REACT_86996 "Translation, Oryza sativa" +xref: Reactome:REACT_95535 "Translation, Mus musculus" +xref: Reactome:REACT_96394 "Translation, Escherichia coli" +xref: Wikipedia:Translation_(genetics) +is_a: GO:0009058 ! biosynthetic process +is_a: GO:0034641 ! cellular nitrogen compound metabolic process +relationship: has_part GO:0009058 ! biosynthetic process +relationship: part_of GO:0008150 ! biological_process + +[Term] +id: GO:0006457 +name: protein folding +namespace: biological_process +alt_id: GO:0007022 +alt_id: GO:0007024 +alt_id: GO:0007025 +def: "The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure." [GOC:go_curators, GOC:rb] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +synonym: "alpha-tubulin folding" NARROW [GOC:mah] +synonym: "beta-tubulin folding" NARROW [GOC:mah] +synonym: "chaperone activity" RELATED [] +synonym: "chaperonin ATPase activity" RELATED [] +synonym: "chaperonin-mediated tubulin folding" NARROW [GOC:mah] +synonym: "co-chaperone activity" RELATED [] +synonym: "co-chaperonin activity" RELATED [] +synonym: "glycoprotein-specific chaperone activity" RELATED [] +synonym: "non-chaperonin molecular chaperone ATPase activity" RELATED [] +synonym: "protein complex assembly, multichaperone pathway" RELATED [] +xref: Reactome:REACT_100411 "Chaperonin-mediated protein folding, Arabidopsis thaliana" +xref: Reactome:REACT_104912 "Chaperonin-mediated protein folding, Caenorhabditis elegans" +xref: Reactome:REACT_105663 "Chaperonin-mediated protein folding, Rattus norvegicus" +xref: Reactome:REACT_106009 "Chaperonin-mediated protein folding, Canis familiaris" +xref: Reactome:REACT_106427 "Chaperonin-mediated protein folding, Mus musculus" +xref: Reactome:REACT_106894 "Formation of tubulin folding intermediates by CCT/TriC, Canis familiaris" +xref: Reactome:REACT_106927 "Chaperonin-mediated protein folding, Drosophila melanogaster" +xref: Reactome:REACT_107029 "Formation of tubulin folding intermediates by CCT/TriC, Drosophila melanogaster" +xref: Reactome:REACT_108248 "Chaperonin-mediated protein folding, Gallus gallus" +xref: Reactome:REACT_109411 "Formation of tubulin folding intermediates by CCT/TriC, Bos taurus" +xref: Reactome:REACT_110417 "Formation of tubulin folding intermediates by CCT/TriC, Rattus norvegicus" +xref: Reactome:REACT_16956 "Formation of tubulin folding intermediates by CCT/TriC, Homo sapiens" +xref: Reactome:REACT_17001 "Formation of tubulin folding intermediates by CCT/TriC, Mus musculus" +xref: Reactome:REACT_17004 "Chaperonin-mediated protein folding, Homo sapiens" +xref: Reactome:REACT_17056 "Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding, Bos taurus" +xref: Reactome:REACT_23878 "N-glycan trimming in the ER and Calnexin/Calreticulin cycle, Homo sapiens" +xref: Reactome:REACT_30906 "Chaperonin-mediated protein folding, Oryza sativa" +xref: Reactome:REACT_32155 "Chaperonin-mediated protein folding, Saccharomyces cerevisiae" +xref: Reactome:REACT_32255 "Chaperonin-mediated protein folding, Schizosaccharomyces pombe" +xref: Reactome:REACT_33395 "Formation of tubulin folding intermediates by CCT/TriC, Mus musculus" +xref: Reactome:REACT_77627 "Chaperonin-mediated protein folding, Plasmodium falciparum" +xref: Reactome:REACT_77963 "Formation of tubulin folding intermediates by CCT/TriC, Saccharomyces cerevisiae" +xref: Reactome:REACT_78530 "Formation of tubulin folding intermediates by CCT/TriC, Gallus gallus" +xref: Reactome:REACT_81155 "Formation of tubulin folding intermediates by CCT/TriC, Caenorhabditis elegans" +xref: Reactome:REACT_83906 "Chaperonin-mediated protein folding, Dictyostelium discoideum" +xref: Reactome:REACT_85492 "Formation of tubulin folding intermediates by CCT/TriC, Sus scrofa" +xref: Reactome:REACT_85496 "Formation of tubulin folding intermediates by CCT/TriC, Plasmodium falciparum" +xref: Reactome:REACT_86318 "Formation of tubulin folding intermediates by CCT/TriC, Arabidopsis thaliana" +xref: Reactome:REACT_91676 "Formation of tubulin folding intermediates by CCT/TriC, Schizosaccharomyces pombe" +xref: Reactome:REACT_92785 "Formation of tubulin folding intermediates by CCT/TriC, Dictyostelium discoideum" +xref: Reactome:REACT_92961 "Chaperonin-mediated protein folding, Xenopus tropicalis" +xref: Reactome:REACT_92981 "Chaperonin-mediated protein folding, Taeniopygia guttata" +xref: Reactome:REACT_94123 "Formation of tubulin folding intermediates by CCT/TriC, Taeniopygia guttata" +xref: Reactome:REACT_94443 "Formation of tubulin folding intermediates by CCT/TriC, Danio rerio" +xref: Reactome:REACT_94772 "Chaperonin-mediated protein folding, Sus scrofa" +xref: Reactome:REACT_96773 "Chaperonin-mediated protein folding, Danio rerio" +xref: Reactome:REACT_97016 "Chaperonin-mediated protein folding, Bos taurus" +xref: Reactome:REACT_97220 "Formation of tubulin folding intermediates by CCT/TriC, Xenopus tropicalis" +xref: Reactome:REACT_98132 "Formation of tubulin folding intermediates by CCT/TriC, Oryza sativa" +xref: Wikipedia:Protein_folding +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0006461 +name: protein complex assembly +namespace: biological_process +def: "The aggregation, arrangement and bonding together of a set of components to form a protein complex." [GOC:ai] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pombe +subset: gosubset_prok +synonym: "chaperone activity" RELATED [] +synonym: "protein complex formation" EXACT [] +is_a: GO:0065003 ! macromolecular complex assembly + +[Term] +id: GO:0006464 +name: cellular protein modification process +namespace: biological_process +def: "The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification)." [GOC:go_curators] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "process resulting in protein modification" RELATED [] +synonym: "protein modification process" BROAD [GOC:bf, GOC:jl] +synonym: "protein tagging activity" RELATED [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0006520 +name: cellular amino acid metabolic process +namespace: biological_process +alt_id: GO:0006519 +def: "The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells." [CHEBI:33709, GOC:curators, ISBN:0198506732] +subset: goslim_aspergillus +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +synonym: "amino acid and derivative metabolism" EXACT [GOC:curators] +synonym: "amino acid metabolic process" EXACT [GOC:curators] +synonym: "cellular amino acid and derivative metabolic process" EXACT [] +synonym: "cellular amino acid metabolism" EXACT [] +xref: Reactome:REACT_116093 "Amino acid metabolism, Gallus gallus" +is_a: GO:0044281 ! small molecule metabolic process + +[Term] +id: GO:0006605 +name: protein targeting +namespace: biological_process +def: "The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif." [GOC:ma] +comment: Note that protein targeting encompasses the transport of the protein to the specified location, and may also include additional steps such as protein processing. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +synonym: "nascent polypeptide association" RELATED [] +synonym: "protein sorting along secretory pathway" NARROW [] +xref: Wikipedia:Protein_targeting +is_a: GO:0006810 ! transport +relationship: occurs_in GO:0005622 ! intracellular +relationship: part_of GO:0008150 ! biological_process + +[Term] +id: GO:0006629 +name: lipid metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids." [GOC:ma] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +synonym: "lipid metabolism" EXACT [] +xref: Reactome:REACT_104930 "Lipid digestion, mobilization, and transport, Drosophila melanogaster" +xref: Reactome:REACT_107479 "Lipid digestion, mobilization, and transport, Xenopus tropicalis" +xref: Reactome:REACT_108775 "Lipid digestion, mobilization, and transport, Canis familiaris" +xref: Reactome:REACT_114669 "Lipid digestion, mobilization, and transport, Staphylococcus aureus N315" +xref: Reactome:REACT_115652 "Lipid metabolism, Gallus gallus" +xref: Reactome:REACT_28745 "Lipid digestion, mobilization, and transport, Saccharomyces cerevisiae" +xref: Reactome:REACT_31395 "Lipid digestion, mobilization, and transport, Sus scrofa" +xref: Reactome:REACT_32539 "Lipid digestion, mobilization, and transport, Bos taurus" +xref: Reactome:REACT_33836 "Lipid digestion, mobilization, and transport, Rattus norvegicus" +xref: Reactome:REACT_602 "Lipid digestion, mobilization, and transport, Homo sapiens" +xref: Reactome:REACT_77176 "Lipid digestion, mobilization, and transport, Danio rerio" +xref: Reactome:REACT_77191 "Lipid digestion, mobilization, and transport, Arabidopsis thaliana" +xref: Reactome:REACT_79244 "Lipid digestion, mobilization, and transport, Plasmodium falciparum" +xref: Reactome:REACT_81778 "Lipid digestion, mobilization, and transport, Oryza sativa" +xref: Reactome:REACT_82512 "Lipid digestion, mobilization, and transport, Taeniopygia guttata" +xref: Reactome:REACT_82723 "Lipid digestion, mobilization, and transport, Escherichia coli" +xref: Reactome:REACT_87884 "Lipid digestion, mobilization, and transport, Caenorhabditis elegans" +xref: Reactome:REACT_90757 "Lipid digestion, mobilization, and transport, Mus musculus" +xref: Reactome:REACT_94607 "Lipid digestion, mobilization, and transport, Mycobacterium tuberculosis" +xref: Reactome:REACT_97906 "Lipid digestion, mobilization, and transport, Gallus gallus" +xref: Reactome:REACT_98129 "Lipid digestion, mobilization, and transport, Schizosaccharomyces pombe" +xref: Reactome:REACT_99706 "Lipid digestion, mobilization, and transport, Dictyostelium discoideum" +xref: Wikipedia:Lipid_metabolism +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0006790 +name: sulfur compound metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione." [GOC:ai] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: gosubset_prok +synonym: "sulfur metabolism" EXACT [] +synonym: "sulphur metabolic process" EXACT [] +synonym: "sulphur metabolism" EXACT [] +xref: Reactome:REACT_27247 "Sulfur compound metabolism, Mycobacterium tuberculosis" +xref: Wikipedia:Sulfur_metabolism +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0006810 +name: transport +namespace: biological_process +alt_id: GO:0015457 +alt_id: GO:0015460 +def: "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC:dph, GOC:jl, GOC:mah] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "auxiliary transport protein activity" RELATED [GOC:mah] +synonym: "small molecule transport" NARROW [] +synonym: "solute:solute exchange" NARROW [] +synonym: "transport accessory protein activity" RELATED [GOC:mah] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0006913 +name: nucleocytoplasmic transport +namespace: biological_process +alt_id: GO:0000063 +def: "The directed movement of molecules between the nucleus and the cytoplasm." [GOC:go_curators] +comment: Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane, and is not traversed. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pombe +synonym: "nucleocytoplasmic shuttling" NARROW [] +is_a: GO:0006810 ! transport +relationship: occurs_in GO:0005622 ! intracellular +relationship: part_of GO:0008150 ! biological_process + +[Term] +id: GO:0006914 +name: autophagy +namespace: biological_process +alt_id: GO:0016238 +def: "The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation." [GOC:autophagy, ISBN:0198547684, PMID:11099404, PMID:9412464] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_pombe +xref: Wikipedia:Autophagy_(cellular) +is_a: GO:0008150 ! biological_process +relationship: has_part GO:0009056 ! catabolic process + +[Term] +id: GO:0006950 +name: response to stress +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_plant +subset: gosubset_prok +synonym: "response to abiotic stress" RELATED [] +synonym: "response to biotic stress" RELATED [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0007005 +name: mitochondrion organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components." [GOC:dph, GOC:jl, GOC:mah, GOC:sgd_curators, PMID:9786946] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_pombe +subset: goslim_yeast +synonym: "mitochondria organization" EXACT [GOC:mah] +synonym: "mitochondrion organisation" EXACT [GOC:mah] +synonym: "mitochondrion organization and biogenesis" RELATED [GOC:curators] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0007009 +name: plasma membrane organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane." [GOC:dph, GOC:jl, GOC:mah] +subset: goslim_chembl +subset: goslim_generic +subset: gosubset_prok +synonym: "plasma membrane organisation" EXACT [GOC:curators] +synonym: "plasma membrane organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0061024 ! membrane organization +relationship: part_of GO:0008150 ! biological_process + +[Term] +id: GO:0007010 +name: cytoskeleton organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures." [GOC:dph, GOC:jl, GOC:mah] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +synonym: "cytoskeletal organization and biogenesis" RELATED [GOC:mah] +synonym: "cytoskeletal regulator activity" RELATED [] +synonym: "cytoskeleton organisation" EXACT [GOC:curators] +synonym: "cytoskeleton organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0007034 +name: vacuolar transport +namespace: biological_process +def: "The directed movement of substances into, out of or within a vacuole." [GOC:ai] +subset: goslim_chembl +subset: goslim_generic +is_a: GO:0006810 ! transport +relationship: occurs_in GO:0005622 ! intracellular +relationship: part_of GO:0008150 ! biological_process + +[Term] +id: GO:0007049 +name: cell cycle +namespace: biological_process +def: "The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division." [GOC:go_curators, GOC:mtg_cell_cycle] +subset: gocheck_do_not_manually_annotate +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "cell-division cycle" EXACT [] +xref: Wikipedia:Cell_cycle +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0007059 +name: chromosome segregation +namespace: biological_process +def: "The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles." [GOC:jl, GOC:mah, GOC:mtg_cell_cycle, GOC:vw] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +synonym: "chromosome division" EXACT [] +synonym: "chromosome transmission" RELATED [] +xref: Wikipedia:Chromosome_segregation +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0007067 +name: mitotic nuclear division +namespace: biological_process +def: "A cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell." [GOC:dph, GOC:ma, GOC:mah, ISBN:0198547684] +subset: goslim_chembl +subset: goslim_generic +synonym: "mitosis" EXACT [] +xref: Wikipedia:Mitosis +is_a: GO:0008150 ! biological_process +relationship: part_of GO:0007049 ! cell cycle + +[Term] +id: GO:0007155 +name: cell adhesion +namespace: biological_process +def: "The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules." [GOC:hb, GOC:pf] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_pombe +subset: gosubset_prok +synonym: "cell adhesion molecule activity" RELATED [] +xref: Wikipedia:Cell_adhesion +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0007165 +name: signal transduction +namespace: biological_process +alt_id: GO:0023033 +def: "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC:go_curators, GOC:mtg_signaling_feb11] +comment: Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_plant +subset: gosubset_prok +synonym: "signaling cascade" NARROW [] +synonym: "signaling pathway" RELATED [] +synonym: "signalling cascade" NARROW [] +synonym: "signalling pathway" RELATED [GOC:mah] +xref: Reactome:REACT_100624 "EGFR interacts with phospholipase C-gamma, Gallus gallus" +xref: Reactome:REACT_102354 "EGFR interacts with phospholipase C-gamma, Canis familiaris" +xref: Reactome:REACT_112130 "EGFR interacts with phospholipase C-gamma, Oryza sativa" +xref: Reactome:REACT_112549 "EGFR interacts with phospholipase C-gamma, Arabidopsis thaliana" +xref: Reactome:REACT_113151 "EGFR interacts with phospholipase C-gamma, Mycobacterium tuberculosis" +xref: Reactome:REACT_113601 "EGFR interacts with phospholipase C-gamma, Drosophila melanogaster" +xref: Reactome:REACT_113964 "EGFR interacts with phospholipase C-gamma, Bos taurus" +xref: Reactome:REACT_114657 "EGFR interacts with phospholipase C-gamma, Dictyostelium discoideum" +xref: Reactome:REACT_114690 "EGFR interacts with phospholipase C-gamma, Saccharomyces cerevisiae" +xref: Reactome:REACT_114820 "EGFR interacts with phospholipase C-gamma, Sus scrofa" +xref: Reactome:REACT_114910 "EGFR interacts with phospholipase C-gamma, Caenorhabditis elegans" +xref: Reactome:REACT_115037 "EGFR interacts with phospholipase C-gamma, Plasmodium falciparum" +xref: Reactome:REACT_115147 "EGFR interacts with phospholipase C-gamma, Schizosaccharomyces pombe" +xref: Reactome:REACT_12478 "EGFR interacts with phospholipase C-gamma, Homo sapiens" +xref: Reactome:REACT_31232 "EGFR interacts with phospholipase C-gamma, Rattus norvegicus" +xref: Reactome:REACT_78535 "EGFR interacts with phospholipase C-gamma, Xenopus tropicalis" +xref: Reactome:REACT_89740 "EGFR interacts with phospholipase C-gamma, Taeniopygia guttata" +xref: Reactome:REACT_93680 "EGFR interacts with phospholipase C-gamma, Danio rerio" +xref: Reactome:REACT_98872 "EGFR interacts with phospholipase C-gamma, Mus musculus" +xref: Wikipedia:Signal_transduction +is_a: GO:0008150 ! biological_process +relationship: part_of GO:0008150 ! biological_process +relationship: regulates GO:0008150 ! biological_process + +[Term] +id: GO:0007267 +name: cell-cell signaling +namespace: biological_process +def: "Any process that mediates the transfer of information from one cell to another." [GOC:mah] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_plant +subset: gosubset_prok +synonym: "cell-cell signalling" EXACT [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0007568 +name: aging +namespace: biological_process +alt_id: GO:0016280 +def: "A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700)." [GOC:PO_curators] +subset: goslim_chembl +subset: goslim_generic +synonym: "ageing" EXACT [] +xref: Wikipedia:Aging +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0008092 +name: cytoskeletal protein binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton)." [GOC:mah] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_yeast +subset: gosubset_prok +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0008134 +name: transcription factor binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription." [ISBN:0198506732] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_yeast +subset: gosubset_prok +synonym: "TF binding" EXACT [] +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0008135 +name: translation factor activity, RNA binding +namespace: molecular_function +def: "Functions during translation by interacting selectively and non-covalently with RNA during polypeptide synthesis at the ribosome." [GOC:ai, GOC:vw] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "translation factor activity, nucleic acid binding" BROAD [GOC:mah] +is_a: GO:0003723 ! RNA binding +relationship: part_of GO:0006412 ! translation + +[Term] +id: GO:0008150 +name: biological_process +namespace: biological_process +alt_id: GO:0000004 +alt_id: GO:0007582 +def: "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." [GOC:go_curators, GOC:isa_complete] +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +synonym: "biological process" EXACT [] +synonym: "physiological process" EXACT [] +xref: Wikipedia:Biological_process + +[Term] +id: GO:0008168 +name: methyltransferase activity +namespace: molecular_function +alt_id: GO:0004480 +def: "Catalysis of the transfer of a methyl group to an acceptor molecule." [ISBN:0198506732] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_yeast +subset: gosubset_prok +synonym: "methylase" BROAD [] +xref: EC:2.1.1 +xref: Reactome:REACT_100745 "Methylation of 3,4-dihydroxypheylacetic acid to homovanillic acid, Bos taurus" +xref: Reactome:REACT_100863 "methylation of Dopamine to form 3-Methoxytyramine, Taeniopygia guttata" +xref: Reactome:REACT_100884 "methylation of Dopamine to form 3-Methoxytyramine, Xenopus tropicalis" +xref: Reactome:REACT_103958 "methylation of Dopamine to form 3-Methoxytyramine, Rattus norvegicus" +xref: Reactome:REACT_104757 "guanidinoacetate + S-adenosylmethionine => creatine + S-adenosylhomocysteine, Danio rerio" +xref: Reactome:REACT_105478 "guanidinoacetate + S-adenosylmethionine => creatine + S-adenosylhomocysteine, Bos taurus" +xref: Reactome:REACT_105909 "Methylation of 3,4-dihydroxypheylacetic acid to homovanillic acid, Xenopus tropicalis" +xref: Reactome:REACT_106465 "Methylation of 3,4-dihydroxypheylacetic acid to homovanillic acid, Sus scrofa" +xref: Reactome:REACT_107676 "Methylation of 3,4-dihydroxypheylacetic acid to homovanillic acid, Schizosaccharomyces pombe" +xref: Reactome:REACT_15531 "methylation of Dopamine to form 3-Methoxytyramine, Homo sapiens" +xref: Reactome:REACT_15553 "Methylation of 3,4-dihydroxypheylacetic acid to homovanillic acid, Homo sapiens" +xref: Reactome:REACT_2094 "guanidinoacetate + S-adenosylmethionine => creatine + S-adenosylhomocysteine, Homo sapiens" +xref: Reactome:REACT_29020 "methylation of Dopamine to form 3-Methoxytyramine, Bos taurus" +xref: Reactome:REACT_29098 "guanidinoacetate + S-adenosylmethionine => creatine + S-adenosylhomocysteine, Canis familiaris" +xref: Reactome:REACT_33644 "Methylation of 3,4-dihydroxypheylacetic acid to homovanillic acid, Mycobacterium tuberculosis" +xref: Reactome:REACT_33779 "methylation of Dopamine to form 3-Methoxytyramine, Mycobacterium tuberculosis" +xref: Reactome:REACT_73401 "guanidinoacetate + S-adenosylmethionine => creatine + S-adenosylhomocysteine, Rattus norvegicus" +xref: Reactome:REACT_77286 "methylation of Dopamine to form 3-Methoxytyramine, Canis familiaris" +xref: Reactome:REACT_78774 "guanidinoacetate + S-adenosylmethionine => creatine + S-adenosylhomocysteine, Mus musculus" +xref: Reactome:REACT_79799 "Methylation of 3,4-dihydroxypheylacetic acid to homovanillic acid, Mus musculus" +xref: Reactome:REACT_83214 "Methylation of 3,4-dihydroxypheylacetic acid to homovanillic acid, Gallus gallus" +xref: Reactome:REACT_84525 "guanidinoacetate + S-adenosylmethionine => creatine + S-adenosylhomocysteine, Taeniopygia guttata" +xref: Reactome:REACT_84974 "methylation of Dopamine to form 3-Methoxytyramine, Sus scrofa" +xref: Reactome:REACT_86817 "methylation of Dopamine to form 3-Methoxytyramine, Schizosaccharomyces pombe" +xref: Reactome:REACT_86905 "Methylation of 3,4-dihydroxypheylacetic acid to homovanillic acid, Rattus norvegicus" +xref: Reactome:REACT_87169 "Methylation of 3,4-dihydroxypheylacetic acid to homovanillic acid, Taeniopygia guttata" +xref: Reactome:REACT_93379 "methylation of Dopamine to form 3-Methoxytyramine, Gallus gallus" +xref: Reactome:REACT_93809 "guanidinoacetate + S-adenosylmethionine => creatine + S-adenosylhomocysteine, Xenopus tropicalis" +xref: Reactome:REACT_94274 "Methylation of 3,4-dihydroxypheylacetic acid to homovanillic acid, Canis familiaris" +xref: Reactome:REACT_96444 "methylation of Dopamine to form 3-Methoxytyramine, Mus musculus" +xref: Reactome:REACT_99316 "guanidinoacetate + S-adenosylmethionine => creatine + S-adenosylhomocysteine, Gallus gallus" +is_a: GO:0003674 ! molecular_function +relationship: part_of GO:0008150 ! biological_process + +[Term] +id: GO:0008219 +name: cell death +namespace: biological_process +def: "Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538)." [GOC:mah, GOC:mtg_apoptosis, PMID:25236395] +comment: This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide) show that cell death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Also, if experimental data suggest that a gene product influences cell death indirectly, rather than being involved in the death process directly, consider annotating to a 'regulation' term. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_plant +subset: gosubset_prok +synonym: "accidental cell death" RELATED [] +synonym: "necrosis" RELATED [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0008233 +name: peptidase activity +namespace: molecular_function +def: "Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid." [GOC:jl, ISBN:0815332181] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_yeast +subset: gosubset_prok +synonym: "hydrolase, acting on peptide bonds" EXACT [] +synonym: "peptide hydrolase activity" EXACT [] +synonym: "protease activity" NARROW [] +synonym: "proteinase activity" NARROW [] +xref: EC:3.4 +xref: Reactome:REACT_106748 "gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6, Rattus norvegicus" +xref: Reactome:REACT_110349 "gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6, Mus musculus" +xref: Reactome:REACT_13710 "gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6, Homo sapiens" +xref: Reactome:REACT_19284 "Proteolytic processing of Slit, Homo sapiens" +xref: Reactome:REACT_93020 "gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6, Bos taurus" +xref: Reactome:REACT_99630 "gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6, Gallus gallus" +is_a: GO:0003674 ! molecular_function +relationship: part_of GO:0008150 ! biological_process + +[Term] +id: GO:0008283 +name: cell proliferation +namespace: biological_process +def: "The multiplication or reproduction of cells, resulting in the expansion of a cell population." [GOC:mah, GOC:mb] +comment: This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0008289 +name: lipid binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a lipid." [GOC:ai] +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0008565 +name: protein transporter activity +namespace: molecular_function +alt_id: GO:0015463 +def: "Enables the directed movement of proteins into, out of or within a cell, or between cells." [ISBN:0198506732] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_yeast +subset: gosubset_prok +synonym: "enzyme transporter activity" NARROW [] +synonym: "holin" RELATED [] +synonym: "protein carrier activity" EXACT [] +synonym: "protein transport chaperone" NARROW [GOC:dph, GOC:mah, GOC:tb] +synonym: "secretin" RELATED [] +is_a: GO:0003674 ! molecular_function +relationship: part_of GO:0006810 ! transport + +[Term] +id: GO:0009056 +name: catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism." [ISBN:0198547684] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_plant +subset: gosubset_prok +synonym: "breakdown" EXACT [] +synonym: "catabolism" EXACT [] +synonym: "degradation" EXACT [] +xref: Wikipedia:Catabolism +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0009058 +name: biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_plant +subset: gosubset_prok +synonym: "anabolism" EXACT [] +synonym: "biosynthesis" EXACT [] +synonym: "formation" EXACT [] +synonym: "synthesis" EXACT [] +xref: Wikipedia:Anabolism +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0009536 +name: plastid +namespace: cellular_component +def: "Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid." [GOC:jl, ISBN:0198547684] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +xref: Wikipedia:Plastid +is_a: GO:0043226 ! organelle +relationship: part_of GO:0005737 ! cytoplasm + +[Term] +id: GO:0009579 +name: thylakoid +namespace: cellular_component +def: "A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation." [GOC:ds, GOC:mtg_sensu, ISBN:0198506732] +comment: A thylakoid is not considered an organelle, but some thylakoids are part of organelles. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "photosynthetic membrane" RELATED [] +xref: Wikipedia:Thylakoid +is_a: GO:0005575 ! cellular_component +relationship: part_of GO:0005622 ! intracellular + +[Term] +id: GO:0009790 +name: embryo development +namespace: biological_process +alt_id: GO:0009795 +def: "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] +subset: gocheck_do_not_manually_annotate +subset: goslim_chembl +subset: goslim_generic +subset: goslim_plant +synonym: "embryogenesis" EXACT [] +synonym: "embryogenesis and morphogenesis" BROAD [] +synonym: "embryonal development" EXACT [] +xref: Wikipedia:Embryogenesis +is_a: GO:0048856 ! anatomical structure development + +[Term] +id: GO:0015979 +name: photosynthesis +namespace: biological_process +def: "The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds." [ISBN:0198547684] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +xref: Wikipedia:Photosynthesis +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0016023 +name: cytoplasmic, membrane-bounded vesicle +namespace: cellular_component +def: "A membrane-bounded vesicle found in the cytoplasm of the cell." [GOC:ai, GOC:mah] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_yeast +subset: gosubset_prok +synonym: "cytoplasmic membrane bounded vesicle" EXACT [] +synonym: "cytoplasmic membrane-enclosed vesicle" EXACT [] +is_a: GO:0043226 ! organelle +relationship: part_of GO:0005737 ! cytoplasm + +[Term] +id: GO:0016192 +name: vesicle-mediated transport +namespace: biological_process +alt_id: GO:0006899 +def: "A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane." [GOC:ai, GOC:mah, ISBN:08789310662000] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_pombe +subset: gosubset_prok +synonym: "nonselective vesicle transport" NARROW [] +synonym: "protein sorting along secretory pathway" RELATED [] +synonym: "vesicle trafficking" RELATED [] +synonym: "vesicle transport" EXACT [] +synonym: "vesicular transport" EXACT [GOC:mah] +is_a: GO:0006810 ! transport + +[Term] +id: GO:0016301 +name: kinase activity +namespace: molecular_function +def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732] +comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "phosphokinase activity" EXACT [] +xref: Reactome:REACT_100073 "Activation of S6K1, Schizosaccharomyces pombe" +xref: Reactome:REACT_100078 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Canis familiaris" +xref: Reactome:REACT_100159 "Inactivation of Myt1 kinase, Mus musculus" +xref: Reactome:REACT_100260 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Taeniopygia guttata" +xref: Reactome:REACT_100298 "Phosphorylation of L1 by CK-II, Rattus norvegicus" +xref: Reactome:REACT_100305 "Regulation of NUDC by phosphorylation, Caenorhabditis elegans" +xref: Reactome:REACT_100311 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Canis familiaris" +xref: Reactome:REACT_100390 "Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3, Canis familiaris" +xref: Reactome:REACT_100465 "Phosphorylation and inactivation of eEF2K by activated S6K1, Dictyostelium discoideum" +xref: Reactome:REACT_100495 "Cdc6 protein is phosphorylated by CDK, Xenopus tropicalis" +xref: Reactome:REACT_100519 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Bos taurus" +xref: Reactome:REACT_100636 "Phosphorylation of proteins involved in the G1/S transition by Cyclin A:Cdk2, Canis familiaris" +xref: Reactome:REACT_100637 "Phosphorylation of the Scc1:Cohesion Complex, Mus musculus" +xref: Reactome:REACT_101024 "Phosphorylation and inactivation of eEF2K by activated S6K1, Bos taurus" +xref: Reactome:REACT_101170 "Phosphorylation of APC component of the destruction complex, Drosophila melanogaster" +xref: Reactome:REACT_101303 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Mus musculus" +xref: Reactome:REACT_101431 "Mcm2-7 is phosphorylated by DDK, Danio rerio" +xref: Reactome:REACT_101543 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Canis familiaris" +xref: Reactome:REACT_101596 "Phosphorylation of Cyclin D:Cdk4/6 complexes, Canis familiaris" +xref: Reactome:REACT_101638 "Phosphorylation and activation of CHK2 by ATM, Bos taurus" +xref: Reactome:REACT_101667 "Down Regulation of Emi1 through Phosphorylation of Emi1, Bos taurus" +xref: Reactome:REACT_101841 "Phosphorylation of Cdc25C at Ser216, Rattus norvegicus" +xref: Reactome:REACT_101862 "Myt-1 mediated phosphorylation of Cyclin A:Cdc2, Xenopus tropicalis" +xref: Reactome:REACT_101914 "Wee1- mediated phosphorylation of Cyclin B1:phospho-Cdc2 complexes, Xenopus tropicalis" +xref: Reactome:REACT_102090 "Phosphoryation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3, Taeniopygia guttata" +xref: Reactome:REACT_102093 "Phosphorylation and activation of eIF4G by activated S6K1, Danio rerio" +xref: Reactome:REACT_102154 "Autophosphorylation of PAK-2p34 in the activation loop, Schizosaccharomyces pombe" +xref: Reactome:REACT_102322 "RAF1 phosphorylates MEK2, Danio rerio" +xref: Reactome:REACT_102330 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Xenopus tropicalis" +xref: Reactome:REACT_102380 "Regulation of KIF23 (MKLP1) by phosphorylation, Xenopus tropicalis" +xref: Reactome:REACT_102475 "Inactivation of Myt1 kinase, Rattus norvegicus" +xref: Reactome:REACT_102499 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes, Canis familiaris" +xref: Reactome:REACT_102552 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Canis familiaris" +xref: Reactome:REACT_102607 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Drosophila melanogaster" +xref: Reactome:REACT_102711 "Phosphorylation of L1 by CK-II, Caenorhabditis elegans" +xref: Reactome:REACT_102729 "RAF1 phosphorylates MEK1, Xenopus tropicalis" +xref: Reactome:REACT_102817 "Phosphorylation of L1 by ERK, Mus musculus" +xref: Reactome:REACT_102887 "Mcm2-7 is phosphorylated by DDK, Rattus norvegicus" +xref: Reactome:REACT_102908 "Phosphorylation of the Scc1:Cohesion Complex, Rattus norvegicus" +xref: Reactome:REACT_102915 "Activation of S6K1, Arabidopsis thaliana" +xref: Reactome:REACT_103060 "Phosphorylation of MDC1/NFBD1 by ATM (within 2 c-term BRCT domains), Arabidopsis thaliana" +xref: Reactome:REACT_103291 "Phosphorylation of complexed TSC2 by PKB, Drosophila melanogaster" +xref: Reactome:REACT_103327 "Phosphorylation of Cyclin E2:Cdk2 complexes by Myt1, Rattus norvegicus" +xref: Reactome:REACT_103359 "Wee1- mediated phosphorylation of Cyclin B1:phospho-Cdc2 complexes, Danio rerio" +xref: Reactome:REACT_103468 "Activation of Cdc25C, Drosophila melanogaster" +xref: Reactome:REACT_103691 "Phosphorylation of COP1 at Ser-387 by ATM, Xenopus tropicalis" +xref: Reactome:REACT_103727 "Phosphorylation of NBS1 by ATM, Drosophila melanogaster" +xref: Reactome:REACT_103804 "Phosphorylation of AKT2 by PDK1, Canis familiaris" +xref: Reactome:REACT_103989 "Phosphorylation of NBS1 by ATM, Danio rerio" +xref: Reactome:REACT_104022 "Phosphorylation of p53 at ser-15 by ATM kinase, Xenopus tropicalis" +xref: Reactome:REACT_104044 "Phosphorylation and activation of Chk1 by ATM, Sus scrofa" +xref: Reactome:REACT_104109 "Phosphorylation of proteins involved in the G1/S transition by Cyclin A:Cdk2, Danio rerio" +xref: Reactome:REACT_104209 "Activation of S6K1, Caenorhabditis elegans" +xref: Reactome:REACT_104323 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Rattus norvegicus" +xref: Reactome:REACT_104386 "Phosphorylation and activation of eIF4B by activated S6K1, Bos taurus" +xref: Reactome:REACT_104523 "Inactivation of Wee1 kinase, Bos taurus" +xref: Reactome:REACT_104644 "Regulation of KIF20A (MKL2) by phosphorylation, Bos taurus" +xref: Reactome:REACT_104687 "Phosphorylation of L1 by CK-II, Canis familiaris" +xref: Reactome:REACT_104730 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Schizosaccharomyces pombe" +xref: Reactome:REACT_104822 "Phosphorylation of COP1 at Ser-387 by ATM, Rattus norvegicus" +xref: Reactome:REACT_104837 "SOS phosphorylation and dissociation (SHC), Mus musculus" +xref: Reactome:REACT_104878 "Phosphorylation of Cyclin E:Cdk2 complexes by Wee-1, Xenopus tropicalis" +xref: Reactome:REACT_105254 "Phosphorylation of Cyclin E:Cdk2 complexes by Wee-1, Danio rerio" +xref: Reactome:REACT_105274 "Regulation of KIF20A (MKL2) by phosphorylation, Danio rerio" +xref: Reactome:REACT_105345 "Phosphoryation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3, Drosophila melanogaster" +xref: Reactome:REACT_105373 "Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3, Gallus gallus" +xref: Reactome:REACT_105503 "Phosphorylation of L1 by ERK, Bos taurus" +xref: Reactome:REACT_105561 "Phosphorylation of complexed TSC2 by PKB, Xenopus tropicalis" +xref: Reactome:REACT_105569 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes, Xenopus tropicalis" +xref: Reactome:REACT_105589 "Phosphorylation of p53 at ser-15 by ATM kinase, Canis familiaris" +xref: Reactome:REACT_105664 "Akt1 phosphorylates BAD protein, Rattus norvegicus" +xref: Reactome:REACT_105700 "Phosphorylation of PDE3B, Rattus norvegicus" +xref: Reactome:REACT_105971 "Phosphorylation of Cyclin A:Cdk2 at Tyr 15, Xenopus tropicalis" +xref: Reactome:REACT_105976 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Xenopus tropicalis" +xref: Reactome:REACT_106075 "Akt1 phosphorylates BAD protein, Canis familiaris" +xref: Reactome:REACT_106144 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Xenopus tropicalis" +xref: Reactome:REACT_106159 "Wee1- mediated phosphorylation of Cyclin B1:phospho-Cdc2 complexes, Canis familiaris" +xref: Reactome:REACT_106186 "Phosphorylation of TSC2 by PKB, Drosophila melanogaster" +xref: Reactome:REACT_106225 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Canis familiaris" +xref: Reactome:REACT_1063 "Phosphorylation of Wee1 kinase by Chk1, Schizosaccharomyces pombe" +xref: Reactome:REACT_106324 "Activation of Cdc25C, Mus musculus" +xref: Reactome:REACT_106383 "Phosphorylation of L1 by ERK, Xenopus tropicalis" +xref: Reactome:REACT_106411 "Phosphorylation and inactivation of eEF2K by activated S6K1, Gallus gallus" +xref: Reactome:REACT_106420 "Regulation of KIF23 (MKLP1) by phosphorylation, Taeniopygia guttata" +xref: Reactome:REACT_106500 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Drosophila melanogaster" +xref: Reactome:REACT_106505 "Phosphorylation of histone H2AX at Serine-139 by ATM at the site of DSB, Rattus norvegicus" +xref: Reactome:REACT_106514 "Phosphorylation of NBS1 by ATM, Mus musculus" +xref: Reactome:REACT_106567 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Mus musculus" +xref: Reactome:REACT_106599 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Xenopus tropicalis" +xref: Reactome:REACT_106681 "Phosphorylation of Cyclin A:Cdk2 at Tyr 15, Rattus norvegicus" +xref: Reactome:REACT_106722 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Xenopus tropicalis" +xref: Reactome:REACT_106738 "SOS phosphorylation and dissociation (IRS, Crk), Canis familiaris" +xref: Reactome:REACT_106897 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Danio rerio" +xref: Reactome:REACT_107009 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Arabidopsis thaliana" +xref: Reactome:REACT_107055 "Phosphorylation of Cdc25C at Ser216, Bos taurus" +xref: Reactome:REACT_107102 "SOS phosphorylation and dissociation (IRS, Crk), Danio rerio" +xref: Reactome:REACT_107243 "Phosphorylation of APC component of the destruction complex, Mus musculus" +xref: Reactome:REACT_107247 "Phosphorylation of TSC2 by PKB, Mus musculus" +xref: Reactome:REACT_107310 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes, Danio rerio" +xref: Reactome:REACT_107424 "Inactivation of Myt1 kinase, Canis familiaris" +xref: Reactome:REACT_107623 "Phosphorylation of histone H2AX at Serine-139 by ATM at the site of DSB, Mus musculus" +xref: Reactome:REACT_107685 "Phosphorylation of Cyclin E:Cdk2 complexes by Wee-1, Sus scrofa" +xref: Reactome:REACT_107732 "Phosphorylation of the Emi1 DSGxxS degron by Plk1, Danio rerio" +xref: Reactome:REACT_107736 "Phosphorylation of Cdc25C at Ser216, Sus scrofa" +xref: Reactome:REACT_107787 "Phosphorylation and activation of CHK2 by ATM, Drosophila melanogaster" +xref: Reactome:REACT_107849 "Phosphorylation of DLC2 by MAPK-8, Bos taurus" +xref: Reactome:REACT_107854 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Canis familiaris" +xref: Reactome:REACT_108002 "Plk1-mediated phosphorylation of Nlp, Bos taurus" +xref: Reactome:REACT_108096 "Phosphorylation of beta-catenin at Ser45 by CK1 alpha, Rattus norvegicus" +xref: Reactome:REACT_108132 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Gallus gallus" +xref: Reactome:REACT_108362 "Phosphorylation of proteins involved in the G1/S transition by Cyclin A:Cdk2, Mus musculus" +xref: Reactome:REACT_108394 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Danio rerio" +xref: Reactome:REACT_108520 "Phosphorylation and activation of Chk1 by ATM, Danio rerio" +xref: Reactome:REACT_108578 "Inactivation of Myt1 kinase, Xenopus tropicalis" +xref: Reactome:REACT_108776 "Free APC/C phosphorylated by Plk1, Taeniopygia guttata" +xref: Reactome:REACT_108840 "Phosphorylation of beta-catenin at Ser45 by CK1 alpha, Canis familiaris" +xref: Reactome:REACT_108871 "Free APC/C phosphorylated by Plk1, Mus musculus" +xref: Reactome:REACT_108971 "Phosphorylation of Cyclin B1 in the CRS domain, Xenopus tropicalis" +xref: Reactome:REACT_108985 "Phosphorylation of cPLA2 by ERK-2, Gallus gallus" +xref: Reactome:REACT_109045 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Danio rerio" +xref: Reactome:REACT_109065 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Taeniopygia guttata" +xref: Reactome:REACT_109117 "Phosphorylation of 4E-BP1 by activated mTORC1, Dictyostelium discoideum" +xref: Reactome:REACT_109197 "SOS phosphorylation and dissociation (IRS), Mus musculus" +xref: Reactome:REACT_109244 "Inactivation of Myt1 kinase, Schizosaccharomyces pombe" +xref: Reactome:REACT_109260 "Free APC/C phosphorylated by Plk1, Xenopus tropicalis" +xref: Reactome:REACT_109264 "SOS phosphorylation and dissociation (IRS), Canis familiaris" +xref: Reactome:REACT_109331 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Drosophila melanogaster" +xref: Reactome:REACT_109367 "Phosphorylation of APC component of the destruction complex, Gallus gallus" +xref: Reactome:REACT_109549 "Regulation of KIF20A (MKL2) by phosphorylation, Xenopus tropicalis" +xref: Reactome:REACT_109641 "CAK-mediated phosphorylation of Cyclin A:Cdk2, Sus scrofa" +xref: Reactome:REACT_109769 "Free APC/C phosphorylated by Plk1, Gallus gallus" +xref: Reactome:REACT_109799 "Phosphorylation of Cyclin E:Cdk2 complexes by Wee-1, Mus musculus" +xref: Reactome:REACT_110175 "Phosphorylation of MDC1/NFBD1 by ATM (within 2 c-term BRCT domains), Mus musculus" +xref: Reactome:REACT_110254 "Phosphorylation of APC component of the destruction complex, Rattus norvegicus" +xref: Reactome:REACT_110296 "Phosphorylation and activation of Chk1 by ATM, Schizosaccharomyces pombe" +xref: Reactome:REACT_110351 "Phosphorylation and inactivation of eEF2K by activated S6K1, Canis familiaris" +xref: Reactome:REACT_110382 "Phosphorylation of MDC1/NFBD1 by ATM (within 2 c-term BRCT domains), Oryza sativa" +xref: Reactome:REACT_110530 "Down Regulation of Emi1 through Phosphorylation of Emi1, Mus musculus" +xref: Reactome:REACT_110583 "Phosphorylation of DLC2 by MAPK-8, Mus musculus" +xref: Reactome:REACT_110643 "Mcm2-7 is phosphorylated by DDK, Xenopus tropicalis" +xref: Reactome:REACT_110679 "Phosphorylation of histone H2AX at Serine-139 by ATM at the site of DSB, Danio rerio" +xref: Reactome:REACT_110774 "Inactivation of Myt1 kinase, Drosophila melanogaster" +xref: Reactome:REACT_110775 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Rattus norvegicus" +xref: Reactome:REACT_110947 "Regulation of KIF23 (MKLP1) by phosphorylation, Drosophila melanogaster" +xref: Reactome:REACT_110995 "Phosphorylation and activation of eIF4G by activated S6K1, Xenopus tropicalis" +xref: Reactome:REACT_111124 "FGFR associated PI3K phosphorylates PIP2 to PIP3, Homo sapiens" +xref: Reactome:REACT_111171 "FGFR-associated PI3K phosphorylates PIP2 to PIP3, Homo sapiens" +xref: Reactome:REACT_1116 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Homo sapiens" +xref: Reactome:REACT_111930 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Caenorhabditis elegans" +xref: Reactome:REACT_1120 "Regulation of KIF20A (MKL2) by phosphorylation, Homo sapiens" +xref: Reactome:REACT_112075 "Mcm2-7 is phosphorylated by DDK, Drosophila melanogaster" +xref: Reactome:REACT_112101 "Phosphorylation of L1 by CK-II, Xenopus tropicalis" +xref: Reactome:REACT_112156 "Phosphorylation of AKT2 by PDK1, Saccharomyces cerevisiae" +xref: Reactome:REACT_112214 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Schizosaccharomyces pombe" +xref: Reactome:REACT_112270 "Akt1 phosphorylates BAD protein, Xenopus tropicalis" +xref: Reactome:REACT_112298 "Autophosphorylation of DNA-PKcs, Dictyostelium discoideum" +xref: Reactome:REACT_112324 "Phosphorylation and activation of eIF4G by activated S6K1, Oryza sativa" +xref: Reactome:REACT_112360 "Regulation of KIF23 (MKLP1) by phosphorylation, Dictyostelium discoideum" +xref: Reactome:REACT_112413 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Saccharomyces cerevisiae" +xref: Reactome:REACT_112480 "Inactivation of Wee1 kinase, Dictyostelium discoideum" +xref: Reactome:REACT_112545 "Phosphorylation and activation of eIF4G by activated S6K1, Drosophila melanogaster" +xref: Reactome:REACT_112633 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Saccharomyces cerevisiae" +xref: Reactome:REACT_112709 "Phosphorylation of L1 by ERK, Saccharomyces cerevisiae" +xref: Reactome:REACT_112722 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Drosophila melanogaster" +xref: Reactome:REACT_112790 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Caenorhabditis elegans" +xref: Reactome:REACT_112846 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Saccharomyces cerevisiae" +xref: Reactome:REACT_112892 "Phosphorylation of BRCA1 at multiple sites by ATM, Oryza sativa" +xref: Reactome:REACT_112948 "Autophosphorylation of DNA-PKcs, Rattus norvegicus" +xref: Reactome:REACT_113022 "Phosphorylation of Cyclin B1 in the CRS domain, Schizosaccharomyces pombe" +xref: Reactome:REACT_113051 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Arabidopsis thaliana" +xref: Reactome:REACT_113121 "Phosphorylation and activation of eIF4B by activated S6K1, Schizosaccharomyces pombe" +xref: Reactome:REACT_113227 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Saccharomyces cerevisiae" +xref: Reactome:REACT_113244 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Drosophila melanogaster" +xref: Reactome:REACT_113269 "Activation of S6K1, Saccharomyces cerevisiae" +xref: Reactome:REACT_113435 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Oryza sativa" +xref: Reactome:REACT_113527 "Autophosphorylation of DNA-PKcs, Bos taurus" +xref: Reactome:REACT_113569 "Activation of Cdc25C, Saccharomyces cerevisiae" +xref: Reactome:REACT_113811 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Bos taurus" +xref: Reactome:REACT_113820 "Phosphorylation of Cyclin B1 in the CRS domain, Saccharomyces cerevisiae" +xref: Reactome:REACT_113894 "PIP2 conversion to PIP3, Caenorhabditis elegans" +xref: Reactome:REACT_113929 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Caenorhabditis elegans" +xref: Reactome:REACT_113990 "Activation of Cdc25C, Schizosaccharomyces pombe" +xref: Reactome:REACT_114160 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes, Saccharomyces cerevisiae" +xref: Reactome:REACT_114198 "Phosphorylation of the Scc1:Cohesion Complex, Schizosaccharomyces pombe" +xref: Reactome:REACT_114207 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Schizosaccharomyces pombe" +xref: Reactome:REACT_114227 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Schizosaccharomyces pombe" +xref: Reactome:REACT_114233 "Autophosphorylation of DNA-PKcs, Sus scrofa" +xref: Reactome:REACT_114255 "Autophosphorylation of DNA-PKcs, Mus musculus" +xref: Reactome:REACT_114268 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Schizosaccharomyces pombe" +xref: Reactome:REACT_114280 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Saccharomyces cerevisiae" +xref: Reactome:REACT_114319 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Caenorhabditis elegans" +xref: Reactome:REACT_114323 "Activation of Cdc25C, Caenorhabditis elegans" +xref: Reactome:REACT_114395 "Phosphorylation of DLC1 by MAPK 8, Xenopus tropicalis" +xref: Reactome:REACT_114434 "Autophosphorylation of DNA-PKcs, Taeniopygia guttata" +xref: Reactome:REACT_114461 "Phosphorylation of AKT2 by PDK1, Schizosaccharomyces pombe" +xref: Reactome:REACT_114522 "Phosphorylation of BRCA1 at multiple sites by ATM, Arabidopsis thaliana" +xref: Reactome:REACT_114553 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Saccharomyces cerevisiae" +xref: Reactome:REACT_114599 "Phosphorylation of TSC2 by PKB, Schizosaccharomyces pombe" +xref: Reactome:REACT_114624 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Drosophila melanogaster" +xref: Reactome:REACT_114771 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Canis familiaris" +xref: Reactome:REACT_114906 "Phosphorylation and activation of eIF4G by activated S6K1, Arabidopsis thaliana" +xref: Reactome:REACT_114984 "Autophosphorylation of DNA-PKcs, Xenopus tropicalis" +xref: Reactome:REACT_115006 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Caenorhabditis elegans" +xref: Reactome:REACT_115135 "Phosphorylation and activation of eIF4G by activated S6K1, Dictyostelium discoideum" +xref: Reactome:REACT_115168 "Autophosphorylation of DNA-PKcs, Gallus gallus" +xref: Reactome:REACT_115199 "Autophosphorylation of DNA-PKcs, Canis familiaris" +xref: Reactome:REACT_115358 "Phosphorylation of Cyclin E:Cdk2 complexes by Wee-1, Drosophila melanogaster" +xref: Reactome:REACT_115384 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes, Schizosaccharomyces pombe" +xref: Reactome:REACT_115440 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Danio rerio" +xref: Reactome:REACT_115472 "Phosphorylation of the SA2 Cohesin Complex, Schizosaccharomyces pombe" +xref: Reactome:REACT_115475 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Schizosaccharomyces pombe" +xref: Reactome:REACT_115521 "Autophosphorylation of DNA-PKcs, Danio rerio" +xref: Reactome:REACT_115527 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Schizosaccharomyces pombe" +xref: Reactome:REACT_115747 "Phosphorylation of H2AX at S139 by ATM at the site of DSB, Gallus gallus" +xref: Reactome:REACT_116149 "Phosphorylation of RAD51 by tyrosine kinase Abelson family protein members, Gallus gallus" +xref: Reactome:REACT_118137 "Phosphorylation of the Scc1:Cohesion Complex, Taeniopygia guttata" +xref: Reactome:REACT_118229 "Phosphorylation of the SA2 Cohesin Complex, Taeniopygia guttata" +xref: Reactome:REACT_118284 "Phosphorylation of the Scc1:Cohesion Complex, Saccharomyces cerevisiae" +xref: Reactome:REACT_118307 "Phosphorylation of the SA2 Cohesin Complex, Gallus gallus" +xref: Reactome:REACT_118367 "Phosphorylation of the Scc1:Cohesion Complex, Gallus gallus" +xref: Reactome:REACT_118462 "Phosphorylation of the SA2 Cohesin Complex, Saccharomyces cerevisiae" +xref: Reactome:REACT_1185 "Phosphorylation (Ser5) of RNA pol II CTD, Homo sapiens" +xref: Reactome:REACT_1279 "Cdc6 protein is phosphorylated by CDK, Homo sapiens" +xref: Reactome:REACT_128 "Phosphorylation of Cdc25C at Ser216, Homo sapiens" +xref: Reactome:REACT_132 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Homo sapiens" +xref: Reactome:REACT_1326 "Regulation of NUDC by phosphorylation, Homo sapiens" +xref: Reactome:REACT_13431 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Homo sapiens" +xref: Reactome:REACT_13581 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Oryctolagus cuniculus" +xref: Reactome:REACT_1362 "Phosphorylation of the Scc1:Cohesion Complex, Homo sapiens" +xref: Reactome:REACT_13817 "Autophosphorylation of PAK-2p34, Oryctolagus cuniculus" +xref: Reactome:REACT_1382 "Phosphorylation of PDE3B by AKT-1, Mus musculus" +xref: Reactome:REACT_13820 "Autophosphorylation of PAK-2p34 in the activation loop, Homo sapiens" +xref: Reactome:REACT_1420 "SOS phosphorylation and dissociation (SHC), Homo sapiens" +xref: Reactome:REACT_1481 "Phosphorylation of the SA2 Cohesin Complex, Homo sapiens" +xref: Reactome:REACT_1517 "Phosphorylation of histone H2AX at Serine-139 by ATM at the site of DSB, Homo sapiens" +xref: Reactome:REACT_15386 "Plk1-mediated phosphorylation of Nlp, Homo sapiens" +xref: Reactome:REACT_1603 "Phosphorylation and activation of CHK2 by ATM, Homo sapiens" +xref: Reactome:REACT_1657 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Homo sapiens" +xref: Reactome:REACT_1680 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Homo sapiens" +xref: Reactome:REACT_169 "SOS phosphorylation and dissociation (IRS), Homo sapiens" +xref: Reactome:REACT_1727 "RAF1 phosphorylates MEK2, Homo sapiens" +xref: Reactome:REACT_1756 "Phosphorylation of p53 at ser-15 by ATM kinase, Homo sapiens" +xref: Reactome:REACT_1782 "Phosphorylation of MDC1/NFBD1 by ATM (within 2 c-term BRCT domains), Homo sapiens" +xref: Reactome:REACT_1808 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Homo sapiens" +xref: Reactome:REACT_1878 "Phosphorylation of PDE3B, Homo sapiens" +xref: Reactome:REACT_188 "Akt1 phosphorylates BAD protein, Homo sapiens" +xref: Reactome:REACT_1888 "Phosphorylation of DLC1 by MAPK 8, Homo sapiens" +xref: Reactome:REACT_1930 "Regulation of KIF23 (MKLP1) by phosphorylation, Homo sapiens" +xref: Reactome:REACT_19312 "Phosphorylation of PD-1, Homo sapiens" +xref: Reactome:REACT_1944 "Inactivation of Wee1 kinase, Homo sapiens" +xref: Reactome:REACT_1981 "Phosphorylation of DLC2 by MAPK-8, Homo sapiens" +xref: Reactome:REACT_2009 "Phosphorylation of NBS1 by ATM, Homo sapiens" +xref: Reactome:REACT_203 "Raf1 phosphorylates MEK1, Rattus norvegicus" +xref: Reactome:REACT_20503 "Phosphorylation of CREB by ribosomal protein S6 kinase, Homo sapiens" +xref: Reactome:REACT_20543 "Phosphorylation of COP1 at Ser-387 by ATM, Homo sapiens" +xref: Reactome:REACT_20562 "Phosphorylation by MAPK/ERK, Homo sapiens" +xref: Reactome:REACT_20578 "Raf activation, Homo sapiens" +xref: Reactome:REACT_20583 "Phosphorylation of CREB by PKA, Homo sapiens" +xref: Reactome:REACT_20631 "Activation of MAPK, Homo sapiens" +xref: Reactome:REACT_20640 "Phophorylation by PDK1, Homo sapiens" +xref: Reactome:REACT_2066 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Homo sapiens" +xref: Reactome:REACT_2111 "Orc1 is phosphorylated by cyclin A/CDK2, Homo sapiens" +xref: Reactome:REACT_2119 "Activation of Cdc25C, Homo sapiens" +xref: Reactome:REACT_215 "Autophosphorylation of DNA-PKcs, Homo sapiens" +xref: Reactome:REACT_22099 "Phosphorylation of L1 by ERK, Homo sapiens" +xref: Reactome:REACT_22378 "Phosphorylation of L1 by CK-II, Homo sapiens" +xref: Reactome:REACT_23976 "Raf1 phosphorylates MEK2, Rattus norvegicus" +xref: Reactome:REACT_23990 "Phosphorylation of cPLA2 by ERK-2, Homo sapiens" +xref: Reactome:REACT_244 "PIP2 conversion to PIP3, Homo sapiens" +xref: Reactome:REACT_26 "SOS phosphorylation and dissociation (IRS, Crk), Homo sapiens" +xref: Reactome:REACT_264 "Phosphorylation of Wee1 kinase by Chk1, Homo sapiens" +xref: Reactome:REACT_28054 "Phosphorylation of BRCA1 at multiple sites by ATM, Mus musculus" +xref: Reactome:REACT_28091 "Inactivation of Wee1 kinase, Canis familiaris" +xref: Reactome:REACT_28113 "RAF1 phosphorylates MEK1, Taeniopygia guttata" +xref: Reactome:REACT_28163 "Phosphorylation of MDC1/NFBD1 by ATM (within 2 c-term BRCT domains), Canis familiaris" +xref: Reactome:REACT_28264 "Phosphorylation of Wee1 kinase by Chk1, Arabidopsis thaliana" +xref: Reactome:REACT_28480 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Danio rerio" +xref: Reactome:REACT_28555 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Xenopus tropicalis" +xref: Reactome:REACT_28681 "Phosphorylation of Cyclin E:Cdk2 complexes by Wee-1, Rattus norvegicus" +xref: Reactome:REACT_28719 "Phosphorylation and activation of eIF4B by activated S6K1, Xenopus tropicalis" +xref: Reactome:REACT_28743 "RAF1 phosphorylates MEK2, Mus musculus" +xref: Reactome:REACT_28746 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Danio rerio" +xref: Reactome:REACT_28824 "Down Regulation of Emi1 through Phosphorylation of Emi1, Danio rerio" +xref: Reactome:REACT_29029 "Phosphorylation of L1 by ERK, Caenorhabditis elegans" +xref: Reactome:REACT_29168 "Phosphorylation of Cyclin A:Cdk2 at Tyr 15, Canis familiaris" +xref: Reactome:REACT_29201 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Saccharomyces cerevisiae" +xref: Reactome:REACT_29213 "Activation of Cdc25C, Rattus norvegicus" +xref: Reactome:REACT_29277 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes, Drosophila melanogaster" +xref: Reactome:REACT_29284 "Phosphorylation of beta-catenin at Ser45 by CK1 alpha, Xenopus tropicalis" +xref: Reactome:REACT_29289 "Activation of S6K1, Gallus gallus" +xref: Reactome:REACT_29300 "Phosphorylation of L1 by ERK, Drosophila melanogaster" +xref: Reactome:REACT_29334 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Rattus norvegicus" +xref: Reactome:REACT_29395 "Phosphorylation of AKT2 by PDK1, Xenopus tropicalis" +xref: Reactome:REACT_29396 "Orc1 is phosphorylated by cyclin A/CDK2, Canis familiaris" +xref: Reactome:REACT_29410 "Regulation of KIF20A (MKL2) by phosphorylation, Rattus norvegicus" +xref: Reactome:REACT_29451 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Bos taurus" +xref: Reactome:REACT_29588 "Phosphorylation of 4E-BP1 by activated mTORC1, Taeniopygia guttata" +xref: Reactome:REACT_29614 "Regulation of NUDC by phosphorylation, Rattus norvegicus" +xref: Reactome:REACT_29689 "Cdc6 protein is phosphorylated by CDK, Bos taurus" +xref: Reactome:REACT_29694 "Phosphorylation of PDE3B, Canis familiaris" +xref: Reactome:REACT_29759 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Bos taurus" +xref: Reactome:REACT_29788 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Xenopus tropicalis" +xref: Reactome:REACT_29873 "Phosphorylation of APC component of the destruction complex, Taeniopygia guttata" +xref: Reactome:REACT_29914 "Down Regulation of Emi1 through Phosphorylation of Emi1, Canis familiaris" +xref: Reactome:REACT_30020 "Phosphorylation (Ser5) of RNA pol II CTD, Rattus norvegicus" +xref: Reactome:REACT_30023 "Phosphorylation (Ser5) of RNA pol II CTD, Xenopus tropicalis" +xref: Reactome:REACT_30052 "Phosphorylation of BRCA1 at multiple sites by ATM, Bos taurus" +xref: Reactome:REACT_30070 "Phosphorylation of L1 by CK-II, Mus musculus" +xref: Reactome:REACT_30084 "PIP2 conversion to PIP3, Canis familiaris" +xref: Reactome:REACT_30113 "SOS phosphorylation and dissociation (IRS, Crk), Drosophila melanogaster" +xref: Reactome:REACT_30116 "Phosphorylation and activation of eIF4B by activated S6K1, Canis familiaris" +xref: Reactome:REACT_30165 "Phosphorylation of the Emi1 DSGxxS degron by Plk1, Gallus gallus" +xref: Reactome:REACT_302 "Phosphorylation and activation of Chk1 by ATM, Homo sapiens" +xref: Reactome:REACT_30230 "Phosphorylation of the SA2 Cohesin Complex, Caenorhabditis elegans" +xref: Reactome:REACT_30345 "RAF1 phosphorylates MEK1, Gallus gallus" +xref: Reactome:REACT_30490 "Inactivation of Myt1 kinase, Danio rerio" +xref: Reactome:REACT_30496 "Phosphorylation of the Scc1:Cohesion Complex, Xenopus tropicalis" +xref: Reactome:REACT_30679 "Phosphorylation and inactivation of eEF2K by activated S6K1, Mus musculus" +xref: Reactome:REACT_30700 "Phosphorylation of BRCA1 at multiple sites by ATM, Gallus gallus" +xref: Reactome:REACT_30836 "Inactivation of Myt1 kinase, Bos taurus" +xref: Reactome:REACT_30921 "Phosphorylation and activation of Chk1 by ATM, Xenopus tropicalis" +xref: Reactome:REACT_30938 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Canis familiaris" +xref: Reactome:REACT_30948 "PIP2 conversion to PIP3, Gallus gallus" +xref: Reactome:REACT_30985 "Plk1-mediated phosphorylation of Nlp, Canis familiaris" +xref: Reactome:REACT_30997 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Rattus norvegicus" +xref: Reactome:REACT_31081 "Phosphorylation of TSC2 by PKB, Canis familiaris" +xref: Reactome:REACT_31149 "Phosphorylation of the Scc1:Cohesion Complex, Danio rerio" +xref: Reactome:REACT_31196 "Phosphorylation of histone H2AX at Serine-139 by ATM at the site of DSB, Canis familiaris" +xref: Reactome:REACT_31227 "Regulation of KIF20A (MKL2) by phosphorylation, Gallus gallus" +xref: Reactome:REACT_31273 "Phosphorylation of the Scc1:Cohesion Complex, Canis familiaris" +xref: Reactome:REACT_31290 "Orc1 is phosphorylated by cyclin A/CDK2, Rattus norvegicus" +xref: Reactome:REACT_31293 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Danio rerio" +xref: Reactome:REACT_31449 "Phosphorylation and activation of CHK2 by ATM, Danio rerio" +xref: Reactome:REACT_31466 "Activation of S6K1, Bos taurus" +xref: Reactome:REACT_31519 "Phosphorylation of the SA2 Cohesin Complex, Danio rerio" +xref: Reactome:REACT_31536 "Phosphorylation of NBS1 by ATM, Taeniopygia guttata" +xref: Reactome:REACT_31571 "Autophosphorylation of PAK-2p34 in the activation loop, Gallus gallus" +xref: Reactome:REACT_31625 "Phosphorylation of L1 by ERK, Taeniopygia guttata" +xref: Reactome:REACT_31639 "SOS phosphorylation and dissociation (SHC), Rattus norvegicus" +xref: Reactome:REACT_31868 "Phosphorylation and activation of CHK2 by ATM, Canis familiaris" +xref: Reactome:REACT_31915 "Phosphorylation of L1 by CK-II, Drosophila melanogaster" +xref: Reactome:REACT_31935 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Sus scrofa" +xref: Reactome:REACT_31984 "Phosphorylation (Ser5) of RNA pol II CTD, Arabidopsis thaliana" +xref: Reactome:REACT_32009 "Wee1- mediated phosphorylation of Cyclin B1:phospho-Cdc2 complexes, Mus musculus" +xref: Reactome:REACT_32077 "Inactivation of Myt1 kinase, Dictyostelium discoideum" +xref: Reactome:REACT_32079 "Phosphorylation of MDC1/NFBD1 by ATM (within 2 c-term BRCT domains), Danio rerio" +xref: Reactome:REACT_32145 "Phosphorylation of COP1 at Ser-387 by ATM, Canis familiaris" +xref: Reactome:REACT_32150 "Phosphorylation of NBS1 by ATM, Arabidopsis thaliana" +xref: Reactome:REACT_32271 "Phosphorylation of cPLA2 by ERK-2, Taeniopygia guttata" +xref: Reactome:REACT_32358 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Canis familiaris" +xref: Reactome:REACT_32374 "Mcm2-7 is phosphorylated by DDK, Canis familiaris" +xref: Reactome:REACT_32438 "Phosphorylation of proteins involved in the G1/S transition by Cyclin A:Cdk2, Sus scrofa" +xref: Reactome:REACT_32492 "Phosphorylation of BRCA1 at multiple sites by ATM, Rattus norvegicus" +xref: Reactome:REACT_32565 "Phosphorylation of NBS1 by ATM, Gallus gallus" +xref: Reactome:REACT_32598 "Phosphorylation and activation of eIF4B by activated S6K1, Taeniopygia guttata" +xref: Reactome:REACT_32620 "Phosphorylation of the Emi1 DSGxxS degron by Plk1, Bos taurus" +xref: Reactome:REACT_32845 "Phosphorylation of Cyclin D:Cdk4/6 complexes, Rattus norvegicus" +xref: Reactome:REACT_32906 "Phosphorylation and inactivation of eEF2K by activated S6K1, Sus scrofa" +xref: Reactome:REACT_32956 "Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3, Mus musculus" +xref: Reactome:REACT_33003 "Phosphorylation of the SA2 Cohesin Complex, Dictyostelium discoideum" +xref: Reactome:REACT_33009 "Phosphorylation of L1 by ERK, Danio rerio" +xref: Reactome:REACT_33080 "Phosphorylation of histone H2AX at Serine-139 by ATM at the site of DSB, Taeniopygia guttata" +xref: Reactome:REACT_33369 "Phosphorylation of NBS1 by ATM, Rattus norvegicus" +xref: Reactome:REACT_33385 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Canis familiaris" +xref: Reactome:REACT_33519 "Phosphorylation of the Emi1 DSGxxS degron by Plk1, Mus musculus" +xref: Reactome:REACT_33532 "Phosphorylation of complexed TSC2 by PKB, Bos taurus" +xref: Reactome:REACT_33692 "Phosphorylation of BRCA1 at multiple sites by ATM, Taeniopygia guttata" +xref: Reactome:REACT_33840 "Regulation of KIF23 (MKLP1) by phosphorylation, Schizosaccharomyces pombe" +xref: Reactome:REACT_33928 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Sus scrofa" +xref: Reactome:REACT_33979 "Phosphorylation of the Emi1 DSGxxS degron by Plk1, Rattus norvegicus" +xref: Reactome:REACT_34080 "Phosphorylation of PD-1, Mus musculus" +xref: Reactome:REACT_34111 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Canis familiaris" +xref: Reactome:REACT_34145 "Phosphorylation of cPLA2 by ERK-2, Xenopus tropicalis" +xref: Reactome:REACT_34222 "Phosphorylation of L1 by ERK, Rattus norvegicus" +xref: Reactome:REACT_34285 "Activation of Cdc25C, Bos taurus" +xref: Reactome:REACT_34310 "Phosphorylation and activation of Chk1 by ATM, Bos taurus" +xref: Reactome:REACT_34403 "Phosphorylation (Ser5) of RNA pol II CTD, Danio rerio" +xref: Reactome:REACT_34514 "Phosphorylation and inactivation of eEF2K by activated S6K1, Danio rerio" +xref: Reactome:REACT_34516 "Cdc6 protein is phosphorylated by CDK, Canis familiaris" +xref: Reactome:REACT_34607 "Phosphorylation of 4E-BP1 by activated mTORC1, Bos taurus" +xref: Reactome:REACT_34741 "Phosphorylation of MDC1/NFBD1 by ATM (within 2 c-term BRCT domains), Rattus norvegicus" +xref: Reactome:REACT_34788 "Phosphorylation and inactivation of eEF2K by activated S6K1, Xenopus tropicalis" +xref: Reactome:REACT_34804 "Phosphoryation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3, Gallus gallus" +xref: Reactome:REACT_384 "Phosphorylation of Cyclin E2:Cdk2 complexes by Myt1, Homo sapiens" +xref: Reactome:REACT_414 "Inactivation of Myt1 kinase, Homo sapiens" +xref: Reactome:REACT_41715 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Mus musculus" +xref: Reactome:REACT_43 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Homo sapiens" +xref: Reactome:REACT_496 "Down Regulation of Emi1 through Phosphorylation of Emi1, Homo sapiens" +xref: Reactome:REACT_54449 "Phosphorylation and activation of eIF4G by activated S6K1, Mus musculus" +xref: Reactome:REACT_545 "RAF1 phosphorylates MEK1, Homo sapiens" +xref: Reactome:REACT_559 "Phosphorylation and activation of Chk1 by ATM kinase, Mus musculus" +xref: Reactome:REACT_58131 "PIP2 conversion to PIP3, Mus musculus" +xref: Reactome:REACT_6139 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes, Homo sapiens" +xref: Reactome:REACT_6170 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by the P-TEFb(Cyclin T1:Cdk9) complex, Homo sapiens" +xref: Reactome:REACT_6178 "Wee1- mediated phosphorylation of Cyclin B1:phospho-Cdc2 complexes, Homo sapiens" +xref: Reactome:REACT_6234 "Phosphorylation (Ser5) of RNA pol II CTD, Homo sapiens" +xref: Reactome:REACT_6297 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Homo sapiens" +xref: Reactome:REACT_6311 "Phosphorylation of NEFL by the P-TEFb(Cyclin T1:Cdk9) complex, Homo sapiens" +xref: Reactome:REACT_6314 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes, Homo sapiens" +xref: Reactome:REACT_6316 "Phosphorylation of DSIF by the P-TEFb(Cyclin T1:Cdk9) complex, Human immunodeficiency virus 1" +xref: Reactome:REACT_6327 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Homo sapiens" +xref: Reactome:REACT_6342 "Myt-1 mediated phosphorylation of Cyclin A:Cdc2, Homo sapiens" +xref: Reactome:REACT_6353 "Phosphorylation of Cyclin B1 in the CRS domain, Homo sapiens" +xref: Reactome:REACT_6725 "Phosphorylation of TSC2 by PKB, Homo sapiens" +xref: Reactome:REACT_6778 "Phosphorylation and activation of eIF4B by activated S6K1, Homo sapiens" +xref: Reactome:REACT_6859 "Free APC/C phosphorylated by Plk1, Homo sapiens" +xref: Reactome:REACT_6861 "Phosphorylation of the Emi1 DSGxxS degron by Plk1, Homo sapiens" +xref: Reactome:REACT_6870 "Phosphorylation and activation of eIF4G by activated S6K1, Homo sapiens" +xref: Reactome:REACT_6873 "Phosphorylation of 4E-BP1 by activated mTORC1, Homo sapiens" +xref: Reactome:REACT_6883 "Phosphorylation and inactivation of eEF2K by activated S6K1, Homo sapiens" +xref: Reactome:REACT_6912 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Homo sapiens" +xref: Reactome:REACT_6948 "Activation of S6K1, Homo sapiens" +xref: Reactome:REACT_6952 "Phosphorylation of complexed TSC2 by PKB, Homo sapiens" +xref: Reactome:REACT_76979 "Phosphorylation of Cyclin D:Cdk4/6 complexes, Danio rerio" +xref: Reactome:REACT_77040 "Phosphorylation of COP1 at Ser-387 by ATM, Oryza sativa" +xref: Reactome:REACT_77074 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Mus musculus" +xref: Reactome:REACT_77179 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Bos taurus" +xref: Reactome:REACT_77231 "Phosphorylation of DLC2 by MAPK-8, Gallus gallus" +xref: Reactome:REACT_77234 "Plk1-mediated phosphorylation of Nlp, Gallus gallus" +xref: Reactome:REACT_773 "Phosphorylation of Cyclin E:Cdk2 complexes by Wee-1, Homo sapiens" +xref: Reactome:REACT_77326 "RAF1 phosphorylates MEK2, Taeniopygia guttata" +xref: Reactome:REACT_77362 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Rattus norvegicus" +xref: Reactome:REACT_77365 "Phosphorylation of the Emi1 DSGxxS degron by Plk1, Xenopus tropicalis" +xref: Reactome:REACT_77397 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Mus musculus" +xref: Reactome:REACT_77407 "Regulation of NUDC by phosphorylation, Bos taurus" +xref: Reactome:REACT_77443 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Danio rerio" +xref: Reactome:REACT_77450 "Phosphorylation of L1 by CK-II, Sus scrofa" +xref: Reactome:REACT_77535 "Phosphorylation of Cyclin D:Cdk4/6 complexes, Mus musculus" +xref: Reactome:REACT_77550 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes, Drosophila melanogaster" +xref: Reactome:REACT_77566 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes, Gallus gallus" +xref: Reactome:REACT_77606 "Phosphoryation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3, Canis familiaris" +xref: Reactome:REACT_77615 "Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3, Gallus gallus" +xref: Reactome:REACT_77654 "CAK-mediated phosphorylation of Cyclin A:Cdk2, Drosophila melanogaster" +xref: Reactome:REACT_77660 "Regulation of KIF23 (MKLP1) by phosphorylation, Caenorhabditis elegans" +xref: Reactome:REACT_77733 "Phosphorylation of PDE3B, Danio rerio" +xref: Reactome:REACT_77834 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Rattus norvegicus" +xref: Reactome:REACT_77857 "Phosphorylation (Ser5) of RNA pol II CTD, Drosophila melanogaster" +xref: Reactome:REACT_77897 "Phosphorylation of Wee1 kinase by Chk1, Taeniopygia guttata" +xref: Reactome:REACT_77911 "Mcm2-7 is phosphorylated by DDK, Taeniopygia guttata" +xref: Reactome:REACT_77928 "Autophosphorylation of PAK-2p34 in the activation loop, Sus scrofa" +xref: Reactome:REACT_77949 "Phosphorylation of Wee1 kinase by Chk1, Drosophila melanogaster" +xref: Reactome:REACT_77977 "Phosphorylation of Cyclin B1 in the CRS domain, Bos taurus" +xref: Reactome:REACT_78014 "Plk1-mediated phosphorylation of Nlp, Taeniopygia guttata" +xref: Reactome:REACT_78035 "Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3, Taeniopygia guttata" +xref: Reactome:REACT_78087 "Phosphorylation of TSC2 by PKB, Xenopus tropicalis" +xref: Reactome:REACT_78121 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Gallus gallus" +xref: Reactome:REACT_78226 "Regulation of NUDC by phosphorylation, Xenopus tropicalis" +xref: Reactome:REACT_78281 "Phosphoryation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3, Rattus norvegicus" +xref: Reactome:REACT_78427 "Myt-1 mediated phosphorylation of Cyclin A:Cdc2, Danio rerio" +xref: Reactome:REACT_78450 "Phosphorylation and activation of eIF4B by activated S6K1, Drosophila melanogaster" +xref: Reactome:REACT_78451 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes, Taeniopygia guttata" +xref: Reactome:REACT_78503 "Phosphorylation of histone H2AX at Serine-139 by ATM at the site of DSB, Bos taurus" +xref: Reactome:REACT_78533 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Danio rerio" +xref: Reactome:REACT_78539 "Down Regulation of Emi1 through Phosphorylation of Emi1, Xenopus tropicalis" +xref: Reactome:REACT_78556 "Free APC/C phosphorylated by Plk1, Drosophila melanogaster" +xref: Reactome:REACT_78625 "Phosphorylation and inactivation of eEF2K by activated S6K1, Caenorhabditis elegans" +xref: Reactome:REACT_78651 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes, Rattus norvegicus" +xref: Reactome:REACT_78696 "Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3, Xenopus tropicalis" +xref: Reactome:REACT_78748 "Cdc6 protein is phosphorylated by CDK, Drosophila melanogaster" +xref: Reactome:REACT_78901 "Phosphorylation (Ser5) of RNA pol II CTD, Mus musculus" +xref: Reactome:REACT_79012 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Schizosaccharomyces pombe" +xref: Reactome:REACT_79039 "Autophosphorylation of PAK-2p34 in the activation loop, Caenorhabditis elegans" +xref: Reactome:REACT_79087 "Phosphorylation of Wee1 kinase by Chk1, Oryza sativa" +xref: Reactome:REACT_79125 "SOS phosphorylation and dissociation (IRS), Bos taurus" +xref: Reactome:REACT_79182 "Phosphorylation of Cyclin B1 in the CRS domain, Canis familiaris" +xref: Reactome:REACT_79208 "Mcm2-7 is phosphorylated by DDK, Bos taurus" +xref: Reactome:REACT_79220 "Phosphorylation of 4E-BP1 by activated mTORC1, Canis familiaris" +xref: Reactome:REACT_79255 "Phosphorylation of p53 at ser-15 by ATM kinase, Danio rerio" +xref: Reactome:REACT_79372 "Cdc6 protein is phosphorylated by CDK, Danio rerio" +xref: Reactome:REACT_79573 "Phosphorylation of p53 at ser-15 by ATM kinase, Mus musculus" +xref: Reactome:REACT_79686 "Phosphorylation of the Scc1:Cohesion Complex, Drosophila melanogaster" +xref: Reactome:REACT_79694 "Autophosphorylation of PAK-2p34 in the activation loop, Xenopus tropicalis" +xref: Reactome:REACT_79700 "Activation of S6K1, Taeniopygia guttata" +xref: Reactome:REACT_79709 "Orc1 is phosphorylated by cyclin A/CDK2, Mus musculus" +xref: Reactome:REACT_79720 "Phosphorylation of Cyclin E2:Cdk2 complexes by Myt1, Danio rerio" +xref: Reactome:REACT_80110 "Phosphorylation of proteins involved in the G1/S transition by Cyclin A:Cdk2, Drosophila melanogaster" +xref: Reactome:REACT_80144 "Phosphorylation of complexed TSC2 by PKB, Sus scrofa" +xref: Reactome:REACT_80185 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Mus musculus" +xref: Reactome:REACT_80213 "Activation of S6K1, Canis familiaris" +xref: Reactome:REACT_80218 "Phosphorylation of the Scc1:Cohesion Complex, Dictyostelium discoideum" +xref: Reactome:REACT_80239 "Regulation of KIF20A (MKL2) by phosphorylation, Dictyostelium discoideum" +xref: Reactome:REACT_80255 "Mcm2-7 is phosphorylated by DDK, Mus musculus" +xref: Reactome:REACT_80591 "Regulation of KIF20A (MKL2) by phosphorylation, Drosophila melanogaster" +xref: Reactome:REACT_80606 "Phosphorylation of NBS1 by ATM, Oryza sativa" +xref: Reactome:REACT_80617 "Inactivation of Wee1 kinase, Xenopus tropicalis" +xref: Reactome:REACT_80632 "Phosphorylation of L1 by ERK, Schizosaccharomyces pombe" +xref: Reactome:REACT_80665 "Down Regulation of Emi1 through Phosphorylation of Emi1, Taeniopygia guttata" +xref: Reactome:REACT_80684 "Phosphorylation of COP1 at Ser-387 by ATM, Arabidopsis thaliana" +xref: Reactome:REACT_80689 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Oryza sativa" +xref: Reactome:REACT_80699 "PIP2 conversion to PIP3, Danio rerio" +xref: Reactome:REACT_80700 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Sus scrofa" +xref: Reactome:REACT_80714 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes, Rattus norvegicus" +xref: Reactome:REACT_80804 "Phosphorylation of PDE3B, Bos taurus" +xref: Reactome:REACT_80853 "Phosphorylation (Ser5) of RNA pol II CTD, Dictyostelium discoideum" +xref: Reactome:REACT_80860 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Rattus norvegicus" +xref: Reactome:REACT_80909 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Drosophila melanogaster" +xref: Reactome:REACT_81027 "PIP2 conversion to PIP3, Sus scrofa" +xref: Reactome:REACT_81148 "Phosphorylation and activation of CHK2 by ATM, Taeniopygia guttata" +xref: Reactome:REACT_81218 "Phosphorylation and activation of CHK2 by ATM, Rattus norvegicus" +xref: Reactome:REACT_81439 "Phosphorylation of APC component of the destruction complex, Xenopus tropicalis" +xref: Reactome:REACT_81458 "Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3, Bos taurus" +xref: Reactome:REACT_81490 "Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3, Xenopus tropicalis" +xref: Reactome:REACT_81590 "Wee1- mediated phosphorylation of Cyclin B1:phospho-Cdc2 complexes, Bos taurus" +xref: Reactome:REACT_81616 "Phosphorylation of Cyclin E2:Cdk2 complexes by Myt1, Canis familiaris" +xref: Reactome:REACT_81647 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Rattus norvegicus" +xref: Reactome:REACT_81652 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Rattus norvegicus" +xref: Reactome:REACT_81693 "Phosphorylation of beta-catenin at Ser45 by CK1 alpha, Drosophila melanogaster" +xref: Reactome:REACT_81715 "Orc1 is phosphorylated by cyclin A/CDK2, Drosophila melanogaster" +xref: Reactome:REACT_81727 "Phosphorylation of Cyclin A:Cdk2 at Tyr 15, Danio rerio" +xref: Reactome:REACT_81864 "Phosphorylation of Cx43 by c-src, Bos taurus" +xref: Reactome:REACT_81941 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Bos taurus" +xref: Reactome:REACT_82037 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Mus musculus" +xref: Reactome:REACT_82115 "Phosphorylation and activation of Chk1 by ATM, Saccharomyces cerevisiae" +xref: Reactome:REACT_82125 "Phosphorylation of complexed TSC2 by PKB, Danio rerio" +xref: Reactome:REACT_82128 "PIP2 conversion to PIP3, Taeniopygia guttata" +xref: Reactome:REACT_82261 "Phosphorylation of DLC2 by MAPK-8, Xenopus tropicalis" +xref: Reactome:REACT_82270 "Autophosphorylation of PAK-2p34 in the activation loop, Rattus norvegicus" +xref: Reactome:REACT_82303 "Phosphorylation of Cyclin D:Cdk4/6 complexes, Xenopus tropicalis" +xref: Reactome:REACT_82310 "Phosphorylation and activation of Chk1 by ATM, Gallus gallus" +xref: Reactome:REACT_82361 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes, Canis familiaris" +xref: Reactome:REACT_82456 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Bos taurus" +xref: Reactome:REACT_82473 "Phosphorylation of the SA2 Cohesin Complex, Canis familiaris" +xref: Reactome:REACT_82616 "Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3, Mus musculus" +xref: Reactome:REACT_82678 "Phosphorylation of complexed TSC2 by PKB, Rattus norvegicus" +xref: Reactome:REACT_82728 "Plk1-mediated phosphorylation of Nlp, Mus musculus" +xref: Reactome:REACT_82751 "Down Regulation of Emi1 through Phosphorylation of Emi1, Rattus norvegicus" +xref: Reactome:REACT_82824 "Inactivation of Wee1 kinase, Rattus norvegicus" +xref: Reactome:REACT_82901 "Phosphorylation of DLC2 by MAPK-8, Canis familiaris" +xref: Reactome:REACT_82927 "PIP2 conversion to PIP3, Rattus norvegicus" +xref: Reactome:REACT_83006 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Caenorhabditis elegans" +xref: Reactome:REACT_83089 "Inactivation of Myt1 kinase, Saccharomyces cerevisiae" +xref: Reactome:REACT_83110 "Phosphorylation (Ser5) of RNA pol II CTD, Schizosaccharomyces pombe" +xref: Reactome:REACT_83178 "Phosphorylation and activation of Chk1 by ATM, Oryza sativa" +xref: Reactome:REACT_83187 "Phosphorylation of the SA2 Cohesin Complex, Mus musculus" +xref: Reactome:REACT_83239 "Phosphorylation and activation of eIF4G by activated S6K1, Gallus gallus" +xref: Reactome:REACT_83279 "Phosphorylation of NBS1 by ATM, Canis familiaris" +xref: Reactome:REACT_83297 "CAK-mediated phosphorylation of Cyclin A:Cdk2, Danio rerio" +xref: Reactome:REACT_83436 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Arabidopsis thaliana" +xref: Reactome:REACT_83476 "Phosphorylation and activation of CHK2 by ATM, Mus musculus" +xref: Reactome:REACT_83529 "Wee1- mediated phosphorylation of Cyclin B1:phospho-Cdc2 complexes, Drosophila melanogaster" +xref: Reactome:REACT_83533 "Phosphorylation and activation of Chk1 by ATM, Rattus norvegicus" +xref: Reactome:REACT_83579 "Phosphorylation of Wee1 kinase by Chk1, Gallus gallus" +xref: Reactome:REACT_83582 "Plk1-mediated phosphorylation of Nlp, Danio rerio" +xref: Reactome:REACT_83671 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Taeniopygia guttata" +xref: Reactome:REACT_83696 "Free APC/C phosphorylated by Plk1, Bos taurus" +xref: Reactome:REACT_83709 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Mus musculus" +xref: Reactome:REACT_83727 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Gallus gallus" +xref: Reactome:REACT_83899 "Phosphorylation of MDC1/NFBD1 by ATM (within 2 c-term BRCT domains), Sus scrofa" +xref: Reactome:REACT_83979 "Phosphorylation of COP1 at Ser-387 by ATM, Mus musculus" +xref: Reactome:REACT_84080 "Phosphorylation of the SA2 Cohesin Complex, Xenopus tropicalis" +xref: Reactome:REACT_84082 "Phosphorylation of Wee1 kinase by Chk1, Rattus norvegicus" +xref: Reactome:REACT_84208 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes, Mus musculus" +xref: Reactome:REACT_84273 "Phosphorylation of L1 by ERK, Sus scrofa" +xref: Reactome:REACT_84348 "Phosphorylation of COP1 at Ser-387 by ATM, Taeniopygia guttata" +xref: Reactome:REACT_84405 "Phosphorylation of p53 at ser-15 by ATM kinase, Rattus norvegicus" +xref: Reactome:REACT_845 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Homo sapiens" +xref: Reactome:REACT_84560 "Cdc6 protein is phosphorylated by CDK, Saccharomyces cerevisiae" +xref: Reactome:REACT_84656 "Phosphoryation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3, Bos taurus" +xref: Reactome:REACT_84932 "Phosphorylation of Wee1 kinase by Chk1, Sus scrofa" +xref: Reactome:REACT_85009 "Phosphorylation of beta-catenin at Ser45 by CK1 alpha, Taeniopygia guttata" +xref: Reactome:REACT_85017 "Activation of S6K1, Dictyostelium discoideum" +xref: Reactome:REACT_85044 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Canis familiaris" +xref: Reactome:REACT_85066 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Taeniopygia guttata" +xref: Reactome:REACT_85256 "Phosphorylation of Cdc25C at Ser216, Mus musculus" +xref: Reactome:REACT_85328 "Regulation of KIF20A (MKL2) by phosphorylation, Mus musculus" +xref: Reactome:REACT_85379 "Phosphorylation of Cx43 by c-src, Sus scrofa" +xref: Reactome:REACT_85449 "Phosphorylation and activation of eIF4G by activated S6K1, Bos taurus" +xref: Reactome:REACT_85586 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Gallus gallus" +xref: Reactome:REACT_85699 "Phosphorylation of Cyclin B1 in the CRS domain, Rattus norvegicus" +xref: Reactome:REACT_85720 "Phosphorylation of L1 by ERK, Canis familiaris" +xref: Reactome:REACT_85745 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes, Xenopus tropicalis" +xref: Reactome:REACT_85751 "Phosphorylation of BRCA1 at multiple sites by ATM, Canis familiaris" +xref: Reactome:REACT_85812 "Phosphorylation and activation of Chk1 by ATM, Drosophila melanogaster" +xref: Reactome:REACT_85836 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Gallus gallus" +xref: Reactome:REACT_85871 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Mus musculus" +xref: Reactome:REACT_86014 "Phosphorylation of the SA2 Cohesin Complex, Bos taurus" +xref: Reactome:REACT_86033 "Phosphorylation and activation of CHK2 by ATM, Schizosaccharomyces pombe" +xref: Reactome:REACT_86061 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Bos taurus" +xref: Reactome:REACT_86092 "Phosphorylation of COP1 at Ser-387 by ATM, Bos taurus" +xref: Reactome:REACT_86211 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Saccharomyces cerevisiae" +xref: Reactome:REACT_86252 "Phosphorylation of Cyclin A:Cdk2 at Tyr 15, Drosophila melanogaster" +xref: Reactome:REACT_86261 "Regulation of NUDC by phosphorylation, Dictyostelium discoideum" +xref: Reactome:REACT_86277 "Phosphorylation of TSC2 by PKB, Bos taurus" +xref: Reactome:REACT_86365 "Phosphorylation and activation of eIF4G by activated S6K1, Rattus norvegicus" +xref: Reactome:REACT_86372 "Akt1 phosphorylates BAD protein, Mus musculus" +xref: Reactome:REACT_86415 "Phosphorylation of Cx43 by c-src, Xenopus tropicalis" +xref: Reactome:REACT_86422 "Phosphorylation of PD-1, Rattus norvegicus" +xref: Reactome:REACT_86533 "Cdc6 protein is phosphorylated by CDK, Sus scrofa" +xref: Reactome:REACT_86736 "Phosphorylation of proteins involved in the G1/S transition by Cyclin A:Cdk2, Rattus norvegicus" +xref: Reactome:REACT_86800 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Danio rerio" +xref: Reactome:REACT_86867 "Phosphorylation of p53 at ser-15 by ATM kinase, Bos taurus" +xref: Reactome:REACT_86952 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Sus scrofa" +xref: Reactome:REACT_86967 "Phosphorylation (Ser5) of RNA pol II CTD, Gallus gallus" +xref: Reactome:REACT_87010 "Regulation of NUDC by phosphorylation, Danio rerio" +xref: Reactome:REACT_87121 "Phosphorylation of cPLA2 by ERK-2, Bos taurus" +xref: Reactome:REACT_87149 "Phosphorylation of L1 by CK-II, Danio rerio" +xref: Reactome:REACT_87212 "Phosphorylation of Cx43 by c-src, Mus musculus" +xref: Reactome:REACT_87222 "Cdc6 protein is phosphorylated by CDK, Schizosaccharomyces pombe" +xref: Reactome:REACT_87298 "Phosphorylation of Cyclin A:Cdk2 at Tyr 15, Sus scrofa" +xref: Reactome:REACT_87329 "Regulation of KIF23 (MKLP1) by phosphorylation, Mus musculus" +xref: Reactome:REACT_87391 "Phosphorylation of Cx43 by c-src, Rattus norvegicus" +xref: Reactome:REACT_87424 "SOS phosphorylation and dissociation (SHC), Danio rerio" +xref: Reactome:REACT_87437 "Phosphorylation of AKT2 by PDK1, Caenorhabditis elegans" +xref: Reactome:REACT_87485 "Activation of S6K1, Xenopus tropicalis" +xref: Reactome:REACT_87497 "Akt1 phosphorylates BAD protein, Bos taurus" +xref: Reactome:REACT_87503 "Phosphorylation of Cyclin E2:Cdk2 complexes by Myt1, Xenopus tropicalis" +xref: Reactome:REACT_87523 "Phosphorylation of Cyclin B1 in the CRS domain, Mus musculus" +xref: Reactome:REACT_87534 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Gallus gallus" +xref: Reactome:REACT_87593 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Gallus gallus" +xref: Reactome:REACT_87650 "Phosphorylation of proteins involved in the G1/S transition by Cyclin A:Cdk2, Xenopus tropicalis" +xref: Reactome:REACT_87679 "Phosphorylation of PDE3B, Xenopus tropicalis" +xref: Reactome:REACT_87753 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Bos taurus" +xref: Reactome:REACT_87880 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes, Danio rerio" +xref: Reactome:REACT_87967 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Xenopus tropicalis" +xref: Reactome:REACT_88025 "Activation of S6K1, Mus musculus" +xref: Reactome:REACT_88055 "Phosphorylation of NBS1 by ATM, Sus scrofa" +xref: Reactome:REACT_88091 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Xenopus tropicalis" +xref: Reactome:REACT_88220 "Regulation of KIF23 (MKLP1) by phosphorylation, Rattus norvegicus" +xref: Reactome:REACT_88298 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Taeniopygia guttata" +xref: Reactome:REACT_88326 "CAK-mediated phosphorylation of Cyclin A:Cdk2, Canis familiaris" +xref: Reactome:REACT_88374 "CAK-mediated phosphorylation of Cyclin A:Cdk2, Xenopus tropicalis" +xref: Reactome:REACT_88421 "Phosphorylation and inactivation of eEF2K by activated S6K1, Rattus norvegicus" +xref: Reactome:REACT_88430 "Orc1 is phosphorylated by cyclin A/CDK2, Bos taurus" +xref: Reactome:REACT_88440 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Caenorhabditis elegans" +xref: Reactome:REACT_88458 "Phosphorylation of cPLA2 by ERK-2, Danio rerio" +xref: Reactome:REACT_88486 "Inactivation of Wee1 kinase, Taeniopygia guttata" +xref: Reactome:REACT_88516 "Cdc6 protein is phosphorylated by CDK, Rattus norvegicus" +xref: Reactome:REACT_88548 "Phosphorylation of the Emi1 DSGxxS degron by Plk1, Taeniopygia guttata" +xref: Reactome:REACT_88564 "Plk1-mediated phosphorylation of Nlp, Xenopus tropicalis" +xref: Reactome:REACT_88590 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Rattus norvegicus" +xref: Reactome:REACT_88665 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Danio rerio" +xref: Reactome:REACT_88668 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Drosophila melanogaster" +xref: Reactome:REACT_88766 "Phosphorylation (Ser5) of RNA pol II CTD, Oryza sativa" +xref: Reactome:REACT_88871 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Rattus norvegicus" +xref: Reactome:REACT_88928 "Autophosphorylation of PAK-2p34 in the activation loop, Drosophila melanogaster" +xref: Reactome:REACT_88987 "Free APC/C phosphorylated by Plk1, Canis familiaris" +xref: Reactome:REACT_89001 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Gallus gallus" +xref: Reactome:REACT_89026 "Phosphorylation of PD-1, Gallus gallus" +xref: Reactome:REACT_89122 "Activation of Cdc25C, Canis familiaris" +xref: Reactome:REACT_89366 "Phosphorylation of APC component of the destruction complex, Canis familiaris" +xref: Reactome:REACT_89427 "Phosphorylation of AKT2 by PDK1, Bos taurus" +xref: Reactome:REACT_89464 "Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3, Taeniopygia guttata" +xref: Reactome:REACT_89547 "Phosphorylation of NBS1 by ATM, Xenopus tropicalis" +xref: Reactome:REACT_89579 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Xenopus tropicalis" +xref: Reactome:REACT_89769 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Taeniopygia guttata" +xref: Reactome:REACT_89794 "Phosphorylation of beta-catenin at Ser45 by CK1 alpha, Mus musculus" +xref: Reactome:REACT_89879 "Phosphoryation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3, Mus musculus" +xref: Reactome:REACT_89988 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Schizosaccharomyces pombe" +xref: Reactome:REACT_9007 "Phosphorylation of proteins involved in the G1/S transition by Cyclin A:Cdk2, Homo sapiens" +xref: Reactome:REACT_90132 "Phosphorylation of AKT2 by PDK1, Sus scrofa" +xref: Reactome:REACT_90167 "Phosphorylation of Wee1 kinase by Chk1, Bos taurus" +xref: Reactome:REACT_90220 "Wee1- mediated phosphorylation of Cyclin B1:phospho-Cdc2 complexes, Rattus norvegicus" +xref: Reactome:REACT_90227 "Phosphorylation of AKT2 by PDK1, Mus musculus" +xref: Reactome:REACT_90290 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Taeniopygia guttata" +xref: Reactome:REACT_90364 "Regulation of NUDC by phosphorylation, Canis familiaris" +xref: Reactome:REACT_90426 "Phosphorylation of Wee1 kinase by Chk1, Mus musculus" +xref: Reactome:REACT_90449 "Phosphorylation of Cyclin E:Cdk2 complexes by Wee-1, Canis familiaris" +xref: Reactome:REACT_90562 "Regulation of NUDC by phosphorylation, Drosophila melanogaster" +xref: Reactome:REACT_9057 "Phosphorylation of Cyclin A:Cdk2 at Tyr 15, Homo sapiens" +xref: Reactome:REACT_9067 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Homo sapiens" +xref: Reactome:REACT_90675 "Phosphorylation (Ser5) of RNA pol II CTD, Caenorhabditis elegans" +xref: Reactome:REACT_907 "Mcm2-7 is phosphorylated by DDK, Homo sapiens" +xref: Reactome:REACT_9070 "CAK-mediated phosphorylation of Cyclin A:Cdk2, Homo sapiens" +xref: Reactome:REACT_908 "Phosphorylation of AKT2 by PDK1, Homo sapiens" +xref: Reactome:REACT_90917 "Phosphorylation of Wee1 kinase by Chk1, Canis familiaris" +xref: Reactome:REACT_91050 "SOS phosphorylation and dissociation (IRS, Crk), Mus musculus" +xref: Reactome:REACT_91062 "Phosphorylation of Cyclin E2:Cdk2 complexes by Myt1, Bos taurus" +xref: Reactome:REACT_91085 "Inactivation of Wee1 kinase, Danio rerio" +xref: Reactome:REACT_91156 "Phosphorylation and activation of CHK2 by ATM, Gallus gallus" +xref: Reactome:REACT_91157 "Phosphorylation (Ser5) of RNA pol II CTD, Saccharomyces cerevisiae" +xref: Reactome:REACT_91196 "Phosphorylation of 4E-BP1 by activated mTORC1, Mus musculus" +xref: Reactome:REACT_91197 "Phosphorylation and activation of eIF4B by activated S6K1, Mus musculus" +xref: Reactome:REACT_91240 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Xenopus tropicalis" +xref: Reactome:REACT_91263 "Down Regulation of Emi1 through Phosphorylation of Emi1, Gallus gallus" +xref: Reactome:REACT_91382 "SOS phosphorylation and dissociation (IRS), Danio rerio" +xref: Reactome:REACT_91470 "Regulation of KIF20A (MKL2) by phosphorylation, Canis familiaris" +xref: Reactome:REACT_91501 "PIP2 conversion to PIP3, Bos taurus" +xref: Reactome:REACT_91541 "Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3, Rattus norvegicus" +xref: Reactome:REACT_91574 "Phosphorylation of DLC2 by MAPK-8, Rattus norvegicus" +xref: Reactome:REACT_91643 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Drosophila melanogaster" +xref: Reactome:REACT_91684 "Phosphorylation of the SA2 Cohesin Complex, Drosophila melanogaster" +xref: Reactome:REACT_91760 "Regulation of KIF23 (MKLP1) by phosphorylation, Danio rerio" +xref: Reactome:REACT_91937 "Phosphorylation of APC component of the destruction complex, Bos taurus" +xref: Reactome:REACT_92033 "Inactivation of Myt1 kinase, Caenorhabditis elegans" +xref: Reactome:REACT_92108 "Myt-1 mediated phosphorylation of Cyclin A:Cdc2, Rattus norvegicus" +xref: Reactome:REACT_92126 "Activation of S6K1, Oryza sativa" +xref: Reactome:REACT_92148 "Autophosphorylation of PAK-2p34 in the activation loop, Danio rerio" +xref: Reactome:REACT_92219 "Phosphorylation of PDE3B, Caenorhabditis elegans" +xref: Reactome:REACT_92247 "Phosphorylation of the Emi1 DSGxxS degron by Plk1, Canis familiaris" +xref: Reactome:REACT_92407 "Regulation of KIF23 (MKLP1) by phosphorylation, Canis familiaris" +xref: Reactome:REACT_92735 "Autophosphorylation of PAK-2p34 in the activation loop, Taeniopygia guttata" +xref: Reactome:REACT_92736 "Phosphorylation of L1 by ERK, Gallus gallus" +xref: Reactome:REACT_92804 "Phosphorylation of Wee1 kinase by Chk1, Danio rerio" +xref: Reactome:REACT_92852 "SOS phosphorylation and dissociation (SHC), Canis familiaris" +xref: Reactome:REACT_92889 "Phosphorylation of TSC2 by PKB, Sus scrofa" +xref: Reactome:REACT_92915 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Danio rerio" +xref: Reactome:REACT_92929 "RAF1 phosphorylates MEK1, Danio rerio" +xref: Reactome:REACT_92951 "Phosphorylation and activation of Chk1 by ATM, Canis familiaris" +xref: Reactome:REACT_93018 "RAF1 phosphorylates MEK1, Bos taurus" +xref: Reactome:REACT_93105 "Phosphorylation of cPLA2 by ERK-2, Rattus norvegicus" +xref: Reactome:REACT_93124 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes, Mus musculus" +xref: Reactome:REACT_93149 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Dictyostelium discoideum" +xref: Reactome:REACT_93166 "Phosphorylation and activation of Chk1 by ATM, Taeniopygia guttata" +xref: Reactome:REACT_93219 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Xenopus tropicalis" +xref: Reactome:REACT_93221 "Phosphoryation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3, Xenopus tropicalis" +xref: Reactome:REACT_93346 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Mus musculus" +xref: Reactome:REACT_93366 "Phosphorylation of cPLA2 by ERK-2, Canis familiaris" +xref: Reactome:REACT_93414 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Drosophila melanogaster" +xref: Reactome:REACT_93440 "Regulation of KIF20A (MKL2) by phosphorylation, Taeniopygia guttata" +xref: Reactome:REACT_93441 "Regulation of KIF23 (MKLP1) by phosphorylation, Gallus gallus" +xref: Reactome:REACT_93613 "CAK-mediated phosphorylation of Cyclin A:Cdk2, Rattus norvegicus" +xref: Reactome:REACT_93615 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Bos taurus" +xref: Reactome:REACT_937 "Phosphorylation of BRCA1 at multiple sites by ATM, Homo sapiens" +xref: Reactome:REACT_93706 "RAF1 phosphorylates MEK1, Canis familiaris" +xref: Reactome:REACT_93746 "Phosphorylation of Cyclin A:Cdk2 at Tyr 15, Mus musculus" +xref: Reactome:REACT_93878 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Gallus gallus" +xref: Reactome:REACT_94017 "SOS phosphorylation and dissociation (IRS, Crk), Bos taurus" +xref: Reactome:REACT_94113 "Phosphorylation of Cx43 by c-src, Canis familiaris" +xref: Reactome:REACT_94151 "Phosphorylation of Wee1 kinase by Chk1, Xenopus tropicalis" +xref: Reactome:REACT_94248 "SOS phosphorylation and dissociation (SHC), Bos taurus" +xref: Reactome:REACT_94258 "Phosphorylation of p53 at ser-15 by ATM kinase, Sus scrofa" +xref: Reactome:REACT_94298 "Phosphorylation of Cyclin B1 in the CRS domain, Danio rerio" +xref: Reactome:REACT_94397 "Orc1 is phosphorylated by cyclin A/CDK2, Danio rerio" +xref: Reactome:REACT_94428 "Phosphorylation of PD-1, Bos taurus" +xref: Reactome:REACT_94452 "Phosphorylation of MDC1/NFBD1 by ATM (within 2 c-term BRCT domains), Bos taurus" +xref: Reactome:REACT_94464 "Phosphorylation and activation of eIF4B by activated S6K1, Danio rerio" +xref: Reactome:REACT_94562 "Phosphorylation of the Scc1:Cohesion Complex, Caenorhabditis elegans" +xref: Reactome:REACT_94615 "SOS phosphorylation and dissociation (IRS, Crk), Rattus norvegicus" +xref: Reactome:REACT_94784 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Rattus norvegicus" +xref: Reactome:REACT_94817 "Phosphorylation of the SA2 Cohesin Complex, Rattus norvegicus" +xref: Reactome:REACT_94947 "Autophosphorylation of PAK-2p34 in the activation loop, Canis familiaris" +xref: Reactome:REACT_95052 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Oryza sativa" +xref: Reactome:REACT_95087 "Phosphorylation of the Scc1:Cohesion Complex, Bos taurus" +xref: Reactome:REACT_95088 "Inactivation of Wee1 kinase, Mus musculus" +xref: Reactome:REACT_95089 "Phosphorylation of Cyclin E:Cdk2 complexes by Wee-1, Bos taurus" +xref: Reactome:REACT_95155 "Regulation of NUDC by phosphorylation, Taeniopygia guttata" +xref: Reactome:REACT_95163 "CAK-mediated phosphorylation of Cyclin A:Cdk2, Mus musculus" +xref: Reactome:REACT_95437 "Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3, Drosophila melanogaster" +xref: Reactome:REACT_95461 "Phosphorylation of proteins involved in the G1/S transition by Cyclin A:Cdk2, Bos taurus" +xref: Reactome:REACT_95504 "Phosphorylation of Cdc25C at Ser216, Xenopus tropicalis" +xref: Reactome:REACT_95769 "PIP2 conversion to PIP3, Xenopus tropicalis" +xref: Reactome:REACT_96 "Phosphorylation of Cyclin D:Cdk4/6 complexes, Homo sapiens" +xref: Reactome:REACT_96039 "Myt-1 mediated phosphorylation of Cyclin A:Cdc2, Canis familiaris" +xref: Reactome:REACT_96088 "Phosphorylation of PDE3B, Sus scrofa" +xref: Reactome:REACT_96097 "SOS phosphorylation and dissociation (IRS), Rattus norvegicus" +xref: Reactome:REACT_96102 "Phosphorylation of Cx43 by c-src, Gallus gallus" +xref: Reactome:REACT_96129 "Phosphorylation and activation of eIF4G by activated S6K1, Taeniopygia guttata" +xref: Reactome:REACT_96200 "Regulation of NUDC by phosphorylation, Gallus gallus" +xref: Reactome:REACT_96208 "Phosphorylation of COP1 at Ser-387 by ATM, Sus scrofa" +xref: Reactome:REACT_96218 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Drosophila melanogaster" +xref: Reactome:REACT_96356 "Free APC/C phosphorylated by Plk1, Rattus norvegicus" +xref: Reactome:REACT_96461 "Phosphorylation of L1 by CK-II, Bos taurus" +xref: Reactome:REACT_96468 "Autophosphorylation of PAK-2p34 in the activation loop, Mus musculus" +xref: Reactome:REACT_96483 "Phosphorylation of COP1 at Ser-387 by ATM, Gallus gallus" +xref: Reactome:REACT_96500 "RAF1 phosphorylates MEK2, Gallus gallus" +xref: Reactome:REACT_96524 "Activation of Cdc25C, Xenopus tropicalis" +xref: Reactome:REACT_96656 "Plk1-mediated phosphorylation of Nlp, Rattus norvegicus" +xref: Reactome:REACT_96666 "Phosphorylation and activation of CHK2 by ATM, Saccharomyces cerevisiae" +xref: Reactome:REACT_96758 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Canis familiaris" +xref: Reactome:REACT_96793 "Activation of S6K1, Danio rerio" +xref: Reactome:REACT_96797 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Rattus norvegicus" +xref: Reactome:REACT_96877 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Sus scrofa" +xref: Reactome:REACT_96899 "Phosphorylation of TSC2 by PKB, Rattus norvegicus" +xref: Reactome:REACT_96968 "Cdc6 protein is phosphorylated by CDK, Mus musculus" +xref: Reactome:REACT_97193 "Phosphorylation and activation of eIF4G by activated S6K1, Canis familiaris" +xref: Reactome:REACT_97218 "Orc1 is phosphorylated by cyclin A/CDK2, Xenopus tropicalis" +xref: Reactome:REACT_97282 "Activation of S6K1, Sus scrofa" +xref: Reactome:REACT_97299 "Phosphorylation of Cyclin E2:Cdk2 complexes by Myt1, Mus musculus" +xref: Reactome:REACT_97458 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Dictyostelium discoideum" +xref: Reactome:REACT_97577 "Myt-1 mediated phosphorylation of Cyclin A:Cdc2, Bos taurus" +xref: Reactome:REACT_97661 "Mcm2-7 is phosphorylated by DDK, Gallus gallus" +xref: Reactome:REACT_97667 "Phosphorylation of complexed TSC2 by PKB, Canis familiaris" +xref: Reactome:REACT_97748 "Phosphorylation of cPLA2 by ERK-2, Mus musculus" +xref: Reactome:REACT_97759 "Phosphorylation of Cx43 by c-src, Danio rerio" +xref: Reactome:REACT_97847 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Mus musculus" +xref: Reactome:REACT_97905 "Phosphorylation of BRCA1 at multiple sites by ATM, Xenopus tropicalis" +xref: Reactome:REACT_98024 "Myt-1 mediated phosphorylation of Cyclin A:Cdc2, Mus musculus" +xref: Reactome:REACT_98050 "Phosphorylation of Cdc25C at Ser216, Canis familiaris" +xref: Reactome:REACT_98066 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Saccharomyces cerevisiae" +xref: Reactome:REACT_98109 "Regulation of NUDC by phosphorylation, Mus musculus" +xref: Reactome:REACT_98176 "Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3, Bos taurus" +xref: Reactome:REACT_98213 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Xenopus tropicalis" +xref: Reactome:REACT_98253 "RAF1 phosphorylates MEK2, Bos taurus" +xref: Reactome:REACT_98296 "Phosphorylation of Cyclin B1 in the CRS domain, Drosophila melanogaster" +xref: Reactome:REACT_98373 "Myt-1 mediated phosphorylation of Cyclin A:Cdc2, Drosophila melanogaster" +xref: Reactome:REACT_98378 "Phosphorylation of COP1 at Ser-387 by ATM, Danio rerio" +xref: Reactome:REACT_98395 "Phosphorylation and activation of Chk1 by ATM, Arabidopsis thaliana" +xref: Reactome:REACT_98434 "Phosphorylation and inactivation of eEF2K by activated S6K1, Taeniopygia guttata" +xref: Reactome:REACT_98436 "Phosphorylation of 4E-BP1 by activated mTORC1, Gallus gallus" +xref: Reactome:REACT_98443 "Inactivation of Wee1 kinase, Gallus gallus" +xref: Reactome:REACT_98493 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Drosophila melanogaster" +xref: Reactome:REACT_98558 "Autophosphorylation of PAK-2p34 in the activation loop, Saccharomyces cerevisiae" +xref: Reactome:REACT_98560 "Phosphorylation and activation of CHK2 by ATM, Xenopus tropicalis" +xref: Reactome:REACT_98663 "Regulation of KIF23 (MKLP1) by phosphorylation, Bos taurus" +xref: Reactome:REACT_98708 "Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3, Drosophila melanogaster" +xref: Reactome:REACT_98731 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Danio rerio" +xref: Reactome:REACT_98738 "Phosphorylation of TSC2 by PKB, Danio rerio" +xref: Reactome:REACT_98741 "Phosphorylation of beta-catenin at Ser45 by CK1 alpha, Bos taurus" +xref: Reactome:REACT_98779 "Phosphorylation of Cx43 by c-src, Taeniopygia guttata" +xref: Reactome:REACT_988 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Homo sapiens" +xref: Reactome:REACT_98847 "Phosphorylation of complexed TSC2 by PKB, Mus musculus" +xref: Reactome:REACT_98908 "Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3, Rattus norvegicus" +xref: Reactome:REACT_98913 "Phosphorylation of PD-1, Canis familiaris" +xref: Reactome:REACT_98971 "Phosphorylation of AKT2 by PDK1, Rattus norvegicus" +xref: Reactome:REACT_98996 "Free APC/C phosphorylated by Plk1, Danio rerio" +xref: Reactome:REACT_99025 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Taeniopygia guttata" +xref: Reactome:REACT_99053 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Sus scrofa" +xref: Reactome:REACT_99141 "Phosphorylation of NBS1 by ATM, Bos taurus" +xref: Reactome:REACT_99158 "Inactivation of Wee1 kinase, Drosophila melanogaster" +xref: Reactome:REACT_99207 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Taeniopygia guttata" +xref: Reactome:REACT_99231 "Phosphorylation of AKT2 by PDK1, Danio rerio" +xref: Reactome:REACT_99266 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Caenorhabditis elegans" +xref: Reactome:REACT_99302 "Phosphorylation of Cyclin D:Cdk4/6 complexes, Sus scrofa" +xref: Reactome:REACT_99311 "RAF1 phosphorylates MEK1, Mus musculus" +xref: Reactome:REACT_9955 "Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3, Homo sapiens" +xref: Reactome:REACT_99556 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Mus musculus" +xref: Reactome:REACT_99560 "RAF1 phosphorylates MEK2, Canis familiaris" +xref: Reactome:REACT_9959 "Phosphoryation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3, Homo sapiens" +xref: Reactome:REACT_99595 "Phosphorylation of Cyclin A:Cdk2 at Tyr 15, Bos taurus" +xref: Reactome:REACT_99713 "Phosphorylation of DLC2 by MAPK-8, Taeniopygia guttata" +xref: Reactome:REACT_9978 "Phosphorylation of beta-catenin at Ser45 by CK1 alpha, Homo sapiens" +xref: Reactome:REACT_99785 "Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3, Canis familiaris" +xref: Reactome:REACT_9983 "Phosphorylation of APC component of the destruction complex, Homo sapiens" +xref: Reactome:REACT_9987 "Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3, Homo sapiens" +xref: Reactome:REACT_99929 "Phosphorylation of beta-catenin at Ser45 by CK1 alpha, Gallus gallus" +xref: Reactome:REACT_99966 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Schizosaccharomyces pombe" +xref: Reactome:REACT_9997 "Phosphorylation of Cx43 by c-src, Homo sapiens" +is_a: GO:0003674 ! molecular_function +relationship: part_of GO:0008150 ! biological_process + +[Term] +id: GO:0016491 +name: oxidoreductase activity +namespace: molecular_function +def: "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC:go_curators] +comment: Note that enzymes of class EC:1.97.-.- should also be annotated to this term. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_yeast +subset: gosubset_prok +synonym: "oxidoreductase activity, acting on other substrates" NARROW [] +synonym: "redox activity" EXACT [] +xref: EC:1 +xref: Reactome:REACT_102858 "Diiodinated tyrosine can be deiodinated, Mus musculus" +xref: Reactome:REACT_102973 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Canis familiaris" +xref: Reactome:REACT_103874 "Monoiodinated tyrosine can be deiodinated, Canis familiaris" +xref: Reactome:REACT_104604 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Danio rerio" +xref: Reactome:REACT_105062 "Monoiodinated tyrosine can be deiodinated, Danio rerio" +xref: Reactome:REACT_105121 "Monoiodinated tyrosine can be deiodinated, Caenorhabditis elegans" +xref: Reactome:REACT_106088 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Rattus norvegicus" +xref: Reactome:REACT_106276 "Monoiodinated tyrosine can be deiodinated, Rattus norvegicus" +xref: Reactome:REACT_107002 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Sus scrofa" +xref: Reactome:REACT_107467 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Rattus norvegicus" +xref: Reactome:REACT_108745 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Taeniopygia guttata" +xref: Reactome:REACT_109500 "Monoiodinated tyrosine can be deiodinated, Bos taurus" +xref: Reactome:REACT_110582 "Diiodinated tyrosine can be deiodinated, Rattus norvegicus" +xref: Reactome:REACT_115316 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Drosophila melanogaster" +xref: Reactome:REACT_15389 "Monoiodinated tyrosine can be deiodinated, Homo sapiens" +xref: Reactome:REACT_15410 "Diiodinated tyrosine can be deiodinated, Homo sapiens" +xref: Reactome:REACT_17006 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Homo sapiens" +xref: Reactome:REACT_17042 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Homo sapiens" +xref: Reactome:REACT_29212 "Diiodinated tyrosine can be deiodinated, Canis familiaris" +xref: Reactome:REACT_30160 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Mus musculus" +xref: Reactome:REACT_31762 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Gallus gallus" +xref: Reactome:REACT_32960 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Bos taurus" +xref: Reactome:REACT_34705 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Mus musculus" +xref: Reactome:REACT_44470 "Monoiodinated tyrosine can be deiodinated, Mus musculus" +xref: Reactome:REACT_78923 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Taeniopygia guttata" +xref: Reactome:REACT_84842 "Diiodinated tyrosine can be deiodinated, Gallus gallus" +xref: Reactome:REACT_86178 "Monoiodinated tyrosine can be deiodinated, Xenopus tropicalis" +xref: Reactome:REACT_88304 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Bos taurus" +xref: Reactome:REACT_89057 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Gallus gallus" +xref: Reactome:REACT_90394 "Diiodinated tyrosine can be deiodinated, Xenopus tropicalis" +xref: Reactome:REACT_91638 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Arabidopsis thaliana" +xref: Reactome:REACT_91952 "Monoiodinated tyrosine can be deiodinated, Gallus gallus" +xref: Reactome:REACT_92075 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Xenopus tropicalis" +xref: Reactome:REACT_92434 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Canis familiaris" +xref: Reactome:REACT_93539 "Diiodinated tyrosine can be deiodinated, Drosophila melanogaster" +xref: Reactome:REACT_93974 "Diiodinated tyrosine can be deiodinated, Taeniopygia guttata" +xref: Reactome:REACT_95169 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Danio rerio" +xref: Reactome:REACT_95558 "Monoiodinated tyrosine can be deiodinated, Sus scrofa" +xref: Reactome:REACT_95573 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Caenorhabditis elegans" +xref: Reactome:REACT_97234 "Diiodinated tyrosine can be deiodinated, Caenorhabditis elegans" +xref: Reactome:REACT_97568 "Diiodinated tyrosine can be deiodinated, Sus scrofa" +xref: Reactome:REACT_97851 "Diiodinated tyrosine can be deiodinated, Bos taurus" +xref: Reactome:REACT_98022 "Monoiodinated tyrosine can be deiodinated, Drosophila melanogaster" +xref: Reactome:REACT_99085 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Oryza sativa" +xref: Reactome:REACT_99794 "Diiodinated tyrosine can be deiodinated, Danio rerio" +xref: Reactome:REACT_99989 "Monoiodinated tyrosine can be deiodinated, Taeniopygia guttata" +is_a: GO:0003674 ! molecular_function +relationship: part_of GO:0008150 ! biological_process + +[Term] +id: GO:0016746 +name: transferase activity, transferring acyl groups +namespace: molecular_function +alt_id: GO:0008415 +def: "Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: gosubset_prok +synonym: "acyltransferase activity" EXACT [] +xref: EC:2.3 +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0016757 +name: transferase activity, transferring glycosyl groups +namespace: molecular_function +alt_id: GO:0016932 +def: "Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732] +comment: Note that enzymes of class EC:2.4.99.- should also be annotated to this term. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_yeast +subset: gosubset_prok +synonym: "glycosyltransferase activity" EXACT [] +synonym: "transferase activity, transferring other glycosyl groups" NARROW [] +synonym: "transglycosidase activity" EXACT [] +synonym: "transglycosylase activity" EXACT [] +xref: EC:2.4 +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0016765 +name: transferase activity, transferring alkyl or aryl (other than methyl) groups +namespace: molecular_function +alt_id: GO:0016766 +def: "Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: gosubset_prok +synonym: "transferase activity, transferring alkyl or aryl groups, other than methyl groups" EXACT [] +xref: EC:2.5 +xref: EC:2.5.1 +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0016779 +name: nucleotidyltransferase activity +namespace: molecular_function +def: "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN:0198506732] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_yeast +subset: gosubset_prok +xref: EC:2.7.7 +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0016791 +name: phosphatase activity +namespace: molecular_function +alt_id: GO:0003869 +alt_id: GO:0016302 +def: "Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate." [EC:3.1.3, EC:3.1.3.41, GOC:curators, GOC:pg] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_yeast +subset: gosubset_prok +synonym: "4-nitrophenylphosphatase activity" NARROW [] +synonym: "4-nitrophenylphosphate phosphohydrolase activity" NARROW [EC:3.1.3.41] +synonym: "ecto-p-nitrophenyl phosphatase activity" NARROW [EC:3.1.3.41] +synonym: "K-pNPPase activity" NARROW [EC:3.1.3.41] +synonym: "nitrophenyl phosphatase activity" NARROW [EC:3.1.3.41] +synonym: "NPPase activity" NARROW [EC:3.1.3.41] +synonym: "p-nitrophenylphosphatase activity" NARROW [EC:3.1.3.41] +synonym: "p-nitrophenylphosphate phosphohydrolase activity" NARROW [EC:3.1.3.41] +synonym: "para-nitrophenyl phosphatase activity" NARROW [EC:3.1.3.41] +synonym: "phosphatase" RELATED [] +synonym: "phosphoric monoester hydrolase activity" EXACT [] +synonym: "PNPPase activity" NARROW [EC:3.1.3.41] +xref: EC:3.1.3 +xref: EC:3.1.3.41 +xref: MetaCyc:4-NITROPHENYLPHOSPHATASE-RXN +xref: RHEA:21667 +is_a: GO:0003674 ! molecular_function +relationship: part_of GO:0008150 ! biological_process + +[Term] +id: GO:0016798 +name: hydrolase activity, acting on glycosyl bonds +namespace: molecular_function +def: "Catalysis of the hydrolysis of any glycosyl bond." [GOC:jl] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_yeast +subset: gosubset_prok +synonym: "glycosidase activity" EXACT [] +synonym: "glycosylase" NARROW [] +synonym: "N-glycosylase" NARROW [] +xref: EC:3.2 +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0016810 +name: hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds +namespace: molecular_function +def: "Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds." [GOC:jl] +comment: Note that enzymes of class EC:3.5.99.- should also be annotated to this term. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: gosubset_prok +synonym: "hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in other compounds" NARROW [] +xref: EC:3.5 +xref: Reactome:REACT_27208 "acetylglucosamine-inositol is deacetylated by Mca, Mycobacterium tuberculosis" +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0016829 +name: lyase activity +namespace: molecular_function +def: "Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring." [EC:4.-.-.-, ISBN:0198547684] +comment: Note that enzymes of class EC:4.99.-.- should also be annotated to this term. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_yeast +subset: gosubset_prok +synonym: "other lyase activity" NARROW [] +xref: EC:4 +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0016853 +name: isomerase activity +namespace: molecular_function +def: "Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5." [ISBN:0198506732] +comment: Note that enzymes of class EC:5.99.-.- should also be annotated to this term. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_yeast +subset: gosubset_prok +synonym: "other isomerase activity" NARROW [] +xref: EC:5 +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0016874 +name: ligase activity +namespace: molecular_function +def: "Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [EC:6, GOC:mah] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_yeast +subset: gosubset_prok +synonym: "synthetase activity" EXACT [GOC:jh2] +xref: EC:6 +xref: Reactome:REACT_115603 "Ligation of DNA at sites of patch replacement, Gallus gallus" +xref: Reactome:REACT_116018 "Ligation of newly synthesized repair patch to incised DNA in GG-NER, Gallus gallus" +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0016887 +name: ATPase activity +namespace: molecular_function +alt_id: GO:0004002 +def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction." [EC:3.6.1.3, GOC:jl] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_yeast +subset: gosubset_prok +synonym: "(Ca2+ + Mg2+)-ATPase" NARROW [EC:3.6.1.3] +synonym: "adenosine 5'-triphosphatase activity" EXACT [EC:3.6.1.3] +synonym: "adenosine triphosphatase activity" EXACT [EC:3.6.1.3] +synonym: "adenosinetriphosphatase activity" EXACT [] +synonym: "ATP hydrolase activity" EXACT [EC:3.6.1.3] +synonym: "ATP monophosphatase activity" EXACT [EC:3.6.1.3] +synonym: "ATP phosphohydrolase activity" EXACT [] +synonym: "complex V (mitochondrial electron transport)" RELATED [EC:3.6.1.3] +synonym: "HCO3--ATPase" NARROW [EC:3.6.1.3] +synonym: "SV40 T-antigen" RELATED [EC:3.6.1.3] +xref: EC:3.6.1.3 +xref: MetaCyc:ADENOSINETRIPHOSPHATASE-RXN +xref: Reactome:REACT_100141 "Trafficking of GluR2-containing AMPA receptors to synapse, Canis familiaris" +xref: Reactome:REACT_108873 "Trafficking of GluR2-containing AMPA receptors to synapse, Bos taurus" +xref: Reactome:REACT_110992 "Trafficking of GluR2-containing AMPA receptors to synapse, Danio rerio" +xref: Reactome:REACT_113271 "Trafficking of GluR2-containing AMPA receptors to synapse, Xenopus tropicalis" +xref: Reactome:REACT_18320 "Trafficking of GluR2-containing AMPA receptors to synapse, Homo sapiens" +xref: Reactome:REACT_27184 "ESCRT Disassembly, Homo sapiens" +xref: Reactome:REACT_33329 "Trafficking of GluR2-containing AMPA receptors to synapse, Gallus gallus" +xref: Reactome:REACT_79964 "Trafficking of GluR2-containing AMPA receptors to synapse, Mus musculus" +xref: Reactome:REACT_84196 "Trafficking of GluR2-containing AMPA receptors to synapse, Drosophila melanogaster" +xref: Reactome:REACT_87020 "Trafficking of GluR2-containing AMPA receptors to synapse, Rattus norvegicus" +xref: Reactome:REACT_89934 "Trafficking of GluR2-containing AMPA receptors to synapse, Taeniopygia guttata" +xref: RHEA:13068 +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0019748 +name: secondary metabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients." [GOC:go_curators] +subset: goslim_aspergillus +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "secondary metabolism" EXACT [] +synonym: "secondary metabolite metabolic process" EXACT [] +synonym: "secondary metabolite metabolism" EXACT [] +xref: Wikipedia:Secondary_metabolism +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0019843 +name: rRNA binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with ribosomal RNA." [GOC:jl] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_yeast +subset: gosubset_prok +is_a: GO:0003723 ! RNA binding + +[Term] +id: GO:0019899 +name: enzyme binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with any enzyme." [GOC:jl] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_yeast +subset: gosubset_prok +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0021700 +name: developmental maturation +namespace: biological_process +def: "A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +subset: goslim_chembl +subset: goslim_generic +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0022607 +name: cellular component assembly +namespace: biological_process +alt_id: GO:0071844 +def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: gosubset_prok +synonym: "cell structure assembly" EXACT [] +synonym: "cellular component assembly at cellular level" EXACT [] +is_a: GO:0008150 ! biological_process +relationship: part_of GO:0008150 ! biological_process + +[Term] +id: GO:0022618 +name: ribonucleoprotein complex assembly +namespace: biological_process +def: "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex." [GOC:jl] +subset: goslim_chembl +subset: goslim_generic +subset: gosubset_prok +synonym: "protein-RNA complex assembly" EXACT [] +synonym: "RNA-protein complex assembly" EXACT [] +synonym: "RNP complex assembly" EXACT [] +is_a: GO:0065003 ! macromolecular complex assembly + +[Term] +id: GO:0022857 +name: transmembrane transporter activity +namespace: molecular_function +alt_id: GO:0005386 +alt_id: GO:0015646 +def: "Enables the transfer of a substance from one side of a membrane to the other." [GOC:mtg_transport, ISBN:0815340729] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_yeast +subset: gosubset_prok +xref: Reactome:REACT_100033 "GLUT9 transports glucose, fructose and urate, Gallus gallus" +xref: Reactome:REACT_106735 "GLUT9 transports glucose, fructose and urate, Xenopus tropicalis" +xref: Reactome:REACT_111088 "Egress of internalized antigen to the cytosol via sec61, Homo sapiens" +xref: Reactome:REACT_111933 "GLUT9 transports glucose, fructose and urate, Plasmodium falciparum" +xref: Reactome:REACT_113047 "GLUT9 transports glucose, fructose and urate, Dictyostelium discoideum" +xref: Reactome:REACT_113116 "GLUT9 transports glucose, fructose and urate, Mycobacterium tuberculosis" +xref: Reactome:REACT_113829 "GLUT9 transports glucose, fructose and urate, Arabidopsis thaliana" +xref: Reactome:REACT_114161 "GLUT9 transports glucose, fructose and urate, Oryza sativa" +xref: Reactome:REACT_19288 "GLUT9 transports glucose, fructose and urate, Homo sapiens" +xref: Reactome:REACT_77235 "GLUT9 transports glucose, fructose and urate, Canis familiaris" +xref: Reactome:REACT_81225 "GLUT9 transports glucose, fructose and urate, Bos taurus" +xref: Reactome:REACT_88503 "GLUT9 transports glucose, fructose and urate, Taeniopygia guttata" +xref: Reactome:REACT_91849 "GLUT9 transports glucose, fructose and urate, Mus musculus" +xref: Reactome:REACT_94185 "GLUT9 transports glucose, fructose and urate, Rattus norvegicus" +is_a: GO:0003674 ! molecular_function +relationship: part_of GO:0055085 ! transmembrane transport + +[Term] +id: GO:0030154 +name: cell differentiation +namespace: biological_process +def: "The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." [ISBN:0198506732] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_plant +subset: gosubset_prok +xref: Wikipedia:Cellular_differentiation +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0030198 +name: extracellular matrix organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix." [GOC:mah] +subset: goslim_chembl +subset: goslim_generic +subset: gosubset_prok +synonym: "extracellular matrix organisation" EXACT [GOC:curators] +synonym: "extracellular matrix organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0030234 +name: enzyme regulator activity +namespace: molecular_function +alt_id: GO:0010576 +def: "Binds to and modulates the activity of an enzyme." [GOC:dph, GOC:mah, GOC:tb] +comment: GO:0030234 is reserved for cases when the regulator directly interacts with the enzyme. When regulation of enzyme activity is achieved without enzyme binding, or when the mechanism of regulation is unknown, instead annotate to 'regulation of catalytic activity ; GO:0050790'. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "catalytic regulator activity" EXACT [GOC:dph] +synonym: "enzyme modulator" EXACT [] +synonym: "metalloenzyme regulator activity" NARROW [] +is_a: GO:0003674 ! molecular_function +relationship: has_part GO:0019899 ! enzyme binding +relationship: part_of GO:0008150 ! biological_process +relationship: regulates GO:0003674 ! molecular_function + +[Term] +id: GO:0030312 +name: external encapsulating structure +namespace: cellular_component +def: "A structure that lies outside the plasma membrane and surrounds the entire cell. This does not include the periplasmic space." [GOC:go_curators] +comment: The outer membrane (of gram negative bacteria) or cell wall (of yeast or Gram positive bacteria) are defined as parts of this structure, see 'external encapsulating structure part'. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +is_a: GO:0005575 ! cellular_component +relationship: part_of GO:0005623 ! cell + +[Term] +id: GO:0030533 +name: triplet codon-amino acid adaptor activity +namespace: molecular_function +def: "The codon binding activity of a tRNA that positions an activated amino acid, mediating its insertion at the correct point in the sequence of a nascent polypeptide chain during protein synthesis." [GOC:hjd, GOC:mtg_MIT_16mar07, ISBN:0198506732] +comment: Note that this term can be used in place of the obsolete term 'transfer RNA ; GO:0005563'. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_yeast +synonym: "transfer RNA" RELATED [] +synonym: "tRNA" RELATED [] +is_a: GO:0003723 ! RNA binding +relationship: part_of GO:0006412 ! translation + +[Term] +id: GO:0030555 +name: RNA modification guide activity +namespace: molecular_function +def: "Specifies the site of a posttranscriptional modification in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565] +comment: Note that this term describes the activity of a nucleic acid, usually RNA, gene product that interacts with other RNA molecules via base pairing; it should not be used to annotate proteins. +subset: goslim_generic +subset: goslim_yeast +is_a: GO:0003723 ! RNA binding + +[Term] +id: GO:0030674 +name: protein binding, bridging +namespace: molecular_function +def: "The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way." [GOC:bf, GOC:mah, GOC:vw] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_yeast +subset: gosubset_prok +synonym: "protein-protein adaptor" NARROW [] +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0030705 +name: cytoskeleton-dependent intracellular transport +namespace: biological_process +def: "The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell." [GOC:mah] +subset: goslim_chembl +subset: goslim_generic +subset: gosubset_prok +is_a: GO:0006810 ! transport +relationship: occurs_in GO:0005622 ! intracellular +relationship: part_of GO:0008150 ! biological_process + +[Term] +id: GO:0032182 +name: ubiquitin-like protein binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a small conjugating protein such as ubiquitin or a ubiquitin-like protein." [GOC:mah] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_yeast +synonym: "small conjugating protein binding" EXACT [GOC:dph] +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0032196 +name: transposition +namespace: biological_process +def: "Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites." [GOC:jp, ISBN:1555812090] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_yeast +subset: gosubset_prok +xref: Wikipedia:Transposon +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0034330 +name: cell junction organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell junction. A cell junction is a specialized region of connection between two cells or between a cell and the extracellular matrix." [GOC:dph, GOC:jl, GOC:mah] +subset: goslim_chembl +subset: goslim_generic +synonym: "cell junction assembly and maintenance" EXACT [] +synonym: "cell junction biogenesis" RELATED [] +synonym: "cell junction organisation" EXACT [GOC:mah] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0034641 +name: cellular nitrogen compound metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells." [GOC:mah] +subset: goslim_chembl +subset: goslim_generic +subset: gosubset_prok +synonym: "cellular nitrogen compound metabolism" EXACT [] +xref: Reactome:REACT_102000 "Metabolism of amino acids and derivatives, Mycobacterium tuberculosis" +xref: Reactome:REACT_103710 "Metabolism of amino acids and derivatives, Escherichia coli" +xref: Reactome:REACT_107293 "Metabolism of amino acids and derivatives, Arabidopsis thaliana" +xref: Reactome:REACT_108179 "Metabolism of amino acids and derivatives, Xenopus tropicalis" +xref: Reactome:REACT_109042 "Metabolism of amino acids and derivatives, Sus scrofa" +xref: Reactome:REACT_13 "Metabolism of amino acids and derivatives, Homo sapiens" +xref: Reactome:REACT_28699 "Metabolism of amino acids and derivatives, Saccharomyces cerevisiae" +xref: Reactome:REACT_29108 "Metabolism of amino acids and derivatives, Caenorhabditis elegans" +xref: Reactome:REACT_32429 "Metabolism of amino acids and derivatives, Rattus norvegicus" +xref: Reactome:REACT_33347 "Metabolism of amino acids and derivatives, Mus musculus" +xref: Reactome:REACT_34326 "Metabolism of amino acids and derivatives, Staphylococcus aureus N315" +xref: Reactome:REACT_55564 "Metabolism of amino acids and derivatives, Gallus gallus" +xref: Reactome:REACT_77741 "Metabolism of amino acids and derivatives, Taeniopygia guttata" +xref: Reactome:REACT_82379 "Metabolism of amino acids and derivatives, Bos taurus" +xref: Reactome:REACT_86268 "Metabolism of amino acids and derivatives, Drosophila melanogaster" +xref: Reactome:REACT_90299 "Metabolism of amino acids and derivatives, Oryza sativa" +xref: Reactome:REACT_91959 "Metabolism of amino acids and derivatives, Plasmodium falciparum" +xref: Reactome:REACT_93580 "Metabolism of amino acids and derivatives, Danio rerio" +xref: Reactome:REACT_95666 "Metabolism of amino acids and derivatives, Canis familiaris" +xref: Reactome:REACT_98086 "Metabolism of amino acids and derivatives, Dictyostelium discoideum" +xref: Reactome:REACT_99241 "Metabolism of amino acids and derivatives, Schizosaccharomyces pombe" +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0034655 +name: nucleobase-containing compound catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:mah] +subset: goslim_chembl +subset: goslim_generic +subset: gosubset_prok +synonym: "nucleobase, nucleoside, nucleotide and nucleic acid breakdown" EXACT [] +synonym: "nucleobase, nucleoside, nucleotide and nucleic acid catabolic process" RELATED [GOC:dph, GOC:tb] +synonym: "nucleobase, nucleoside, nucleotide and nucleic acid catabolism" EXACT [] +synonym: "nucleobase, nucleoside, nucleotide and nucleic acid degradation" EXACT [] +is_a: GO:0009056 ! catabolic process +is_a: GO:0034641 ! cellular nitrogen compound metabolic process + +[Term] +id: GO:0040007 +name: growth +namespace: biological_process +alt_id: GO:0048590 +def: "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC:bf, GOC:ma] +comment: See also the biological process term 'cell growth ; GO:0016049'. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "growth pattern" RELATED [] +synonym: "non-developmental growth" RELATED [GOC:mah] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0040011 +name: locomotion +namespace: biological_process +def: "Self-propelled movement of a cell or organism from one location to another." [GOC:dgh] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0042254 +name: ribosome biogenesis +namespace: biological_process +alt_id: GO:0007046 +def: "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis." [GOC:ma] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_pombe +subset: gosubset_prok +synonym: "ribosomal chaperone activity" RELATED [] +synonym: "ribosome biogenesis and assembly" EXACT [] +xref: Wikipedia:Ribosome_biogenesis +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0042393 +name: histone binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of plant and animal chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity." [GOC:jl] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_yeast +synonym: "histone-specific chaperone activity" RELATED [] +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0042592 +name: homeostatic process +namespace: biological_process +def: "Any biological process involved in the maintenance of an internal steady state." [GOC:jl, ISBN:0395825172] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: gosubset_prok +synonym: "homeostasis" RELATED [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0043167 +name: ion binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with ions, charged atoms or groups of atoms." [GOC:jl] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_yeast +subset: gosubset_prok +synonym: "atom binding" RELATED [] +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0043226 +name: organelle +namespace: cellular_component +def: "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane." [GOC:go_curators] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: gosubset_prok +xref: NIF_Subcellular:sao1539965131 +xref: Wikipedia:Organelle +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0043234 +name: protein complex +namespace: cellular_component +def: "A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical." [GOC:go_curators, http://www.ebi.ac.uk/intact/complex/documentation/] +comment: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: gosubset_prok +synonym: "protein-protein complex" EXACT [] +xref: Wikipedia:Protein_complex +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0043473 +name: pigmentation +namespace: biological_process +def: "The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells." [GOC:jl] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0044281 +name: small molecule metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:vw] +comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +synonym: "small molecule metabolism" EXACT [] +xref: Reactome:REACT_111217 "Metabolism, Homo sapiens" +xref: Reactome:REACT_112077 "Metabolism, Xenopus tropicalis" +xref: Reactome:REACT_112140 "Metabolism, Dictyostelium discoideum" +xref: Reactome:REACT_112621 "Metabolism, Mus musculus" +xref: Reactome:REACT_112912 "Metabolism, Arabidopsis thaliana" +xref: Reactome:REACT_113131 "Metabolism, Schizosaccharomyces pombe" +xref: Reactome:REACT_113305 "Metabolism, Canis familiaris" +xref: Reactome:REACT_113457 "Metabolism, Mycobacterium tuberculosis" +xref: Reactome:REACT_113568 "Metabolism, Rattus norvegicus" +xref: Reactome:REACT_113610 "Metabolism, Caenorhabditis elegans" +xref: Reactome:REACT_113934 "Metabolism, Escherichia coli" +xref: Reactome:REACT_114081 "Metabolism, Gallus gallus" +xref: Reactome:REACT_114137 "Metabolism, Sus scrofa" +xref: Reactome:REACT_114421 "Metabolism, Saccharomyces cerevisiae" +xref: Reactome:REACT_114473 "Metabolism, Danio rerio" +xref: Reactome:REACT_114495 "Metabolism, Staphylococcus aureus N315" +xref: Reactome:REACT_114668 "Metabolism, Plasmodium falciparum" +xref: Reactome:REACT_114983 "Metabolism, Drosophila melanogaster" +xref: Reactome:REACT_115063 "Metabolism, Taeniopygia guttata" +xref: Reactome:REACT_115388 "Metabolism, Oryza sativa" +xref: Reactome:REACT_115420 "Metabolism, Bos taurus" +xref: Reactome:REACT_115655 "Metabolism, Gallus gallus" +is_a: GO:0008150 ! biological_process +created_by: jane +creation_date: 2010-01-26T12:05:20Z + +[Term] +id: GO:0044403 +name: symbiosis, encompassing mutualism through parasitism +namespace: biological_process +alt_id: GO:0043298 +alt_id: GO:0044404 +def: "An interaction between two organisms living together in more or less intimate association. Microscopic symbionts are often referred to as endosymbionts. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs." [GOC:cc, http://www.free-definition.com] +comment: Note that this term encompasses all symbiotic relationships between species along a continuum from mutualism through to parasitism, as outlined in the definition. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: gosubset_prok +synonym: "host-pathogen interaction" RELATED [] +synonym: "symbiosis" EXACT [] +synonym: "symbiotic interaction" EXACT [] +synonym: "symbiotic interaction between host and organism" RELATED [] +synonym: "symbiotic interaction between organisms" EXACT [] +synonym: "symbiotic interaction between species" EXACT [] +synonym: "symbiotic interaction with other non-host organism" RELATED [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0048646 +name: anatomical structure formation involved in morphogenesis +namespace: biological_process +def: "The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GOC:dph, GOC:jid, GOC:tb] +comment: Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense. +subset: goslim_chembl +subset: goslim_generic +synonym: "formation of an anatomical structure involved in morphogenesis" EXACT [GOC:dph, GOC:tb] +is_a: GO:0008150 ! biological_process +relationship: part_of GO:0048856 ! anatomical structure development + +[Term] +id: GO:0048856 +name: anatomical structure development +namespace: biological_process +def: "The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GO_REF:0000021, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +subset: goslim_chembl +subset: goslim_generic +synonym: "development of an anatomical structure" EXACT [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0048870 +name: cell motility +namespace: biological_process +def: "Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another." [GOC:dgh, GOC:dph, GOC:isa_complete, GOC:mlg] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: gosubset_prok +synonym: "cell locomotion" EXACT [] +synonym: "cell movement" RELATED [] +synonym: "movement of a cell" EXACT [] +is_a: GO:0040011 ! locomotion +relationship: part_of GO:0008150 ! biological_process + +[Term] +id: GO:0050877 +name: neurological system process +namespace: biological_process +def: "A organ system process carried out by any of the organs or tissues of neurological system." [GOC:ai, GOC:mtg_cardio] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +synonym: "neurophysiological process" EXACT [] +synonym: "pan-neural process" RELATED [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0051082 +name: unfolded protein binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with an unfolded protein." [GOC:ai] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_yeast +subset: gosubset_prok +synonym: "binding unfolded ER proteins" NARROW [] +synonym: "chaperone activity" RELATED [] +synonym: "fimbrium-specific chaperone activity" RELATED [] +synonym: "glycoprotein-specific chaperone activity" RELATED [] +synonym: "histone-specific chaperone activity" RELATED [] +synonym: "ribosomal chaperone activity" RELATED [] +synonym: "tubulin-specific chaperone activity" RELATED [] +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0051186 +name: cofactor metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate." [GOC:ai] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +synonym: "cofactor metabolism" EXACT [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0051276 +name: chromosome organization +namespace: biological_process +alt_id: GO:0007001 +alt_id: GO:0051277 +def: "A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: gosubset_prok +synonym: "chromosome organisation" EXACT [] +synonym: "chromosome organization and biogenesis" RELATED [GOC:mah] +synonym: "maintenance of genome integrity" RELATED [] +synonym: "nuclear genome maintenance" RELATED [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0051301 +name: cell division +namespace: biological_process +def: "The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells." [GOC:di, GOC:go_curators, GOC:pr] +comment: Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: gosubset_prok +xref: Wikipedia:Cell_division +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0051604 +name: protein maturation +namespace: biological_process +def: "Any process leading to the attainment of the full functional capacity of a protein." [GOC:ai] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +is_a: GO:0008150 ! biological_process +relationship: part_of GO:0008150 ! biological_process + +[Term] +id: GO:0055085 +name: transmembrane transport +namespace: biological_process +def: "The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other" [GOC:dph, GOC:jid] +comment: Transmembrane transport requires transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pombe +subset: goslim_yeast +synonym: "membrane transport" EXACT [] +xref: Reactome:REACT_100480 "SLC-mediated transmembrane transport, Taeniopygia guttata" +xref: Reactome:REACT_101577 "SLC-mediated transmembrane transport, Caenorhabditis elegans" +xref: Reactome:REACT_101877 "SLC-mediated transmembrane transport, Escherichia coli" +xref: Reactome:REACT_101975 "SLC-mediated transmembrane transport, Sus scrofa" +xref: Reactome:REACT_102348 "Transmembrane transport of small molecules, Staphylococcus aureus N315" +xref: Reactome:REACT_102897 "Transmembrane transport of small molecules, Caenorhabditis elegans" +xref: Reactome:REACT_102974 "SLC-mediated transmembrane transport, Canis familiaris" +xref: Reactome:REACT_104555 "SLC-mediated transmembrane transport, Xenopus tropicalis" +xref: Reactome:REACT_108243 "SLC-mediated transmembrane transport, Staphylococcus aureus N315" +xref: Reactome:REACT_109832 "Transmembrane transport of small molecules, Plasmodium falciparum" +xref: Reactome:REACT_110770 "ABC-family proteins mediated transport, Mus musculus" +xref: Reactome:REACT_114546 "ABC-family proteins mediated transport, Staphylococcus aureus N315" +xref: Reactome:REACT_114763 "ABC-family proteins mediated transport, Escherichia coli" +xref: Reactome:REACT_114890 "ABC-family proteins mediated transport, Plasmodium falciparum" +xref: Reactome:REACT_115378 "ABC-family proteins mediated transport, Mycobacterium tuberculosis" +xref: Reactome:REACT_15480 "ABC-family proteins mediated transport, Homo sapiens" +xref: Reactome:REACT_15518 "Transmembrane transport of small molecules, Homo sapiens" +xref: Reactome:REACT_19118 "SLC-mediated transmembrane transport, Homo sapiens" +xref: Reactome:REACT_29093 "ABC-family proteins mediated transport, Taeniopygia guttata" +xref: Reactome:REACT_29184 "SLC-mediated transmembrane transport, Gallus gallus" +xref: Reactome:REACT_29635 "Transmembrane transport of small molecules, Canis familiaris" +xref: Reactome:REACT_30969 "ABC-family proteins mediated transport, Canis familiaris" +xref: Reactome:REACT_32055 "Transmembrane transport of small molecules, Saccharomyces cerevisiae" +xref: Reactome:REACT_32223 "Transmembrane transport of small molecules, Rattus norvegicus" +xref: Reactome:REACT_32423 "SLC-mediated transmembrane transport, Bos taurus" +xref: Reactome:REACT_32713 "ABC-family proteins mediated transport, Sus scrofa" +xref: Reactome:REACT_33571 "SLC-mediated transmembrane transport, Danio rerio" +xref: Reactome:REACT_61245 "Transmembrane transport of small molecules, Bos taurus" +xref: Reactome:REACT_79086 "SLC-mediated transmembrane transport, Plasmodium falciparum" +xref: Reactome:REACT_79921 "SLC-mediated transmembrane transport, Saccharomyces cerevisiae" +xref: Reactome:REACT_80022 "ABC-family proteins mediated transport, Bos taurus" +xref: Reactome:REACT_80510 "ABC-family proteins mediated transport, Rattus norvegicus" +xref: Reactome:REACT_80848 "ABC-family proteins mediated transport, Schizosaccharomyces pombe" +xref: Reactome:REACT_80977 "ABC-family proteins mediated transport, Caenorhabditis elegans" +xref: Reactome:REACT_81024 "Transmembrane transport of small molecules, Oryza sativa" +xref: Reactome:REACT_81153 "SLC-mediated transmembrane transport, Mus musculus" +xref: Reactome:REACT_82725 "SLC-mediated transmembrane transport, Rattus norvegicus" +xref: Reactome:REACT_83770 "Transmembrane transport of small molecules, Escherichia coli" +xref: Reactome:REACT_86135 "ABC-family proteins mediated transport, Oryza sativa" +xref: Reactome:REACT_86409 "Transmembrane transport of small molecules, Drosophila melanogaster" +xref: Reactome:REACT_86576 "Transmembrane transport of small molecules, Schizosaccharomyces pombe" +xref: Reactome:REACT_87124 "SLC-mediated transmembrane transport, Oryza sativa" +xref: Reactome:REACT_88059 "ABC-family proteins mediated transport, Xenopus tropicalis" +xref: Reactome:REACT_88521 "Transmembrane transport of small molecules, Taeniopygia guttata" +xref: Reactome:REACT_88894 "Transmembrane transport of small molecules, Gallus gallus" +xref: Reactome:REACT_89376 "SLC-mediated transmembrane transport, Schizosaccharomyces pombe" +xref: Reactome:REACT_91272 "ABC-family proteins mediated transport, Arabidopsis thaliana" +xref: Reactome:REACT_91803 "SLC-mediated transmembrane transport, Mycobacterium tuberculosis" +xref: Reactome:REACT_92006 "Transmembrane transport of small molecules, Mycobacterium tuberculosis" +xref: Reactome:REACT_92624 "ABC-family proteins mediated transport, Gallus gallus" +xref: Reactome:REACT_93747 "Transmembrane transport of small molecules, Dictyostelium discoideum" +xref: Reactome:REACT_94160 "Transmembrane transport of small molecules, Mus musculus" +xref: Reactome:REACT_94393 "ABC-family proteins mediated transport, Drosophila melanogaster" +xref: Reactome:REACT_94944 "ABC-family proteins mediated transport, Danio rerio" +xref: Reactome:REACT_94972 "SLC-mediated transmembrane transport, Dictyostelium discoideum" +xref: Reactome:REACT_96633 "Transmembrane transport of small molecules, Sus scrofa" +xref: Reactome:REACT_96636 "SLC-mediated transmembrane transport, Arabidopsis thaliana" +xref: Reactome:REACT_97365 "Transmembrane transport of small molecules, Arabidopsis thaliana" +xref: Reactome:REACT_97867 "ABC-family proteins mediated transport, Saccharomyces cerevisiae" +xref: Reactome:REACT_98509 "Transmembrane transport of small molecules, Xenopus tropicalis" +xref: Reactome:REACT_98716 "SLC-mediated transmembrane transport, Drosophila melanogaster" +xref: Reactome:REACT_99579 "Transmembrane transport of small molecules, Danio rerio" +xref: Reactome:REACT_99829 "ABC-family proteins mediated transport, Dictyostelium discoideum" +is_a: GO:0006810 ! transport + +[Term] +id: GO:0061024 +name: membrane organization +namespace: biological_process +alt_id: GO:0016044 +def: "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:dph, GOC:tb] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pombe +synonym: "cellular membrane organisation" EXACT [GOC:curators] +synonym: "cellular membrane organization" EXACT [] +synonym: "membrane organisation" EXACT [GOC:mah] +synonym: "membrane organization and biogenesis" RELATED [GOC:mah] +xref: Reactome:REACT_101524 "Membrane Trafficking, Dictyostelium discoideum" +xref: Reactome:REACT_103082 "Membrane Trafficking, Schizosaccharomyces pombe" +xref: Reactome:REACT_11123 "Membrane Trafficking, Homo sapiens" +xref: Reactome:REACT_29278 "Membrane Trafficking, Sus scrofa" +xref: Reactome:REACT_32337 "Membrane Trafficking, Taeniopygia guttata" +xref: Reactome:REACT_33741 "Membrane Trafficking, Bos taurus" +xref: Reactome:REACT_34084 "Membrane Trafficking, Caenorhabditis elegans" +xref: Reactome:REACT_78213 "Membrane Trafficking, Plasmodium falciparum" +xref: Reactome:REACT_78288 "Membrane Trafficking, Xenopus tropicalis" +xref: Reactome:REACT_83546 "Membrane Trafficking, Oryza sativa" +xref: Reactome:REACT_86557 "Membrane Trafficking, Arabidopsis thaliana" +xref: Reactome:REACT_87431 "Membrane Trafficking, Drosophila melanogaster" +xref: Reactome:REACT_88307 "Membrane Trafficking, Mus musculus" +xref: Reactome:REACT_91154 "Membrane Trafficking, Saccharomyces cerevisiae" +xref: Reactome:REACT_93714 "Membrane Trafficking, Danio rerio" +xref: Reactome:REACT_95586 "Membrane Trafficking, Gallus gallus" +xref: Reactome:REACT_96516 "Membrane Trafficking, Canis familiaris" +xref: Reactome:REACT_97881 "Membrane Trafficking, Rattus norvegicus" +is_a: GO:0008150 ! biological_process +created_by: dph +creation_date: 2010-02-08T02:43:11Z + +[Term] +id: GO:0065003 +name: macromolecular complex assembly +namespace: biological_process +def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a complex." [GOC:jl] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: gosubset_prok +synonym: "macromolecule complex assembly" EXACT [] +is_a: GO:0022607 ! cellular component assembly + +[Term] +id: GO:0071554 +name: cell wall organization or biogenesis +namespace: biological_process +alt_id: GO:0070882 +def: "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cell wall." [GOC:mah] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +synonym: "cell wall organisation or biogenesis" EXACT [GOC:mah] +synonym: "cell wall organization or biogenesis at cellular level" EXACT [GOC:mah] +synonym: "cellular cell wall organisation or biogenesis" EXACT [GOC:mah] +synonym: "cellular cell wall organization or biogenesis" EXACT [] +is_a: GO:0008150 ! biological_process +created_by: midori +creation_date: 2010-01-13T03:19:38Z + +[Term] +id: GO:0071941 +name: nitrogen cycle metabolic process +namespace: biological_process +def: "A nitrogen compound metabolic process that contributes to the nitrogen cycle. The nitrogen cycle is a series of metabolic pathways by which nitrogen is converted between various forms and redox states; it encompasses pathways in which nitrogen is acted upon directly, such as nitrification, denitrification, nitrogen fixation, and mineralization." [GOC:mah, PMID:16675690, Wikipedia:Nitrogen_cycle] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pombe +xref: Wikipedia:Nitrogen_cycle +is_a: GO:0008150 ! biological_process +created_by: midori +creation_date: 2010-09-30T05:21:03Z + +[Typedef] +id: ends_during +name: ends_during +namespace: external +xref: RO:0002093 + +[Typedef] +id: happens_during +name: happens_during +namespace: external +xref: RO:0002092 +is_transitive: true +is_a: ends_during ! ends_during + +[Typedef] +id: has_part +name: has_part +namespace: external +xref: BFO:0000051 +is_transitive: true + +[Typedef] +id: negatively_regulates +name: negatively regulates +namespace: external +xref: RO:0002212 +is_a: regulates ! regulates +transitive_over: part_of ! part of + +[Typedef] +id: never_in_taxon +name: never_in_taxon +namespace: external +xref: RO:0002161 +expand_assertion_to: "Class: ?X DisjointWith: RO_0002162 some ?Y" [] +is_metadata_tag: true +is_class_level: true + +[Typedef] +id: occurs_in +name: occurs in +namespace: external +xref: BFO:0000066 +holds_over_chain: part_of occurs_in +transitive_over: part_of ! part of + +[Typedef] +id: part_of +name: part of +namespace: external +xref: BFO:0000050 +is_transitive: true +inverse_of: has_part ! has_part + +[Typedef] +id: positively_regulates +name: positively regulates +namespace: external +xref: RO:0002213 +holds_over_chain: negatively_regulates negatively_regulates +is_a: regulates ! regulates +transitive_over: part_of ! part of + +[Typedef] +id: regulates +name: regulates +namespace: external +xref: RO:0002211 +is_transitive: true +transitive_over: part_of ! part of + +[Typedef] +id: starts_during +name: starts_during +namespace: external +xref: RO:0002091 + diff --git a/tests/data/ontologies/so-xp-simple.obo b/tests/data/ontologies/so-xp-simple.obo new file mode 100644 index 000000000..aa9f94e7a --- /dev/null +++ b/tests/data/ontologies/so-xp-simple.obo @@ -0,0 +1,21087 @@ +format-version: 1.2 +data-version: so-xp/releases/2015-11-24/so-xp.owl +date: 26:04:2016 15:44 +saved-by: nicole +auto-generated-by: OBO-Edit 2.3.1 +subsetdef: biosapiens "biosapiens protein feature ontology" +subsetdef: DBVAR "database of genomic structural variation" +subsetdef: SOFA "SO feature annotation" +synonymtypedef: aa1 "amino acid 1 letter code" +synonymtypedef: aa3 "amino acid 3 letter code" +synonymtypedef: AAMOD "amino acid modification" +synonymtypedef: BS "biosapiens" +synonymtypedef: dbsnp "dbsnp variant terms" +synonymtypedef: dbvar "DBVAR" +synonymtypedef: ebi_variants "ensembl variant terms" +synonymtypedef: RNAMOD "RNA modification" EXACT +synonymtypedef: VAR "variant annotation term" +default-namespace: sequence +ontology: so-xp.obo + +[Term] +id: SO:0000000 +name: Sequence_Ontology +subset: SOFA +is_obsolete: true + +[Term] +id: SO:0000001 +name: region +def: "A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke] +subset: SOFA +synonym: "sequence" EXACT [] +is_a: SO:0000110 ! sequence_feature + +[Term] +id: SO:0000002 +name: sequence_secondary_structure +def: "A folded sequence." [SO:ke] +synonym: "sequence secondary structure" EXACT [] +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0000003 +name: G_quartet +def: "G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet." [http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract] +synonym: "G quartet" EXACT [] +synonym: "G tetrad" EXACT [] +synonym: "G-quadruplex" EXACT [] +synonym: "G-quartet" EXACT [] +synonym: "G-tetrad" EXACT [] +synonym: "G_quadruplex" EXACT [] +synonym: "guanine tetrad" EXACT [] +xref: http://en.wikipedia.org/wiki/G-quadruplex "wiki" +is_a: SO:0000002 ! sequence_secondary_structure + +[Term] +id: SO:0000004 +name: interior_coding_exon +subset: SOFA +synonym: "interior coding exon" EXACT [] +is_a: SO:0000195 ! coding_exon + +[Term] +id: SO:0000005 +name: satellite_DNA +def: "The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +subset: SOFA +synonym: "satellite DNA" EXACT [] +xref: http://en.wikipedia.org/wiki/Satellite_DNA "wiki" +is_a: SO:0000705 ! tandem_repeat + +[Term] +id: SO:0000006 +name: PCR_product +def: "A region amplified by a PCR reaction." [SO:ke] +comment: This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406. +subset: SOFA +synonym: "amplicon" RELATED [] +synonym: "PCR product" EXACT [] +xref: http://en.wikipedia.org/wiki/RAPD "wiki" +is_a: SO:0000695 ! reagent + +[Term] +id: SO:0000007 +name: read_pair +def: "One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls] +subset: SOFA +synonym: "mate pair" EXACT [] +synonym: "read-pair" EXACT [] +is_a: SO:0000150 ! read +relationship: part_of SO:0000149 ! contig +relationship: part_of SO:0001790 ! paired_end_fragment + +[Term] +id: SO:0000008 +name: gene_sensu_your_favorite_organism +is_obsolete: true + +[Term] +id: SO:0000009 +name: gene_class +is_obsolete: true + +[Term] +id: SO:0000010 +name: protein_coding +synonym: "protein-coding" EXACT [] +is_a: SO:0000401 ! gene_attribute + +[Term] +id: SO:0000011 +name: non_protein_coding +synonym: "non protein-coding" EXACT [] +is_a: SO:0000401 ! gene_attribute + +[Term] +id: SO:0000012 +name: scRNA_primary_transcript +def: "The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html] +synonym: "scRNA primary transcript" EXACT [] +synonym: "scRNA transcript" EXACT [] +synonym: "small cytoplasmic RNA" RELATED [] +synonym: "small cytoplasmic RNA transcript" EXACT [] +synonym: "small_cytoplasmic_RNA" RELATED [] +is_a: SO:0000483 ! nc_primary_transcript + +[Term] +id: SO:0000013 +name: scRNA +def: "A small non coding RNA sequence, present in the cytoplasm." [SO:ke] +subset: SOFA +synonym: "small cytoplasmic RNA" EXACT [] +is_a: SO:0000655 ! ncRNA +relationship: derives_from SO:0000012 ! scRNA_primary_transcript + +[Term] +id: SO:0000014 +name: INR_motif +def: "A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867] +comment: Binds TAF1, TAF2. +synonym: "DMp2" RELATED [] +synonym: "initiator" EXACT [] +synonym: "initiator motif" EXACT [] +synonym: "INR motif" EXACT [] +is_a: SO:0001660 ! core_promoter_element +relationship: part_of SO:0001669 ! RNApol_II_core_promoter + +[Term] +id: SO:0000015 +name: DPE_motif +def: "A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739\:12537576, PMID:16858867] +comment: Binds TAF6, TAF9. +synonym: "CRWMGCGWKCGCTTS" NARROW [] +synonym: "downstream core promoter element" EXACT [] +synonym: "DPE motif" EXACT [] +is_a: SO:0001660 ! core_promoter_element +relationship: part_of SO:0001669 ! RNApol_II_core_promoter + +[Term] +id: SO:0000016 +name: BREu_motif +def: "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867] +comment: Binds TFIIB. +synonym: "B-recognition element" EXACT [] +synonym: "BRE motif" EXACT [] +synonym: "BREu" RELATED [] +synonym: "BREu motif" EXACT [] +synonym: "TFIIB recognition element" RELATED [] +synonym: "transcription factor B-recognition element" EXACT [] +is_a: SO:0001660 ! core_promoter_element +relationship: part_of SO:0001669 ! RNApol_II_core_promoter + +[Term] +id: SO:0000017 +name: PSE_motif +def: "A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739] +synonym: "proximal sequence element" EXACT [] +synonym: "PSE motif" EXACT [] +is_a: SO:0000713 ! DNA_motif +relationship: part_of SO:0000167 ! promoter + +[Term] +id: SO:0000018 +name: linkage_group +def: "A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned." [ISBN:038752046] +synonym: "linkage group" EXACT [] +xref: http://en.wikipedia.org/wiki/Linkage_group "wiki" +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0000020 +name: RNA_internal_loop +def: "A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." [SO:ke] +synonym: "RNA internal loop" EXACT [] +is_a: SO:0000715 ! RNA_motif + +[Term] +id: SO:0000021 +name: asymmetric_RNA_internal_loop +def: "An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke] +synonym: "asymmetric RNA internal loop" EXACT [] +is_a: SO:0000020 ! RNA_internal_loop + +[Term] +id: SO:0000022 +name: A_minor_RNA_motif +def: "A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix." [SO:ke] +synonym: "A minor RNA motif" EXACT [] +is_a: SO:0000715 ! RNA_motif + +[Term] +id: SO:0000023 +name: K_turn_RNA_motif +def: "The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." [SO:ke] +synonym: "K turn RNA motif" EXACT [] +synonym: "K-turn" EXACT [] +synonym: "kink turn" EXACT [] +synonym: "kink-turn motif" EXACT [] +xref: http://en.wikipedia.org/wiki/K-turn "wiki" +is_a: SO:0000021 ! asymmetric_RNA_internal_loop + +[Term] +id: SO:0000024 +name: sarcin_like_RNA_motif +def: "A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." [http://www.ncbi.nlm.nih.gov/pubmed/7897662] +synonym: "sarcin like RNA motif" EXACT [] +synonym: "sarcin/ricin domain" EXACT [] +synonym: "sarcin/ricin loop" EXACT [] +synonym: "sarcin/ricin RNA domain" EXACT [] +is_a: SO:0000021 ! asymmetric_RNA_internal_loop + +[Term] +id: SO:0000025 +name: symmetric_RNA_internal_loop +def: "An internal RNA loop where the extent of the loop on both stands is the same size." [SO:ke] +synonym: "A-minor RNA motif" EXACT [] +is_a: SO:0000020 ! RNA_internal_loop + +[Term] +id: SO:0000026 +name: RNA_junction_loop +synonym: "RNA junction loop" EXACT [] +is_a: SO:0000715 ! RNA_motif + +[Term] +id: SO:0000027 +name: RNA_hook_turn +synonym: "hook turn" RELATED [] +synonym: "hook-turn motif" EXACT [] +synonym: "RNA hook turn" EXACT [] +is_a: SO:0000026 ! RNA_junction_loop + +[Term] +id: SO:0000028 +name: base_pair +synonym: "base pair" EXACT [] +xref: http://en.wikipedia.org/wiki/Base_pair "wiki" +is_a: SO:0000002 ! sequence_secondary_structure + +[Term] +id: SO:0000029 +name: WC_base_pair +def: "The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation." [PMID:12177293] +synonym: "canonical base pair" EXACT [] +synonym: "Watson Crick base pair" EXACT [] +synonym: "Watson-Crick base pair" RELATED [] +synonym: "Watson-Crick pair" EXACT [] +synonym: "WC base pair" EXACT [] +is_a: SO:0000028 ! base_pair + +[Term] +id: SO:0000030 +name: sugar_edge_base_pair +def: "A type of non-canonical base-pairing." [PMID:12177293] +synonym: "sugar edge base pair" EXACT [] +is_a: SO:0000028 ! base_pair + +[Term] +id: SO:0000031 +name: aptamer +def: "DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu] +xref: http://en.wikipedia.org/wiki/Aptamer "wiki" +is_a: SO:0000696 ! oligo + +[Term] +id: SO:0000032 +name: DNA_aptamer +def: "DNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:aptamer.icmb.utexas.edu] +synonym: "DNA aptamer" EXACT [] +is_a: SO:0000031 ! aptamer + +[Term] +id: SO:0000033 +name: RNA_aptamer +def: "RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu] +synonym: "RNA aptamer" EXACT [] +is_a: SO:0000031 ! aptamer + +[Term] +id: SO:0000034 +name: morpholino_oligo +def: "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [http://www.gene-tools.com/] +synonym: "morphant" BROAD [] +synonym: "morpholino" EXACT [] +synonym: "morpholino oligo" EXACT [] +is_a: SO:0001247 ! synthetic_oligo +relationship: has_quality SO:0001183 ! morpholino_backbone + +[Term] +id: SO:0000035 +name: riboswitch +def: "A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954] +synonym: "riboswitch RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/Riboswitch "wiki" +is_a: SO:0000836 ! mRNA_region +relationship: part_of SO:0000234 ! mRNA + +[Term] +id: SO:0000036 +name: matrix_attachment_site +def: "A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma] +synonym: "MAR" EXACT [] +synonym: "matrix association region" EXACT [] +synonym: "matrix attachment region" EXACT [] +synonym: "matrix attachment site" EXACT [] +synonym: "nuclear matrix association region" EXACT [] +synonym: "nuclear matrix attachment site" EXACT [] +synonym: "S/MAR" EXACT [] +synonym: "S/MAR element" RELATED [] +synonym: "scaffold attachment site" EXACT [] +synonym: "scaffold matrix attachment region" EXACT [] +synonym: "SMAR" EXACT [] +xref: http://en.wikipedia.org/wiki/Matrix_attachment_site "wiki" +is_a: SO:0000626 ! chromosomal_regulatory_element + +[Term] +id: SO:0000037 +name: locus_control_region +def: "A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." [SO:ma] +synonym: "LCR" EXACT [] +synonym: "locus control element" RELATED [] +synonym: "locus control region" EXACT [] +xref: http://en.wikipedia.org/wiki/Locus_control_region "wiki" +is_a: SO:0000727 ! CRM + +[Term] +id: SO:0000038 +name: match_set +def: "A collection of match parts." [SO:ke] +subset: SOFA +is_obsolete: true + +[Term] +id: SO:0000039 +name: match_part +def: "A part of a match, for example an hsp from blast is a match_part." [SO:ke] +subset: SOFA +synonym: "match part" EXACT [] +is_a: SO:0001410 ! experimental_feature +relationship: part_of SO:0000343 ! match + +[Term] +id: SO:0000040 +name: genomic_clone +def: "A clone of a DNA region of a genome." [SO:ma] +synonym: "genomic clone" EXACT [] +is_a: SO:0000151 ! clone +relationship: has_quality SO:0000991 ! genomic_DNA + +[Term] +id: SO:0000041 +name: sequence_operation +def: "An operation that can be applied to a sequence, that results in a change." [SO:ke] +synonym: "sequence operation" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000042 +name: pseudogene_attribute +def: "An attribute of a pseudogene (SO:0000336)." [SO:ma] +synonym: "pseudogene attribute" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000043 +name: processed_pseudogene +def: "A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail." [SO:xp] +comment: Please not the synonym R psi M uses the spelled out form of the greek letter. +synonym: "processed pseudogene" EXACT [] +synonym: "pseudogene by reverse transcription" RELATED [] +synonym: "R psi G" RELATED [] +synonym: "retropseudogene" EXACT [] +is_a: SO:0000336 ! pseudogene + +[Term] +id: SO:0000044 +name: pseudogene_by_unequal_crossing_over +def: "A pseudogene caused by unequal crossing over at recombination." [SO:ke] +synonym: "pseudogene by unequal crossing over" EXACT [] +is_a: SO:0001760 ! non_processed_pseudogene + +[Term] +id: SO:0000045 +name: delete +def: "To remove a subsection of sequence." [SO:ke] +is_obsolete: true + +[Term] +id: SO:0000046 +name: insert +def: "To insert a subsection of sequence." [SO:ke] +is_obsolete: true + +[Term] +id: SO:0000047 +name: invert +def: "To invert a subsection of sequence." [SO:ke] +is_obsolete: true + +[Term] +id: SO:0000048 +name: substitute +def: "To substitute a subsection of sequence for another." [SO:ke] +is_obsolete: true + +[Term] +id: SO:0000049 +name: translocate +def: "To translocate a subsection of sequence." [SO:ke] +is_obsolete: true + +[Term] +id: SO:0000050 +name: gene_part +def: "A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene." [SO:ke] +subset: SOFA +is_obsolete: true + +[Term] +id: SO:0000051 +name: probe +def: "A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [SO:ma] +xref: http://en.wikipedia.org/wiki/Hybridization_probe "wiki" +is_a: SO:0000696 ! oligo + +[Term] +id: SO:0000052 +name: assortment_derived_deficiency +synonym: "assortment-derived_deficiency" RELATED [] +is_obsolete: true + +[Term] +id: SO:0000053 +name: sequence_variant_affecting_regulatory_region +def: "A sequence_variant_effect which changes the regulatory region of a gene." [SO:ke] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting regulatory region" RELATED [] +synonym: "sequence variant affecting regulatory region" EXACT [] +is_obsolete: true +replaced_by: SO:0001556 + +[Term] +id: SO:0000054 +name: aneuploid +def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke] +xref: http://en.wikipedia.org/wiki/Aneuploid "wiki" +is_a: SO:1000182 ! chromosome_number_variation + +[Term] +id: SO:0000055 +name: hyperploid +def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present." [SO:ke] +xref: http://en.wikipedia.org/wiki/Hyperploid "wiki" +is_a: SO:0000054 ! aneuploid + +[Term] +id: SO:0000056 +name: hypoploid +def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing." [SO:ke] +xref: http://en.wikipedia.org/wiki/Hypoploid "wiki" +is_a: SO:0000054 ! aneuploid + +[Term] +id: SO:0000057 +name: operator +def: "A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma] +subset: SOFA +synonym: "operator segment" EXACT [] +xref: http://en.wikipedia.org/wiki/Operator_(biology)#Operator "wiki" +is_a: SO:0000752 ! gene_group_regulatory_region + +[Term] +id: SO:0000058 +name: assortment_derived_aneuploid +synonym: "assortment-derived_aneuploid" RELATED [] +is_obsolete: true + +[Term] +id: SO:0000059 +name: nuclease_binding_site +def: "A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb] +subset: SOFA +synonym: "nuclease binding site" EXACT [] +is_a: SO:0001654 ! nucleotide_to_protein_binding_site + +[Term] +id: SO:0000060 +name: compound_chromosome_arm +comment: FLAG - this term is should probably be a part of rather than an is_a. +synonym: "compound chromosome arm" EXACT [] +is_a: SO:1000042 ! compound_chromosome + +[Term] +id: SO:0000061 +name: restriction_enzyme_binding_site +def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme." [SO:cb] +comment: A region of a molecule that binds to a restriction enzyme. +synonym: "restriction endonuclease binding site" EXACT [] +synonym: "restriction enzyme binding site" EXACT [] +is_a: SO:0000059 ! nuclease_binding_site + +[Term] +id: SO:0000062 +name: deficient_intrachromosomal_transposition +def: "An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual] +synonym: "deficient intrachromosomal transposition" EXACT [] +is_a: SO:1000029 ! chromosomal_deletion +is_a: SO:1000041 ! intrachromosomal_transposition +relationship: has_part SO:0000159 ! deletion + +[Term] +id: SO:0000063 +name: deficient_interchromosomal_transposition +def: "An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke] +synonym: "deficient interchromosomal transposition" EXACT [] +is_a: SO:1000155 ! interchromosomal_transposition + +[Term] +id: SO:0000064 +name: gene_by_transcript_attribute +comment: This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004. +is_obsolete: true + +[Term] +id: SO:0000065 +name: free_chromosome_arm +def: "A chromosome structure variation whereby an arm exists as an individual chromosome element." [SO:ke] +synonym: "free chromosome arm" EXACT [] +is_a: SO:1000183 ! chromosome_structure_variation + +[Term] +id: SO:0000066 +name: gene_by_polyadenylation_attribute +is_obsolete: true + +[Term] +id: SO:0000067 +name: gene_to_gene_feature +synonym: "gene to gene feature" EXACT [] +is_a: SO:0000401 ! gene_attribute + +[Term] +id: SO:0000068 +name: overlapping +def: "An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke] +is_a: SO:0000067 ! gene_to_gene_feature + +[Term] +id: SO:0000069 +name: inside_intron +def: "An attribute to describe a gene when it is located within the intron of another gene." [SO:ke] +synonym: "inside intron" EXACT [] +is_a: SO:0000068 ! overlapping + +[Term] +id: SO:0000070 +name: inside_intron_antiparallel +def: "An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand." [SO:ke] +synonym: "inside intron antiparallel" EXACT [] +is_a: SO:0000069 ! inside_intron + +[Term] +id: SO:0000071 +name: inside_intron_parallel +def: "An attribute to describe a gene when it is located within the intron of another gene and on the same strand." [SO:ke] +synonym: "inside intron parallel" EXACT [] +is_a: SO:0000069 ! inside_intron + +[Term] +id: SO:0000072 +name: end_overlapping_gene +is_obsolete: true + +[Term] +id: SO:0000073 +name: five_prime_three_prime_overlap +def: "An attribute to describe a gene when the five prime region overlaps with another gene's 3' region." [SO:ke] +synonym: "five prime-three prime overlap" EXACT [] +is_a: SO:0000068 ! overlapping + +[Term] +id: SO:0000074 +name: five_prime_five_prime_overlap +def: "An attribute to describe a gene when the five prime region overlaps with another gene's five prime region." [SO:ke] +synonym: "five prime-five prime overlap" EXACT [] +is_a: SO:0000068 ! overlapping + +[Term] +id: SO:0000075 +name: three_prime_three_prime_overlap +def: "An attribute to describe a gene when the 3' region overlaps with another gene's 3' region." [SO:ke] +synonym: "three prime-three prime overlap" EXACT [] +is_a: SO:0000068 ! overlapping + +[Term] +id: SO:0000076 +name: three_prime_five_prime_overlap +def: "An attribute to describe a gene when the 3' region overlaps with another gene's 5' region." [SO:ke] +synonym: "5' 3' overlap" EXACT [] +synonym: "three prime five prime overlap" EXACT [] +is_a: SO:0000068 ! overlapping + +[Term] +id: SO:0000077 +name: antisense +def: "A region sequence that is complementary to a sequence of messenger RNA." [SO:ke] +xref: http://en.wikipedia.org/wiki/Antisense "wiki" +is_a: SO:0000068 ! overlapping + +[Term] +id: SO:0000078 +name: polycistronic_transcript +def: "A transcript that is polycistronic." [SO:xp] +synonym: "polycistronic transcript" EXACT [] +is_a: SO:0000673 ! transcript +relationship: has_quality SO:0000880 ! polycistronic + +[Term] +id: SO:0000079 +name: dicistronic_transcript +def: "A transcript that is dicistronic." [SO:ke] +synonym: "dicistronic transcript" EXACT [] +is_a: SO:0000078 ! polycistronic_transcript +relationship: has_quality SO:0000879 ! dicistronic + +[Term] +id: SO:0000080 +name: operon_member +synonym: "operon member" EXACT [] +is_a: SO:0000081 ! gene_array_member + +[Term] +id: SO:0000081 +name: gene_array_member +synonym: "gene array member" EXACT [] +is_a: SO:0000401 ! gene_attribute + +[Term] +id: SO:0000082 +name: processed_transcript_attribute +is_obsolete: true + +[Term] +id: SO:0000083 +name: macronuclear_sequence +synonym: "macronuclear sequence" EXACT [] +is_a: SO:0000736 ! organelle_sequence + +[Term] +id: SO:0000084 +name: micronuclear_sequence +synonym: "micronuclear sequence" EXACT [] +is_a: SO:0000736 ! organelle_sequence + +[Term] +id: SO:0000085 +name: gene_by_genome_location +is_obsolete: true + +[Term] +id: SO:0000086 +name: gene_by_organelle_of_genome +is_obsolete: true + +[Term] +id: SO:0000087 +name: nuclear_gene +def: "A gene from nuclear sequence." [SO:xp] +synonym: "nuclear gene" EXACT [] +xref: http://en.wikipedia.org/wiki/Nuclear_gene "wiki" +is_a: SO:0000704 ! gene +relationship: has_origin SO:0000738 ! nuclear_sequence + +[Term] +id: SO:0000088 +name: mt_gene +def: "A gene located in mitochondrial sequence." [SO:xp] +synonym: "mitochondrial gene" EXACT [] +synonym: "mt gene" EXACT [] +xref: http://en.wikipedia.org/wiki/Mitochondrial_gene "wiki" +is_a: SO:0000704 ! gene +relationship: has_origin SO:0000737 ! mitochondrial_sequence + +[Term] +id: SO:0000089 +name: kinetoplast_gene +def: "A gene located in kinetoplast sequence." [SO:xp] +synonym: "kinetoplast gene" EXACT [] +is_a: SO:0000088 ! mt_gene +relationship: has_origin SO:0000741 ! kinetoplast + +[Term] +id: SO:0000090 +name: plastid_gene +def: "A gene from plastid sequence." [SO:xp] +synonym: "plastid gene" EXACT [] +is_a: SO:0000704 ! gene +relationship: has_origin SO:0000740 ! plastid_sequence + +[Term] +id: SO:0000091 +name: apicoplast_gene +def: "A gene from apicoplast sequence." [SO:xp] +synonym: "apicoplast gene" EXACT [] +is_a: SO:0000090 ! plastid_gene +relationship: has_origin SO:0000743 ! apicoplast_sequence + +[Term] +id: SO:0000092 +name: ct_gene +def: "A gene from chloroplast sequence." [SO:xp] +synonym: "chloroplast gene" EXACT [] +synonym: "ct gene" EXACT [] +is_a: SO:0000090 ! plastid_gene +relationship: has_origin SO:0000745 ! chloroplast_sequence + +[Term] +id: SO:0000093 +name: chromoplast_gene +def: "A gene from chromoplast_sequence." [SO:xp] +synonym: "chromoplast gene" EXACT [] +is_a: SO:0000090 ! plastid_gene +relationship: has_origin SO:0000744 ! chromoplast_sequence + +[Term] +id: SO:0000094 +name: cyanelle_gene +def: "A gene from cyanelle sequence." [SO:xp] +synonym: "cyanelle gene" EXACT [] +is_a: SO:0000090 ! plastid_gene +relationship: has_origin SO:0000746 ! cyanelle_sequence + +[Term] +id: SO:0000095 +name: leucoplast_gene +def: "A plastid gene from leucoplast sequence." [SO:xp] +synonym: "leucoplast gene" EXACT [] +is_a: SO:0000090 ! plastid_gene +relationship: has_origin SO:0000747 ! leucoplast_sequence + +[Term] +id: SO:0000096 +name: proplastid_gene +def: "A gene from proplastid sequence." [SO:ke] +synonym: "proplastid gene" EXACT [] +is_a: SO:0000090 ! plastid_gene +relationship: has_origin SO:0000748 ! proplastid_sequence + +[Term] +id: SO:0000097 +name: nucleomorph_gene +def: "A gene from nucleomorph sequence." [SO:xp] +synonym: "nucleomorph gene" EXACT [] +is_a: SO:0000704 ! gene +relationship: has_origin SO:0000739 ! nucleomorphic_sequence + +[Term] +id: SO:0000098 +name: plasmid_gene +def: "A gene from plasmid sequence." [SO:xp] +synonym: "plasmid gene" EXACT [] +is_a: SO:0000704 ! gene +relationship: has_origin SO:0000749 ! plasmid_location + +[Term] +id: SO:0000099 +name: proviral_gene +def: "A gene from proviral sequence." [SO:xp] +synonym: "proviral gene" EXACT [] +is_a: SO:0000704 ! gene +relationship: has_origin SO:0000751 ! proviral_location + +[Term] +id: SO:0000100 +name: endogenous_retroviral_gene +def: "A proviral gene with origin endogenous retrovirus." [SO:xp] +synonym: "endogenous retroviral gene" EXACT [] +is_a: SO:0000099 ! proviral_gene +relationship: has_origin SO:0000903 ! endogenous_retroviral_sequence + +[Term] +id: SO:0000101 +name: transposable_element +def: "A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html] +subset: SOFA +synonym: "transposable element" EXACT [] +synonym: "transposon" EXACT [] +xref: http://en.wikipedia.org/wiki/Transposable_element "wiki" +is_a: SO:0001039 ! integrated_mobile_genetic_element + +[Term] +id: SO:0000102 +name: expressed_sequence_match +def: "A match to an EST or cDNA sequence." [SO:ke] +subset: SOFA +synonym: "expressed sequence match" EXACT [] +is_a: SO:0000347 ! nucleotide_match + +[Term] +id: SO:0000103 +name: clone_insert_end +def: "The end of the clone insert." [SO:ke] +subset: SOFA +synonym: "clone insert end" EXACT [] +is_a: SO:0000699 ! junction +relationship: part_of SO:0000753 ! clone_insert + +[Term] +id: SO:0000104 +name: polypeptide +alt_id: SO:0000358 +def: "A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute. +subset: SOFA +synonym: "protein" EXACT [] +xref: http://en.wikipedia.org/wiki/Polypeptide "wiki" +is_a: SO:0001411 ! biological_region +relationship: derives_from SO:0000316 ! CDS + +[Term] +id: SO:0000105 +name: chromosome_arm +def: "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.medterms.com/script/main/art.asp?articlekey=5152] +synonym: "chromosome arm" EXACT [] +is_a: SO:0000830 ! chromosome_part + +[Term] +id: SO:0000106 +name: non_capped_primary_transcript +is_obsolete: true + +[Term] +id: SO:0000107 +name: sequencing_primer +synonym: "sequencing primer" EXACT [] +is_a: SO:0000112 ! primer + +[Term] +id: SO:0000108 +name: mRNA_with_frameshift +def: "An mRNA with a frameshift." [SO:xp] +synonym: "frameshifted mRNA" EXACT [] +synonym: "mRNA with frameshift" EXACT [] +is_a: SO:0000234 ! mRNA +relationship: has_quality SO:0000865 ! frameshift + +[Term] +id: SO:0000109 +name: sequence_variant_obs +def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke] +subset: SOFA +synonym: "mutation" RELATED [] +is_obsolete: true + +[Term] +id: SO:0000110 +name: sequence_feature +def: "Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke] +subset: SOFA +synonym: "located sequence feature" RELATED [] +synonym: "located_sequence_feature" EXACT [] +synonym: "sequence feature" EXACT [] +disjoint_from: SO:0000400 ! sequence_attribute + +[Term] +id: SO:0000111 +name: transposable_element_gene +def: "A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke] +synonym: "transposable element gene" EXACT [] +is_a: SO:0000704 ! gene +relationship: part_of SO:0000101 ! transposable_element + +[Term] +id: SO:0000112 +name: primer +def: "An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke] +subset: SOFA +synonym: "DNA primer" EXACT [] +synonym: "primer oligonucleotide" EXACT [] +synonym: "primer polynucleotide" EXACT [] +synonym: "primer sequence" EXACT [] +xref: http://en.wikipedia.org/wiki/Primer_(molecular_biology) "wiki" +is_a: SO:0000441 ! ss_oligo + +[Term] +id: SO:0000113 +name: proviral_region +def: "A viral sequence which has integrated into a host genome." [SO:ke] +subset: SOFA +synonym: "proviral region" EXACT [] +synonym: "proviral sequence" RELATED [] +is_a: SO:0001039 ! integrated_mobile_genetic_element + +[Term] +id: SO:0000114 +name: methylated_cytosine +def: "A methylated deoxy-cytosine." [SO:ke] +subset: SOFA +synonym: "methylated C" EXACT [] +synonym: "methylated cytosine" EXACT [] +synonym: "methylated cytosine base" EXACT [] +synonym: "methylated cytosine residue" EXACT [] +synonym: "methylated_C" EXACT [] +is_a: SO:0000306 ! methylated_DNA_base_feature +is_a: SO:0001963 ! modified_cytosine + +[Term] +id: SO:0000115 +name: transcript_feature +is_obsolete: true + +[Term] +id: SO:0000116 +name: edited +def: "An attribute describing a sequence that is modified by editing." [SO:ke] +is_a: SO:0000237 ! transcript_attribute + +[Term] +id: SO:0000117 +name: transcript_with_readthrough_stop_codon +is_obsolete: true + +[Term] +id: SO:0000118 +name: transcript_with_translational_frameshift +def: "A transcript with a translational frameshift." [SO:xp] +synonym: "transcript with translational frameshift" EXACT [] +is_a: SO:0000673 ! transcript +relationship: has_quality SO:0000887 ! translationally_frameshifted + +[Term] +id: SO:0000119 +name: regulated +def: "An attribute to describe a sequence that is regulated." [SO:ke] +is_a: SO:0000401 ! gene_attribute + +[Term] +id: SO:0000120 +name: protein_coding_primary_transcript +def: "A primary transcript that, at least in part, encodes one or more proteins." [SO:ke] +comment: May contain introns. +subset: SOFA +synonym: "pre mRNA" RELATED [] +synonym: "protein coding primary transcript" EXACT [] +is_a: SO:0000185 ! primary_transcript + +[Term] +id: SO:0000121 +name: forward_primer +def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +synonym: "DNA forward primer" EXACT [] +synonym: "forward DNA primer" EXACT [] +synonym: "forward primer" EXACT [] +synonym: "forward primer oligo" EXACT [] +synonym: "forward primer oligonucleotide" EXACT [] +synonym: "forward primer polynucleotide" EXACT [] +synonym: "forward primer sequence" EXACT [] +is_a: SO:0000112 ! primer +relationship: has_quality SO:0001030 ! forward + +[Term] +id: SO:0000122 +name: RNA_sequence_secondary_structure +def: "A folded RNA sequence." [SO:ke] +synonym: "RNA sequence secondary structure" EXACT [] +is_a: SO:0000002 ! sequence_secondary_structure + +[Term] +id: SO:0000123 +name: transcriptionally_regulated +def: "An attribute describing a gene that is regulated at transcription." [SO:ma] +comment: By:. +synonym: "transcriptionally regulated" EXACT [] +is_a: SO:0000119 ! regulated + +[Term] +id: SO:0000124 +name: transcriptionally_constitutive +def: "Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate." [SO:ke] +synonym: "transcriptionally constitutive" EXACT [] +is_a: SO:0000123 ! transcriptionally_regulated + +[Term] +id: SO:0000125 +name: transcriptionally_induced +def: "An inducer molecule is required for transcription to occur." [SO:ke] +synonym: "transcriptionally induced" EXACT [] +is_a: SO:0000123 ! transcriptionally_regulated + +[Term] +id: SO:0000126 +name: transcriptionally_repressed +def: "A repressor molecule is required for transcription to stop." [SO:ke] +synonym: "transcriptionally repressed" EXACT [] +is_a: SO:0000123 ! transcriptionally_regulated + +[Term] +id: SO:0000127 +name: silenced_gene +def: "A gene that is silenced." [SO:xp] +synonym: "silenced gene" EXACT [] +is_a: SO:0000704 ! gene +relationship: has_quality SO:0000893 ! silenced + +[Term] +id: SO:0000128 +name: gene_silenced_by_DNA_modification +def: "A gene that is silenced by DNA modification." [SO:xp] +synonym: "gene silenced by DNA modification" EXACT [] +is_a: SO:0000127 ! silenced_gene +relationship: has_quality SO:0000894 ! silenced_by_DNA_modification + +[Term] +id: SO:0000129 +name: gene_silenced_by_DNA_methylation +def: "A gene that is silenced by DNA methylation." [SO:xp] +synonym: "gene silenced by DNA methylation" EXACT [] +synonym: "methylation-silenced gene" EXACT [] +is_a: SO:0000128 ! gene_silenced_by_DNA_modification +relationship: has_quality SO:0000895 ! silenced_by_DNA_methylation + +[Term] +id: SO:0000130 +name: post_translationally_regulated +def: "An attribute describing a gene that is regulated after it has been translated." [SO:ke] +synonym: "post translationally regulated" EXACT [] +synonym: "post-translationally regulated" EXACT [] +is_a: SO:0000119 ! regulated + +[Term] +id: SO:0000131 +name: translationally_regulated +def: "An attribute describing a gene that is regulated as it is translated." [SO:ke] +synonym: "translationally regulated" EXACT [] +is_a: SO:0000119 ! regulated + +[Term] +id: SO:0000132 +name: reverse_primer +def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +synonym: "DNA reverse primer" EXACT [] +synonym: "reverse DNA primer" EXACT [] +synonym: "reverse primer" EXACT [] +synonym: "reverse primer oligo" EXACT [] +synonym: "reverse primer oligonucleotide" EXACT [] +synonym: "reverse primer sequence" EXACT [] +is_a: SO:0000112 ! primer +relationship: has_quality SO:0001031 ! reverse + +[Term] +id: SO:0000133 +name: epigenetically_modified +def: "This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones." [SO:ke] +synonym: "epigenetically modified" EXACT [] +is_a: SO:0000401 ! gene_attribute + +[Term] +id: SO:0000134 +name: genomically_imprinted +def: "Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke] +synonym: "genomically imprinted" EXACT [] +synonym: "imprinted" BROAD [] +xref: http:http\://en.wikipedia.org/wiki/Genomic_imprinting "wiki" +is_a: SO:0000119 ! regulated +is_a: SO:0000133 ! epigenetically_modified + +[Term] +id: SO:0000135 +name: maternally_imprinted +def: "The maternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke] +synonym: "maternally imprinted" EXACT [] +is_a: SO:0000134 ! genomically_imprinted + +[Term] +id: SO:0000136 +name: paternally_imprinted +def: "The paternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke] +synonym: "paternally imprinted" EXACT [] +is_a: SO:0000134 ! genomically_imprinted + +[Term] +id: SO:0000137 +name: allelically_excluded +def: "Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell." [SO:ke] +comment: Examples are x-inactivation and immunoglobulin formation. +synonym: "allelically excluded" EXACT [] +is_a: SO:0000133 ! epigenetically_modified + +[Term] +id: SO:0000138 +name: gene_rearranged_at_DNA_level +def: "An epigenetically modified gene, rearranged at the DNA level." [SO:xp] +synonym: "gene rearranged at DNA level" EXACT [] +is_a: SO:0000898 ! epigenetically_modified_gene +relationship: has_quality SO:0000904 ! rearranged_at_DNA_level + +[Term] +id: SO:0000139 +name: ribosome_entry_site +def: "Region in mRNA where ribosome assembles." [SO:ke] +subset: SOFA +synonym: "ribosome entry site" EXACT [] +is_a: SO:0000836 ! mRNA_region +relationship: part_of SO:0000204 ! five_prime_UTR + +[Term] +id: SO:0000140 +name: attenuator +def: "A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as] +subset: SOFA +synonym: "attenuator sequence" EXACT [] +xref: http://en.wikipedia.org/wiki/Attenuator "wiki" +is_a: SO:0001680 ! translation_regulatory_region +relationship: part_of SO:0000234 ! mRNA + +[Term] +id: SO:0000141 +name: terminator +def: "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +subset: SOFA +synonym: "terminator sequence" EXACT [] +xref: http://en.wikipedia.org/wiki/Terminator_(genetics) "wiki" +is_a: SO:0001679 ! transcription_regulatory_region +relationship: part_of SO:0000673 ! transcript + +[Term] +id: SO:0000142 +name: DNA_sequence_secondary_structure +def: "A folded DNA sequence." [SO:ke] +synonym: "DNA sequence secondary structure" EXACT [] +is_a: SO:0000002 ! sequence_secondary_structure + +[Term] +id: SO:0000143 +name: assembly_component +def: "A region of known length which may be used to manufacture a longer region." [SO:ke] +subset: SOFA +synonym: "assembly component" EXACT [] +is_a: SO:0001410 ! experimental_feature + +[Term] +id: SO:0000144 +name: primary_transcript_attribute +is_obsolete: true + +[Term] +id: SO:0000145 +name: recoded_codon +def: "A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp] +synonym: "recoded codon" EXACT [] +is_a: SO:0000360 ! codon + +[Term] +id: SO:0000146 +name: capped +def: "An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end." [SO:ke] +is_a: SO:0000237 ! transcript_attribute + +[Term] +id: SO:0000147 +name: exon +def: "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +subset: SOFA +xref: http://en.wikipedia.org/wiki/Exon "wiki" +is_a: SO:0000833 ! transcript_region + +[Term] +id: SO:0000148 +name: supercontig +def: "One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls] +subset: SOFA +synonym: "scaffold" RELATED [] +is_a: SO:0001876 ! partial_genomic_sequence_assembly +relationship: part_of SO:0000719 ! ultracontig + +[Term] +id: SO:0000149 +name: contig +def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls] +subset: SOFA +xref: http://en.wikipedia.org/wiki/Contig "wiki" +is_a: SO:0000143 ! assembly_component +is_a: SO:0000353 ! sequence_assembly +relationship: part_of SO:0000148 ! supercontig + +[Term] +id: SO:0000150 +name: read +def: "A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd] +subset: SOFA +is_a: SO:0000143 ! assembly_component +relationship: part_of SO:0000149 ! contig + +[Term] +id: SO:0000151 +name: clone +def: "A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke] +subset: SOFA +xref: http:http\://en.wikipedia.org/wiki/Clone_(genetics) "wiki" +is_a: SO:0000695 ! reagent + +[Term] +id: SO:0000152 +name: YAC +def: "Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +synonym: "yeast artificial chromosome" EXACT [] +is_a: SO:0000440 ! vector_replicon + +[Term] +id: SO:0000153 +name: BAC +def: "Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +synonym: "bacterial artificial chromosome" EXACT [] +is_a: SO:0000440 ! vector_replicon + +[Term] +id: SO:0000154 +name: PAC +def: "The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Drosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome. +synonym: "P1" EXACT [] +synonym: "P1 artificial chromosome" EXACT [] +xref: http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome "wiki" +is_a: SO:0000440 ! vector_replicon + +[Term] +id: SO:0000155 +name: plasmid +def: "A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +synonym: "plasmid sequence" EXACT [] +is_a: SO:0001235 ! replicon + +[Term] +id: SO:0000156 +name: cosmid +def: "A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma] +comment: Paper: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1):9-20. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +synonym: "cosmid vector" EXACT [] +xref: http://en.wikipedia.org/wiki/Cosmid "wiki" +is_a: SO:0000440 ! vector_replicon + +[Term] +id: SO:0000157 +name: phagemid +def: "A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \"helper\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma] +synonym: "phagemid vector" RELATED [] +xref: http://en.wikipedia.org/wiki/Phagemid "wiki" +is_a: SO:0000440 ! vector_replicon + +[Term] +id: SO:0000158 +name: fosmid +def: "A cloning vector that utilizes the E. coli F factor." [SO:ma] +comment: Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996. +synonym: "fosmid vector" RELATED [] +xref: http://en.wikipedia.org/wiki/Fosmid "wiki" +is_a: SO:0000440 ! vector_replicon + +[Term] +id: SO:0000159 +name: deletion +alt_id: SO:1000033 +def: "The point at which one or more contiguous nucleotides were excised." [SO:ke] +subset: SOFA +synonym: "deleted_sequence" EXACT [] +synonym: "nucleotide deletion" EXACT [] +synonym: "nucleotide_deletion" EXACT [] +xref: http://en.wikipedia.org/wiki/Nucleotide_deletion "wiki" +xref: loinc:LA6692-3 "Deletion" +is_a: SO:0001059 ! sequence_alteration +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0000160 +name: lambda_clone +def: "A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8] +is_obsolete: true + +[Term] +id: SO:0000161 +name: methylated_adenine +def: "A modified base in which adenine has been methylated." [SO:ke] +subset: SOFA +synonym: "methylated A" EXACT [] +synonym: "methylated adenine" EXACT [] +synonym: "methylated adenine base" EXACT [] +synonym: "methylated adenine residue" EXACT [] +synonym: "methylated_A" EXACT [] +is_a: SO:0000306 ! methylated_DNA_base_feature +is_a: SO:0001962 ! modified_adenine + +[Term] +id: SO:0000162 +name: splice_site +def: "Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke] +comment: With spliceosomal introns, the splice sites bind the spliceosomal machinery. +subset: SOFA +synonym: "splice site" EXACT [] +xref: http://en.wikipedia.org/wiki/Splice_site "wiki" +is_a: SO:0000835 ! primary_transcript_region + +[Term] +id: SO:0000163 +name: five_prime_cis_splice_site +def: "Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke] +subset: SOFA +synonym: "5' splice site" EXACT [] +synonym: "donor" RELATED [] +synonym: "donor splice site" EXACT [] +synonym: "five prime splice site" EXACT [] +synonym: "splice donor site" EXACT [] +is_a: SO:0001419 ! cis_splice_site + +[Term] +id: SO:0000164 +name: three_prime_cis_splice_site +def: "Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke] +subset: SOFA +synonym: "3' splice site" RELATED [] +synonym: "acceptor" RELATED [] +synonym: "acceptor splice site" EXACT [] +synonym: "splice acceptor site" EXACT [] +synonym: "three prime splice site" EXACT [] +is_a: SO:0001419 ! cis_splice_site + +[Term] +id: SO:0000165 +name: enhancer +def: "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +comment: An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO. +subset: SOFA +xref: http://en.wikipedia.org/wiki/Enhancer_(genetics) "wiki" +is_a: SO:0000727 ! CRM + +[Term] +id: SO:0000166 +name: enhancer_bound_by_factor +def: "An enhancer bound by a factor." [SO:xp] +synonym: "enhancer bound by factor" EXACT [] +is_a: SO:0000165 ! enhancer +relationship: has_quality SO:0000277 ! bound_by_factor + +[Term] +id: SO:0000167 +name: promoter +def: "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription. +subset: SOFA +synonym: "promoter sequence" EXACT [] +xref: http://en.wikipedia.org/wiki/Promoter "wiki" +is_a: SO:0001055 ! transcriptional_cis_regulatory_region + +[Term] +id: SO:0000168 +name: restriction_enzyme_cut_site +def: "A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA." [SO:ma] +is_obsolete: true + +[Term] +id: SO:0000169 +name: RNApol_I_promoter +def: "A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke] +synonym: "pol I promoter" EXACT [] +synonym: "polymerase I promoter" EXACT [] +synonym: "RNA polymerase A promoter" EXACT [] +synonym: "RNApol I promoter" EXACT [] +is_a: SO:0001203 ! RNA_polymerase_promoter + +[Term] +id: SO:0000170 +name: RNApol_II_promoter +def: "A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke] +synonym: "pol II promoter" RELATED [] +synonym: "polymerase II promoter" EXACT [] +synonym: "RNA polymerase B promoter" EXACT [] +synonym: "RNApol II promoter" EXACT [] +is_a: SO:0001203 ! RNA_polymerase_promoter + +[Term] +id: SO:0000171 +name: RNApol_III_promoter +def: "A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke] +synonym: "pol III promoter" EXACT [] +synonym: "polymerase III promoter" EXACT [] +synonym: "RNA polymerase C promoter" EXACT [] +synonym: "RNApol III promoter" EXACT [] +is_a: SO:0001203 ! RNA_polymerase_promoter + +[Term] +id: SO:0000172 +name: CAAT_signal +def: "Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +synonym: "CAAT box" EXACT [] +synonym: "CAAT signal" EXACT [] +synonym: "CAAT-box" EXACT [] +xref: http://en.wikipedia.org/wiki/CAAT_box "wiki" +is_a: SO:0000713 ! DNA_motif +relationship: part_of SO:0000170 ! RNApol_II_promoter + +[Term] +id: SO:0000173 +name: GC_rich_promoter_region +def: "A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +synonym: "GC rich promoter region" EXACT [] +synonym: "GC-rich region" EXACT [] +is_a: SO:0001659 ! promoter_element +relationship: part_of SO:0000170 ! RNApol_II_promoter + +[Term] +id: SO:0000174 +name: TATA_box +def: "A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:16858867] +comment: Binds TBP. +synonym: "Goldstein-Hogness box" EXACT [] +synonym: "TATA box" EXACT [] +xref: http://en.wikipedia.org/wiki/TATA_box "wiki" +is_a: SO:0001660 ! core_promoter_element + +[Term] +id: SO:0000175 +name: minus_10_signal +def: "A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +synonym: "-10 signal" EXACT [] +synonym: "minus 10 signal" EXACT [] +synonym: "Pribnow box" EXACT [] +synonym: "Pribnow Schaller box" EXACT [] +synonym: "Pribnow-Schaller box" EXACT [] +xref: http://en.wikipedia.org/wiki/Pribnow_box "wiki" +is_a: SO:0000713 ! DNA_motif +relationship: part_of SO:0001671 ! bacterial_RNApol_promoter_sigma_70 +relationship: part_of SO:0001913 ! bacterial_RNApol_promoter_sigma_ecf + +[Term] +id: SO:0000176 +name: minus_35_signal +def: "A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +synonym: "-35 signal" EXACT [] +synonym: "minus 35 signal" EXACT [] +is_a: SO:0000713 ! DNA_motif +relationship: part_of SO:0001671 ! bacterial_RNApol_promoter_sigma_70 +relationship: part_of SO:0001913 ! bacterial_RNApol_promoter_sigma_ecf + +[Term] +id: SO:0000177 +name: cross_genome_match +def: "A nucleotide match against a sequence from another organism." [SO:ma] +subset: SOFA +synonym: "cross genome match" EXACT [] +is_a: SO:0000347 ! nucleotide_match + +[Term] +id: SO:0000178 +name: operon +def: "A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +subset: SOFA +xref: http://en.wikipedia.org/wiki/Operon "wiki" +is_a: SO:0005855 ! gene_group + +[Term] +id: SO:0000179 +name: clone_insert_start +def: "The start of the clone insert." [SO:ke] +subset: SOFA +synonym: "clone insert start" EXACT [] +is_a: SO:0000699 ! junction +relationship: part_of SO:0000753 ! clone_insert + +[Term] +id: SO:0000180 +name: retrotransposon +def: "A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r] +synonym: "class I" RELATED [] +synonym: "class I transposon" EXACT [] +synonym: "retrotransposon element" EXACT [] +xref: http://en.wikipedia.org/wiki/Retrotransposon "wiki" +is_a: SO:0000101 ! transposable_element + +[Term] +id: SO:0000181 +name: translated_nucleotide_match +def: "A match against a translated sequence." [SO:ke] +subset: SOFA +synonym: "translated nucleotide match" EXACT [] +is_a: SO:0000347 ! nucleotide_match + +[Term] +id: SO:0000182 +name: DNA_transposon +def: "A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke] +synonym: "class II" RELATED [] +synonym: "class II transposon" EXACT [] +synonym: "DNA transposon" EXACT [] +is_a: SO:0000101 ! transposable_element + +[Term] +id: SO:0000183 +name: non_transcribed_region +def: "A region of the gene which is not transcribed." [SO:ke] +subset: SOFA +synonym: "non transcribed region" EXACT [] +synonym: "non-transcribed sequence" EXACT [] +synonym: "nontranscribed region" EXACT [] +synonym: "nontranscribed sequence" EXACT [] +is_a: SO:0000842 ! gene_component_region + +[Term] +id: SO:0000184 +name: U2_intron +def: "A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511] +comment: May have either GT-AG or AT-AG 5' and 3' boundaries. +synonym: "U2 intron" EXACT [] +is_a: SO:0000662 ! spliceosomal_intron + +[Term] +id: SO:0000185 +name: primary_transcript +def: "A transcript that in its initial state requires modification to be functional." [SO:ma] +subset: SOFA +synonym: "precursor RNA" EXACT [] +synonym: "primary transcript" EXACT [] +xref: http://en.wikipedia.org/wiki/Primary_transcript "wiki" +is_a: SO:0000673 ! transcript + +[Term] +id: SO:0000186 +name: LTR_retrotransposon +def: "A retrotransposon flanked by long terminal repeat sequences." [SO:ke] +synonym: "long terminal repeat retrotransposon" EXACT [] +synonym: "LTR retrotransposon" EXACT [] +is_a: SO:0000180 ! retrotransposon + +[Term] +id: SO:0000187 +name: repeat_family +def: "A group of characterized repeat sequences." [SO:ke] +subset: SOFA +is_obsolete: true + +[Term] +id: SO:0000188 +name: intron +def: "A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +subset: SOFA +xref: http://en.wikipedia.org/wiki/Intron "wiki" +is_a: SO:0000835 ! primary_transcript_region + +[Term] +id: SO:0000189 +name: non_LTR_retrotransposon +def: "A retrotransposon without long terminal repeat sequences." [SO:ke] +synonym: "non LTR retrotransposon" EXACT [] +is_a: SO:0000180 ! retrotransposon + +[Term] +id: SO:0000190 +name: five_prime_intron +synonym: "5' intron" EXACT [] +synonym: "5' intron sequence" EXACT [] +synonym: "five prime intron" EXACT [] +is_a: SO:0000188 ! intron + +[Term] +id: SO:0000191 +name: interior_intron +synonym: "interior intron" EXACT [] +is_a: SO:0000188 ! intron + +[Term] +id: SO:0000192 +name: three_prime_intron +synonym: "3' intron" EXACT [] +synonym: "3' intron sequence" RELATED [] +synonym: "three prime intron" EXACT [] +is_a: SO:0000188 ! intron + +[Term] +id: SO:0000193 +name: RFLP_fragment +def: "A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme." [GOC:pj] +subset: SOFA +synonym: "restriction fragment length polymorphism" EXACT [] +synonym: "RFLP" EXACT [] +synonym: "RFLP fragment" EXACT [] +xref: http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism "wiki" +is_a: SO:0000412 ! restriction_fragment + +[Term] +id: SO:0000194 +name: LINE_element +def: "A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html] +synonym: "LINE" EXACT [] +synonym: "LINE element" EXACT [] +synonym: "Long interspersed element" EXACT [] +synonym: "Long interspersed nuclear element" EXACT [] +is_a: SO:0000189 ! non_LTR_retrotransposon + +[Term] +id: SO:0000195 +name: coding_exon +def: "An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke] +subset: SOFA +synonym: "coding exon" EXACT [] +is_a: SO:0000147 ! exon + +[Term] +id: SO:0000196 +name: five_prime_coding_exon_coding_region +def: "The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm] +subset: SOFA +synonym: "five prime exon coding region" EXACT [] +is_a: SO:0001215 ! coding_region_of_exon +relationship: part_of SO:0000200 ! five_prime_coding_exon + +[Term] +id: SO:0000197 +name: three_prime_coding_exon_coding_region +def: "The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm] +subset: SOFA +synonym: "three prime exon coding region" EXACT [] +is_a: SO:0001215 ! coding_region_of_exon +relationship: part_of SO:0000202 ! three_prime_coding_exon + +[Term] +id: SO:0000198 +name: noncoding_exon +def: "An exon that does not contain any codons." [SO:ke] +subset: SOFA +synonym: "noncoding exon" EXACT [] +is_a: SO:0000147 ! exon + +[Term] +id: SO:0000199 +name: translocation +def: "A region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions." [NCBI:th, SO:ke] +subset: DBVAR +synonym: "transchr" RELATED [http://www.ncbi.nlm.nih.gov/dbvar/] +synonym: "translocated sequence" EXACT [] +is_a: SO:0001785 ! structural_alteration + +[Term] +id: SO:0000200 +name: five_prime_coding_exon +def: "The 5' most coding exon." [SO:ke] +subset: SOFA +synonym: "5' coding exon" EXACT [] +synonym: "five prime coding exon" EXACT [] +is_a: SO:0000195 ! coding_exon + +[Term] +id: SO:0000201 +name: interior_exon +def: "An exon that is bounded by 5' and 3' splice sites." [PMID:10373547] +synonym: "interior exon" EXACT [] +is_a: SO:0000147 ! exon + +[Term] +id: SO:0000202 +name: three_prime_coding_exon +def: "The coding exon that is most 3-prime on a given transcript." [SO:ma] +synonym: "3' coding exon" RELATED [] +synonym: "three prime coding exon" EXACT [] +is_a: SO:0000195 ! coding_exon + +[Term] +id: SO:0000203 +name: UTR +def: "Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke] +subset: SOFA +synonym: "untranslated region" EXACT [] +is_a: SO:0000836 ! mRNA_region + +[Term] +id: SO:0000204 +name: five_prime_UTR +def: "A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +subset: SOFA +synonym: "5' UTR" EXACT [] +synonym: "five prime UTR" EXACT [] +synonym: "five_prime_untranslated_region" EXACT [] +xref: http://en.wikipedia.org/wiki/5'_UTR "wiki" +is_a: SO:0000203 ! UTR + +[Term] +id: SO:0000205 +name: three_prime_UTR +def: "A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +subset: SOFA +synonym: "three prime untranslated region" EXACT [] +synonym: "three prime UTR" EXACT [] +xref: http://en.wikipedia.org/wiki/Three_prime_untranslated_region "wiki" +is_a: SO:0000203 ! UTR + +[Term] +id: SO:0000206 +name: SINE_element +def: "A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke] +synonym: "Short interspersed element" EXACT [] +synonym: "Short interspersed nuclear element" EXACT [] +synonym: "SINE element" EXACT [] +xref: http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element "wiki" +is_a: SO:0000189 ! non_LTR_retrotransposon + +[Term] +id: SO:0000207 +name: simple_sequence_length_variation +synonym: "simple sequence length polymorphism" RELATED [] +synonym: "simple sequence length variation" EXACT [] +synonym: "SSLP" RELATED [] +is_a: SO:0000248 ! sequence_length_variation + +[Term] +id: SO:0000208 +name: terminal_inverted_repeat_element +def: "A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf] +synonym: "terminal inverted repeat element" EXACT [] +synonym: "TIR element" EXACT [] +is_a: SO:0000182 ! DNA_transposon + +[Term] +id: SO:0000209 +name: rRNA_primary_transcript +def: "A primary transcript encoding a ribosomal RNA." [SO:ke] +subset: SOFA +synonym: "ribosomal RNA primary transcript" EXACT [] +synonym: "rRNA primary transcript" EXACT [] +is_a: SO:0000483 ! nc_primary_transcript + +[Term] +id: SO:0000210 +name: tRNA_primary_transcript +def: "A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke] +synonym: "tRNA primary transcript" EXACT [] +is_a: SO:0000483 ! nc_primary_transcript + +[Term] +id: SO:0000211 +name: alanine_tRNA_primary_transcript +def: "A primary transcript encoding alanyl tRNA." [SO:ke] +synonym: "alanine tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000212 +name: arginine_tRNA_primary_transcript +def: "A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke] +synonym: "arginine tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000213 +name: asparagine_tRNA_primary_transcript +def: "A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke] +synonym: "asparagine tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000214 +name: aspartic_acid_tRNA_primary_transcript +def: "A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke] +synonym: "aspartic acid tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000215 +name: cysteine_tRNA_primary_transcript +def: "A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke] +synonym: "cysteine tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000216 +name: glutamic_acid_tRNA_primary_transcript +def: "A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke] +synonym: "glutamic acid tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000217 +name: glutamine_tRNA_primary_transcript +def: "A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke] +synonym: "glutamine tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000218 +name: glycine_tRNA_primary_transcript +def: "A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke] +synonym: "glycine tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000219 +name: histidine_tRNA_primary_transcript +def: "A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke] +synonym: "histidine tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000220 +name: isoleucine_tRNA_primary_transcript +def: "A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke] +synonym: "isoleucine tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000221 +name: leucine_tRNA_primary_transcript +def: "A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke] +synonym: "leucine tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000222 +name: lysine_tRNA_primary_transcript +def: "A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke] +synonym: "lysine tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000223 +name: methionine_tRNA_primary_transcript +def: "A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke] +synonym: "methionine tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000224 +name: phenylalanine_tRNA_primary_transcript +def: "A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke] +synonym: "phenylalanine tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000225 +name: proline_tRNA_primary_transcript +def: "A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke] +synonym: "proline tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000226 +name: serine_tRNA_primary_transcript +def: "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke] +synonym: "serine tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000227 +name: threonine_tRNA_primary_transcript +def: "A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke] +synonym: "threonine tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000228 +name: tryptophan_tRNA_primary_transcript +def: "A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke] +synonym: "tryptophan tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000229 +name: tyrosine_tRNA_primary_transcript +def: "A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke] +synonym: "tyrosine tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000230 +name: valine_tRNA_primary_transcript +def: "A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke] +synonym: "valine tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000231 +name: snRNA_primary_transcript +def: "A primary transcript encoding a small nuclear RNA (SO:0000274)." [SO:ke] +synonym: "snRNA primary transcript" EXACT [] +is_a: SO:0000483 ! nc_primary_transcript + +[Term] +id: SO:0000232 +name: snoRNA_primary_transcript +def: "A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke] +synonym: "snoRNA primary transcript" EXACT [] +is_a: SO:0000483 ! nc_primary_transcript + +[Term] +id: SO:0000233 +name: mature_transcript +def: "A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke] +comment: A processed transcript cannot contain introns. +subset: SOFA +synonym: "mature transcript" EXACT [] +xref: http://en.wikipedia.org/wiki/Mature_transcript "wiki" +is_a: SO:0000673 ! transcript +relationship: derives_from SO:0000185 ! primary_transcript + +[Term] +id: SO:0000234 +name: mRNA +def: "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma] +comment: An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +subset: SOFA +synonym: "messenger RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/MRNA "wiki" +is_a: SO:0000233 ! mature_transcript + +[Term] +id: SO:0000235 +name: TF_binding_site +def: "A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke] +subset: SOFA +synonym: "TF binding site" EXACT [] +synonym: "transcription factor binding site" EXACT [] +is_a: SO:0001654 ! nucleotide_to_protein_binding_site +is_a: SO:0001679 ! transcription_regulatory_region + +[Term] +id: SO:0000236 +name: ORF +def: "The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma] +comment: The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +subset: SOFA +synonym: "open reading frame" EXACT [] +is_a: SO:0000717 ! reading_frame + +[Term] +id: SO:0000237 +name: transcript_attribute +synonym: "transcript attribute" EXACT [] +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000238 +name: foldback_element +def: "A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf] +synonym: "foldback element" EXACT [] +synonym: "long inverted repeat element" RELATED [] +synonym: "LVR element" RELATED [] +is_a: SO:0000182 ! DNA_transposon + +[Term] +id: SO:0000239 +name: flanking_region +def: "The sequences extending on either side of a specific region." [SO:ke] +subset: SOFA +synonym: "flanking region" EXACT [] +is_a: SO:0001412 ! topologically_defined_region + +[Term] +id: SO:0000240 +name: chromosome_variation +synonym: "chromosome variation" EXACT [] +is_a: SO:0001507 ! variant_collection +relationship: part_of SO:0001524 ! chromosomally_aberrant_genome + +[Term] +id: SO:0000241 +name: internal_UTR +def: "A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm] +synonym: "internal UTR" EXACT [] +is_a: SO:0000203 ! UTR + +[Term] +id: SO:0000242 +name: untranslated_region_polycistronic_mRNA +def: "The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke] +synonym: "untranslated region polycistronic mRNA" EXACT [] +is_a: SO:0000203 ! UTR + +[Term] +id: SO:0000243 +name: internal_ribosome_entry_site +def: "Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke] +synonym: "internal ribosomal entry sequence" EXACT [] +synonym: "internal ribosomal entry site" EXACT [] +synonym: "internal ribosome entry sequence" RELATED [] +synonym: "internal ribosome entry site" EXACT [] +synonym: "IRES" EXACT [] +xref: http://en.wikipedia.org/wiki/Internal_ribosome_entry_site "wiki" +is_a: SO:0000139 ! ribosome_entry_site + +[Term] +id: SO:0000244 +name: four_cutter_restriction_site +synonym: "4-cutter_restriction_site" RELATED [] +synonym: "four-cutter_restriction_sit" RELATED [] +is_obsolete: true + +[Term] +id: SO:0000245 +name: mRNA_by_polyadenylation_status +is_obsolete: true + +[Term] +id: SO:0000246 +name: polyadenylated +def: "A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule." [SO:ke] +is_a: SO:0000863 ! mRNA_attribute + +[Term] +id: SO:0000247 +name: mRNA_not_polyadenylated +is_obsolete: true + +[Term] +id: SO:0000248 +name: sequence_length_variation +synonym: "sequence length variation" EXACT [] +is_a: SO:1000002 ! substitution + +[Term] +id: SO:0000249 +name: six_cutter_restriction_site +synonym: "6-cutter_restriction_site" RELATED [] +synonym: "six-cutter_restriction_site" RELATED [] +is_obsolete: true + +[Term] +id: SO:0000250 +name: modified_RNA_base_feature +def: "A post_transcriptionally modified base." [SO:ke] +synonym: "modified RNA base feature" EXACT [] +is_a: SO:0001236 ! base + +[Term] +id: SO:0000251 +name: eight_cutter_restriction_site +synonym: "8-cutter_restriction_site" RELATED [] +synonym: "eight-cutter_restriction_site" RELATED [] +is_obsolete: true + +[Term] +id: SO:0000252 +name: rRNA +def: "RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732] +subset: SOFA +synonym: "ribosomal ribonucleic acid" EXACT [] +synonym: "ribosomal RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/RRNA "wiki" +is_a: SO:0000655 ! ncRNA +relationship: derives_from SO:0000209 ! rRNA_primary_transcript + +[Term] +id: SO:0000253 +name: tRNA +def: "Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +subset: SOFA +synonym: "transfer ribonucleic acid" RELATED [] +synonym: "transfer RNA" RELATED [] +xref: http://en.wikipedia.org/wiki/TRNA "wiki" +is_a: SO:0000655 ! ncRNA +relationship: derives_from SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0000254 +name: alanyl_tRNA +def: "A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." [SO:ke] +synonym: "alanyl tRNA" EXACT [] +synonym: "alanyl-transfer ribonucleic acid" EXACT [] +synonym: "alanyl-transfer RNA" EXACT [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000211 ! alanine_tRNA_primary_transcript + +[Term] +id: SO:0000255 +name: rRNA_small_subunit_primary_transcript +def: "A primary transcript encoding a small ribosomal subunit RNA." [SO:ke] +synonym: "rRNA small subunit primary transcript" EXACT [] +is_a: SO:0000209 ! rRNA_primary_transcript + +[Term] +id: SO:0000256 +name: asparaginyl_tRNA +def: "A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." [SO:ke] +synonym: "asparaginyl tRNA" EXACT [] +synonym: "asparaginyl-transfer ribonucleic acid" EXACT [] +synonym: "asparaginyl-transfer RNA" EXACT [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000213 ! asparagine_tRNA_primary_transcript + +[Term] +id: SO:0000257 +name: aspartyl_tRNA +def: "A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." [SO:ke] +synonym: "aspartyl tRNA" EXACT [] +synonym: "aspartyl-transfer ribonucleic acid" EXACT [] +synonym: "aspartyl-transfer RNA" EXACT [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000214 ! aspartic_acid_tRNA_primary_transcript + +[Term] +id: SO:0000258 +name: cysteinyl_tRNA +def: "A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." [SO:ke] +synonym: "cysteinyl tRNA" EXACT [] +synonym: "cysteinyl-transfer ribonucleic acid" EXACT [] +synonym: "cysteinyl-transfer RNA" EXACT [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000215 ! cysteine_tRNA_primary_transcript + +[Term] +id: SO:0000259 +name: glutaminyl_tRNA +def: "A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." [SO:ke] +synonym: "glutaminyl tRNA" EXACT [] +synonym: "glutaminyl-transfer ribonucleic acid" EXACT [] +synonym: "glutaminyl-transfer RNA" EXACT [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000216 ! glutamic_acid_tRNA_primary_transcript + +[Term] +id: SO:0000260 +name: glutamyl_tRNA +def: "A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." [SO:ke] +synonym: "glutamyl tRNA" EXACT [] +synonym: "glutamyl-transfer ribonucleic acid" EXACT [] +synonym: "glutamyl-transfer RNA" RELATED [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000217 ! glutamine_tRNA_primary_transcript + +[Term] +id: SO:0000261 +name: glycyl_tRNA +def: "A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." [SO:ke] +synonym: "glycyl tRNA" EXACT [] +synonym: "glycyl-transfer ribonucleic acid" RELATED [] +synonym: "glycyl-transfer RNA" RELATED [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000218 ! glycine_tRNA_primary_transcript + +[Term] +id: SO:0000262 +name: histidyl_tRNA +def: "A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." [SO:ke] +synonym: "histidyl tRNA" EXACT [] +synonym: "histidyl-transfer ribonucleic acid" EXACT [] +synonym: "histidyl-transfer RNA" EXACT [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000219 ! histidine_tRNA_primary_transcript + +[Term] +id: SO:0000263 +name: isoleucyl_tRNA +def: "A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." [SO:ke] +synonym: "isoleucyl tRNA" EXACT [] +synonym: "isoleucyl-transfer ribonucleic acid" EXACT [] +synonym: "isoleucyl-transfer RNA" EXACT [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000220 ! isoleucine_tRNA_primary_transcript + +[Term] +id: SO:0000264 +name: leucyl_tRNA +def: "A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." [SO:ke] +synonym: "leucyl tRNA" EXACT [] +synonym: "leucyl-transfer ribonucleic acid" EXACT [] +synonym: "leucyl-transfer RNA" EXACT [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000221 ! leucine_tRNA_primary_transcript + +[Term] +id: SO:0000265 +name: lysyl_tRNA +def: "A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." [SO:ke] +synonym: "lysyl tRNA" EXACT [] +synonym: "lysyl-transfer ribonucleic acid" EXACT [] +synonym: "lysyl-transfer RNA" EXACT [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000222 ! lysine_tRNA_primary_transcript + +[Term] +id: SO:0000266 +name: methionyl_tRNA +def: "A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." [SO:ke] +synonym: "methionyl tRNA" EXACT [] +synonym: "methionyl-transfer ribonucleic acid" EXACT [] +synonym: "methionyl-transfer RNA" EXACT [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000223 ! methionine_tRNA_primary_transcript + +[Term] +id: SO:0000267 +name: phenylalanyl_tRNA +def: "A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." [SO:ke] +synonym: "phenylalanyl tRNA" EXACT [] +synonym: "phenylalanyl-transfer ribonucleic acid" EXACT [] +synonym: "phenylalanyl-transfer RNA" EXACT [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000224 ! phenylalanine_tRNA_primary_transcript + +[Term] +id: SO:0000268 +name: prolyl_tRNA +def: "A tRNA sequence that has a proline anticodon, and a 3' proline binding region." [SO:ke] +synonym: "prolyl tRNA" EXACT [] +synonym: "prolyl-transfer ribonucleic acid" EXACT [] +synonym: "prolyl-transfer RNA" EXACT [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000225 ! proline_tRNA_primary_transcript + +[Term] +id: SO:0000269 +name: seryl_tRNA +def: "A tRNA sequence that has a serine anticodon, and a 3' serine binding region." [SO:ke] +synonym: "seryl tRNA" EXACT [] +synonym: "seryl-transfer ribonucleic acid" RELATED [] +synonym: "seryl-transfer RNA" EXACT [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000226 ! serine_tRNA_primary_transcript + +[Term] +id: SO:0000270 +name: threonyl_tRNA +def: "A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." [SO:ke] +synonym: "threonyl tRNA" EXACT [] +synonym: "threonyl-transfer ribonucleic acid" EXACT [] +synonym: "threonyl-transfer RNA" RELATED [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000227 ! threonine_tRNA_primary_transcript + +[Term] +id: SO:0000271 +name: tryptophanyl_tRNA +def: "A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." [SO:ke] +synonym: "tryptophanyl tRNA" EXACT [] +synonym: "tryptophanyl-transfer ribonucleic acid" EXACT [] +synonym: "tryptophanyl-transfer RNA" EXACT [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000228 ! tryptophan_tRNA_primary_transcript + +[Term] +id: SO:0000272 +name: tyrosyl_tRNA +def: "A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." [SO:ke] +synonym: "tyrosyl tRNA" EXACT [] +synonym: "tyrosyl-transfer ribonucleic acid" EXACT [] +synonym: "tyrosyl-transfer RNA" RELATED [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000229 ! tyrosine_tRNA_primary_transcript + +[Term] +id: SO:0000273 +name: valyl_tRNA +def: "A tRNA sequence that has a valine anticodon, and a 3' valine binding region." [SO:ke] +synonym: "valyl tRNA" EXACT [] +synonym: "valyl-transfer ribonucleic acid" EXACT [] +synonym: "valyl-transfer RNA" RELATED [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000230 ! valine_tRNA_primary_transcript + +[Term] +id: SO:0000274 +name: snRNA +def: "A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +subset: SOFA +synonym: "small nuclear RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/SnRNA "wiki" +is_a: SO:0000655 ! ncRNA +relationship: derives_from SO:0000231 ! snRNA_primary_transcript + +[Term] +id: SO:0000275 +name: snoRNA +def: "A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc] +subset: SOFA +synonym: "small nucleolar RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/SnoRNA "wiki" +is_a: SO:0000655 ! ncRNA +relationship: derives_from SO:0000232 ! snoRNA_primary_transcript + +[Term] +id: SO:0000276 +name: miRNA +alt_id: SO:0000649 +def: "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:11081512, PMID:12592000] +subset: SOFA +synonym: "micro RNA" EXACT [] +synonym: "microRNA" EXACT [] +synonym: "small temporal RNA" EXACT [] +synonym: "stRNA" EXACT [] +xref: http://en.wikipedia.org/wiki/MiRNA "wiki" +xref: http://en.wikipedia.org/wiki/StRNA "wiki" +is_a: SO:0000370 ! small_regulatory_ncRNA +relationship: part_of SO:0001244 ! pre_miRNA + +[Term] +id: SO:0000277 +name: bound_by_factor +def: "An attribute describing a sequence that is bound by another molecule." [SO:ke] +comment: Formerly called transcript_by_bound_factor. +synonym: "bound by factor" EXACT [] +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000278 +name: transcript_bound_by_nucleic_acid +def: "A transcript that is bound by a nucleic acid." [SO:xp] +comment: Formerly called transcript_by_bound_nucleic_acid. +synonym: "transcript bound by nucleic acid" EXACT [] +is_a: SO:0000673 ! transcript +relationship: has_quality SO:0000876 ! bound_by_nucleic_acid + +[Term] +id: SO:0000279 +name: transcript_bound_by_protein +def: "A transcript that is bound by a protein." [SO:xp] +comment: Formerly called transcript_by_bound_protein. +synonym: "transcript bound by protein" EXACT [] +is_a: SO:0000673 ! transcript +relationship: has_quality SO:0000875 ! bound_by_protein + +[Term] +id: SO:0000280 +name: engineered_gene +def: "A gene that is engineered." [SO:xp] +synonym: "engineered gene" EXACT [] +is_a: SO:0000704 ! gene +is_a: SO:0000804 ! engineered_region +relationship: has_quality SO:0000783 ! engineered + +[Term] +id: SO:0000281 +name: engineered_foreign_gene +def: "A gene that is engineered and foreign." [SO:xp] +synonym: "engineered foreign gene" EXACT [] +is_a: SO:0000280 ! engineered_gene +is_a: SO:0000285 ! foreign_gene +is_a: SO:0000805 ! engineered_foreign_region +relationship: has_quality SO:0000783 ! engineered +relationship: has_quality SO:0000784 ! foreign + +[Term] +id: SO:0000282 +name: mRNA_with_minus_1_frameshift +def: "An mRNA with a minus 1 frameshift." [SO:xp] +synonym: "mRNA with minus 1 frameshift" EXACT [] +is_a: SO:0000108 ! mRNA_with_frameshift +relationship: has_quality SO:0000866 ! minus_1_frameshift + +[Term] +id: SO:0000283 +name: engineered_foreign_transposable_element_gene +def: "A transposable_element that is engineered and foreign." [SO:xp] +synonym: "engineered foreign transposable element gene" EXACT [] +is_a: SO:0000111 ! transposable_element_gene +is_a: SO:0000281 ! engineered_foreign_gene +relationship: has_quality SO:0000783 ! engineered +relationship: has_quality SO:0000784 ! foreign + +[Term] +id: SO:0000284 +name: type_I_enzyme_restriction_site +def: "The recognition site is bipartite and interrupted." [http://www.promega.com] +is_obsolete: true + +[Term] +id: SO:0000285 +name: foreign_gene +def: "A gene that is foreign." [SO:xp] +synonym: "foreign gene" EXACT [] +is_a: SO:0000704 ! gene +relationship: has_quality SO:0000784 ! foreign + +[Term] +id: SO:0000286 +name: long_terminal_repeat +def: "A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +synonym: "direct terminal repeat" RELATED [] +synonym: "long terminal repeat" EXACT [] +synonym: "LTR" EXACT [] +xref: http://en.wikipedia.org/wiki/Long_terminal_repeat "wiki" +is_a: SO:0000657 ! repeat_region +relationship: part_of SO:0000186 ! LTR_retrotransposon + +[Term] +id: SO:0000287 +name: fusion_gene +def: "A gene that is a fusion." [SO:xp] +synonym: "fusion gene" EXACT [] +xref: http://en.wikipedia.org/wiki/Fusion_gene "wiki" +is_a: SO:0000704 ! gene +relationship: has_quality SO:0000806 ! fusion + +[Term] +id: SO:0000288 +name: engineered_fusion_gene +def: "A fusion gene that is engineered." [SO:xp] +synonym: "engineered fusion gene" EXACT [] +is_a: SO:0000280 ! engineered_gene +is_a: SO:0000287 ! fusion_gene +relationship: has_quality SO:0000783 ! engineered + +[Term] +id: SO:0000289 +name: microsatellite +def: "A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th] +subset: SOFA +synonym: "microsatellite locus" EXACT [] +synonym: "microsatellite marker" EXACT [] +synonym: "STR" EXACT [http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9651/] +xref: http://en.wikipedia.org/wiki/Microsatellite "wiki" +is_a: SO:0000005 ! satellite_DNA + +[Term] +id: SO:0000290 +name: dinucleotide_repeat_microsatellite_feature +synonym: "dinucleotide repeat microsatellite" EXACT [] +synonym: "dinucleotide repeat microsatellite feature" EXACT [] +synonym: "dinucleotide repeat microsatellite locus" EXACT [] +synonym: "dinucleotide repeat microsatellite marker" EXACT [] +is_a: SO:0000289 ! microsatellite + +[Term] +id: SO:0000291 +name: trinucleotide_repeat_microsatellite_feature +synonym: "dinucleotide repeat microsatellite marker" RELATED [] +synonym: "rinucleotide repeat microsatellite" EXACT [] +synonym: "trinucleotide repeat microsatellite feature" EXACT [] +synonym: "trinucleotide repeat microsatellite locus" EXACT [] +is_a: SO:0000289 ! microsatellite + +[Term] +id: SO:0000292 +name: repetitive_element +is_obsolete: true + +[Term] +id: SO:0000293 +name: engineered_foreign_repetitive_element +def: "A repetitive element that is engineered and foreign." [SO:xp] +synonym: "engineered foreign repetitive element" EXACT [] +is_a: SO:0000657 ! repeat_region +is_a: SO:0000805 ! engineered_foreign_region +relationship: has_quality SO:0000783 ! engineered +relationship: has_quality SO:0000784 ! foreign + +[Term] +id: SO:0000294 +name: inverted_repeat +def: "The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:ke] +subset: SOFA +synonym: "inverted repeat" EXACT [] +synonym: "inverted repeat sequence" EXACT [] +xref: http://en.wikipedia.org/wiki/Inverted_repeat "wiki" +is_a: SO:0000657 ! repeat_region + +[Term] +id: SO:0000295 +name: U12_intron +def: "A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511] +comment: May have either GT-AC or AT-AC 5' and 3' boundaries. +synonym: "U12 intron" EXACT [] +synonym: "U12-dependent intron" EXACT [] +is_a: SO:0000662 ! spliceosomal_intron + +[Term] +id: SO:0000296 +name: origin_of_replication +def: "The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +subset: SOFA +synonym: "ori" EXACT [] +synonym: "origin of replication" EXACT [] +xref: http://en.wikipedia.org/wiki/Origin_of_replication "wiki" +is_a: SO:0001411 ! biological_region +relationship: part_of SO:0001235 ! replicon + +[Term] +id: SO:0000297 +name: D_loop +def: "Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +synonym: "D-loop" EXACT [] +synonym: "displacement loop" RELATED [] +xref: http://en.wikipedia.org/wiki/D_loop "wiki" +is_a: SO:0000296 ! origin_of_replication + +[Term] +id: SO:0000298 +name: recombination_feature +synonym: "recombination feature" EXACT [] +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0000299 +name: specific_recombination_site +synonym: "specific recombination site" EXACT [] +is_a: SO:0000669 ! sequence_rearrangement_feature + +[Term] +id: SO:0000300 +name: recombination_feature_of_rearranged_gene +synonym: "recombination feature of rearranged gene" EXACT [] +is_a: SO:0000299 ! specific_recombination_site + +[Term] +id: SO:0000301 +name: vertebrate_immune_system_gene_recombination_feature +synonym: "vertebrate immune system gene recombination feature" EXACT [] +is_a: SO:0000300 ! recombination_feature_of_rearranged_gene + +[Term] +id: SO:0000302 +name: J_gene_recombination_feature +def: "Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "J gene recombination feature" EXACT [] +synonym: "J-RS" EXACT [] +is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature + +[Term] +id: SO:0000303 +name: clip +def: "Part of the primary transcript that is clipped off during processing." [SO:ke] +subset: SOFA +is_a: SO:0000835 ! primary_transcript_region + +[Term] +id: SO:0000304 +name: type_II_enzyme_restriction_site +def: "The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site." [http://www.promega.com] +is_obsolete: true + +[Term] +id: SO:0000305 +name: modified_DNA_base +def: "A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +comment: Modified base:. +subset: SOFA +synonym: "modified base site" EXACT [] +is_a: SO:0001236 ! base +is_a: SO:0001720 ! epigenetically_modified_region + +[Term] +id: SO:0000306 +name: methylated_DNA_base_feature +def: "A nucleotide modified by methylation." [SO:ke] +subset: SOFA +synonym: "methylated base feature" EXACT [] +is_a: SO:0000305 ! modified_DNA_base + +[Term] +id: SO:0000307 +name: CpG_island +def: "Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." [SO:rd] +subset: SOFA +synonym: "CG island" EXACT [] +synonym: "CpG island" EXACT [] +xref: http://en.wikipedia.org/wiki/CpG_island "wiki" +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0000308 +name: sequence_feature_locating_method +is_obsolete: true + +[Term] +id: SO:0000309 +name: computed_feature +is_obsolete: true + +[Term] +id: SO:0000310 +name: predicted_ab_initio_computation +is_obsolete: true + +[Term] +id: SO:0000311 +name: computed_feature_by_similarity +def: "." [SO:ma] +comment: similar to: +is_obsolete: true + +[Term] +id: SO:0000312 +name: experimentally_determined +def: "Attribute to describe a feature that has been experimentally verified." [SO:ke] +synonym: "experimentally determined" EXACT [] +is_a: SO:0000789 ! validated + +[Term] +id: SO:0000313 +name: stem_loop +alt_id: SO:0000019 +def: "A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +synonym: "RNA_hairpin_loop" EXACT [] +synonym: "stem loop" EXACT [] +synonym: "stem-loop" EXACT [] +xref: http://en.wikipedia.org/wiki/Stem_loop "wiki" +is_a: SO:0000122 ! RNA_sequence_secondary_structure + +[Term] +id: SO:0000314 +name: direct_repeat +def: "A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA." [SO:ke] +subset: SOFA +synonym: "direct repeat" EXACT [] +xref: http://en.wikipedia.org/wiki/Direct_repeat "wiki" +is_a: SO:0000657 ! repeat_region + +[Term] +id: SO:0000315 +name: TSS +def: "The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke] +subset: SOFA +synonym: "transcription start site" EXACT [] +synonym: "transcription_start_site" EXACT [] +is_a: SO:0000835 ! primary_transcript_region + +[Term] +id: SO:0000316 +name: CDS +def: "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma] +subset: SOFA +synonym: "coding sequence" EXACT [] +synonym: "coding_sequence" EXACT [] +is_a: SO:0000836 ! mRNA_region + +[Term] +id: SO:0000317 +name: cDNA_clone +def: "Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +synonym: "cDNA clone" EXACT [] +is_a: SO:0000151 ! clone +relationship: has_quality SO:0000756 ! cDNA + +[Term] +id: SO:0000318 +name: start_codon +def: "First codon to be translated by a ribosome." [SO:ke] +subset: SOFA +synonym: "initiation codon" EXACT [] +synonym: "start codon" EXACT [] +xref: http://en.wikipedia.org/wiki/Start_codon "wiki" +is_a: SO:0000360 ! codon + +[Term] +id: SO:0000319 +name: stop_codon +def: "In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke] +subset: SOFA +synonym: "stop codon" EXACT [] +xref: http://en.wikipedia.org/wiki/Stop_codon "wiki" +is_a: SO:0000360 ! codon + +[Term] +id: SO:0000320 +name: intronic_splice_enhancer +def: "Sequences within the intron that modulate splice site selection for some introns." [SO:ke] +synonym: "intronic splice enhancer" EXACT [] +is_a: SO:0000344 ! splice_enhancer +relationship: part_of SO:0000841 ! spliceosomal_intron_region + +[Term] +id: SO:0000321 +name: mRNA_with_plus_1_frameshift +def: "An mRNA with a plus 1 frameshift." [SO:ke] +synonym: "mRNA with plus 1 frameshift" EXACT [] +is_a: SO:0000108 ! mRNA_with_frameshift +relationship: has_quality SO:0000868 ! plus_1_frameshift + +[Term] +id: SO:0000322 +name: nuclease_hypersensitive_site +synonym: "nuclease hypersensitive site" EXACT [] +is_a: SO:0000684 ! nuclease_sensitive_site + +[Term] +id: SO:0000323 +name: coding_start +def: "The first base to be translated into protein." [SO:ke] +synonym: "coding start" EXACT [] +synonym: "translation initiation site" EXACT [] +synonym: "translation start" RELATED [] +is_a: SO:0000851 ! CDS_region + +[Term] +id: SO:0000324 +name: tag +def: "A nucleotide sequence that may be used to identify a larger sequence." [SO:ke] +subset: SOFA +is_a: SO:0000696 ! oligo + +[Term] +id: SO:0000325 +name: rRNA_large_subunit_primary_transcript +def: "A primary transcript encoding a large ribosomal subunit RNA." [SO:ke] +subset: SOFA +synonym: "35S rRNA primary transcript" EXACT [] +synonym: "rRNA large subunit primary transcript" EXACT [] +is_a: SO:0000209 ! rRNA_primary_transcript + +[Term] +id: SO:0000326 +name: SAGE_tag +def: "A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract] +subset: SOFA +synonym: "SAGE tag" EXACT [] +is_a: SO:0000324 ! tag + +[Term] +id: SO:0000327 +name: coding_end +def: "The last base to be translated into protein. It does not include the stop codon." [SO:ke] +synonym: "coding end" EXACT [] +synonym: "translation termination site" EXACT [] +synonym: "translation_end" EXACT [] +is_a: SO:0000851 ! CDS_region + +[Term] +id: SO:0000328 +name: microarray_oligo +synonym: "microarray oligo" EXACT [] +synonym: "microarray oligonucleotide" EXACT [] +is_a: SO:0000051 ! probe + +[Term] +id: SO:0000329 +name: mRNA_with_plus_2_frameshift +def: "An mRNA with a plus 2 frameshift." [SO:xp] +synonym: "mRNA with plus 2 frameshift" EXACT [] +is_a: SO:0000108 ! mRNA_with_frameshift +relationship: has_quality SO:0000869 ! plus_2_framshift + +[Term] +id: SO:0000330 +name: conserved_region +def: "Region of sequence similarity by descent from a common ancestor." [SO:ke] +subset: SOFA +synonym: "conserved region" EXACT [] +xref: http://en.wikipedia.org/wiki/Conserved_region "wiki" +is_a: SO:0001410 ! experimental_feature + +[Term] +id: SO:0000331 +name: STS +def: "Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com] +subset: SOFA +synonym: "sequence tag site" EXACT [] +is_a: SO:0000324 ! tag + +[Term] +id: SO:0000332 +name: coding_conserved_region +def: "Coding region of sequence similarity by descent from a common ancestor." [SO:ke] +subset: SOFA +synonym: "coding conserved region" EXACT [] +is_a: SO:0000330 ! conserved_region + +[Term] +id: SO:0000333 +name: exon_junction +def: "The boundary between two exons in a processed transcript." [SO:ke] +subset: SOFA +synonym: "exon junction" EXACT [] +is_a: SO:0000699 ! junction +relationship: part_of SO:0000233 ! mature_transcript + +[Term] +id: SO:0000334 +name: nc_conserved_region +def: "Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke] +subset: SOFA +synonym: "nc conserved region" EXACT [] +synonym: "noncoding conserved region" EXACT [] +is_a: SO:0000330 ! conserved_region + +[Term] +id: SO:0000335 +name: mRNA_with_minus_2_frameshift +def: "A mRNA with a minus 2 frameshift." [SO:ke] +synonym: "mRNA with minus 2 frameshift" EXACT [] +is_a: SO:0000108 ! mRNA_with_frameshift +relationship: has_quality SO:0000867 ! minus_2_frameshift + +[Term] +id: SO:0000336 +name: pseudogene +def: "A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html] +subset: SOFA +xref: http://en.wikipedia.org/wiki/Pseudogene "wiki" +is_a: SO:0001411 ! biological_region +relationship: non_functional_homolog_of SO:0000704 ! gene + +[Term] +id: SO:0000337 +name: RNAi_reagent +def: "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd] +subset: SOFA +synonym: "RNAi reagent" EXACT [] +is_a: SO:0000442 ! ds_oligo + +[Term] +id: SO:0000338 +name: MITE +def: "A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." [http://www.pnas.org/cgi/content/full/97/18/10083] +synonym: "miniature inverted repeat transposable element" EXACT [] +is_a: SO:0000208 ! terminal_inverted_repeat_element + +[Term] +id: SO:0000339 +name: recombination_hotspot +def: "A region in a genome which promotes recombination." [SO:rd] +synonym: "recombination hotspot" EXACT [] +xref: http://en.wikipedia.org/wiki/Recombination_hotspot "wiki" +is_a: SO:0000298 ! recombination_feature + +[Term] +id: SO:0000340 +name: chromosome +def: "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +subset: SOFA +xref: http://en.wikipedia.org/wiki/Chromosome "wiki" +is_a: SO:0001235 ! replicon + +[Term] +id: SO:0000341 +name: chromosome_band +def: "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma] +subset: SOFA +synonym: "chromosome band" EXACT [] +synonym: "cytoband" EXACT [] +synonym: "cytological band" EXACT [] +xref: http://en.wikipedia.org/wiki/Cytological_band "wiki" +is_a: SO:0000830 ! chromosome_part + +[Term] +id: SO:0000342 +name: site_specific_recombination_target_region +synonym: "site specific recombination target region" EXACT [] +is_a: SO:0000299 ! specific_recombination_site + +[Term] +id: SO:0000343 +name: match +def: "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke] +subset: SOFA +is_a: SO:0001410 ! experimental_feature + +[Term] +id: SO:0000344 +name: splice_enhancer +def: "Region of a transcript that regulates splicing." [SO:ke] +subset: SOFA +synonym: "splice enhancer" EXACT [] +is_a: SO:0000165 ! enhancer +is_a: SO:0001056 ! splicing_regulatory_region + +[Term] +id: SO:0000345 +name: EST +def: "A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +subset: SOFA +synonym: "expressed sequence tag" EXACT [] +is_a: SO:0000324 ! tag +relationship: derives_from SO:0000234 ! mRNA + +[Term] +id: SO:0000346 +name: loxP_site +synonym: "Cre-recombination target region" RELATED [] +synonym: "loxP site" EXACT [] +is_a: SO:0000947 ! resolution_site + +[Term] +id: SO:0000347 +name: nucleotide_match +def: "A match against a nucleotide sequence." [SO:ke] +subset: SOFA +synonym: "nucleotide match" EXACT [] +is_a: SO:0000343 ! match + +[Term] +id: SO:0000348 +name: nucleic_acid +def: "An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb] +synonym: "nucleic acid" EXACT [] +xref: http://en.wikipedia.org/wiki/Nucleic_acid "wiki" +is_a: SO:0000443 ! polymer_attribute + +[Term] +id: SO:0000349 +name: protein_match +def: "A match against a protein sequence." [SO:ke] +subset: SOFA +synonym: "protein match" EXACT [] +is_a: SO:0000343 ! match + +[Term] +id: SO:0000350 +name: FRT_site +def: "An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma] +synonym: "FLP recombination target region" EXACT [] +synonym: "FRT site" EXACT [] +is_a: SO:0000948 ! inversion_site + +[Term] +id: SO:0000351 +name: synthetic_sequence +def: "An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence." [SO:ma] +synonym: "synthetic sequence" EXACT [] +is_a: SO:0000443 ! polymer_attribute + +[Term] +id: SO:0000352 +name: DNA +def: "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone." [RSC:cb] +is_a: SO:0000348 ! nucleic_acid + +[Term] +id: SO:0000353 +name: sequence_assembly +def: "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma] +subset: SOFA +synonym: "sequence assembly" EXACT [] +xref: http://en.wikipedia.org/wiki/Sequence_assembly "wiki" +is_a: SO:0001248 ! assembly + +[Term] +id: SO:0000354 +name: group_1_intron_homing_endonuclease_target_region +def: "A region of intronic nucleotide sequence targeted by a nuclease enzyme." [SO:ke] +synonym: "group 1 intron homing endonuclease target region" EXACT [] +is_a: SO:0000684 ! nuclease_sensitive_site + +[Term] +id: SO:0000355 +name: haplotype_block +def: "A region of the genome which is co-inherited as the result of the lack of historic recombination within it." [SO:ma] +synonym: "haplotype block" EXACT [] +is_a: SO:0000298 ! recombination_feature + +[Term] +id: SO:0000356 +name: RNA +def: "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone." [RSC:cb] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +is_a: SO:0000348 ! nucleic_acid + +[Term] +id: SO:0000357 +name: flanked +def: "An attribute describing a region that is bounded either side by a particular kind of region." [SO:ke] +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000359 +name: floxed +def: "An attribute describing sequence that is flanked by Lox-P sites." [SO:ke] +xref: http://en.wikipedia.org/wiki/Floxed "wiki" +is_a: SO:0000357 ! flanked + +[Term] +id: SO:0000360 +name: codon +def: "A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke] +subset: SOFA +xref: http://en.wikipedia.org/wiki/Codon "wiki" +is_a: SO:0000851 ! CDS_region + +[Term] +id: SO:0000361 +name: FRT_flanked +def: "An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT." [SO:ke] +synonym: "FRT flanked" EXACT [] +is_a: SO:0000357 ! flanked + +[Term] +id: SO:0000362 +name: invalidated_by_chimeric_cDNA +def: "A cDNA clone constructed from more than one mRNA. Usually an experimental artifact." [SO:ma] +synonym: "invalidated by chimeric cDNA" EXACT [] +is_a: SO:0000790 ! invalidated + +[Term] +id: SO:0000363 +name: floxed_gene +def: "A transgene that is floxed." [SO:xp] +synonym: "floxed gene" EXACT [] +is_a: SO:0000902 ! transgene +relationship: has_quality SO:0000359 ! floxed + +[Term] +id: SO:0000364 +name: transposable_element_flanking_region +def: "The region of sequence surrounding a transposable element." [SO:ke] +synonym: "transposable element flanking region" EXACT [] +is_a: SO:0000239 ! flanking_region + +[Term] +id: SO:0000365 +name: integron +def: "A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site." [SO:as] +xref: http://en.wikipedia.org/wiki/Integron "wiki" +is_a: SO:0001039 ! integrated_mobile_genetic_element + +[Term] +id: SO:0000366 +name: insertion_site +def: "The junction where an insertion occurred." [SO:ke] +subset: SOFA +synonym: "insertion site" EXACT [] +is_a: SO:0000699 ! junction + +[Term] +id: SO:0000367 +name: attI_site +def: "A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as] +synonym: "attI site" EXACT [] +is_a: SO:0000946 ! integration_excision_site +relationship: part_of SO:0000365 ! integron + +[Term] +id: SO:0000368 +name: transposable_element_insertion_site +def: "The junction in a genome where a transposable_element has inserted." [SO:ke] +subset: SOFA +synonym: "transposable element insertion site" EXACT [] +is_a: SO:0000366 ! insertion_site + +[Term] +id: SO:0000369 +name: integrase_coding_region +is_obsolete: true + +[Term] +id: SO:0000370 +name: small_regulatory_ncRNA +def: "A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma] +subset: SOFA +synonym: "small regulatory ncRNA" EXACT [] +is_a: SO:0000655 ! ncRNA + +[Term] +id: SO:0000371 +name: conjugative_transposon +def: "A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html] +synonym: "conjugative transposon" EXACT [] +is_a: SO:0000182 ! DNA_transposon + +[Term] +id: SO:0000372 +name: enzymatic_RNA +def: "An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb] +comment: This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts. +subset: SOFA +synonym: "enzymatic RNA" EXACT [] +is_a: SO:0000673 ! transcript +relationship: has_quality SO:0001185 ! enzymatic + +[Term] +id: SO:0000373 +name: recombinationally_inverted_gene +def: "A recombinationally rearranged gene by inversion." [SO:xp] +synonym: "recombinationally inverted gene" EXACT [] +is_a: SO:0000456 ! recombinationally_rearranged_gene +relationship: has_quality SO:1000036 ! inversion + +[Term] +id: SO:0000374 +name: ribozyme +def: "An RNA with catalytic activity." [SO:ma] +subset: SOFA +xref: http://en.wikipedia.org/wiki/Ribozyme "wiki" +is_a: SO:0000372 ! enzymatic_RNA +relationship: has_quality SO:0001186 ! ribozymic + +[Term] +id: SO:0000375 +name: rRNA_5_8S +def: "5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002] +subset: SOFA +synonym: "5.8S LSU rRNA" EXACT [] +synonym: "5.8S ribosomal RNA" EXACT [] +synonym: "5.8S rRNA" EXACT [] +synonym: "rRNA 5 8S" EXACT [] +xref: http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA "wiki" +is_a: SO:0000651 ! large_subunit_rRNA + +[Term] +id: SO:0000376 +name: RNA_6S +def: "A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013] +synonym: "6S RNA" EXACT [] +synonym: "RNA 6S" EXACT [] +xref: http://en.wikipedia.org/wiki/6S_RNA "wiki" +is_a: SO:0000370 ! small_regulatory_ncRNA + +[Term] +id: SO:0000377 +name: CsrB_RsmB_RNA +def: "An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018] +synonym: "CsrB RsmB RNA" EXACT [] +synonym: "CsrB-RsmB RNA" EXACT [] +is_a: SO:0000370 ! small_regulatory_ncRNA + +[Term] +id: SO:0000378 +name: DsrA_RNA +def: "DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014] +synonym: "DsrA RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/DsrA_RNA "wiki" +is_a: SO:0000370 ! small_regulatory_ncRNA + +[Term] +id: SO:0000379 +name: GcvB_RNA +def: "A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022] +synonym: "GcvB RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/GcvB_RNA "wiki" +is_a: SO:0000378 ! DsrA_RNA + +[Term] +id: SO:0000380 +name: hammerhead_ribozyme +def: "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [PMID:2436805] +subset: SOFA +synonym: "hammerhead ribozyme" EXACT [] +xref: http://en.wikipedia.org/wiki/Hammerhead_ribozyme "wiki" +is_a: SO:0000715 ! RNA_motif +relationship: has_quality SO:0001186 ! ribozymic + +[Term] +id: SO:0000381 +name: group_IIA_intron +synonym: "group IIA intron" EXACT [] +is_a: SO:0000603 ! group_II_intron + +[Term] +id: SO:0000382 +name: group_IIB_intron +synonym: "group IIB intron" EXACT [] +is_a: SO:0000603 ! group_II_intron + +[Term] +id: SO:0000383 +name: MicF_RNA +def: "A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033] +synonym: "MicF RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/MicF_RNA "wiki" +is_a: SO:0000644 ! antisense_RNA + +[Term] +id: SO:0000384 +name: OxyS_RNA +def: "A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035] +synonym: "OxyS RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/OxyS_RNA "wiki" +is_a: SO:0000370 ! small_regulatory_ncRNA + +[Term] +id: SO:0000385 +name: RNase_MRP_RNA +def: "The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030] +subset: SOFA +synonym: "RNase MRP RNA" EXACT [] +is_a: SO:0000655 ! ncRNA + +[Term] +id: SO:0000386 +name: RNase_P_RNA +def: "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010] +subset: SOFA +synonym: "RNase P RNA" EXACT [] +is_a: SO:0000655 ! ncRNA + +[Term] +id: SO:0000387 +name: RprA_RNA +def: "Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034] +synonym: "RprA RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/RprA_RNA "wiki" +is_a: SO:0000370 ! small_regulatory_ncRNA + +[Term] +id: SO:0000388 +name: RRE_RNA +def: "The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036] +synonym: "RRE RNA" EXACT [] +is_a: SO:0000370 ! small_regulatory_ncRNA + +[Term] +id: SO:0000389 +name: spot_42_RNA +def: "A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021] +synonym: "spot-42 RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/Spot_42_RNA "wiki" +is_a: SO:0000370 ! small_regulatory_ncRNA + +[Term] +id: SO:0000390 +name: telomerase_RNA +def: "The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025] +subset: SOFA +synonym: "telomerase RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/Telomerase_RNA "wiki" +is_a: SO:0000655 ! ncRNA + +[Term] +id: SO:0000391 +name: U1_snRNA +def: "U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003] +subset: SOFA +synonym: "small nuclear RNA U1" EXACT [RSC:cb] +synonym: "snRNA U1" EXACT [RSC:cb] +synonym: "U1 small nuclear RNA" EXACT [RSC:cb] +synonym: "U1 snRNA" EXACT [] +xref: http://en.wikipedia.org/wiki/U1_snRNA "wiki" +is_a: SO:0000274 ! snRNA + +[Term] +id: SO:0000392 +name: U2_snRNA +def: "U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004] +subset: SOFA +synonym: "small nuclear RNA U2" EXACT [RSC:CB] +synonym: "snRNA U2" EXACT [RSC:CB] +synonym: "U2 small nuclear RNA" EXACT [RSC:CB] +synonym: "U2 snRNA" EXACT [] +xref: http://en.wikipedia.org/wiki/U2_snRNA "wiki" +is_a: SO:0000274 ! snRNA + +[Term] +id: SO:0000393 +name: U4_snRNA +def: "U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015] +subset: SOFA +synonym: "small nuclear RNA U4" EXACT [RSC:cb] +synonym: "snRNA U4" EXACT [RSC:cb] +synonym: "U4 small nuclear RNA" EXACT [RSC:cb] +synonym: "U4 snRNA" EXACT [] +xref: http://en.wikipedia.org/wiki/U4_snRNA "wiki" +is_a: SO:0000274 ! snRNA + +[Term] +id: SO:0000394 +name: U4atac_snRNA +def: "An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455] +subset: SOFA +synonym: "small nuclear RNA U4atac" EXACT [RSC:cb] +synonym: "snRNA U4atac" EXACT [RSC:cb] +synonym: "U4atac small nuclear RNA" EXACT [RSC:cb] +synonym: "U4atac snRNA" EXACT [] +is_a: SO:0000274 ! snRNA + +[Term] +id: SO:0000395 +name: U5_snRNA +def: "U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020] +subset: SOFA +synonym: "small nuclear RNA U5" EXACT [RSC:cb] +synonym: "snRNA U5" EXACT [RSC:cb] +synonym: "U5 small nuclear RNA" EXACT [RSC:cb] +synonym: "U5 snRNA" EXACT [] +xref: http://en.wikipedia.org/wiki/U5_snRNA "wiki" +is_a: SO:0000274 ! snRNA + +[Term] +id: SO:0000396 +name: U6_snRNA +def: "U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015] +subset: SOFA +synonym: "small nuclear RNA U6" EXACT [RSC:cb] +synonym: "snRNA U6" EXACT [RSC:cb] +synonym: "U6 small nuclear RNA" EXACT [RSC:cb] +synonym: "U6 snRNA" EXACT [] +xref: http://en.wikipedia.org/wiki/U6_snRNA "wiki" +is_a: SO:0000274 ! snRNA + +[Term] +id: SO:0000397 +name: U6atac_snRNA +def: "U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract] +subset: SOFA +synonym: "snRNA U6atac" EXACT [RSC:cb] +synonym: "U6atac small nuclear RNA" EXACT [RSC:cb] +synonym: "U6atac snRNA" EXACT [RSC:cb] +is_a: SO:0000274 ! snRNA + +[Term] +id: SO:0000398 +name: U11_snRNA +def: "U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129] +subset: SOFA +synonym: "small nuclear RNA U11" EXACT [RSC:cb] +synonym: "snRNA U11" EXACT [RSC:cb] +synonym: "U11 small nuclear RNA" EXACT [RSC:cb] +synonym: "U11 snRNA" EXACT [] +xref: http://en.wikipedia.org/wiki/U11_snRNA "wiki" +is_a: SO:0000274 ! snRNA + +[Term] +id: SO:0000399 +name: U12_snRNA +def: "The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007] +subset: SOFA +synonym: "small nuclear RNA U12" EXACT [RSC:cb] +synonym: "snRNA U12" EXACT [RSC:cb] +synonym: "U12 small nuclear RNA" EXACT [RSC:cb] +synonym: "U12 snRNA" EXACT [] +xref: http://en.wikipedia.org/wiki/U12_snRNA "wiki" +is_a: SO:0000274 ! snRNA + +[Term] +id: SO:0000400 +name: sequence_attribute +def: "An attribute describes a quality of sequence." [SO:ke] +synonym: "sequence attribute" EXACT [] + +[Term] +id: SO:0000401 +name: gene_attribute +synonym: "gene attribute" EXACT [] +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000402 +name: enhancer_attribute +is_obsolete: true + +[Term] +id: SO:0000403 +name: U14_snoRNA +alt_id: SO:0005839 +def: "U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119] +comment: An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA. +subset: SOFA +synonym: "small nucleolar RNA U14" EXACT [] +synonym: "snoRNA U14" EXACT [] +synonym: "U14 small nucleolar RNA" EXACT [] +synonym: "U14 snoRNA" EXACT [] +is_a: SO:0000593 ! C_D_box_snoRNA +relationship: derives_from SO:0005837 ! U14_snoRNA_primary_transcript + +[Term] +id: SO:0000404 +name: vault_RNA +def: "A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006] +subset: SOFA +synonym: "vault RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/Vault_RNA "wiki" +is_a: SO:0000655 ! ncRNA + +[Term] +id: SO:0000405 +name: Y_RNA +def: "Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019] +subset: SOFA +synonym: "Y RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/Y_RNA "wiki" +is_a: SO:0000655 ! ncRNA + +[Term] +id: SO:0000406 +name: twintron +def: "An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908] +xref: http://en.wikipedia.org/wiki/Twintron "wiki" +is_a: SO:0000188 ! intron + +[Term] +id: SO:0000407 +name: rRNA_18S +def: "A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke] +subset: SOFA +synonym: "18S ribosomal RNA" EXACT [] +synonym: "18S rRNA" EXACT [] +synonym: "rRNA 18S" EXACT [] +xref: http://en.wikipedia.org/wiki/18S_ribosomal_RNA "wiki" +is_a: SO:0000650 ! small_subunit_rRNA + +[Term] +id: SO:0000408 +name: site +def: "The interbase position where something (eg an aberration) occurred." [SO:ke] +is_obsolete: true + +[Term] +id: SO:0000409 +name: binding_site +alt_id: BS:00033 +def: "A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke] +comment: See GO:0005488 : binding. +subset: biosapiens +subset: SOFA +synonym: "binding_or_interaction_site" EXACT [] +synonym: "site" RELATED [] +xref: http://en.wikipedia.org/wiki/Binding_site "wiki" +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0000410 +name: protein_binding_site +def: "A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke] +comment: See GO:0042277 : peptide binding. +subset: SOFA +synonym: "protein binding site" EXACT [] +is_a: SO:0000409 ! binding_site + +[Term] +id: SO:0000411 +name: rescue_region +def: "A region that rescues." [SO:xp] +synonym: "rescue fragment" EXACT [] +synonym: "rescue region" EXACT [] +synonym: "rescue segment" RELATED [] +is_a: SO:0000695 ! reagent +relationship: has_quality SO:0000814 ! rescue + +[Term] +id: SO:0000412 +name: restriction_fragment +def: "A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke] +subset: SOFA +synonym: "restriction fragment" EXACT [] +xref: http://en.wikipedia.org/wiki/Restriction_fragment "wiki" +is_a: SO:0000143 ! assembly_component + +[Term] +id: SO:0000413 +name: sequence_difference +def: "A region where the sequence differs from that of a specified sequence." [SO:ke] +subset: SOFA +synonym: "sequence difference" EXACT [] +is_a: SO:0000700 ! remark + +[Term] +id: SO:0000414 +name: invalidated_by_genomic_contamination +def: "An attribute to describe a feature that is invalidated due to genomic contamination." [SO:ke] +synonym: "invalidated by genomic contamination" EXACT [] +is_a: SO:0000790 ! invalidated + +[Term] +id: SO:0000415 +name: invalidated_by_genomic_polyA_primed_cDNA +def: "An attribute to describe a feature that is invalidated due to polyA priming." [SO:ke] +synonym: "invalidated by genomic polyA primed cDNA" EXACT [] +is_a: SO:0000790 ! invalidated + +[Term] +id: SO:0000416 +name: invalidated_by_partial_processing +def: "An attribute to describe a feature that is invalidated due to partial processing." [SO:ke] +synonym: "invalidated by partial processing" EXACT [] +is_a: SO:0000790 ! invalidated + +[Term] +id: SO:0000417 +name: polypeptide_domain +alt_id: BS:00012 +alt_id: BS:00134 +alt_id: SO:0001069 +def: "A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR] +comment: Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains. +subset: biosapiens +synonym: "domain" BROAD BS [uniprot:feature_type] +synonym: "polypeptide domain" EXACT [] +synonym: "polypeptide_structural_domain" EXACT BS [] +synonym: "structural domain" BROAD BS [] +is_a: SO:0001070 ! polypeptide_structural_region +is_a: SO:0100021 ! polypeptide_conserved_region + +[Term] +id: SO:0000418 +name: signal_peptide +alt_id: BS:00159 +def: "The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +comment: Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence. +subset: biosapiens +subset: SOFA +synonym: "signal" RELATED [uniprot:feature_type] +synonym: "signal peptide" EXACT [] +synonym: "signal peptide coding sequence" EXACT [] +xref: http://en.wikipedia.org/wiki/Signal_peptide "wiki" +is_a: SO:0001527 ! peptide_localization_signal +relationship: part_of SO:0001062 ! propeptide + +[Term] +id: SO:0000419 +name: mature_protein_region +alt_id: BS:00149 +def: "The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb] +comment: This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification. +subset: biosapiens +subset: SOFA +synonym: "chain" RELATED [uniprot:feature_type] +synonym: "mature peptide" RELATED [] +synonym: "mature protein region" EXACT [] +is_a: SO:0000839 ! polypeptide_region +relationship: part_of SO:0001063 ! immature_peptide_region + +[Term] +id: SO:0000420 +name: five_prime_terminal_inverted_repeat +synonym: "5' TIR" EXACT [] +synonym: "five prime terminal inverted repeat" EXACT [] +is_a: SO:0000481 ! terminal_inverted_repeat + +[Term] +id: SO:0000421 +name: three_prime_terminal_inverted_repeat +synonym: "3' TIR" EXACT [] +synonym: "three prime terminal inverted repeat" EXACT [] +is_a: SO:0000481 ! terminal_inverted_repeat + +[Term] +id: SO:0000422 +name: U5_LTR_region +synonym: "U5 long terminal repeat region" EXACT [] +synonym: "U5 LTR region" EXACT [] +is_a: SO:0000848 ! LTR_component + +[Term] +id: SO:0000423 +name: R_LTR_region +synonym: "R long terminal repeat region" EXACT [] +synonym: "R LTR region" EXACT [] +is_a: SO:0000848 ! LTR_component + +[Term] +id: SO:0000424 +name: U3_LTR_region +synonym: "U3 long terminal repeat region" EXACT [] +synonym: "U3 LTR region" EXACT [] +is_a: SO:0000848 ! LTR_component + +[Term] +id: SO:0000425 +name: five_prime_LTR +synonym: "5' long terminal repeat" EXACT [] +synonym: "5' LTR" EXACT [] +synonym: "five prime LTR" EXACT [] +is_a: SO:0000286 ! long_terminal_repeat + +[Term] +id: SO:0000426 +name: three_prime_LTR +synonym: "3' long terminal repeat" EXACT [] +synonym: "3' LTR" EXACT [] +synonym: "three prime LTR" EXACT [] +is_a: SO:0000286 ! long_terminal_repeat + +[Term] +id: SO:0000427 +name: R_five_prime_LTR_region +synonym: "R 5' long term repeat region" EXACT [] +synonym: "R five prime LTR region" EXACT [] +is_a: SO:0000423 ! R_LTR_region +is_a: SO:0000850 ! five_prime_LTR_component + +[Term] +id: SO:0000428 +name: U5_five_prime_LTR_region +synonym: "U5 5' long terminal repeat region" EXACT [] +synonym: "U5 five prime LTR region" EXACT [] +is_a: SO:0000422 ! U5_LTR_region +is_a: SO:0000850 ! five_prime_LTR_component + +[Term] +id: SO:0000429 +name: U3_five_prime_LTR_region +synonym: "U3 5' long term repeat region" EXACT [] +synonym: "U3 five prime LTR region" EXACT [] +is_a: SO:0000424 ! U3_LTR_region +is_a: SO:0000850 ! five_prime_LTR_component + +[Term] +id: SO:0000430 +name: R_three_prime_LTR_region +synonym: "R 3' long terminal repeat region" EXACT [] +synonym: "R three prime LTR region" EXACT [] +is_a: SO:0000849 ! three_prime_LTR_component + +[Term] +id: SO:0000431 +name: U3_three_prime_LTR_region +synonym: "U3 3' long terminal repeat region" EXACT [] +synonym: "U3 three prime LTR region" EXACT [] +is_a: SO:0000849 ! three_prime_LTR_component + +[Term] +id: SO:0000432 +name: U5_three_prime_LTR_region +synonym: "U5 3' long terminal repeat region" EXACT [] +synonym: "U5 three prime LTR region" EXACT [] +is_a: SO:0000849 ! three_prime_LTR_component + +[Term] +id: SO:0000433 +name: non_LTR_retrotransposon_polymeric_tract +def: "A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke] +synonym: "non LTR retrotransposon polymeric tract" EXACT [] +is_a: SO:0000657 ! repeat_region +is_a: SO:0000840 ! repeat_component +relationship: part_of SO:0000189 ! non_LTR_retrotransposon + +[Term] +id: SO:0000434 +name: target_site_duplication +def: "A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion." [http://www.koko.gov.my/CocoaBioTech/Glossaryt.html] +synonym: "target site duplication" EXACT [] +is_a: SO:0000314 ! direct_repeat +relationship: derives_from SO:0000101 ! transposable_element + +[Term] +id: SO:0000435 +name: RR_tract +def: "A polypurine tract within an LTR_retrotransposon." [SO:ke] +synonym: "LTR retrotransposon poly purine tract" RELATED [] +synonym: "RR tract" EXACT [] +is_a: SO:0000330 ! conserved_region +relationship: part_of SO:0000186 ! LTR_retrotransposon + +[Term] +id: SO:0000436 +name: ARS +def: "A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma] +subset: SOFA +synonym: "autonomously replicating sequence" EXACT [] +is_a: SO:0000296 ! origin_of_replication + +[Term] +id: SO:0000437 +name: assortment_derived_duplication +is_obsolete: true + +[Term] +id: SO:0000438 +name: gene_not_polyadenylated +is_obsolete: true + +[Term] +id: SO:0000439 +name: inverted_ring_chromosome +synonym: "inverted ring chromosome" EXACT [] +is_a: SO:1000030 ! chromosomal_inversion +is_a: SO:1000045 ! ring_chromosome + +[Term] +id: SO:0000440 +name: vector_replicon +def: "A replicon that has been modified to act as a vector for foreign sequence." [SO:ma] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +synonym: "vector" EXACT [] +synonym: "vector replicon" EXACT [] +xref: http://en.wikipedia.org/wiki/Vector_(molecular_biology) "wiki" +is_a: SO:0001235 ! replicon +relationship: part_of SO:0000151 ! clone + +[Term] +id: SO:0000441 +name: ss_oligo +def: "A single stranded oligonucleotide." [SO:ke] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +subset: SOFA +synonym: "single strand oligo" EXACT [] +synonym: "single strand oligonucleotide" EXACT [] +synonym: "single stranded oligonucleotide" EXACT [] +synonym: "ss oligo" EXACT [] +synonym: "ss oligonucleotide" EXACT [] +is_a: SO:0000696 ! oligo + +[Term] +id: SO:0000442 +name: ds_oligo +def: "A double stranded oligonucleotide." [SO:ke] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +subset: SOFA +synonym: "double stranded oligonucleotide" EXACT [] +synonym: "ds oligo" EXACT [] +synonym: "ds-oligonucleotide" EXACT [] +is_a: SO:0000696 ! oligo + +[Term] +id: SO:0000443 +name: polymer_attribute +def: "An attribute to describe the kind of biological sequence." [SO:ke] +synonym: "polymer attribute" EXACT [] +is_a: SO:0000400 ! sequence_attribute + +[Term] +id: SO:0000444 +name: three_prime_noncoding_exon +def: "Non-coding exon in the 3' UTR." [SO:ke] +synonym: "three prime noncoding exon" EXACT [] +is_a: SO:0000198 ! noncoding_exon + +[Term] +id: SO:0000445 +name: five_prime_noncoding_exon +def: "Non-coding exon in the 5' UTR." [SO:ke] +synonym: "5' nc exon" EXACT [] +synonym: "5' non coding exon" EXACT [] +synonym: "five prime noncoding exon" EXACT [] +is_a: SO:0000198 ! noncoding_exon + +[Term] +id: SO:0000446 +name: UTR_intron +def: "Intron located in the untranslated region." [SO:ke] +synonym: "UTR intron" EXACT [] +is_a: SO:0000188 ! intron + +[Term] +id: SO:0000447 +name: five_prime_UTR_intron +def: "An intron located in the 5' UTR." [SO:ke] +synonym: "five prime UTR intron" EXACT [] +is_a: SO:0000446 ! UTR_intron + +[Term] +id: SO:0000448 +name: three_prime_UTR_intron +def: "An intron located in the 3' UTR." [SO:ke] +synonym: "three prime UTR intron" EXACT [] +is_a: SO:0000446 ! UTR_intron + +[Term] +id: SO:0000449 +name: random_sequence +def: "A sequence of nucleotides or amino acids which, by design, has a \"random\" order of components, given a predetermined input frequency of these components." [SO:ma] +synonym: "random sequence" EXACT [] +is_a: SO:0000351 ! synthetic_sequence + +[Term] +id: SO:0000450 +name: interband +def: "A light region between two darkly staining bands in a polytene chromosome." [SO:ma] +synonym: "chromosome interband" RELATED [] +is_a: SO:0000830 ! chromosome_part + +[Term] +id: SO:0000451 +name: gene_with_polyadenylated_mRNA +def: "A gene that encodes a polyadenylated mRNA." [SO:xp] +synonym: "gene with polyadenylated mRNA" EXACT [] +is_a: SO:0001217 ! protein_coding_gene +relationship: transcribed_to SO:0000871 ! polyadenylated_mRNA + +[Term] +id: SO:0000452 +name: transgene_attribute +is_obsolete: true + +[Term] +id: SO:0000453 +name: chromosomal_transposition +def: "A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke] +synonym: "chromosomal transposition" EXACT [] +synonym: "transposition" NARROW [] +is_a: SO:1000183 ! chromosome_structure_variation + +[Term] +id: SO:0000454 +name: rasiRNA +def: "A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284] +subset: SOFA +synonym: "repeat associated small interfering RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/RasiRNA "wiki" +is_a: SO:0000655 ! ncRNA + +[Term] +id: SO:0000455 +name: gene_with_mRNA_with_frameshift +def: "A gene that encodes an mRNA with a frameshift." [SO:xp] +synonym: "gene with mRNA with frameshift" EXACT [] +is_a: SO:0001217 ! protein_coding_gene +relationship: has_quality SO:0000865 ! frameshift + +[Term] +id: SO:0000456 +name: recombinationally_rearranged_gene +def: "A gene that is recombinationally rearranged." [SO:ke] +synonym: "recombinationally rearranged gene" EXACT [] +is_a: SO:0000704 ! gene +relationship: has_quality SO:0000940 ! recombinationally_rearranged + +[Term] +id: SO:0000457 +name: interchromosomal_duplication +def: "A chromosome duplication involving an insertion from another chromosome." [SO:ke] +synonym: "interchromosomal duplication" EXACT [] +is_a: SO:1000037 ! chromosomal_duplication + +[Term] +id: SO:0000458 +name: D_gene_segment +def: "Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "D gene" EXACT [] +synonym: "D-GENE" EXACT [] +is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment + +[Term] +id: SO:0000459 +name: gene_with_trans_spliced_transcript +def: "A gene with a transcript that is trans-spliced." [SO:xp] +synonym: "gene with trans spliced transcript" EXACT [] +is_a: SO:0000704 ! gene +relationship: transcribed_to SO:0000479 ! trans_spliced_transcript + +[Term] +id: SO:0000460 +name: vertebrate_immunoglobulin_T_cell_receptor_segment +comment: I am using the term segment instead of gene here to avoid confusion with the region 'gene'. +synonym: "vertebrate immunoglobulin T cell receptor segment" EXACT [] +synonym: "vertebrate_immunoglobulin/T-cell receptor gene" EXACT [] +is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature + +[Term] +id: SO:0000461 +name: inversion_derived_bipartite_deficiency +def: "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km] +synonym: "inversion derived bipartite deficiency" EXACT [] +is_a: SO:1000029 ! chromosomal_deletion + +[Term] +id: SO:0000462 +name: pseudogenic_region +def: "A non-functional descendant of a functional entity." [SO:cjm] +subset: SOFA +synonym: "pseudogenic region" EXACT [] +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0000463 +name: encodes_alternately_spliced_transcripts +def: "A gene that encodes more than one transcript." [SO:ke] +synonym: "encodes alternately spliced transcripts" EXACT [] +is_a: SO:0000401 ! gene_attribute + +[Term] +id: SO:0000464 +name: decayed_exon +def: "A non-functional descendant of an exon." [SO:ke] +comment: Does not have to be part of a pseudogene. +subset: SOFA +synonym: "decayed exon" EXACT [] +is_a: SO:0000462 ! pseudogenic_region +relationship: non_functional_homolog_of SO:0000147 ! exon + +[Term] +id: SO:0000465 +name: inversion_derived_deficiency_plus_duplication +def: "A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km] +synonym: "inversion derived deficiency plus duplication" EXACT [] +is_a: SO:1000029 ! chromosomal_deletion +is_a: SO:1000038 ! intrachromosomal_duplication + +[Term] +id: SO:0000466 +name: V_gene_segment +def: "Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V gene" EXACT [] +synonym: "V-GENE" EXACT [] +synonym: "variable_gene" EXACT [] +is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment + +[Term] +id: SO:0000467 +name: post_translationally_regulated_by_protein_stability +def: "An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein." [SO:ke] +synonym: "post translationally regulated by protein stability" EXACT [] +synonym: "post-translationally regulated by protein stability" EXACT [] +is_a: SO:0000130 ! post_translationally_regulated + +[Term] +id: SO:0000468 +name: golden_path_fragment +def: "One of the pieces of sequence that make up a golden path." [SO:rd] +subset: SOFA +synonym: "golden path fragment" EXACT [] +is_a: SO:0000143 ! assembly_component +relationship: part_of SO:0000688 ! golden_path + +[Term] +id: SO:0000469 +name: post_translationally_regulated_by_protein_modification +def: "An attribute describing a gene sequence where the resulting protein is modified to regulate it." [SO:ke] +synonym: "post translationally regulated by protein modification" EXACT [] +synonym: "post-translationally regulated by protein modification" EXACT [] +is_a: SO:0000130 ! post_translationally_regulated + +[Term] +id: SO:0000470 +name: J_gene_segment +def: "Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "J gene" EXACT [] +synonym: "J-GENE" EXACT [] +is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment + +[Term] +id: SO:0000471 +name: autoregulated +def: "The gene product is involved in its own transcriptional regulation." [SO:ke] +is_a: SO:0000123 ! transcriptionally_regulated + +[Term] +id: SO:0000472 +name: tiling_path +def: "A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm] +subset: SOFA +synonym: "tiling path" EXACT [] +is_a: SO:0000353 ! sequence_assembly + +[Term] +id: SO:0000473 +name: negatively_autoregulated +def: "The gene product is involved in its own transcriptional regulation where it decreases transcription." [SO:ke] +synonym: "negatively autoregulated" EXACT [] +is_a: SO:0000126 ! transcriptionally_repressed +is_a: SO:0000471 ! autoregulated + +[Term] +id: SO:0000474 +name: tiling_path_fragment +def: "A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke] +subset: SOFA +synonym: "tiling path fragment" EXACT [] +is_a: SO:0000143 ! assembly_component +relationship: part_of SO:0000472 ! tiling_path + +[Term] +id: SO:0000475 +name: positively_autoregulated +def: "The gene product is involved in its own transcriptional regulation, where it increases transcription." [SO:ke] +synonym: "positively autoregulated" EXACT [] +is_a: SO:0000125 ! transcriptionally_induced +is_a: SO:0000471 ! autoregulated + +[Term] +id: SO:0000476 +name: contig_read +def: "A DNA sequencer read which is part of a contig." [SO:ke] +synonym: "contig read" EXACT [] +is_a: SO:0000150 ! read + +[Term] +id: SO:0000477 +name: polycistronic_gene +def: "A gene that is polycistronic." [SO:ke] +is_obsolete: true + +[Term] +id: SO:0000478 +name: C_gene_segment +def: "Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "C gene" EXACT [] +synonym: "C_GENE" EXACT [] +synonym: "constant gene" EXACT [] +is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment + +[Term] +id: SO:0000479 +name: trans_spliced_transcript +def: "A transcript that is trans-spliced." [SO:xp] +synonym: "trans spliced transcript" EXACT [] +synonym: "trans-spliced transcript" EXACT [] +is_a: SO:0000673 ! transcript +relationship: has_quality SO:0000870 ! trans_spliced + +[Term] +id: SO:0000480 +name: tiling_path_clone +def: "A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke] +synonym: "tiling path clone" EXACT [] +is_a: SO:0000151 ! clone +is_a: SO:0000474 ! tiling_path_fragment + +[Term] +id: SO:0000481 +name: terminal_inverted_repeat +def: "An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke] +synonym: "terminal inverted repeat" EXACT [] +synonym: "TIR" EXACT [] +is_a: SO:0000294 ! inverted_repeat +relationship: part_of SO:0000208 ! terminal_inverted_repeat_element + +[Term] +id: SO:0000482 +name: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster +synonym: "vertebrate immunoglobulin T cell receptor gene cluster" EXACT [] +synonym: "vertebrate_immunoglobulin/T-cell receptor gene cluster" EXACT [] +is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature + +[Term] +id: SO:0000483 +name: nc_primary_transcript +def: "A primary transcript that is never translated into a protein." [SO:ke] +subset: SOFA +synonym: "nc primary transcript" EXACT [] +synonym: "noncoding primary transcript" EXACT [] +is_a: SO:0000185 ! primary_transcript + +[Term] +id: SO:0000484 +name: three_prime_coding_exon_noncoding_region +def: "The sequence of the 3' exon that is not coding." [SO:ke] +subset: SOFA +synonym: "three prime coding exon noncoding region" EXACT [] +synonym: "three_prime_exon_noncoding_region" EXACT [] +is_a: SO:0001214 ! noncoding_region_of_exon +relationship: part_of SO:0000202 ! three_prime_coding_exon + +[Term] +id: SO:0000485 +name: DJ_J_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "(DJ)-J-CLUSTER" EXACT [] +synonym: "DJ J cluster" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000572 ! DJ_gene_segment + +[Term] +id: SO:0000486 +name: five_prime_coding_exon_noncoding_region +def: "The sequence of the 5' exon preceding the start codon." [SO:ke] +subset: SOFA +synonym: "five prime coding exon noncoding region" EXACT [] +synonym: "five_prime_exon_noncoding_region" EXACT [] +is_a: SO:0001214 ! noncoding_region_of_exon +relationship: part_of SO:0000200 ! five_prime_coding_exon + +[Term] +id: SO:0000487 +name: VDJ_J_C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "(VDJ)-J-C-CLUSTER" EXACT [] +synonym: "VDJ J C cluster" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000478 ! C_gene_segment +relationship: has_part SO:0000574 ! VDJ_gene_segment + +[Term] +id: SO:0000488 +name: VDJ_J_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "(VDJ)-J-CLUSTER" EXACT [] +synonym: "VDJ J cluster" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000574 ! VDJ_gene_segment + +[Term] +id: SO:0000489 +name: VJ_C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "(VJ)-C-CLUSTER" RELATED [] +synonym: "VJ C cluster" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000478 ! C_gene_segment +relationship: has_part SO:0000576 ! VJ_gene_segment + +[Term] +id: SO:0000490 +name: VJ_J_C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "(VJ)-J-C-CLUSTER" EXACT [] +synonym: "VJ J C cluster" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000478 ! C_gene_segment +relationship: has_part SO:0000576 ! VJ_gene_segment + +[Term] +id: SO:0000491 +name: VJ_J_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "(VJ)-J-CLUSTER" EXACT [] +synonym: "VJ J cluster" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000576 ! VJ_gene_segment + +[Term] +id: SO:0000492 +name: D_gene_recombination_feature +synonym: "D gene recombination feature" EXACT [] +is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature + +[Term] +id: SO:0000493 +name: three_prime_D_heptamer +def: "7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "3'D-HEPTAMER" EXACT [] +synonym: "three prime D heptamer" EXACT [] +is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene +relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence + +[Term] +id: SO:0000494 +name: three_prime_D_nonamer +def: "A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "3'D-NOMAMER" EXACT [] +synonym: "three prime D nonamer" EXACT [] +is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene +relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence + +[Term] +id: SO:0000495 +name: three_prime_D_spacer +def: "A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "3'D-SPACER" EXACT [] +synonym: "three prime D spacer" EXACT [] +is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer +relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence + +[Term] +id: SO:0000496 +name: five_prime_D_heptamer +def: "7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "5'D-HEPTAMER" EXACT [] +synonym: "five prime D heptamer" EXACT [] +is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene +relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence + +[Term] +id: SO:0000497 +name: five_prime_D_nonamer +def: "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "5'D-NONAMER" EXACT [] +synonym: "five prime D nonamer" EXACT [] +is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene +relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence + +[Term] +id: SO:0000498 +name: five_prime_D_spacer +def: "12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "5'-SPACER" EXACT [] +synonym: "five prime D spacer" EXACT [] +synonym: "five prime D-spacer" EXACT [] +is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer +relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence + +[Term] +id: SO:0000499 +name: virtual_sequence +def: "A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke] +subset: SOFA +synonym: "virtual sequence" EXACT [] +is_a: SO:0000353 ! sequence_assembly + +[Term] +id: SO:0000500 +name: Hoogsteen_base_pair +def: "A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds." [PMID:12177293] +synonym: "Hoogsteen base pair" EXACT [] +xref: http://en.wikipedia.org/wiki/Hoogsteen_base_pair "wiki" +is_a: SO:0000028 ! base_pair + +[Term] +id: SO:0000501 +name: reverse_Hoogsteen_base_pair +def: "A type of non-canonical base-pairing." [SO:ke] +synonym: "reverse Hoogsteen base pair" EXACT [] +is_a: SO:0000028 ! base_pair + +[Term] +id: SO:0000502 +name: transcribed_region +def: "A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes." [SO:ke] +comment: This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being. +subset: SOFA +is_obsolete: true + +[Term] +id: SO:0000503 +name: alternately_spliced_gene_encodeing_one_transcript +is_obsolete: true + +[Term] +id: SO:0000504 +name: D_DJ_C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "D DJ C cluster" EXACT [] +synonym: "D-(DJ)-C-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000458 ! D_gene_segment +relationship: has_part SO:0000478 ! C_gene_segment +relationship: has_part SO:0000572 ! DJ_gene_segment + +[Term] +id: SO:0000505 +name: D_DJ_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "D DJ cluster" EXACT [] +synonym: "D-(DJ)-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000458 ! D_gene_segment +relationship: has_part SO:0000572 ! DJ_gene_segment + +[Term] +id: SO:0000506 +name: D_DJ_J_C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "D DJ J C cluster" EXACT [] +synonym: "D-(DJ)-J-C-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000458 ! D_gene_segment +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000478 ! C_gene_segment +relationship: has_part SO:0000572 ! DJ_gene_segment + +[Term] +id: SO:0000507 +name: pseudogenic_exon +def: "A non functional descendant of an exon, part of a pseudogene." [SO:ke] +comment: This is the analog of the exon of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations. +synonym: "pseudogenic exon" EXACT [] +is_a: SO:0000462 ! pseudogenic_region +relationship: non_functional_homolog_of SO:0000147 ! exon +relationship: part_of SO:0000516 ! pseudogenic_transcript + +[Term] +id: SO:0000508 +name: D_DJ_J_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "D DJ J cluster" EXACT [] +synonym: "D-(DJ)-J-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000458 ! D_gene_segment +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000572 ! DJ_gene_segment + +[Term] +id: SO:0000509 +name: D_J_C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "D J C cluster" EXACT [] +synonym: "D-J-C-CLUSTER" EXACT [] +is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster +relationship: has_part SO:0000458 ! D_gene_segment +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000478 ! C_gene_segment + +[Term] +id: SO:0000510 +name: VD_gene_segment +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V_D_GENE" EXACT [] +synonym: "VD gene" EXACT [] +is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment + +[Term] +id: SO:0000511 +name: J_C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "J C cluster" EXACT [] +synonym: "J-C-CLUSTER" EXACT [] +is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000478 ! C_gene_segment + +[Term] +id: SO:0000512 +name: inversion_derived_deficiency_plus_aneuploid +def: "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km] +synonym: "inversion derived deficiency plus aneuploid" EXACT [] +is_a: SO:1000029 ! chromosomal_deletion + +[Term] +id: SO:0000513 +name: J_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "J cluster" EXACT [] +synonym: "J-CLUSTER" EXACT [] +is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster +relationship: has_part SO:0000470 ! J_gene_segment + +[Term] +id: SO:0000514 +name: J_nonamer +def: "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "J nonamer" EXACT [] +synonym: "J-NONAMER" EXACT [] +is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene +relationship: part_of SO:0000302 ! J_gene_recombination_feature + +[Term] +id: SO:0000515 +name: J_heptamer +def: "7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "J heptamer" EXACT [] +synonym: "J-HEPTAMER" EXACT [] +is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene +relationship: part_of SO:0000302 ! J_gene_recombination_feature + +[Term] +id: SO:0000516 +name: pseudogenic_transcript +def: "A non functional descendant of a transcript, part of a pseudogene." [SO:ke] +comment: This is the analog of the transcript of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations. +synonym: "pseudogenic transcript" EXACT [] +is_a: SO:0000462 ! pseudogenic_region +relationship: non_functional_homolog_of SO:0000673 ! transcript +relationship: part_of SO:0000336 ! pseudogene + +[Term] +id: SO:0000517 +name: J_spacer +def: "12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "J spacer" EXACT [] +synonym: "J-SPACER" EXACT [] +is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer +relationship: part_of SO:0000302 ! J_gene_recombination_feature + +[Term] +id: SO:0000518 +name: V_DJ_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V DJ cluster" EXACT [] +synonym: "V-(DJ)-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000572 ! DJ_gene_segment + +[Term] +id: SO:0000519 +name: V_DJ_J_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V DJ J cluster" EXACT [] +synonym: "V-(DJ)-J-CLUSTER" RELATED [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000572 ! DJ_gene_segment + +[Term] +id: SO:0000520 +name: V_VDJ_C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V VDJ C cluster" EXACT [] +synonym: "V-(VDJ)-C-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000478 ! C_gene_segment +relationship: has_part SO:0000574 ! VDJ_gene_segment + +[Term] +id: SO:0000521 +name: V_VDJ_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V VDJ cluster" EXACT [] +synonym: "V-(VDJ)-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000574 ! VDJ_gene_segment + +[Term] +id: SO:0000522 +name: V_VDJ_J_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V VDJ J cluster" EXACT [] +synonym: "V-(VDJ)-J-CLUSTER" RELATED [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000574 ! VDJ_gene_segment + +[Term] +id: SO:0000523 +name: V_VJ_C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V VJ C cluster" EXACT [] +synonym: "V-(VJ)-C-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000478 ! C_gene_segment +relationship: has_part SO:0000576 ! VJ_gene_segment + +[Term] +id: SO:0000524 +name: V_VJ_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V VJ cluster" EXACT [] +synonym: "V-(VJ)-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000576 ! VJ_gene_segment + +[Term] +id: SO:0000525 +name: V_VJ_J_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V VJ J cluster" EXACT [] +synonym: "V-(VJ)-J-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000576 ! VJ_gene_segment + +[Term] +id: SO:0000526 +name: V_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V cluster" EXACT [] +synonym: "V-CLUSTER" EXACT [] +is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster +relationship: has_part SO:0000466 ! V_gene_segment + +[Term] +id: SO:0000527 +name: V_D_DJ_C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V D DJ C cluster" EXACT [] +synonym: "V-D-(DJ)-C-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000458 ! D_gene_segment +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000478 ! C_gene_segment +relationship: has_part SO:0000572 ! DJ_gene_segment + +[Term] +id: SO:0000528 +name: V_D_DJ_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V D DJ cluster" EXACT [] +synonym: "V-D-(DJ)-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000458 ! D_gene_segment +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000572 ! DJ_gene_segment + +[Term] +id: SO:0000529 +name: V_D_DJ_J_C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V D DJ J C cluster" EXACT [] +synonym: "V-D-(DJ)-J-C-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000458 ! D_gene_segment +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000478 ! C_gene_segment +relationship: has_part SO:0000572 ! DJ_gene_segment + +[Term] +id: SO:0000530 +name: V_D_DJ_J_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V D DJ J cluster" EXACT [] +synonym: "V-D-(DJ)-J-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000458 ! D_gene_segment +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000572 ! DJ_gene_segment + +[Term] +id: SO:0000531 +name: V_D_J_C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V D J C cluster" EXACT [] +synonym: "V-D-J-C-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000458 ! D_gene_segment +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000478 ! C_gene_segment + +[Term] +id: SO:0000532 +name: V_D_J_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V D J cluster" EXACT [] +synonym: "V-D-J-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000458 ! D_gene_segment +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000470 ! J_gene_segment + +[Term] +id: SO:0000533 +name: V_heptamer +def: "7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V heptamer" EXACT [] +synonym: "V-HEPTAMER" EXACT [] +is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene +relationship: part_of SO:0000538 ! V_gene_recombination_feature + +[Term] +id: SO:0000534 +name: V_J_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V J cluster" EXACT [] +synonym: "V-J-CLUSTER" EXACT [] +is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000470 ! J_gene_segment + +[Term] +id: SO:0000535 +name: V_J_C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V J C cluster" EXACT [] +synonym: "V-J-C-CLUSTER" EXACT [] +is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000478 ! C_gene_segment + +[Term] +id: SO:0000536 +name: V_nonamer +def: "9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V nonamer" EXACT [] +synonym: "V-NONAMER" EXACT [] +is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene +relationship: part_of SO:0000538 ! V_gene_recombination_feature + +[Term] +id: SO:0000537 +name: V_spacer +def: "12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V spacer" EXACT [] +synonym: "V-SPACER" EXACT [] +is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer +relationship: part_of SO:0000538 ! V_gene_recombination_feature + +[Term] +id: SO:0000538 +name: V_gene_recombination_feature +def: "Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V gene recombination feature" EXACT [] +synonym: "V-RS" EXACT [] +is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature + +[Term] +id: SO:0000539 +name: DJ_C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "(DJ)-C-CLUSTER" EXACT [] +synonym: "DJ C cluster" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000478 ! C_gene_segment +relationship: has_part SO:0000572 ! DJ_gene_segment + +[Term] +id: SO:0000540 +name: DJ_J_C_cluster +def: "Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "(DJ)-J-C-CLUSTER" EXACT [] +synonym: "DJ J C cluster" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000478 ! C_gene_segment +relationship: has_part SO:0000572 ! DJ_gene_segment + +[Term] +id: SO:0000541 +name: VDJ_C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "(VDJ)-C-CLUSTER" EXACT [] +synonym: "VDJ C cluster" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000478 ! C_gene_segment +relationship: has_part SO:0000574 ! VDJ_gene_segment + +[Term] +id: SO:0000542 +name: V_DJ_C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V DJ C cluster" EXACT [] +synonym: "V-(DJ)-C-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000478 ! C_gene_segment +relationship: has_part SO:0000572 ! DJ_gene_segment + +[Term] +id: SO:0000543 +name: alternately_spliced_gene_encoding_greater_than_one_transcript +is_obsolete: true + +[Term] +id: SO:0000544 +name: helitron +def: "A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569] +synonym: "ISCR" RELATED [] +xref: http://en.wikipedia.org/wiki/Helitron "wiki" +is_a: SO:0000182 ! DNA_transposon + +[Term] +id: SO:0000545 +name: recoding_pseudoknot +def: "The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937] +synonym: "recoding pseudoknot" EXACT [] +is_a: SO:0000591 ! pseudoknot +relationship: part_of SO:1001268 ! recoding_stimulatory_region + +[Term] +id: SO:0000546 +name: designed_sequence +synonym: "designed sequence" EXACT [] +is_a: SO:0000351 ! synthetic_sequence + +[Term] +id: SO:0000547 +name: inversion_derived_bipartite_duplication +def: "A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km] +synonym: "inversion derived bipartite duplication" EXACT [] +is_a: SO:1000038 ! intrachromosomal_duplication + +[Term] +id: SO:0000548 +name: gene_with_edited_transcript +def: "A gene that encodes a transcript that is edited." [SO:xp] +synonym: "gene with edited transcript" EXACT [] +is_a: SO:0001217 ! protein_coding_gene +relationship: transcribed_to SO:0000873 ! edited_transcript + +[Term] +id: SO:0000549 +name: inversion_derived_duplication_plus_aneuploid +def: "A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km] +synonym: "inversion derived duplication plus aneuploid" EXACT [] +is_a: SO:1000038 ! intrachromosomal_duplication + +[Term] +id: SO:0000550 +name: aneuploid_chromosome +def: "A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke] +comment: Examples are Nullo-4, Haplo-4 and triplo-4 in Drosophila. +synonym: "aneuploid chromosome" EXACT [] +is_a: SO:1000183 ! chromosome_structure_variation + +[Term] +id: SO:0000551 +name: polyA_signal_sequence +def: "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +subset: SOFA +synonym: "poly(A) signal" EXACT [] +synonym: "polyA signal sequence" EXACT [] +synonym: "polyadenylation termination signal" EXACT [] +is_a: SO:0001679 ! transcription_regulatory_region + +[Term] +id: SO:0000552 +name: Shine_Dalgarno_sequence +def: "A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh] +comment: Not found in Eukaryotic sequence. +synonym: "five prime ribosome binding site" EXACT [] +synonym: "RBS" RELATED [] +synonym: "Shine Dalgarno sequence" EXACT [] +synonym: "Shine-Dalgarno sequence" EXACT [] +xref: http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence "wiki" +is_a: SO:0000139 ! ribosome_entry_site + +[Term] +id: SO:0000553 +name: polyA_site +alt_id: SO:0001430 +def: "The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +subset: SOFA +synonym: "polyA cleavage site" EXACT [] +synonym: "polyA junction" EXACT [] +synonym: "polyA site" EXACT [] +synonym: "polyA_junction" EXACT [] +synonym: "polyadenylation site" RELATED [] +is_a: SO:0000699 ! junction +relationship: part_of SO:0000205 ! three_prime_UTR +relationship: part_of SO:0000233 ! mature_transcript + +[Term] +id: SO:0000554 +name: assortment_derived_deficiency_plus_duplication +is_obsolete: true + +[Term] +id: SO:0000555 +name: five_prime_clip +def: "5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +synonym: "5' clip" RELATED [] +synonym: "five prime clip" EXACT [] +is_a: SO:0000303 ! clip + +[Term] +id: SO:0000556 +name: five_prime_D_recombination_signal_sequence +def: "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "5'RS" EXACT [] +synonym: "five prime D recombination signal sequence" EXACT [] +synonym: "five prime D-recombination signal sequence" EXACT [] +is_a: SO:0000492 ! D_gene_recombination_feature + +[Term] +id: SO:0000557 +name: three_prime_clip +def: "3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +synonym: "3'-clip" EXACT [] +synonym: "three prime clip" EXACT [] +is_a: SO:0000303 ! clip + +[Term] +id: SO:0000558 +name: C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "C cluster" EXACT [] +synonym: "C-CLUSTER" EXACT [] +is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster +relationship: has_part SO:0000478 ! C_gene_segment + +[Term] +id: SO:0000559 +name: D_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "D cluster" EXACT [] +synonym: "D-CLUSTER" EXACT [] +is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster +relationship: has_part SO:0000458 ! D_gene_segment + +[Term] +id: SO:0000560 +name: D_J_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "D J cluster" EXACT [] +synonym: "D-J-CLUSTER" EXACT [] +is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster +relationship: has_part SO:0000458 ! D_gene_segment +relationship: has_part SO:0000470 ! J_gene_segment + +[Term] +id: SO:0000561 +name: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene +def: "Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "HEPTAMER" RELATED [] +synonym: "heptamer of recombination feature of vertebrate immune system gene" EXACT [] +is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature + +[Term] +id: SO:0000562 +name: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene +synonym: "nonamer of recombination feature of vertebrate immune system gene" EXACT [] +is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature + +[Term] +id: SO:0000563 +name: vertebrate_immune_system_gene_recombination_spacer +synonym: "vertebrate immune system gene recombination spacer" EXACT [] +is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature + +[Term] +id: SO:0000564 +name: V_DJ_J_C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V DJ J C cluster" EXACT [] +synonym: "V-(DJ)-J-C-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000478 ! C_gene_segment +relationship: has_part SO:0000572 ! DJ_gene_segment + +[Term] +id: SO:0000565 +name: V_VDJ_J_C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V VDJ J C cluster" EXACT [] +synonym: "V-(VDJ)-J-C-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000478 ! C_gene_segment +relationship: has_part SO:0000574 ! VDJ_gene_segment + +[Term] +id: SO:0000566 +name: V_VJ_J_C_cluster +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V VJ J C cluster" EXACT [] +synonym: "V-(VJ)-J-C-CLUSTER" EXACT [] +is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +relationship: has_part SO:0000466 ! V_gene_segment +relationship: has_part SO:0000470 ! J_gene_segment +relationship: has_part SO:0000478 ! C_gene_segment +relationship: has_part SO:0000576 ! VJ_gene_segment + +[Term] +id: SO:0000567 +name: inversion_derived_aneuploid_chromosome +def: "A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km] +synonym: "inversion derived aneuploid chromosome" EXACT [] +is_a: SO:0000550 ! aneuploid_chromosome + +[Term] +id: SO:0000568 +name: bidirectional_promoter +def: "An unregulated promoter that allows continuous expression." [SO:ke] +synonym: "bidirectional promoter" EXACT [] +is_a: SO:0000167 ! promoter + +[Term] +id: SO:0000569 +name: retrotransposed +alt_id: SO:0100042 +def: "An attribute of a feature that occurred as the product of a reverse transcriptase mediated event." [SO:ke] +comment: GO:0003964 RNA-directed DNA polymerase activity. +xref: http://en.wikipedia.org/wiki/Retrotransposed "wiki" +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000570 +name: three_prime_D_recombination_signal_sequence +def: "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "3'D-RS" EXACT [] +synonym: "three prime D recombination signal sequence" EXACT [] +synonym: "three_prime_D-recombination_signal_sequence" EXACT [] +is_a: SO:0000492 ! D_gene_recombination_feature + +[Term] +id: SO:0000571 +name: miRNA_encoding +synonym: "miRNA encoding" EXACT [] +is_a: SO:0000011 ! non_protein_coding + +[Term] +id: SO:0000572 +name: DJ_gene_segment +def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "D-J-GENE" EXACT [] +synonym: "DJ gene" EXACT [] +is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment + +[Term] +id: SO:0000573 +name: rRNA_encoding +synonym: "rRNA encoding" EXACT [] +is_a: SO:0000011 ! non_protein_coding + +[Term] +id: SO:0000574 +name: VDJ_gene_segment +def: "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V-D-J-GENE" EXACT [] +synonym: "VDJ gene" EXACT [] +is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment + +[Term] +id: SO:0000575 +name: scRNA_encoding +synonym: "scRNA encoding" EXACT [] +is_a: SO:0000011 ! non_protein_coding + +[Term] +id: SO:0000576 +name: VJ_gene_segment +def: "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] +synonym: "V-J-GENE" EXACT [] +synonym: "VJ gene" EXACT [] +is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment + +[Term] +id: SO:0000577 +name: centromere +def: "A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke] +subset: SOFA +xref: http://en.wikipedia.org/wiki/Centromere "wiki" +is_a: SO:0000628 ! chromosomal_structural_element + +[Term] +id: SO:0000578 +name: snoRNA_encoding +synonym: "snoRNA encoding" EXACT [] +is_a: SO:0000011 ! non_protein_coding + +[Term] +id: SO:0000579 +name: edited_transcript_feature +def: "A locatable feature on a transcript that is edited." [SO:ma] +synonym: "edited transcript feature" EXACT [] +is_a: SO:0000833 ! transcript_region + +[Term] +id: SO:0000580 +name: methylation_guide_snoRNA_primary_transcript +def: "A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke] +synonym: "methylation guide snoRNA primary transcript" EXACT [] +is_a: SO:0000232 ! snoRNA_primary_transcript + +[Term] +id: SO:0000581 +name: cap +def: "A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html] +subset: SOFA +xref: http://en.wikipedia.org/wiki/5%27_cap "wiki" +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0000582 +name: rRNA_cleavage_snoRNA_primary_transcript +def: "A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke] +synonym: "rRNA cleavage snoRNA primary transcript" EXACT [] +is_a: SO:0000232 ! snoRNA_primary_transcript + +[Term] +id: SO:0000583 +name: pre_edited_region +def: "The region of a transcript that will be edited." [http://dna.kdna.ucla.edu/rna/index.aspx] +synonym: "pre edited region" EXACT [] +synonym: "pre-edited region" EXACT [] +is_a: SO:0000579 ! edited_transcript_feature + +[Term] +id: SO:0000584 +name: tmRNA +def: "A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023] +synonym: "10Sa RNA" RELATED [] +synonym: "ssrA" RELATED [] +xref: http://en.wikipedia.org/wiki/TmRNA "wiki" +is_a: SO:0000370 ! small_regulatory_ncRNA + +[Term] +id: SO:0000585 +name: C_D_box_snoRNA_encoding +synonym: "C/D box snoRNA encoding" EXACT [] +is_a: SO:0000578 ! snoRNA_encoding + +[Term] +id: SO:0000586 +name: tmRNA_primary_transcript +def: "A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke] +synonym: "10Sa RNA primary transcript" RELATED [] +synonym: "ssrA RNA primary transcript" RELATED [] +synonym: "tmRNA primary transcript" EXACT [] +is_a: SO:0000483 ! nc_primary_transcript + +[Term] +id: SO:0000587 +name: group_I_intron +def: "Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028] +comment: GO:0000372. +subset: SOFA +synonym: "group I intron" EXACT [] +xref: http://en.wikipedia.org/wiki/Group_I_intron "wiki" +is_a: SO:0000588 ! autocatalytically_spliced_intron + +[Term] +id: SO:0000588 +name: autocatalytically_spliced_intron +def: "A self spliced intron." [SO:ke] +subset: SOFA +synonym: "autocatalytically spliced intron" EXACT [] +is_a: SO:0000188 ! intron +relationship: has_quality SO:0001186 ! ribozymic + +[Term] +id: SO:0000589 +name: SRP_RNA_primary_transcript +def: "A primary transcript encoding a signal recognition particle RNA." [SO:ke] +synonym: "SRP RNA primary transcript" EXACT [] +is_a: SO:0000483 ! nc_primary_transcript + +[Term] +id: SO:0000590 +name: SRP_RNA +def: "The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017] +subset: SOFA +synonym: "7S RNA" RELATED [] +synonym: "signal recognition particle RNA" RELATED [] +synonym: "SRP RNA" EXACT [] +is_a: SO:0000655 ! ncRNA +relationship: derives_from SO:0000589 ! SRP_RNA_primary_transcript + +[Term] +id: SO:0000591 +name: pseudoknot +def: "A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop." [RSC:cb] +xref: http://en.wikipedia.org/wiki/Pseudoknot "wiki" +is_a: SO:0000002 ! sequence_secondary_structure + +[Term] +id: SO:0000592 +name: H_pseudoknot +def: "A pseudoknot which contains two stems and at least two loops." [http://www.ncbi.nlm.nih.gov\:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract] +synonym: "classical pseudoknot" EXACT [] +synonym: "H pseudoknot" EXACT [] +synonym: "H-pseudoknot" EXACT [] +synonym: "H-type pseudoknot" EXACT [] +synonym: "hairpin-type pseudoknot" EXACT [] +is_a: SO:0000591 ! pseudoknot + +[Term] +id: SO:0000593 +name: C_D_box_snoRNA +def: "Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html] +subset: SOFA +synonym: "box C/D snoRNA" EXACT [] +synonym: "C D box snoRNA" EXACT [] +synonym: "C/D box snoRNA" EXACT [] +is_a: SO:0000275 ! snoRNA +relationship: derives_from SO:0000595 ! C_D_box_snoRNA_primary_transcript + +[Term] +id: SO:0000594 +name: H_ACA_box_snoRNA +def: "Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html] +synonym: "box H/ACA snoRNA" EXACT [] +synonym: "H ACA box snoRNA" EXACT [] +synonym: "H/ACA box snoRNA" EXACT [] +is_a: SO:0000275 ! snoRNA +relationship: derives_from SO:0000596 ! H_ACA_box_snoRNA_primary_transcript + +[Term] +id: SO:0000595 +name: C_D_box_snoRNA_primary_transcript +def: "A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke] +synonym: "C/D box snoRNA primary transcript" EXACT [] +is_a: SO:0000232 ! snoRNA_primary_transcript + +[Term] +id: SO:0000596 +name: H_ACA_box_snoRNA_primary_transcript +def: "A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke] +synonym: "H ACA box snoRNA primary transcript" EXACT [] +is_a: SO:0000232 ! snoRNA_primary_transcript + +[Term] +id: SO:0000597 +name: transcript_edited_by_U_insertion/deletion +def: "The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa." [http://www.rna.ucla.edu/index.html] +is_obsolete: true + +[Term] +id: SO:0000598 +name: edited_by_C_insertion_and_dinucleotide_insertion +synonym: "transcript_edited_by_C-insertion_and_dinucleotide_insertion" RELATED [] +is_obsolete: true + +[Term] +id: SO:0000599 +name: edited_by_C_to_U_substitution +is_obsolete: true + +[Term] +id: SO:0000600 +name: edited_by_A_to_I_substitution +is_obsolete: true + +[Term] +id: SO:0000601 +name: edited_by_G_addition +is_obsolete: true + +[Term] +id: SO:0000602 +name: guide_RNA +def: "A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html] +subset: SOFA +synonym: "gRNA" EXACT [] +synonym: "guide RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/Guide_RNA "wiki" +is_a: SO:0000655 ! ncRNA + +[Term] +id: SO:0000603 +name: group_II_intron +def: "Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron to intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml] +comment: GO:0000373. +subset: SOFA +synonym: "group II intron" EXACT [] +xref: http://en.wikipedia.org/wiki/Group_II_intron "wiki" +is_a: SO:0000588 ! autocatalytically_spliced_intron + +[Term] +id: SO:0000604 +name: editing_block +def: "Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx] +synonym: "editing block" EXACT [] +is_a: SO:0000579 ! edited_transcript_feature + +[Term] +id: SO:0000605 +name: intergenic_region +def: "A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome." [SO:cjm] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +subset: SOFA +synonym: "intergenic region" EXACT [] +xref: http://en.wikipedia.org/wiki/Intergenic_region "wiki" +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0000606 +name: editing_domain +def: "Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx] +synonym: "editing domain" EXACT [] +is_a: SO:0000579 ! edited_transcript_feature + +[Term] +id: SO:0000607 +name: unedited_region +def: "The region of an edited transcript that will not be edited." [http://dna.kdna.ucla.edu/rna/index.aspx] +synonym: "unedited region" EXACT [] +is_a: SO:0000579 ! edited_transcript_feature + +[Term] +id: SO:0000608 +name: H_ACA_box_snoRNA_encoding +synonym: "H ACA box snoRNA encoding" EXACT [] +is_a: SO:0000578 ! snoRNA_encoding + +[Term] +id: SO:0000609 +name: oligo_U_tail +def: "The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602)." [http://www.rna.ucla.edu/] +synonym: "oligo U tail" EXACT [] +is_a: SO:0001411 ! biological_region +relationship: adjacent_to SO:0000602 ! guide_RNA + +[Term] +id: SO:0000610 +name: polyA_sequence +def: "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke] +subset: SOFA +synonym: "polyA sequence" EXACT [] +is_a: SO:0001411 ! biological_region +relationship: adjacent_to SO:0000234 ! mRNA + +[Term] +id: SO:0000611 +name: branch_site +def: "A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke] +subset: SOFA +synonym: "branch point" EXACT [] +synonym: "branch site" EXACT [] +synonym: "branch_point" EXACT [] +is_a: SO:0000841 ! spliceosomal_intron_region + +[Term] +id: SO:0000612 +name: polypyrimidine_tract +def: "The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888] +subset: SOFA +synonym: "polypyrimidine tract" EXACT [] +xref: http://en.wikipedia.org/wiki/Polypyrimidine_tract "wiki" +is_a: SO:0000841 ! spliceosomal_intron_region + +[Term] +id: SO:0000613 +name: bacterial_RNApol_promoter +def: "A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke] +synonym: "bacterial RNApol promoter" EXACT [] +is_a: SO:0000752 ! gene_group_regulatory_region +is_a: SO:0001203 ! RNA_polymerase_promoter + +[Term] +id: SO:0000614 +name: bacterial_terminator +def: "A terminator signal for bacterial transcription." [SO:ke] +synonym: "bacterial terminator" EXACT [] +is_a: SO:0000141 ! terminator +is_a: SO:0000752 ! gene_group_regulatory_region + +[Term] +id: SO:0000615 +name: terminator_of_type_2_RNApol_III_promoter +def: "A terminator signal for RNA polymerase III transcription." [SO:ke] +synonym: "terminator of type 2 RNApol III promoter" EXACT [] +is_a: SO:0000951 ! eukaryotic_terminator + +[Term] +id: SO:0000616 +name: transcription_end_site +def: "The base where transcription ends." [SO:ke] +subset: SOFA +synonym: "transcription end site" EXACT [] +is_a: SO:0000835 ! primary_transcript_region + +[Term] +id: SO:0000617 +name: RNApol_III_promoter_type_1 +synonym: "RNApol III promoter type 1" EXACT [] +is_a: SO:0000171 ! RNApol_III_promoter + +[Term] +id: SO:0000618 +name: RNApol_III_promoter_type_2 +synonym: "RNApol III promoter type 2" EXACT [] +synonym: "tRNA promoter" RELATED [] +is_a: SO:0000171 ! RNApol_III_promoter + +[Term] +id: SO:0000619 +name: A_box +def: "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke] +comment: Binds TFIIIC. +synonym: "A-box" EXACT [] +xref: http://en.wikipedia.org/wiki/A-box "wiki" +is_a: SO:0001660 ! core_promoter_element + +[Term] +id: SO:0000620 +name: B_box +def: "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke] +comment: Binds TFIIIC. +synonym: "B-box" EXACT [] +is_a: SO:0001660 ! core_promoter_element +relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2 + +[Term] +id: SO:0000621 +name: RNApol_III_promoter_type_3 +synonym: "RNApol III promoter type 3" EXACT [] +is_a: SO:0000171 ! RNApol_III_promoter + +[Term] +id: SO:0000622 +name: C_box +def: "An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke] +synonym: "C-box" EXACT [] +is_a: SO:0001660 ! core_promoter_element +relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1 + +[Term] +id: SO:0000623 +name: snRNA_encoding +synonym: "snRNA encoding" EXACT [] +is_a: SO:0000011 ! non_protein_coding + +[Term] +id: SO:0000624 +name: telomere +def: "A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma] +subset: SOFA +synonym: "telomeric DNA" EXACT [] +synonym: "telomeric sequence" EXACT [] +xref: http://en.wikipedia.org/wiki/Telomere "wiki" +is_a: SO:0000628 ! chromosomal_structural_element + +[Term] +id: SO:0000625 +name: silencer +def: "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke] +subset: SOFA +xref: http://en.wikipedia.org/wiki/Silencer_(DNA) "wiki" +is_a: SO:0000727 ! CRM + +[Term] +id: SO:0000626 +name: chromosomal_regulatory_element +synonym: "chromosomal regulatory element" EXACT [] +is_a: SO:0000830 ! chromosome_part + +[Term] +id: SO:0000627 +name: insulator +def: "A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative] +subset: SOFA +synonym: "insulator element" EXACT [] +xref: http://en.wikipedia.org/wiki/Insulator_(genetics) "wiki" +is_a: SO:0001055 ! transcriptional_cis_regulatory_region + +[Term] +id: SO:0000628 +name: chromosomal_structural_element +subset: SOFA +synonym: "chromosomal structural element" EXACT [] +is_a: SO:0000830 ! chromosome_part + +[Term] +id: SO:0000629 +name: five_prime_open_reading_frame +synonym: "five prime open reading frame" EXACT [] +is_a: SO:0000836 ! mRNA_region +relationship: part_of SO:0000204 ! five_prime_UTR + +[Term] +id: SO:0000630 +name: upstream_AUG_codon +def: "A start codon upstream of the ORF." [SO:ke] +synonym: "upstream AUG codon" EXACT [] +is_a: SO:0000837 ! UTR_region +relationship: part_of SO:0000203 ! UTR + +[Term] +id: SO:0000631 +name: polycistronic_primary_transcript +def: "A primary transcript encoding for more than one gene product." [SO:ke] +synonym: "polycistronic primary transcript" EXACT [] +is_a: SO:0000078 ! polycistronic_transcript +is_a: SO:0000185 ! primary_transcript +relationship: has_quality SO:0000880 ! polycistronic + +[Term] +id: SO:0000632 +name: monocistronic_primary_transcript +def: "A primary transcript encoding for one gene product." [SO:ke] +synonym: "monocistronic primary transcript" EXACT [] +is_a: SO:0000185 ! primary_transcript +is_a: SO:0000665 ! monocistronic_transcript +relationship: has_quality SO:0000878 ! monocistronic + +[Term] +id: SO:0000633 +name: monocistronic_mRNA +def: "An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd] +synonym: "monocistronic mRNA" EXACT [] +synonym: "monocistronic processed transcript" EXACT [] +xref: http://en.wikipedia.org/wiki/Monocistronic_mRNA "wiki" +is_a: SO:0000234 ! mRNA +is_a: SO:0000665 ! monocistronic_transcript +relationship: has_quality SO:0000878 ! monocistronic + +[Term] +id: SO:0000634 +name: polycistronic_mRNA +def: "An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd] +synonym: "polycistronic mRNA" EXACT [] +synonym: "polycistronic processed transcript" RELATED [] +xref: http://en.wikipedia.org/wiki/Polycistronic_mRNA "wiki" +is_a: SO:0000078 ! polycistronic_transcript +is_a: SO:0000234 ! mRNA +relationship: has_quality SO:0000880 ! polycistronic + +[Term] +id: SO:0000635 +name: mini_exon_donor_RNA +def: "A primary transcript that donates the spliced leader to other mRNA." [SO:ke] +synonym: "mini exon donor RNA" EXACT [] +synonym: "mini-exon donor RNA" EXACT [] +is_a: SO:0000185 ! primary_transcript + +[Term] +id: SO:0000636 +name: spliced_leader_RNA +synonym: "mini-exon" RELATED [] +synonym: "spliced leader RNA" EXACT [] +is_a: SO:0000835 ! primary_transcript_region +relationship: part_of SO:0000635 ! mini_exon_donor_RNA + +[Term] +id: SO:0000637 +name: engineered_plasmid +def: "A plasmid that is engineered." [SO:xp] +synonym: "engineered plasmid" EXACT [] +synonym: "engineered plasmid gene" RELATED [] +is_a: SO:0000155 ! plasmid +is_a: SO:0000804 ! engineered_region +relationship: has_quality SO:0000783 ! engineered + +[Term] +id: SO:0000638 +name: transcribed_spacer_region +def: "Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html] +synonym: "transcribed spacer region" EXACT [] +is_a: SO:0000838 ! rRNA_primary_transcript_region + +[Term] +id: SO:0000639 +name: internal_transcribed_spacer_region +def: "Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke] +synonym: "internal transcribed spacer region" EXACT [] +is_a: SO:0000638 ! transcribed_spacer_region + +[Term] +id: SO:0000640 +name: external_transcribed_spacer_region +def: "Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke] +synonym: "external transcribed spacer region" EXACT [] +is_a: SO:0000638 ! transcribed_spacer_region + +[Term] +id: SO:0000641 +name: tetranucleotide_repeat_microsatellite_feature +synonym: "tetranucleotide repeat microsatellite feature" EXACT [] +is_a: SO:0000289 ! microsatellite + +[Term] +id: SO:0000642 +name: SRP_RNA_encoding +synonym: "SRP RNA encoding" EXACT [] +is_a: SO:0000011 ! non_protein_coding + +[Term] +id: SO:0000643 +name: minisatellite +def: "A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml] +subset: SOFA +synonym: "VNTR" EXACT [http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9655/] +xref: http://en.wikipedia.org/wiki/Minisatellite "wiki" +is_a: SO:0000005 ! satellite_DNA + +[Term] +id: SO:0000644 +name: antisense_RNA +def: "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke] +subset: SOFA +synonym: "antisense RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/Antisense_RNA "wiki" +is_a: SO:0000655 ! ncRNA +relationship: derives_from SO:0000645 ! antisense_primary_transcript + +[Term] +id: SO:0000645 +name: antisense_primary_transcript +def: "The reverse complement of the primary transcript." [SO:ke] +subset: SOFA +synonym: "antisense primary transcript" EXACT [] +is_a: SO:0000185 ! primary_transcript + +[Term] +id: SO:0000646 +name: siRNA +def: "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000] +subset: SOFA +synonym: "small interfering RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/SiRNA "wiki" +is_a: SO:0000655 ! ncRNA + +[Term] +id: SO:0000647 +name: miRNA_primary_transcript +alt_id: SO:0000648 +def: "A primary transcript encoding a micro RNA." [SO:ke] +synonym: "micro RNA primary transcript" EXACT [] +synonym: "miRNA primary transcript" EXACT [] +synonym: "small temporal RNA primary transcript" EXACT [] +synonym: "stRNA primary transcript" EXACT [] +synonym: "stRNA_primary_transcript" EXACT [] +is_a: SO:0000483 ! nc_primary_transcript +relationship: has_part SO:0001244 ! pre_miRNA + +[Term] +id: SO:0000650 +name: small_subunit_rRNA +def: "Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke] +subset: SOFA +synonym: "small subunit rRNA" EXACT [] +synonym: "SSU RNA" EXACT [RSC:cb] +synonym: "SSU rRNA" EXACT [RSC:cb] +is_a: SO:0000252 ! rRNA +relationship: derives_from SO:0000255 ! rRNA_small_subunit_primary_transcript + +[Term] +id: SO:0000651 +name: large_subunit_rRNA +def: "Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke] +subset: SOFA +synonym: "large subunit rRNA" EXACT [] +synonym: "LSU RNA" EXACT [RSC:cb] +synonym: "LSU rRNA" EXACT [RSC:cb] +is_a: SO:0000252 ! rRNA +relationship: derives_from SO:0000325 ! rRNA_large_subunit_primary_transcript + +[Term] +id: SO:0000652 +name: rRNA_5S +def: "5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001] +subset: SOFA +synonym: "5S LSU rRNA" EXACT [] +synonym: "5S ribosomal RNA" EXACT [] +synonym: "5S rRNA" EXACT [] +synonym: "rRNA 5S" EXACT [] +xref: http://en.wikipedia.org/wiki/5S_ribosomal_RNA "wiki" +is_a: SO:0000651 ! large_subunit_rRNA + +[Term] +id: SO:0000653 +name: rRNA_28S +def: "A component of the large ribosomal subunit." [SO:ke] +subset: SOFA +synonym: "28S LSU rRNA" EXACT [] +synonym: "28S ribosomal RNA" EXACT [] +synonym: "28S rRNA" EXACT [] +synonym: "rRNA 28S" EXACT [] +xref: http://en.wikipedia.org/wiki/28S_ribosomal_RNA "wiki" +is_a: SO:0000651 ! large_subunit_rRNA + +[Term] +id: SO:0000654 +name: maxicircle_gene +def: "A mitochondrial gene located in a maxicircle." [SO:xp] +synonym: "maxi-circle gene" EXACT [] +synonym: "maxicircle gene" EXACT [] +is_a: SO:0000089 ! kinetoplast_gene +relationship: part_of SO:0000742 ! maxicircle + +[Term] +id: SO:0000655 +name: ncRNA +def: "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke] +comment: A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript. +subset: SOFA +synonym: "noncoding RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/NcRNA "wiki" +is_a: SO:0000233 ! mature_transcript + +[Term] +id: SO:0000656 +name: stRNA_encoding +synonym: "stRNA encoding" EXACT [] +is_a: SO:0000011 ! non_protein_coding + +[Term] +id: SO:0000657 +name: repeat_region +def: "A region of sequence containing one or more repeat units." [SO:ke] +subset: SOFA +synonym: "repeat region" EXACT [] +is_a: SO:0001411 ! biological_region +relationship: has_part SO:0000726 ! repeat_unit + +[Term] +id: SO:0000658 +name: dispersed_repeat +def: "A repeat that is located at dispersed sites in the genome." [SO:ke] +subset: SOFA +synonym: "dispersed repeat" EXACT [] +synonym: "interspersed repeat" EXACT [] +xref: http://en.wikipedia.org/wiki/Interspersed_repeat "wiki" +is_a: SO:0000657 ! repeat_region + +[Term] +id: SO:0000659 +name: tmRNA_encoding +synonym: "tmRNA encoding" EXACT [] +is_a: SO:0000011 ! non_protein_coding + +[Term] +id: SO:0000660 +name: DNA_invertase_target_sequence +is_obsolete: true + +[Term] +id: SO:0000661 +name: intron_attribute +is_obsolete: true + +[Term] +id: SO:0000662 +name: spliceosomal_intron +def: "An intron which is spliced by the spliceosome." [SO:ke] +comment: GO:0000398. +subset: SOFA +synonym: "spliceosomal intron" EXACT [] +is_a: SO:0000188 ! intron + +[Term] +id: SO:0000663 +name: tRNA_encoding +synonym: "tRNA encoding" EXACT [] +is_a: SO:0000011 ! non_protein_coding + +[Term] +id: SO:0000664 +name: introgressed_chromosome_region +synonym: "introgressed chromosome region" EXACT [] +is_a: SO:0000830 ! chromosome_part + +[Term] +id: SO:0000665 +name: monocistronic_transcript +def: "A transcript that is monocistronic." [SO:xp] +synonym: "monocistronic transcript" EXACT [] +is_a: SO:0000673 ! transcript +relationship: has_quality SO:0000878 ! monocistronic + +[Term] +id: SO:0000666 +name: mobile_intron +def: "An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke] +synonym: "mobile intron" EXACT [] +is_a: SO:0000188 ! intron +is_a: SO:0001037 ! mobile_genetic_element +relationship: has_quality SO:0001234 ! mobile + +[Term] +id: SO:0000667 +name: insertion +alt_id: SO:1000034 +def: "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke] +subset: DBVAR +subset: SOFA +synonym: "insertion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] +synonym: "nucleotide insertion" EXACT [] +synonym: "nucleotide_insertion" EXACT [] +xref: loinc:LA6687-3 "Insertion" +is_a: SO:0001059 ! sequence_alteration +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0000668 +name: EST_match +def: "A match against an EST sequence." [SO:ke] +subset: SOFA +synonym: "EST match" EXACT [] +is_a: SO:0000102 ! expressed_sequence_match + +[Term] +id: SO:0000669 +name: sequence_rearrangement_feature +synonym: "sequence rearrangement feature" EXACT [] +is_a: SO:0000298 ! recombination_feature + +[Term] +id: SO:0000670 +name: chromosome_breakage_sequence +def: "A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation." [SO:ma] +synonym: "chromosome breakage sequence" EXACT [] +is_a: SO:0000669 ! sequence_rearrangement_feature + +[Term] +id: SO:0000671 +name: internal_eliminated_sequence +def: "A sequence eliminated from the genome of ciliates during nuclear differentiation." [SO:ma] +synonym: "internal eliminated sequence" EXACT [] +is_a: SO:0000669 ! sequence_rearrangement_feature + +[Term] +id: SO:0000672 +name: macronucleus_destined_segment +def: "A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome." [SO:ma] +synonym: "macronucleus destined segment" EXACT [] +is_a: SO:0000669 ! sequence_rearrangement_feature + +[Term] +id: SO:0000673 +name: transcript +def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma] +subset: SOFA +xref: http://en.wikipedia.org/wiki/RNA "wiki" +is_a: SO:0000831 ! gene_member_region + +[Term] +id: SO:0000674 +name: non_canonical_splice_site +def: "A splice site where the donor and acceptor sites differ from the canonical form." [SO:ke] +synonym: "non canonical splice site" EXACT [] +synonym: "non-canonical splice site" EXACT [] +is_obsolete: true +consider: SO:0000678 +consider: SO:0000679 + +[Term] +id: SO:0000675 +name: canonical_splice_site +def: "The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively." [SO:ke] +synonym: "canonical splice site" EXACT [] +is_obsolete: true +consider: SO:0000676 +consider: SO:0000677 + +[Term] +id: SO:0000676 +name: canonical_three_prime_splice_site +def: "The canonical 3' splice site has the sequence \"AG\"." [SO:ke] +synonym: "canonical 3' splice site" EXACT [] +synonym: "canonical three prime splice site" EXACT [] +is_a: SO:0000164 ! three_prime_cis_splice_site + +[Term] +id: SO:0000677 +name: canonical_five_prime_splice_site +def: "The canonical 5' splice site has the sequence \"GT\"." [SO:ke] +synonym: "canonical 5' splice site" EXACT [] +synonym: "canonical five prime splice site" EXACT [] +is_a: SO:0000163 ! five_prime_cis_splice_site + +[Term] +id: SO:0000678 +name: non_canonical_three_prime_splice_site +def: "A 3' splice site that does not have the sequence \"AG\"." [SO:ke] +synonym: "non canonical 3' splice site" RELATED [] +synonym: "non canonical three prime splice site" EXACT [] +synonym: "non-canonical three prime splice site" EXACT [] +is_a: SO:0000164 ! three_prime_cis_splice_site + +[Term] +id: SO:0000679 +name: non_canonical_five_prime_splice_site +def: "A 5' splice site which does not have the sequence \"GT\"." [SO:ke] +synonym: "non canonical 5' splice site" EXACT [] +synonym: "non canonical five prime splice site" EXACT [] +synonym: "non-canonical five prime splice site" EXACT [] +is_a: SO:0000163 ! five_prime_cis_splice_site + +[Term] +id: SO:0000680 +name: non_canonical_start_codon +def: "A start codon that is not the usual AUG sequence." [SO:ke] +synonym: "non ATG start codon" EXACT [] +synonym: "non canonical start codon" EXACT [] +synonym: "non-canonical start codon" EXACT [] +is_a: SO:0000318 ! start_codon + +[Term] +id: SO:0000681 +name: aberrant_processed_transcript +def: "A transcript that has been processed \"incorrectly\", for example by the failure of splicing of one or more exons." [SO:ke] +synonym: "aberrant processed transcript" EXACT [] +is_a: SO:0000673 ! transcript + +[Term] +id: SO:0000682 +name: splicing_feature +is_obsolete: true + +[Term] +id: SO:0000683 +name: exonic_splice_enhancer +def: "Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [http://www.ncbi.nlm.nih.gov\:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract] +synonym: "exonic splice enhancer" EXACT [] +is_a: SO:0000344 ! splice_enhancer + +[Term] +id: SO:0000684 +name: nuclease_sensitive_site +def: "A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma] +subset: SOFA +synonym: "nuclease sensitive site" EXACT [] +is_a: SO:0000059 ! nuclease_binding_site + +[Term] +id: SO:0000685 +name: DNAseI_hypersensitive_site +synonym: "DHS" EXACT [] +synonym: "DNAseI hypersensitive site" EXACT [] +is_a: SO:0000322 ! nuclease_hypersensitive_site + +[Term] +id: SO:0000686 +name: translocation_element +def: "A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma] +synonym: "translocation element" EXACT [] +is_a: SO:1000044 ! chromosomal_translocation + +[Term] +id: SO:0000687 +name: deletion_junction +def: "The space between two bases in a sequence which marks the position where a deletion has occurred." [SO:ke] +subset: SOFA +synonym: "deletion junction" EXACT [] +is_a: SO:0000699 ! junction + +[Term] +id: SO:0000688 +name: golden_path +def: "A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls] +subset: SOFA +synonym: "golden path" EXACT [] +is_a: SO:0000353 ! sequence_assembly + +[Term] +id: SO:0000689 +name: cDNA_match +def: "A match against cDNA sequence." [SO:ke] +subset: SOFA +synonym: "cDNA match" EXACT [] +is_a: SO:0000102 ! expressed_sequence_match + +[Term] +id: SO:0000690 +name: gene_with_polycistronic_transcript +def: "A gene that encodes a polycistronic transcript." [SO:xp] +synonym: "gene with polycistronic transcript" EXACT [] +is_a: SO:0000704 ! gene +relationship: transcribed_to SO:0000078 ! polycistronic_transcript + +[Term] +id: SO:0000691 +name: cleaved_initiator_methionine +alt_id: BS:00067 +def: "The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR] +subset: biosapiens +synonym: "cleaved initiator methionine" EXACT [] +synonym: "init_met" RELATED [uniprot:feature_type] +synonym: "initiator methionine" RELATED [] +is_a: SO:0100011 ! cleaved_peptide_region + +[Term] +id: SO:0000692 +name: gene_with_dicistronic_transcript +def: "A gene that encodes a dicistronic transcript." [SO:xp] +synonym: "gene with dicistronic transcript" EXACT [] +is_a: SO:0000690 ! gene_with_polycistronic_transcript +relationship: transcribed_to SO:0000079 ! dicistronic_transcript + +[Term] +id: SO:0000693 +name: gene_with_recoded_mRNA +def: "A gene that encodes an mRNA that is recoded." [SO:xp] +synonym: "gene with recoded mRNA" EXACT [] +is_a: SO:0001217 ! protein_coding_gene +relationship: has_quality SO:0000881 ! recoded + +[Term] +id: SO:0000694 +name: SNP +def: "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb] +subset: SOFA +synonym: "single nucleotide polymorphism" EXACT [] +is_a: SO:0001483 ! SNV + +[Term] +id: SO:0000695 +name: reagent +def: "A sequence used in experiment." [SO:ke] +comment: Requested by Lynn Crosby, jan 2006. +subset: SOFA +is_a: SO:0001409 ! biomaterial_region + +[Term] +id: SO:0000696 +name: oligo +def: "A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma] +subset: SOFA +synonym: "oligonucleotide" EXACT [] +xref: http://en.wikipedia.org/wiki/Oligonucleotide "wiki" +is_a: SO:0000695 ! reagent + +[Term] +id: SO:0000697 +name: gene_with_stop_codon_read_through +def: "A gene that encodes a transcript with stop codon readthrough." [SO:xp] +synonym: "gene with stop codon read through" EXACT [] +is_a: SO:0000693 ! gene_with_recoded_mRNA +relationship: has_part SO:0000883 ! stop_codon_read_through + +[Term] +id: SO:0000698 +name: gene_with_stop_codon_redefined_as_pyrrolysine +def: "A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp] +synonym: "gene with stop codon redefined as pyrrolysine" EXACT [] +is_a: SO:0000697 ! gene_with_stop_codon_read_through +relationship: has_part SO:0000884 ! stop_codon_redefined_as_pyrrolysine + +[Term] +id: SO:0000699 +name: junction +def: "A sequence_feature with an extent of zero." [SO:ke] +comment: A junction is a boundary between regions. A boundary has an extent of zero. +subset: SOFA +synonym: "boundary" EXACT [] +synonym: "breakpoint" EXACT [] +is_a: SO:0000110 ! sequence_feature + +[Term] +id: SO:0000700 +name: remark +def: "A comment about the sequence." [SO:ke] +subset: SOFA +is_a: SO:0001410 ! experimental_feature + +[Term] +id: SO:0000701 +name: possible_base_call_error +def: "A region of sequence where the validity of the base calling is questionable." [SO:ke] +subset: SOFA +synonym: "possible base call error" EXACT [] +is_a: SO:0000413 ! sequence_difference + +[Term] +id: SO:0000702 +name: possible_assembly_error +def: "A region of sequence where there may have been an error in the assembly." [SO:ke] +subset: SOFA +synonym: "possible assembly error" EXACT [] +is_a: SO:0000413 ! sequence_difference + +[Term] +id: SO:0000703 +name: experimental_result_region +def: "A region of sequence implicated in an experimental result." [SO:ke] +subset: SOFA +synonym: "experimental result region" EXACT [] +is_a: SO:0000700 ! remark + +[Term] +id: SO:0000704 +name: gene +def: "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance. +subset: SOFA +xref: http://en.wikipedia.org/wiki/Gene "wiki" +is_a: SO:0001411 ! biological_region +relationship: member_of SO:0005855 ! gene_group + +[Term] +id: SO:0000705 +name: tandem_repeat +def: "Two or more adjacent copies of a region (of length greater than 1)." [SO:ke] +subset: SOFA +synonym: "tandem repeat" EXACT [] +xref: http://en.wikipedia.org/wiki/Tandem_repeat "wiki" +xref: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html +is_a: SO:0000657 ! repeat_region + +[Term] +id: SO:0000706 +name: trans_splice_acceptor_site +def: "The 3' splice site of the acceptor primary transcript." [SO:ke] +comment: This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans. +subset: SOFA +synonym: "3' trans splice site" RELATED [] +synonym: "trans splice acceptor site" EXACT [] +is_a: SO:0001420 ! trans_splice_site + +[Term] +id: SO:0000707 +name: trans_splice_donor_site +def: "The 5' five prime splice site region of the donor RNA." [SO:ke] +comment: SL RNA contains a donor site. +synonym: "5 prime trans splice site" RELATED [] +synonym: "trans splice donor site" EXACT [] +synonym: "trans-splice donor site" EXACT [] +is_a: SO:0001420 ! trans_splice_site + +[Term] +id: SO:0000708 +name: SL1_acceptor_site +def: "A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw] +synonym: "SL1 acceptor site" EXACT [] +is_a: SO:0000706 ! trans_splice_acceptor_site + +[Term] +id: SO:0000709 +name: SL2_acceptor_site +def: "A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] +synonym: "SL2 acceptor site" EXACT [] +is_a: SO:0000706 ! trans_splice_acceptor_site + +[Term] +id: SO:0000710 +name: gene_with_stop_codon_redefined_as_selenocysteine +def: "A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp] +synonym: "gene with stop codon redefined as selenocysteine" EXACT [] +is_a: SO:0000697 ! gene_with_stop_codon_read_through +relationship: has_part SO:0000885 ! stop_codon_redefined_as_selenocysteine + +[Term] +id: SO:0000711 +name: gene_with_mRNA_recoded_by_translational_bypass +def: "A gene with mRNA recoded by translational bypass." [SO:xp] +synonym: "gene with mRNA recoded by translational bypass" EXACT [] +is_a: SO:0000693 ! gene_with_recoded_mRNA +relationship: has_quality SO:0000886 ! recoded_by_translational_bypass + +[Term] +id: SO:0000712 +name: gene_with_transcript_with_translational_frameshift +def: "A gene encoding a transcript that has a translational frameshift." [SO:xp] +synonym: "gene with transcript with translational frameshift" EXACT [] +is_a: SO:0000693 ! gene_with_recoded_mRNA +relationship: has_quality SO:0000887 ! translationally_frameshifted + +[Term] +id: SO:0000713 +name: DNA_motif +def: "A motif that is active in the DNA form of the sequence." [SO:ke] +synonym: "DNA motif" EXACT [] +xref: http://en.wikipedia.org/wiki/DNA_motif "wiki" +is_a: SO:0000714 ! nucleotide_motif + +[Term] +id: SO:0000714 +name: nucleotide_motif +def: "A region of nucleotide sequence corresponding to a known motif." [SO:ke] +subset: SOFA +synonym: "nucleotide motif" EXACT [] +is_a: SO:0001683 ! sequence_motif + +[Term] +id: SO:0000715 +name: RNA_motif +def: "A motif that is active in RNA sequence." [SO:ke] +subset: SOFA +synonym: "RNA motif" EXACT [] +is_a: SO:0000714 ! nucleotide_motif + +[Term] +id: SO:0000716 +name: dicistronic_mRNA +def: "An mRNA that has the quality dicistronic." [SO:ke] +synonym: "dicistronic mRNA" EXACT [] +synonym: "dicistronic processed transcript" RELATED [] +is_a: SO:0000079 ! dicistronic_transcript +is_a: SO:0000634 ! polycistronic_mRNA +relationship: has_quality SO:0000879 ! dicistronic + +[Term] +id: SO:0000717 +name: reading_frame +def: "A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb] +comment: This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop. +subset: SOFA +synonym: "reading frame" EXACT [] +xref: http://en.wikipedia.org/wiki/Reading_frame "wiki" +is_a: SO:0001410 ! experimental_feature + +[Term] +id: SO:0000718 +name: blocked_reading_frame +def: "A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons." [SGD:rb] +comment: Term requested by Rama from SGD. +synonym: "blocked reading frame" EXACT [] +is_a: SO:0000717 ! reading_frame + +[Term] +id: SO:0000719 +name: ultracontig +def: "An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG] +subset: SOFA +synonym: "superscaffold" RELATED [] +is_a: SO:0001876 ! partial_genomic_sequence_assembly + +[Term] +id: SO:0000720 +name: foreign_transposable_element +def: "A transposable element that is foreign." [SO:ke] +comment: requested by Michael on 19 Nov 2004. +synonym: "foreign transposable element" EXACT [] +is_a: SO:0000101 ! transposable_element +relationship: has_quality SO:0000784 ! foreign + +[Term] +id: SO:0000721 +name: gene_with_dicistronic_primary_transcript +def: "A gene that encodes a dicistronic primary transcript." [SO:xp] +comment: Requested by Michael, 19 nov 2004. +synonym: "gene with dicistronic primary transcript" EXACT [] +is_a: SO:0000692 ! gene_with_dicistronic_transcript +relationship: transcribed_to SO:1001197 ! dicistronic_primary_transcript + +[Term] +id: SO:0000722 +name: gene_with_dicistronic_mRNA +def: "A gene that encodes a polycistronic mRNA." [SO:xp] +comment: Requested by MA nov 19 2004. +synonym: "gene with dicistronic mRNA" EXACT [] +synonym: "gene with dicistronic processed transcript" EXACT [] +is_a: SO:0000692 ! gene_with_dicistronic_transcript +relationship: transcribed_to SO:0000716 ! dicistronic_mRNA + +[Term] +id: SO:0000723 +name: iDNA +def: "Genomic sequence removed from the genome, as a normal event, by a process of recombination." [SO:ma] +synonym: "intervening DNA" EXACT [] +xref: http://en.wikipedia.org/wiki/IDNA "wiki" +is_a: SO:0000298 ! recombination_feature + +[Term] +id: SO:0000724 +name: oriT +def: "A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +subset: SOFA +synonym: "origin of transfer" EXACT [] +xref: http://en.wikipedia.org/wiki/Origin_of_transfer "wiki" +is_a: SO:0000296 ! origin_of_replication + +[Term] +id: SO:0000725 +name: transit_peptide +alt_id: BS:00055 +def: "The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +comment: Added to bring SO inline with the EMBL, DDBJ, GenBank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle. +subset: biosapiens +subset: SOFA +synonym: "signal" RELATED [] +synonym: "transit" RELATED [uniprot:feature_type] +synonym: "transit peptide" EXACT [] +is_a: SO:0001527 ! peptide_localization_signal + +[Term] +id: SO:0000726 +name: repeat_unit +def: "The simplest repeated component of a repeat region. A single repeat." [SO:ke] +comment: Added to comply with the feature table. A single repeat. +synonym: "repeat unit" EXACT [] +xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0000727 +name: CRM +def: "A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG] +comment: Requested by Stephen Grossmann Dec 2004. +subset: SOFA +synonym: "cis regulatory module" EXACT [] +synonym: "TF module" EXACT [] +synonym: "transcription factor module" EXACT [] +is_a: SO:0001055 ! transcriptional_cis_regulatory_region +relationship: has_part SO:0000235 ! TF_binding_site + +[Term] +id: SO:0000728 +name: intein +def: "A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke] +comment: Intein-mediated protein splicing occurs after mRNA has been translated into a protein. +synonym: "protein intron" RELATED [] +xref: http://en.wikipedia.org/wiki/Intein "wiki" +is_a: SO:0100011 ! cleaved_peptide_region + +[Term] +id: SO:0000729 +name: intein_containing +def: "An attribute of protein-coding genes where the initial protein product contains an intein." [SO:ke] +synonym: "intein containing" EXACT [] +is_a: SO:0000010 ! protein_coding + +[Term] +id: SO:0000730 +name: gap +def: "A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke] +subset: SOFA +is_a: SO:0000143 ! assembly_component +relationship: part_of SO:0000353 ! sequence_assembly + +[Term] +id: SO:0000731 +name: fragmentary +def: "An attribute to describe a feature that is incomplete." [SO:ke] +comment: Term added because of request by MO people. +synonym: "fragment" EXACT [] +is_a: SO:0000905 ! status + +[Term] +id: SO:0000732 +name: predicted +def: "An attribute describing an unverified region." [SO:ke] +xref: http://en.wikipedia.org/wiki/Predicted "wiki" +is_a: SO:0000905 ! status + +[Term] +id: SO:0000733 +name: feature_attribute +def: "An attribute describing a located_sequence_feature." [SO:ke] +synonym: "feature attribute" EXACT [] +is_a: SO:0000400 ! sequence_attribute + +[Term] +id: SO:0000734 +name: exemplar_mRNA +def: "An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http://mged.sourceforge.net/ontologies/MGEDontology.php] +comment: Added for the MO people. +synonym: "exemplar mRNA" EXACT [] +is_a: SO:0000234 ! mRNA +relationship: has_quality SO:0000864 ! exemplar + +[Term] +id: SO:0000735 +name: sequence_location +synonym: "sequence location" EXACT [] +is_a: SO:0000400 ! sequence_attribute + +[Term] +id: SO:0000736 +name: organelle_sequence +synonym: "organelle sequence" EXACT [] +is_a: SO:0000735 ! sequence_location + +[Term] +id: SO:0000737 +name: mitochondrial_sequence +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +synonym: "mitochondrial sequence" EXACT [] +is_a: SO:0000736 ! organelle_sequence + +[Term] +id: SO:0000738 +name: nuclear_sequence +synonym: "nuclear sequence" EXACT [] +is_a: SO:0000736 ! organelle_sequence + +[Term] +id: SO:0000739 +name: nucleomorphic_sequence +synonym: "nucleomorphic sequence" EXACT [] +is_a: SO:0000736 ! organelle_sequence + +[Term] +id: SO:0000740 +name: plastid_sequence +synonym: "plastid sequence" EXACT [] +is_a: SO:0000736 ! organelle_sequence + +[Term] +id: SO:0000741 +name: kinetoplast +alt_id: SO:0000826 +def: "A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species." [PMID:8395055] +synonym: "kinetoplast_chromosome" EXACT [] +xref: http://en.wikipedia.org/wiki/Kinetoplast "wiki" +is_a: SO:0001026 ! genome +relationship: has_part SO:0000742 ! maxicircle +relationship: has_part SO:0000980 ! minicircle + +[Term] +id: SO:0000742 +name: maxicircle +alt_id: SO:0000827 +def: "A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method." [PMID:8395055] +synonym: "maxicircle_chromosome" EXACT [] +is_a: SO:0001235 ! replicon + +[Term] +id: SO:0000743 +name: apicoplast_sequence +synonym: "apicoplast sequence" EXACT [] +is_a: SO:0000740 ! plastid_sequence + +[Term] +id: SO:0000744 +name: chromoplast_sequence +synonym: "chromoplast sequence" EXACT [] +is_a: SO:0000740 ! plastid_sequence + +[Term] +id: SO:0000745 +name: chloroplast_sequence +synonym: "chloroplast sequence" EXACT [] +is_a: SO:0000740 ! plastid_sequence + +[Term] +id: SO:0000746 +name: cyanelle_sequence +synonym: "cyanelle sequence" EXACT [] +is_a: SO:0000740 ! plastid_sequence + +[Term] +id: SO:0000747 +name: leucoplast_sequence +synonym: "leucoplast sequence" EXACT [] +is_a: SO:0000740 ! plastid_sequence + +[Term] +id: SO:0000748 +name: proplastid_sequence +synonym: "proplastid sequence" EXACT [] +is_a: SO:0000740 ! plastid_sequence + +[Term] +id: SO:0000749 +name: plasmid_location +synonym: "plasmid location" EXACT [] +is_a: SO:0000735 ! sequence_location + +[Term] +id: SO:0000750 +name: amplification_origin +def: "An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence." [SO:ma] +synonym: "amplification origin" EXACT [] +is_a: SO:0000296 ! origin_of_replication + +[Term] +id: SO:0000751 +name: proviral_location +synonym: "proviral location" EXACT [] +is_a: SO:0000735 ! sequence_location + +[Term] +id: SO:0000752 +name: gene_group_regulatory_region +subset: SOFA +synonym: "gene group regulatory region" EXACT [] +is_a: SO:0001679 ! transcription_regulatory_region +relationship: member_of SO:0005855 ! gene_group + +[Term] +id: SO:0000753 +name: clone_insert +def: "The region of sequence that has been inserted and is being propagated by the clone." [SO:ke] +subset: SOFA +synonym: "clone insert" EXACT [] +is_a: SO:0000695 ! reagent +relationship: part_of SO:0000151 ! clone + +[Term] +id: SO:0000754 +name: lambda_vector +def: "The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8] +synonym: "lambda vector" EXACT [] +is_a: SO:0000440 ! vector_replicon + +[Term] +id: SO:0000755 +name: plasmid_vector +synonym: "plasmid vector" EXACT [] +xref: http://en.wikipedia.org/wiki/Plasmid_vector#Vectors "wiki" +is_a: SO:0000440 ! vector_replicon +relationship: derives_from SO:0000155 ! plasmid + +[Term] +id: SO:0000756 +name: cDNA +def: "DNA synthesized by reverse transcriptase using RNA as a template." [SO:ma] +synonym: "complementary DNA" EXACT [] +xref: http://en.wikipedia.org/wiki/CDNA "wiki" +is_a: SO:0000352 ! DNA + +[Term] +id: SO:0000757 +name: single_stranded_cDNA +synonym: "single strand cDNA" EXACT [] +synonym: "single stranded cDNA" EXACT [] +synonym: "single-strand cDNA" RELATED [] +is_a: SO:0000756 ! cDNA + +[Term] +id: SO:0000758 +name: double_stranded_cDNA +synonym: "double strand cDNA" RELATED [] +synonym: "double stranded cDNA" EXACT [] +synonym: "double-strand cDNA" RELATED [] +is_a: SO:0000756 ! cDNA + +[Term] +id: SO:0000759 +name: plasmid_clone +is_obsolete: true + +[Term] +id: SO:0000760 +name: YAC_clone +is_obsolete: true + +[Term] +id: SO:0000761 +name: phagemid_clone +is_obsolete: true + +[Term] +id: SO:0000762 +name: PAC_clone +synonym: "P1_clone" RELATED [] +is_obsolete: true + +[Term] +id: SO:0000763 +name: fosmid_clone +is_obsolete: true + +[Term] +id: SO:0000764 +name: BAC_clone +is_obsolete: true + +[Term] +id: SO:0000765 +name: cosmid_clone +is_obsolete: true + +[Term] +id: SO:0000766 +name: pyrrolysyl_tRNA +def: "A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." [SO:ke] +synonym: "pyrrolysyl tRNA" EXACT [] +synonym: "pyrrolysyl-transfer ribonucleic acid" EXACT [] +synonym: "pyrrolysyl-transfer RNA" EXACT [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0001178 ! pyrrolysine_tRNA_primary_transcript + +[Term] +id: SO:0000767 +name: clone_insert_start +is_obsolete: true + +[Term] +id: SO:0000768 +name: episome +def: "A plasmid that may integrate with a chromosome." [SO:ma] +is_a: SO:0000155 ! plasmid + +[Term] +id: SO:0000769 +name: tmRNA_coding_piece +def: "The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962] +comment: Added in response to comment from Kelly Williams from Indiana. Nov 2005. +synonym: "tmRNA coding piece" EXACT [] +is_a: SO:0000847 ! tmRNA_region + +[Term] +id: SO:0000770 +name: tmRNA_acceptor_piece +def: "The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw] +comment: Added in response to Kelly Williams from Indiana. Date: Nov 2005. +synonym: "tmRNA acceptor piece" EXACT [] +is_a: SO:0000847 ! tmRNA_region + +[Term] +id: SO:0000771 +name: QTL +def: "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [http://rgd.mcw.edu/tu/qtls/] +comment: Added in respose to request by Simon Twigger November 14th 2005. +synonym: "quantitative trait locus" EXACT [] +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0000772 +name: genomic_island +def: "A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke] +comment: Genomic islands are transmissible elements characterized by large size (>10kb). +synonym: "genomic island" EXACT [] +xref: http://en.wikipedia.org/wiki/Genomic_island "wiki" +is_a: SO:0001039 ! integrated_mobile_genetic_element + +[Term] +id: SO:0000773 +name: pathogenic_island +def: "Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." [SO:ke] +comment: Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker. +synonym: "pathogenic island" EXACT [] +is_a: SO:0000772 ! genomic_island + +[Term] +id: SO:0000774 +name: metabolic_island +def: "A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke] +comment: Genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands. +synonym: "metabolic island" EXACT [] +is_a: SO:0000772 ! genomic_island + +[Term] +id: SO:0000775 +name: adaptive_island +def: "An adaptive island is a genomic island that provides an adaptive advantage to the host." [SO:ke] +comment: The iron-uptake ability of many pathogens are conveyed by adaptive islands. Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker. +synonym: "adaptive island" EXACT [] +is_a: SO:0000772 ! genomic_island + +[Term] +id: SO:0000776 +name: symbiosis_island +def: "A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke] +comment: Nitrogen fixation in Rhizobiaceae species is encoded by symbiosis islands. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. John T. Sullivan and Clive W. Ronso PNAS 1998 Apr 28 95 (9) 5145-5149. +synonym: "symbiosis island" EXACT [] +is_a: SO:0000772 ! genomic_island + +[Term] +id: SO:0000777 +name: pseudogenic_rRNA +def: "A non functional descendant of an rRNA." [SO:ke] +comment: Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations. +subset: SOFA +synonym: "pseudogenic rRNA" EXACT [] +is_a: SO:0000516 ! pseudogenic_transcript + +[Term] +id: SO:0000778 +name: pseudogenic_tRNA +def: "A non functional descendent of a tRNA." [SO:ke] +comment: Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations. +subset: SOFA +synonym: "pseudogenic tRNA" EXACT [] +is_a: SO:0000516 ! pseudogenic_transcript + +[Term] +id: SO:0000779 +name: engineered_episome +def: "An episome that is engineered." [SO:xp] +comment: Requested by Lynn Crosby Jan 2006. +synonym: "engineered episome" EXACT [] +is_a: SO:0000637 ! engineered_plasmid +is_a: SO:0000768 ! episome +relationship: has_quality SO:0000783 ! engineered + +[Term] +id: SO:0000780 +name: transposable_element_attribute +comment: Added by KE Jan 2006 to capture the kinds of attributes of TEs +is_obsolete: true + +[Term] +id: SO:0000781 +name: transgenic +def: "Attribute describing sequence that has been integrated with foreign sequence." [SO:ke] +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000782 +name: natural +def: "An attribute describing a feature that occurs in nature." [SO:ke] +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000783 +name: engineered +def: "An attribute to describe a region that was modified in vitro." [SO:ke] +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000784 +name: foreign +def: "An attribute to describe a region from another species." [SO:ke] +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000785 +name: cloned_region +comment: Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions. +synonym: "cloned region" EXACT [] +synonym: "cloned segment" EXACT [] +is_a: SO:0000695 ! reagent +relationship: part_of SO:0000753 ! clone_insert + +[Term] +id: SO:0000786 +name: reagent_attribute +comment: Added jan 2006 by KE. +synonym: "reagent attribute" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000787 +name: clone_attribute +is_obsolete: true + +[Term] +id: SO:0000788 +name: cloned +is_obsolete: true + +[Term] +id: SO:0000789 +name: validated +def: "An attribute to describe a feature that has been proven." [SO:ke] +is_a: SO:0000905 ! status + +[Term] +id: SO:0000790 +name: invalidated +def: "An attribute describing a feature that is invalidated." [SO:ke] +is_a: SO:0000905 ! status + +[Term] +id: SO:0000791 +name: cloned_genomic +is_obsolete: true + +[Term] +id: SO:0000792 +name: cloned_cDNA +is_obsolete: true + +[Term] +id: SO:0000793 +name: engineered_DNA +is_obsolete: true + +[Term] +id: SO:0000794 +name: engineered_rescue_region +def: "A rescue region that is engineered." [SO:xp] +synonym: "engineered rescue fragment" EXACT [] +synonym: "engineered rescue region" EXACT [] +synonym: "engineered rescue segment" EXACT [] +is_a: SO:0000411 ! rescue_region +is_a: SO:0000804 ! engineered_region +relationship: has_quality SO:0000783 ! engineered + +[Term] +id: SO:0000795 +name: rescue_mini_gene +def: "A mini_gene that rescues." [SO:xp] +synonym: "rescue mini gene" EXACT [] +synonym: "rescue mini-gene" EXACT [] +is_a: SO:0000815 ! mini_gene +relationship: has_quality SO:0000814 ! rescue + +[Term] +id: SO:0000796 +name: transgenic_transposable_element +def: "TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE." [FB:mc] +comment: Modified as requested by Lynn - FB. May 2007. +synonym: "transgenic transposable element" EXACT [] +is_a: SO:0000101 ! transposable_element +relationship: derives_from SO:0000151 ! clone +relationship: has_quality SO:0000781 ! transgenic + +[Term] +id: SO:0000797 +name: natural_transposable_element +def: "TE that exists (or existed) in nature." [FB:mc] +synonym: "natural transposable element" EXACT [] +is_a: SO:0000101 ! transposable_element +is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element +relationship: has_quality SO:0000782 ! natural + +[Term] +id: SO:0000798 +name: engineered_transposable_element +def: "TE that has been modified by manipulations in vitro." [FB:mc] +synonym: "engineered transposable element" EXACT [] +is_a: SO:0000101 ! transposable_element +is_a: SO:0000804 ! engineered_region +relationship: has_quality SO:0000783 ! engineered + +[Term] +id: SO:0000799 +name: engineered_foreign_transposable_element +def: "A transposable_element that is engineered and foreign." [FB:mc] +synonym: "engineered foreign transposable element" EXACT [] +is_a: SO:0000720 ! foreign_transposable_element +is_a: SO:0000798 ! engineered_transposable_element +is_a: SO:0000805 ! engineered_foreign_region +relationship: has_quality SO:0000783 ! engineered +relationship: has_quality SO:0000784 ! foreign + +[Term] +id: SO:0000800 +name: assortment_derived_duplication +def: "A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm] +synonym: "assortment derived duplication" EXACT [] +is_a: SO:0001504 ! assortment_derived_variation + +[Term] +id: SO:0000801 +name: assortment_derived_deficiency_plus_duplication +def: "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm] +synonym: "assortment derived deficiency plus duplication" EXACT [] +is_a: SO:0001504 ! assortment_derived_variation + +[Term] +id: SO:0000802 +name: assortment_derived_deficiency +def: "A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm] +synonym: "assortment-derived deficiency" EXACT [] +is_a: SO:0001504 ! assortment_derived_variation + +[Term] +id: SO:0000803 +name: assortment_derived_aneuploid +def: "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [FB:gm] +synonym: "assortment derived aneuploid" EXACT [] +is_a: SO:0001504 ! assortment_derived_variation + +[Term] +id: SO:0000804 +name: engineered_region +def: "A region that is engineered." [SO:xp] +synonym: "construct" EXACT [] +synonym: "engineered region" EXACT [] +synonym: "engineered sequence" EXACT [] +is_a: SO:0001409 ! biomaterial_region +relationship: has_quality SO:0000783 ! engineered + +[Term] +id: SO:0000805 +name: engineered_foreign_region +def: "A region that is engineered and foreign." [SO:xp] +synonym: "engineered foreign region" EXACT [] +is_a: SO:0000804 ! engineered_region +relationship: has_quality SO:0000783 ! engineered +relationship: has_quality SO:0000784 ! foreign + +[Term] +id: SO:0000806 +name: fusion +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000807 +name: engineered_tag +def: "A tag that is engineered." [SO:xp] +synonym: "engineered tag" EXACT [] +is_a: SO:0000324 ! tag +is_a: SO:0000804 ! engineered_region +relationship: has_quality SO:0000783 ! engineered + +[Term] +id: SO:0000808 +name: validated_cDNA_clone +def: "A cDNA clone that has been validated." [SO:xp] +synonym: "validated cDNA clone" EXACT [] +is_a: SO:0000317 ! cDNA_clone +relationship: has_quality SO:0000789 ! validated + +[Term] +id: SO:0000809 +name: invalidated_cDNA_clone +def: "A cDNA clone that is invalid." [SO:xp] +synonym: "invalidated cDNA clone" EXACT [] +is_a: SO:0000317 ! cDNA_clone +relationship: has_quality SO:0000790 ! invalidated + +[Term] +id: SO:0000810 +name: chimeric_cDNA_clone +def: "A cDNA clone invalidated because it is chimeric." [SO:xp] +synonym: "chimeric cDNA clone" EXACT [] +is_a: SO:0000809 ! invalidated_cDNA_clone +relationship: has_quality SO:0000362 ! invalidated_by_chimeric_cDNA + +[Term] +id: SO:0000811 +name: genomically_contaminated_cDNA_clone +def: "A cDNA clone invalidated by genomic contamination." [SO:xp] +synonym: "genomically contaminated cDNA clone" EXACT [] +is_a: SO:0000809 ! invalidated_cDNA_clone +relationship: has_quality SO:0000414 ! invalidated_by_genomic_contamination + +[Term] +id: SO:0000812 +name: polyA_primed_cDNA_clone +def: "A cDNA clone invalidated by polyA priming." [SO:xp] +synonym: "polyA primed cDNA clone" EXACT [] +is_a: SO:0000809 ! invalidated_cDNA_clone +relationship: has_quality SO:0000415 ! invalidated_by_genomic_polyA_primed_cDNA + +[Term] +id: SO:0000813 +name: partially_processed_cDNA_clone +def: "A cDNA invalidated clone by partial processing." [SO:xp] +synonym: "partially processed cDNA clone" EXACT [] +is_a: SO:0000809 ! invalidated_cDNA_clone +relationship: has_quality SO:0000416 ! invalidated_by_partial_processing + +[Term] +id: SO:0000814 +name: rescue +def: "An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype." [SO:ke] +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000815 +name: mini_gene +def: "By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA." [PMID:15992143] +synonym: "mini gene" EXACT [] +is_a: SO:0000236 ! ORF + +[Term] +id: SO:0000816 +name: rescue_gene +def: "A gene that rescues." [SO:xp] +synonym: "rescue gene" EXACT [] +is_a: SO:0000704 ! gene +relationship: has_quality SO:0000814 ! rescue + +[Term] +id: SO:0000817 +name: wild_type +def: "An attribute describing sequence with the genotype found in nature and/or standard laboratory stock." [SO:ke] +synonym: "wild type" EXACT [] +xref: http://en.wikipedia.org/wiki/Wild_type "wiki" +xref: loinc:LA9658-1 "wild type" +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000818 +name: wild_type_rescue_gene +def: "A gene that rescues." [SO:xp] +synonym: "wild type rescue gene" EXACT [] +is_a: SO:0000816 ! rescue_gene +relationship: has_quality SO:0000817 ! wild_type + +[Term] +id: SO:0000819 +name: mitochondrial_chromosome +def: "A chromosome originating in a mitochondria." [SO:xp] +synonym: "mitochondrial chromosome" EXACT [] +is_a: SO:0000340 ! chromosome +relationship: has_origin SO:0000737 ! mitochondrial_sequence + +[Term] +id: SO:0000820 +name: chloroplast_chromosome +def: "A chromosome originating in a chloroplast." [SO:xp] +synonym: "chloroplast chromosome" EXACT [] +is_a: SO:0000340 ! chromosome +relationship: has_origin SO:0000745 ! chloroplast_sequence + +[Term] +id: SO:0000821 +name: chromoplast_chromosome +def: "A chromosome originating in a chromoplast." [SO:xp] +synonym: "chromoplast chromosome" EXACT [] +is_a: SO:0000340 ! chromosome +relationship: has_origin SO:0000744 ! chromoplast_sequence + +[Term] +id: SO:0000822 +name: cyanelle_chromosome +def: "A chromosome originating in a cyanelle." [SO:xp] +synonym: "cyanelle chromosome" EXACT [] +is_a: SO:0000340 ! chromosome +relationship: has_origin SO:0000746 ! cyanelle_sequence + +[Term] +id: SO:0000823 +name: leucoplast_chromosome +def: "A chromosome with origin in a leucoplast." [SO:xp] +synonym: "leucoplast chromosome" EXACT [] +is_a: SO:0000340 ! chromosome +relationship: has_origin SO:0000747 ! leucoplast_sequence + +[Term] +id: SO:0000824 +name: macronuclear_chromosome +def: "A chromosome originating in a macronucleus." [SO:xp] +synonym: "macronuclear chromosome" EXACT [] +is_a: SO:0000340 ! chromosome +relationship: has_origin SO:0000083 ! macronuclear_sequence + +[Term] +id: SO:0000825 +name: micronuclear_chromosome +def: "A chromosome originating in a micronucleus." [SO:xp] +synonym: "micronuclear chromosome" EXACT [] +is_a: SO:0000340 ! chromosome +relationship: has_origin SO:0000084 ! micronuclear_sequence + +[Term] +id: SO:0000828 +name: nuclear_chromosome +def: "A chromosome originating in a nucleus." [SO:xp] +synonym: "nuclear chromosome" EXACT [] +is_a: SO:0000340 ! chromosome +relationship: has_origin SO:0000738 ! nuclear_sequence + +[Term] +id: SO:0000829 +name: nucleomorphic_chromosome +def: "A chromosome originating in a nucleomorph." [SO:xp] +synonym: "nucleomorphic chromosome" EXACT [] +is_a: SO:0000340 ! chromosome +relationship: has_origin SO:0000739 ! nucleomorphic_sequence + +[Term] +id: SO:0000830 +name: chromosome_part +def: "A region of a chromosome." [SO:ke] +comment: This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root. +subset: SOFA +synonym: "chromosome part" EXACT [] +is_a: SO:0001411 ! biological_region +relationship: part_of SO:0000340 ! chromosome + +[Term] +id: SO:0000831 +name: gene_member_region +def: "A region of a gene." [SO:ke] +comment: A manufactured term used to allow the parts of a gene to have an is_a path to the root. +subset: SOFA +synonym: "gene member region" EXACT [] +is_a: SO:0001411 ! biological_region +relationship: member_of SO:0000704 ! gene + +[Term] +id: SO:0000832 +name: promoter_region +def: "A region of sequence which is part of a promoter." [SO:ke] +comment: This is a manufactured term to allow the parts of promoter to have an is_a path back to the root. +is_obsolete: true + +[Term] +id: SO:0000833 +name: transcript_region +def: "A region of a transcript." [SO:ke] +comment: This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root. +subset: SOFA +synonym: "transcript region" EXACT [] +is_a: SO:0001411 ! biological_region +relationship: part_of SO:0000673 ! transcript + +[Term] +id: SO:0000834 +name: mature_transcript_region +def: "A region of a mature transcript." [SO:ke] +comment: A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root. +subset: SOFA +synonym: "mature transcript region" EXACT [] +is_a: SO:0000833 ! transcript_region + +[Term] +id: SO:0000835 +name: primary_transcript_region +def: "A part of a primary transcript." [SO:ke] +comment: This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root. +subset: SOFA +synonym: "primary transcript region" EXACT [] +is_a: SO:0000833 ! transcript_region +relationship: part_of SO:0000185 ! primary_transcript + +[Term] +id: SO:0000836 +name: mRNA_region +def: "A region of an mRNA." [SO:cb] +comment: This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root. +subset: SOFA +synonym: "mRNA region" EXACT [] +is_a: SO:0000834 ! mature_transcript_region +relationship: part_of SO:0000234 ! mRNA + +[Term] +id: SO:0000837 +name: UTR_region +def: "A region of UTR." [SO:ke] +comment: A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root. +subset: SOFA +synonym: "UTR region" EXACT [] +is_a: SO:0000836 ! mRNA_region + +[Term] +id: SO:0000838 +name: rRNA_primary_transcript_region +def: "A region of an rRNA primary transcript." [SO:ke] +comment: To allow transcribed_spacer_region to have a path to the root. +synonym: "rRNA primary transcript region" EXACT [] +is_a: SO:0000835 ! primary_transcript_region +relationship: part_of SO:0000209 ! rRNA_primary_transcript + +[Term] +id: SO:0000839 +name: polypeptide_region +alt_id: BS:00124 +alt_id: BS:00331 +def: "Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke] +comment: Added to allow the polypeptide regions to have is_a paths back to the root. +subset: biosapiens +subset: SOFA +synonym: "positional" RELATED [] +synonym: "positional polypeptide feature" RELATED [] +synonym: "region" NARROW [uniprot:feature_type] +synonym: "region or site annotation" RELATED [] +synonym: "site" NARROW [uniprot:feature_type] +is_a: SO:0001411 ! biological_region +relationship: part_of SO:0000104 ! polypeptide + +[Term] +id: SO:0000840 +name: repeat_component +def: "A region of a repeated sequence." [SO:ke] +comment: A manufactured to group the parts of repeats, to give them an is_a path back to the root. +synonym: "repeat component" EXACT [] +is_a: SO:0001412 ! topologically_defined_region + +[Term] +id: SO:0000841 +name: spliceosomal_intron_region +def: "A region within an intron." [SO:ke] +comment: A terms added to allow the parts of introns to have is_a paths to the root. +subset: SOFA +synonym: "spliceosomal intron region" EXACT [] +is_a: SO:0000835 ! primary_transcript_region +relationship: part_of SO:0000662 ! spliceosomal_intron + +[Term] +id: SO:0000842 +name: gene_component_region +subset: SOFA +synonym: "gene component region" EXACT [] +is_a: SO:0001411 ! biological_region +relationship: part_of SO:0000704 ! gene + +[Term] +id: SO:0000843 +name: bacterial_RNApol_promoter_region +def: "A region which is part of a bacterial RNA polymerase promoter." [SO:ke] +comment: This is a manufactured term to allow the parts of bacterial_RNApol_promoter to have an is_a path back to the root. +is_obsolete: true + +[Term] +id: SO:0000844 +name: RNApol_II_promoter_region +def: "A region of sequence which is a promoter for RNA polymerase II." [SO:ke] +comment: This is a manufactured term to allow the parts of RNApol_II_promoter to have an is_a path back to the root. +is_obsolete: true + +[Term] +id: SO:0000845 +name: RNApol_III_promoter_type_1_region +def: "A region of sequence which is a promoter for RNA polymerase III type 1." [SO:ke] +comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_1 to have an is_a path back to the root. +is_obsolete: true + +[Term] +id: SO:0000846 +name: RNApol_III_promoter_type_2_region +def: "A region of sequence which is a promoter for RNA polymerase III type 2." [SO:ke] +comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_2 to have an is_a path back to the root. +is_obsolete: true + +[Term] +id: SO:0000847 +name: tmRNA_region +def: "A region of a tmRNA." [SO:cb] +comment: This term was added to provide a grouping term for the region parts of tmRNA, thus giving them an is_a path back to the root. +synonym: "tmRNA region" EXACT [] +is_a: SO:0000834 ! mature_transcript_region +relationship: part_of SO:0000584 ! tmRNA + +[Term] +id: SO:0000848 +name: LTR_component +synonym: "long term repeat component" EXACT [] +synonym: "LTR component" EXACT [] +is_a: SO:0000840 ! repeat_component +relationship: part_of SO:0000286 ! long_terminal_repeat + +[Term] +id: SO:0000849 +name: three_prime_LTR_component +synonym: "3' long terminal repeat component" EXACT [] +synonym: "three prime LTR component" EXACT [] +is_a: SO:0000848 ! LTR_component +relationship: part_of SO:0000426 ! three_prime_LTR + +[Term] +id: SO:0000850 +name: five_prime_LTR_component +synonym: "5' long term repeat component" EXACT [] +synonym: "five prime LTR component" EXACT [] +is_a: SO:0000848 ! LTR_component +relationship: part_of SO:0000425 ! five_prime_LTR + +[Term] +id: SO:0000851 +name: CDS_region +def: "A region of a CDS." [SO:cb] +subset: SOFA +synonym: "CDS region" EXACT [] +is_a: SO:0000836 ! mRNA_region +relationship: part_of SO:0000316 ! CDS + +[Term] +id: SO:0000852 +name: exon_region +def: "A region of an exon." [RSC:cb] +subset: SOFA +synonym: "exon region" EXACT [] +is_a: SO:0000833 ! transcript_region +relationship: part_of SO:0000147 ! exon + +[Term] +id: SO:0000853 +name: homologous_region +def: "A region that is homologous to another region." [SO:ke] +synonym: "homolog" EXACT [] +synonym: "homologous region" EXACT [] +synonym: "homologue" EXACT [] +xref: http://en.wikipedia.org/wiki/Homology_(biology) "wiki" +is_a: SO:0000330 ! conserved_region +relationship: has_quality SO:0000857 ! homologous + +[Term] +id: SO:0000854 +name: paralogous_region +def: "A homologous_region that is paralogous to another region." [SO:ke] +comment: A term to be used in conjunction with the paralogous_to relationship. +synonym: "paralog" EXACT [] +synonym: "paralogous region" EXACT [] +synonym: "paralogue" EXACT [] +xref: http://en.wikipedia.org/wiki/Paralog#Paralogy "wiki" +is_a: SO:0000853 ! homologous_region +relationship: has_quality SO:0000859 ! paralogous + +[Term] +id: SO:0000855 +name: orthologous_region +def: "A homologous_region that is orthologous to another region." [SO:ke] +comment: This term should be used in conjunction with the similarity relationships defined in SO. +synonym: "ortholog" EXACT [] +synonym: "orthologous region" EXACT [] +synonym: "orthologue" EXACT [] +xref: http://en.wikipedia.org/wiki/Ortholog#Orthology "wiki" +is_a: SO:0000853 ! homologous_region +relationship: has_quality SO:0000858 ! orthologous + +[Term] +id: SO:0000856 +name: conserved +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000857 +name: homologous +def: "Similarity due to common ancestry." [SO:ke] +is_a: SO:0000856 ! conserved + +[Term] +id: SO:0000858 +name: orthologous +def: "An attribute describing a kind of homology where divergence occurred after a speciation event." [SO:ke] +is_a: SO:0000857 ! homologous + +[Term] +id: SO:0000859 +name: paralogous +def: "An attribute describing a kind of homology where divergence occurred after a duplication event." [SO:ke] +is_a: SO:0000857 ! homologous + +[Term] +id: SO:0000860 +name: syntenic +def: "Attribute describing sequence regions occurring in same order on chromosome of different species." [SO:ke] +xref: http://en.wikipedia.org/wiki/Syntenic "wiki" +is_a: SO:0000856 ! conserved + +[Term] +id: SO:0000861 +name: capped_primary_transcript +def: "A primary transcript that is capped." [SO:xp] +synonym: "capped primary transcript" EXACT [] +is_a: SO:0000185 ! primary_transcript +relationship: adjacent_to SO:0000581 ! cap +relationship: has_quality SO:0000146 ! capped + +[Term] +id: SO:0000862 +name: capped_mRNA +def: "An mRNA that is capped." [SO:xp] +synonym: "capped mRNA" EXACT [] +is_a: SO:0000234 ! mRNA +relationship: adjacent_to SO:0000581 ! cap +relationship: has_quality SO:0000146 ! capped + +[Term] +id: SO:0000863 +name: mRNA_attribute +def: "An attribute describing an mRNA feature." [SO:ke] +synonym: "mRNA attribute" EXACT [] +is_a: SO:0000237 ! transcript_attribute + +[Term] +id: SO:0000864 +name: exemplar +def: "An attribute describing a sequence is representative of a class of similar sequences." [SO:ke] +is_a: SO:0000863 ! mRNA_attribute + +[Term] +id: SO:0000865 +name: frameshift +def: "An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." [SO:ke] +xref: http://en.wikipedia.org/wiki/Frameshift "wiki" +is_a: SO:0000863 ! mRNA_attribute + +[Term] +id: SO:0000866 +name: minus_1_frameshift +def: "A frameshift caused by deleting one base." [SO:ke] +synonym: "minus 1 frameshift" EXACT [] +is_a: SO:0000865 ! frameshift + +[Term] +id: SO:0000867 +name: minus_2_frameshift +def: "A frameshift caused by deleting two bases." [SO:ke] +synonym: "minus 2 frameshift" EXACT [] +is_a: SO:0000865 ! frameshift + +[Term] +id: SO:0000868 +name: plus_1_frameshift +def: "A frameshift caused by inserting one base." [SO:ke] +synonym: "plus 1 frameshift" EXACT [] +is_a: SO:0000865 ! frameshift + +[Term] +id: SO:0000869 +name: plus_2_framshift +def: "A frameshift caused by inserting two bases." [SO:ke] +synonym: "plus 2 framshift" EXACT [] +is_a: SO:0000865 ! frameshift + +[Term] +id: SO:0000870 +name: trans_spliced +def: "An attribute describing transcript sequence that is created by splicing exons from diferent genes." [SO:ke] +synonym: "trans-spliced" EXACT [] +is_a: SO:0000237 ! transcript_attribute + +[Term] +id: SO:0000871 +name: polyadenylated_mRNA +def: "An mRNA that is polyadenylated." [SO:xp] +synonym: "polyadenylated mRNA" EXACT [] +is_a: SO:0000234 ! mRNA +relationship: adjacent_to SO:0000610 ! polyA_sequence +relationship: has_quality SO:0000246 ! polyadenylated + +[Term] +id: SO:0000872 +name: trans_spliced_mRNA +def: "An mRNA that is trans-spliced." [SO:xp] +synonym: "trans-spliced mRNA" EXACT [] +is_a: SO:0000234 ! mRNA +is_a: SO:0000479 ! trans_spliced_transcript +relationship: adjacent_to SO:0000636 ! spliced_leader_RNA +relationship: has_quality SO:0000870 ! trans_spliced + +[Term] +id: SO:0000873 +name: edited_transcript +def: "A transcript that is edited." [SO:ke] +synonym: "edited transcript" EXACT [] +is_a: SO:0000673 ! transcript +relationship: guided_by SO:0000602 ! guide_RNA +relationship: has_part SO:0000977 ! anchor_binding_site +relationship: has_quality SO:0000116 ! edited + +[Term] +id: SO:0000874 +name: edited_transcript_by_A_to_I_substitution +def: "A transcript that has been edited by A to I substitution." [SO:ke] +synonym: "edited transcript by A to I substitution" EXACT [] +is_a: SO:0000873 ! edited_transcript + +[Term] +id: SO:0000875 +name: bound_by_protein +def: "An attribute describing a sequence that is bound by a protein." [SO:ke] +synonym: "bound by protein" EXACT [] +is_a: SO:0000277 ! bound_by_factor + +[Term] +id: SO:0000876 +name: bound_by_nucleic_acid +def: "An attribute describing a sequence that is bound by a nucleic acid." [SO:ke] +synonym: "bound by nucleic acid" EXACT [] +is_a: SO:0000277 ! bound_by_factor + +[Term] +id: SO:0000877 +name: alternatively_spliced +def: "An attribute describing a situation where a gene may encode for more than 1 transcript." [SO:ke] +synonym: "alternatively spliced" EXACT [] +is_a: SO:0000237 ! transcript_attribute + +[Term] +id: SO:0000878 +name: monocistronic +def: "An attribute describing a sequence that contains the code for one gene product." [SO:ke] +is_a: SO:0000237 ! transcript_attribute + +[Term] +id: SO:0000879 +name: dicistronic +def: "An attribute describing a sequence that contains the code for two gene products." [SO:ke] +is_a: SO:0000880 ! polycistronic + +[Term] +id: SO:0000880 +name: polycistronic +def: "An attribute describing a sequence that contains the code for more than one gene product." [SO:ke] +is_a: SO:0000237 ! transcript_attribute + +[Term] +id: SO:0000881 +name: recoded +def: "An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke] +is_a: SO:0000863 ! mRNA_attribute + +[Term] +id: SO:0000882 +name: codon_redefined +def: "An attribute describing the alteration of codon meaning." [SO:ke] +synonym: "codon redefined" EXACT [] +is_a: SO:0000881 ! recoded + +[Term] +id: SO:0000883 +name: stop_codon_read_through +def: "A stop codon redefined to be a new amino acid." [SO:ke] +synonym: "stop codon read through" EXACT [] +synonym: "stop codon readthrough" RELATED [] +is_a: SO:0000145 ! recoded_codon + +[Term] +id: SO:0000884 +name: stop_codon_redefined_as_pyrrolysine +def: "A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke] +synonym: "stop codon redefined as pyrrolysine" EXACT [] +is_a: SO:0000883 ! stop_codon_read_through + +[Term] +id: SO:0000885 +name: stop_codon_redefined_as_selenocysteine +def: "A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke] +synonym: "stop codon redefined as selenocysteine" EXACT [] +is_a: SO:0000883 ! stop_codon_read_through + +[Term] +id: SO:0000886 +name: recoded_by_translational_bypass +def: "Recoded mRNA where a block of nucleotides is not translated." [SO:ke] +synonym: "recoded by translational bypass" EXACT [] +is_a: SO:0000881 ! recoded + +[Term] +id: SO:0000887 +name: translationally_frameshifted +def: "Recoding by frameshifting a particular site." [SO:ke] +synonym: "translationally frameshifted" EXACT [] +is_a: SO:0000881 ! recoded + +[Term] +id: SO:0000888 +name: maternally_imprinted_gene +def: "A gene that is maternally_imprinted." [SO:xp] +synonym: "maternally imprinted gene" EXACT [] +is_a: SO:0000898 ! epigenetically_modified_gene +relationship: has_quality SO:0000135 ! maternally_imprinted + +[Term] +id: SO:0000889 +name: paternally_imprinted_gene +def: "A gene that is paternally imprinted." [SO:xp] +synonym: "paternally imprinted gene" EXACT [] +is_a: SO:0000898 ! epigenetically_modified_gene +relationship: has_quality SO:0000136 ! paternally_imprinted + +[Term] +id: SO:0000890 +name: post_translationally_regulated_gene +def: "A gene that is post translationally regulated." [SO:xp] +synonym: "post translationally regulated gene" EXACT [] +is_a: SO:0000704 ! gene +relationship: has_quality SO:0000130 ! post_translationally_regulated + +[Term] +id: SO:0000891 +name: negatively_autoregulated_gene +def: "A gene that is negatively autoreguated." [SO:xp] +synonym: "negatively autoregulated gene" EXACT [] +is_a: SO:0000704 ! gene +relationship: has_quality SO:0000473 ! negatively_autoregulated + +[Term] +id: SO:0000892 +name: positively_autoregulated_gene +def: "A gene that is positively autoregulated." [SO:xp] +synonym: "positively autoregulated gene" EXACT [] +is_a: SO:0000704 ! gene +relationship: has_quality SO:0000475 ! positively_autoregulated + +[Term] +id: SO:0000893 +name: silenced +def: "An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke] +xref: http://en.wikipedia.org/wiki/Silenced "wiki" +is_a: SO:0000126 ! transcriptionally_repressed + +[Term] +id: SO:0000894 +name: silenced_by_DNA_modification +def: "An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." [SO:ke] +synonym: "silenced by DNA modification" EXACT [] +is_a: SO:0000893 ! silenced + +[Term] +id: SO:0000895 +name: silenced_by_DNA_methylation +def: "An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." [SO:ke] +synonym: "silenced by DNA methylation" EXACT [] +is_a: SO:0000894 ! silenced_by_DNA_modification + +[Term] +id: SO:0000896 +name: translationally_regulated_gene +def: "A gene that is translationally regulated." [SO:xp] +synonym: "translationally regulated gene" EXACT [] +is_a: SO:0000704 ! gene +relationship: has_quality SO:0000131 ! translationally_regulated + +[Term] +id: SO:0000897 +name: allelically_excluded_gene +def: "A gene that is allelically_excluded." [SO:xp] +synonym: "allelically excluded gene" EXACT [] +is_a: SO:0000898 ! epigenetically_modified_gene +relationship: has_quality SO:0000137 ! allelically_excluded + +[Term] +id: SO:0000898 +name: epigenetically_modified_gene +def: "A gene that is epigenetically modified." [SO:ke] +synonym: "epigenetically modified gene" EXACT [] +is_a: SO:0000704 ! gene +is_a: SO:0001720 ! epigenetically_modified_region +relationship: has_quality SO:0000133 ! epigenetically_modified + +[Term] +id: SO:0000899 +name: nuclear_mitochondrial +def: "An attribute describing a nuclear pseudogene of a mitochndrial gene." [SO:ke] +synonym: "nuclear mitochondrial" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000900 +name: processed +def: "An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail." [SO:ke] +is_obsolete: true + +[Term] +id: SO:0000901 +name: unequally_crossed_over +def: "An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination." [SO:ke] +synonym: "unequally crossed over" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000902 +name: transgene +def: "A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another." [SO:xp] +xref: http://en.wikipedia.org/wiki/Transgene "wiki" +is_a: SO:0000704 ! gene +relationship: has_quality SO:0000781 ! transgenic + +[Term] +id: SO:0000903 +name: endogenous_retroviral_sequence +synonym: "endogenous retroviral sequence" EXACT [] +is_a: SO:0000751 ! proviral_location + +[Term] +id: SO:0000904 +name: rearranged_at_DNA_level +def: "An attribute to describe the sequence of a feature, where the DNA is rearranged." [SO:ke] +synonym: "rearranged at DNA level" EXACT [] +is_a: SO:0000133 ! epigenetically_modified + +[Term] +id: SO:0000905 +name: status +def: "An attribute describing the status of a feature, based on the available evidence." [SO:ke] +comment: This term is the hypernym of attributes and should not be annotated to. +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000906 +name: independently_known +def: "Attribute to describe a feature that is independently known - not predicted." [SO:ke] +synonym: "independently known" EXACT [] +is_a: SO:0000905 ! status + +[Term] +id: SO:0000907 +name: supported_by_sequence_similarity +def: "An attribute to describe a feature that has been predicted using sequence similarity techniques." [SO:ke] +synonym: "supported by sequence similarity" EXACT [] +is_a: SO:0000732 ! predicted + +[Term] +id: SO:0000908 +name: supported_by_domain_match +def: "An attribute to describe a feature that has been predicted using sequence similarity of a known domain." [SO:ke] +synonym: "supported by domain match" EXACT [] +is_a: SO:0000907 ! supported_by_sequence_similarity + +[Term] +id: SO:0000909 +name: supported_by_EST_or_cDNA +def: "An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data." [SO:ke] +synonym: "supported by EST or cDNA" EXACT [] +is_a: SO:0000907 ! supported_by_sequence_similarity + +[Term] +id: SO:0000910 +name: orphan +is_a: SO:0000732 ! predicted + +[Term] +id: SO:0000911 +name: predicted_by_ab_initio_computation +def: "An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity." [SO:ke] +synonym: "predicted by ab initio computation" EXACT [] +is_a: SO:0000732 ! predicted + +[Term] +id: SO:0000912 +name: asx_turn +alt_id: BS:00203 +def: "A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "asx turn" EXACT [] +is_a: SO:0001128 ! polypeptide_turn_motif + +[Term] +id: SO:0000913 +name: cloned_cDNA_insert +def: "A clone insert made from cDNA." [SO:xp] +synonym: "cloned cDNA insert" EXACT [] +is_a: SO:0000753 ! clone_insert +relationship: has_quality SO:0000756 ! cDNA + +[Term] +id: SO:0000914 +name: cloned_genomic_insert +def: "A clone insert made from genomic DNA." [SO:xp] +synonym: "cloned genomic insert" EXACT [] +is_a: SO:0000753 ! clone_insert +relationship: has_quality SO:0000991 ! genomic_DNA + +[Term] +id: SO:0000915 +name: engineered_insert +def: "A clone insert that is engineered." [SO:xp] +synonym: "engineered insert" EXACT [] +is_a: SO:0000753 ! clone_insert +is_a: SO:0000804 ! engineered_region +relationship: has_quality SO:0000783 ! engineered + +[Term] +id: SO:0000916 +name: edit_operation +synonym: "edit operation" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000917 +name: insert_U +def: "An edit to insert a U." [SO:ke] +comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa. +synonym: "insert U" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000918 +name: delete_U +def: "An edit to delete a uridine." [SO:ke] +comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa. +synonym: "delete U" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000919 +name: substitute_A_to_I +def: "An edit to substitute an I for an A." [SO:ke] +synonym: "substitute A to I" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000920 +name: insert_C +def: "An edit to insert a cytidine." [SO:ke] +synonym: "insert C" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000921 +name: insert_dinucleotide +def: "An edit to insert a dinucleotide." [SO:ke] +synonym: "insert dinucleotide" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000922 +name: substitute_C_to_U +def: "An edit to substitute an U for a C." [SO:ke] +synonym: "substitute C to U" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000923 +name: insert_G +def: "An edit to insert a G." [SO:ke] +synonym: "insert G" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000924 +name: insert_GC +def: "An edit to insert a GC dinucleotide." [SO:ke] +comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. +synonym: "insert GC" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000925 +name: insert_GU +def: "An edit to insert a GU dinucleotide." [SO:ke] +comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. +synonym: "insert GU" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000926 +name: insert_CU +def: "An edit to insert a CU dinucleotide." [SO:ke] +comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. +synonym: "insert CU" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000927 +name: insert_AU +def: "An edit to insert a AU dinucleotide." [SO:ke] +comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. +synonym: "insert AU" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000928 +name: insert_AA +def: "An edit to insert a AA dinucleotide." [SO:ke] +comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. +synonym: "insert AA" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000929 +name: edited_mRNA +def: "An mRNA that is edited." [SO:xp] +synonym: "edited mRNA" EXACT [] +is_a: SO:0000234 ! mRNA +is_a: SO:0000873 ! edited_transcript +relationship: has_quality SO:0000116 ! edited + +[Term] +id: SO:0000930 +name: guide_RNA_region +def: "A region of guide RNA." [SO:ma] +synonym: "guide RNA region" EXACT [] +is_a: SO:0000834 ! mature_transcript_region +relationship: part_of SO:0000602 ! guide_RNA + +[Term] +id: SO:0000931 +name: anchor_region +def: "A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk] +synonym: "anchor region" EXACT [] +is_a: SO:0000930 ! guide_RNA_region + +[Term] +id: SO:0000932 +name: pre_edited_mRNA +synonym: "pre-edited mRNA" EXACT [] +is_a: SO:0000120 ! protein_coding_primary_transcript + +[Term] +id: SO:0000933 +name: intermediate +def: "An attribute to describe a feature between stages of processing." [SO:ke] +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000934 +name: miRNA_target_site +def: "A miRNA target site is a binding site where the molecule is a micro RNA." [FB:cds] +synonym: "miRNA target site" EXACT [] +is_a: SO:0001655 ! nucleotide_binding_site + +[Term] +id: SO:0000935 +name: edited_CDS +def: "A CDS that is edited." [SO:xp] +synonym: "edited CDS" EXACT [] +is_a: SO:0000316 ! CDS +relationship: has_quality SO:0000116 ! edited + +[Term] +id: SO:0000936 +name: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment +synonym: "vertebrate immunoglobulin T cell receptor rearranged segment" EXACT [] +is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature + +[Term] +id: SO:0000937 +name: vertebrate_immune_system_feature +is_obsolete: true + +[Term] +id: SO:0000938 +name: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +synonym: "vertebrate immunoglobulin T cell receptor rearranged gene cluster" EXACT [] +is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature + +[Term] +id: SO:0000939 +name: vertebrate_immune_system_gene_recombination_signal_feature +synonym: "vertebrate immune system gene recombination signal feature" EXACT [] +is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature + +[Term] +id: SO:0000940 +name: recombinationally_rearranged +synonym: "recombinationally rearranged" EXACT [] +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000941 +name: recombinationally_rearranged_vertebrate_immune_system_gene +def: "A recombinationally rearranged gene of the vertebrate immune system." [SO:xp] +synonym: "recombinationally rearranged vertebrate immune system gene" EXACT [] +is_a: SO:0000456 ! recombinationally_rearranged_gene + +[Term] +id: SO:0000942 +name: attP_site +def: "An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as] +synonym: "attP site" EXACT [] +is_a: SO:0000946 ! integration_excision_site +relationship: part_of SO:0001042 ! phage_sequence + +[Term] +id: SO:0000943 +name: attB_site +def: "An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:as] +synonym: "attB site" EXACT [] +is_a: SO:0000946 ! integration_excision_site + +[Term] +id: SO:0000944 +name: attL_site +def: "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." [SO:as] +synonym: "attBP'" RELATED [] +synonym: "attL site" RELATED [] +is_a: SO:0000946 ! integration_excision_site + +[Term] +id: SO:0000945 +name: attR_site +def: "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." [SO:as] +synonym: "attPB'" RELATED [] +synonym: "attR site" EXACT [] +is_a: SO:0000946 ! integration_excision_site + +[Term] +id: SO:0000946 +name: integration_excision_site +def: "A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as] +synonym: "attachment site" RELATED [] +synonym: "integration excision site" EXACT [] +is_a: SO:0000342 ! site_specific_recombination_target_region + +[Term] +id: SO:0000947 +name: resolution_site +def: "A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as] +synonym: "res site" EXACT [] +synonym: "resolution site" EXACT [] +is_a: SO:0000342 ! site_specific_recombination_target_region + +[Term] +id: SO:0000948 +name: inversion_site +def: "A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma] +comment: A target region for site-specific inversion of a DNA region and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase. +synonym: "inversion site" EXACT [] +is_a: SO:0000342 ! site_specific_recombination_target_region + +[Term] +id: SO:0000949 +name: dif_site +def: "A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as] +synonym: "dif site" EXACT [] +is_a: SO:0000947 ! resolution_site + +[Term] +id: SO:0000950 +name: attC_site +def: "An attC site is a sequence required for the integration of a DNA of an integron." [SO:as] +synonym: "attC site" EXACT [] +is_a: SO:0000946 ! integration_excision_site +relationship: part_of SO:0000365 ! integron + +[Term] +id: SO:0000951 +name: eukaryotic_terminator +synonym: "eukaryotic terminator" EXACT [] +is_a: SO:0000141 ! terminator + +[Term] +id: SO:0000952 +name: oriV +def: "An origin of vegetative replication in plasmids and phages." [SO:as] +synonym: "origin of vegetative replication" EXACT [] +is_a: SO:0000296 ! origin_of_replication + +[Term] +id: SO:0000953 +name: oriC +def: "An origin of bacterial chromosome replication." [SO:as] +synonym: "origin of bacterial chromosome replication" EXACT [] +is_a: SO:0000296 ! origin_of_replication + +[Term] +id: SO:0000954 +name: DNA_chromosome +def: "Structural unit composed of a self-replicating, DNA molecule." [SO:ma] +synonym: "DNA chromosome" EXACT [] +is_a: SO:0000340 ! chromosome +relationship: has_quality SO:0000352 ! DNA + +[Term] +id: SO:0000955 +name: double_stranded_DNA_chromosome +def: "Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma] +synonym: "double stranded DNA chromosome" EXACT [] +is_a: SO:0000954 ! DNA_chromosome +relationship: has_quality SO:0000985 ! double + +[Term] +id: SO:0000956 +name: single_stranded_DNA_chromosome +def: "Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma] +synonym: "single stranded DNA chromosome" EXACT [] +is_a: SO:0000954 ! DNA_chromosome +relationship: has_quality SO:0000984 ! single + +[Term] +id: SO:0000957 +name: linear_double_stranded_DNA_chromosome +def: "Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." [SO:ma] +synonym: "linear double stranded DNA chromosome" EXACT [] +is_a: SO:0000955 ! double_stranded_DNA_chromosome +relationship: has_quality SO:0000987 ! linear + +[Term] +id: SO:0000958 +name: circular_double_stranded_DNA_chromosome +def: "Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." [SO:ma] +synonym: "circular double stranded DNA chromosome" EXACT [] +is_a: SO:0000955 ! double_stranded_DNA_chromosome +relationship: has_quality SO:0000988 ! circular + +[Term] +id: SO:0000959 +name: linear_single_stranded_DNA_chromosome +def: "Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." [SO:ma] +synonym: "linear single stranded DNA chromosome" EXACT [] +is_a: SO:0000956 ! single_stranded_DNA_chromosome +relationship: has_quality SO:0000987 ! linear + +[Term] +id: SO:0000960 +name: circular_single_stranded_DNA_chromosome +def: "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma] +synonym: "circular single stranded DNA chromosome" EXACT [] +is_a: SO:0000956 ! single_stranded_DNA_chromosome +relationship: has_quality SO:0000988 ! circular + +[Term] +id: SO:0000961 +name: RNA_chromosome +def: "Structural unit composed of a self-replicating, RNA molecule." [SO:ma] +synonym: "RNA chromosome" EXACT [] +is_a: SO:0000340 ! chromosome +relationship: has_quality SO:0000356 ! RNA + +[Term] +id: SO:0000962 +name: single_stranded_RNA_chromosome +def: "Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma] +synonym: "single stranded RNA chromosome" EXACT [] +is_a: SO:0000961 ! RNA_chromosome +relationship: has_quality SO:0000984 ! single + +[Term] +id: SO:0000963 +name: linear_single_stranded_RNA_chromosome +def: "Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." [SO:ma] +synonym: "linear single stranded RNA chromosome" EXACT [] +is_a: SO:0000962 ! single_stranded_RNA_chromosome +relationship: has_quality SO:0000987 ! linear + +[Term] +id: SO:0000964 +name: linear_double_stranded_RNA_chromosome +def: "Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." [SO:ma] +synonym: "linear double stranded RNA chromosome" EXACT [] +is_a: SO:0000965 ! double_stranded_RNA_chromosome +relationship: has_quality SO:0000987 ! linear + +[Term] +id: SO:0000965 +name: double_stranded_RNA_chromosome +def: "Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma] +synonym: "double stranded RNA chromosome" EXACT [] +is_a: SO:0000961 ! RNA_chromosome +relationship: has_quality SO:0000985 ! double + +[Term] +id: SO:0000966 +name: circular_single_stranded_RNA_chromosome +def: "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma] +synonym: "circular single stranded RNA chromosome" EXACT [] +is_a: SO:0000962 ! single_stranded_RNA_chromosome +relationship: has_quality SO:0000988 ! circular + +[Term] +id: SO:0000967 +name: circular_double_stranded_RNA_chromosome +def: "Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." [SO:ma] +synonym: "circular double stranded RNA chromosome" EXACT [] +is_a: SO:0000965 ! double_stranded_RNA_chromosome +relationship: has_quality SO:0000988 ! circular + +[Term] +id: SO:0000968 +name: sequence_replication_mode +comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961. +synonym: "sequence replication mode" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000969 +name: rolling_circle +comment: This has been obsoleted as it represents a process. replaced_by: GO:0070581. +synonym: "rolling circle" EXACT [] +xref: http://en.wikipedia.org/wiki/Rolling_circle "wiki" +is_obsolete: true + +[Term] +id: SO:0000970 +name: theta_replication +comment: This has been obsoleted as it represents a process. replaced_by: GO:0070582 +synonym: "theta replication" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000971 +name: DNA_replication_mode +comment: This has been obsoleted as it represents a process. replaced_by: GO:0006260. +synonym: "DNA replication mode" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000972 +name: RNA_replication_mode +comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961. +synonym: "RNA replication mode" EXACT [] +is_obsolete: true + +[Term] +id: SO:0000973 +name: insertion_sequence +def: "A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as] +synonym: "insertion sequence" EXACT [] +synonym: "IS" RELATED [] +xref: http://en.wikipedia.org/wiki/Insertion_sequence "wiki" +is_a: SO:0000208 ! terminal_inverted_repeat_element + +[Term] +id: SO:0000975 +name: minicircle_gene +synonym: "minicircle gene" EXACT [] +is_a: SO:0000089 ! kinetoplast_gene +relationship: part_of SO:0000980 ! minicircle + +[Term] +id: SO:0000976 +name: cryptic +def: "A feature_attribute describing a feature that is not manifest under normal conditions." [SO:ke] +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000977 +name: anchor_binding_site +comment: Part of an edited transcript only. +synonym: "anchor binding site" EXACT [] +is_a: SO:0000833 ! transcript_region + +[Term] +id: SO:0000978 +name: template_region +def: "A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk] +synonym: "information region" EXACT [] +synonym: "template region" EXACT [] +is_a: SO:0000930 ! guide_RNA_region + +[Term] +id: SO:0000979 +name: gRNA_encoding +def: "A non-protein_coding gene that encodes a guide_RNA." [SO:ma] +synonym: "gRNA encoding" EXACT [] +is_a: SO:0000011 ! non_protein_coding + +[Term] +id: SO:0000980 +name: minicircle +alt_id: SO:0000974 +def: "A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs." [PMID:8395055] +synonym: "minicircle_chromosome" EXACT [] +xref: http://en.wikipedia.org/wiki/Minicircle "wiki" +is_a: SO:0001235 ! replicon + +[Term] +id: SO:0000981 +name: rho_dependent_bacterial_terminator +synonym: "rho dependent bacterial terminator" EXACT [] +is_a: SO:0000614 ! bacterial_terminator + +[Term] +id: SO:0000982 +name: rho_independent_bacterial_terminator +synonym: "rho independent bacterial terminator" EXACT [] +is_a: SO:0000614 ! bacterial_terminator + +[Term] +id: SO:0000983 +name: strand_attribute +comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. +synonym: "strand attribute" EXACT [] +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000984 +name: single +comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. +is_a: SO:0000983 ! strand_attribute + +[Term] +id: SO:0000985 +name: double +comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. +is_a: SO:0000983 ! strand_attribute + +[Term] +id: SO:0000986 +name: topology_attribute +comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. +synonym: "topology attribute" EXACT [] +is_a: SO:0000443 ! polymer_attribute + +[Term] +id: SO:0000987 +name: linear +def: "A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue." [SO:cb] +comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. +synonym: "two-ended" RELATED [] +is_a: SO:0000986 ! topology_attribute +disjoint_from: SO:0000988 ! circular + +[Term] +id: SO:0000988 +name: circular +def: "A quality of a nucleotide polymer that has no terminal nucleotide residues." [SO:cb] +comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. +synonym: "zero-ended" RELATED [] +is_a: SO:0000986 ! topology_attribute + +[Term] +id: SO:0000989 +name: class_II_RNA +def: "Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696] +synonym: "class II RNA" EXACT [] +is_a: SO:0000655 ! ncRNA + +[Term] +id: SO:0000990 +name: class_I_RNA +def: "Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696] +comment: Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577. +synonym: "class I RNA" EXACT [] +is_a: SO:0000655 ! ncRNA + +[Term] +id: SO:0000991 +name: genomic_DNA +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +synonym: "genomic DNA" EXACT [] +is_a: SO:0000352 ! DNA + +[Term] +id: SO:0000992 +name: BAC_cloned_genomic_insert +comment: Requested by Andy Schroder - Flybase Harvard, Nov 2006. +synonym: "BAC cloned genomic insert" EXACT [] +is_a: SO:0000914 ! cloned_genomic_insert +relationship: derives_from SO:0000153 ! BAC + +[Term] +id: SO:0000993 +name: consensus +comment: Term added Dec 06 to comply with mapping to MGED terms. It should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA. +is_a: SO:0000905 ! status + +[Term] +id: SO:0000994 +name: consensus_region +comment: DO not obsolete without considering MGED mapping. +synonym: "consensus region" EXACT [] +is_a: SO:0001410 ! experimental_feature +relationship: has_quality SO:0000993 ! consensus + +[Term] +id: SO:0000995 +name: consensus_mRNA +comment: DO not obsolete without considering MGED mapping. +synonym: "consensus mRNA" EXACT [] +is_a: SO:0000234 ! mRNA +is_a: SO:0000994 ! consensus_region +relationship: has_quality SO:0000993 ! consensus + +[Term] +id: SO:0000996 +name: predicted_gene +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +synonym: "predicted gene" EXACT [] +is_a: SO:0000704 ! gene +relationship: has_quality SO:0000732 ! predicted + +[Term] +id: SO:0000997 +name: gene_fragment +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +synonym: "gene fragment" EXACT [] +is_a: SO:0000842 ! gene_component_region +relationship: has_quality SO:0000731 ! fragmentary + +[Term] +id: SO:0000998 +name: recursive_splice_site +def: "A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661] +synonym: "recursive splice site" EXACT [] +is_a: SO:0001419 ! cis_splice_site + +[Term] +id: SO:0000999 +name: BAC_end +def: "A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke] +comment: Requested by Keith Boroevich December, 2006. +synonym: "BAC end" EXACT [] +synonym: "BAC end sequence" EXACT [] +synonym: "BES" EXACT [] +is_a: SO:0000150 ! read +relationship: part_of SO:0000153 ! BAC + +[Term] +id: SO:0001000 +name: rRNA_16S +def: "A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke] +subset: SOFA +synonym: "16S ribosomal RNA" EXACT [] +synonym: "16S rRNA" RELATED [] +synonym: "16S SSU RNA" EXACT [] +synonym: "rRNA 16S" EXACT [] +xref: http://en.wikipedia.org/wiki/16S_ribosomal_RNA "wiki" +is_a: SO:0000650 ! small_subunit_rRNA + +[Term] +id: SO:0001001 +name: rRNA_23S +def: "A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke] +subset: SOFA +synonym: "23S LSU rRNA" EXACT [] +synonym: "23S ribosomal RNA" RELATED [] +synonym: "23S rRNA" EXACT [] +synonym: "rRNA 23S" EXACT [] +is_a: SO:0000651 ! large_subunit_rRNA + +[Term] +id: SO:0001002 +name: rRNA_25S +def: "A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb] +subset: SOFA +synonym: "25S LSU rRNA" EXACT [] +synonym: "25S ribosomal RNA" EXACT [] +synonym: "25S rRNA" EXACT [] +synonym: "rRNA 25S" EXACT [] +is_a: SO:0000651 ! large_subunit_rRNA + +[Term] +id: SO:0001003 +name: solo_LTR +def: "A recombination product between the 2 LTR of the same element." [SO:ke] +comment: Requested by Hadi Quesneville January 2007. +synonym: "solo LTR" EXACT [] +is_a: SO:0000286 ! long_terminal_repeat + +[Term] +id: SO:0001004 +name: low_complexity +synonym: "low complexity" EXACT [] +is_a: SO:0000905 ! status + +[Term] +id: SO:0001005 +name: low_complexity_region +synonym: "low complexity region" EXACT [] +is_a: SO:0001410 ! experimental_feature +relationship: has_quality SO:0001004 ! low_complexity + +[Term] +id: SO:0001006 +name: prophage +def: "A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \"island\"." [GOC:jl] +xref: http://en.wikipedia.org/wiki/Prophage "wiki" +is_a: SO:0000113 ! proviral_region + +[Term] +id: SO:0001007 +name: cryptic_prophage +def: "A remnant of an integrated prophage in the host genome or an \"island\" in the host genome that includes phage like-genes." [GOC:jl] +comment: This is not cryptic in the same sense as a cryptic gene or cryptic splice site. +synonym: "cryptic prophage" EXACT [] +xref: http://ecoliwiki.net/colipedia/index.php/Category\:Cryptic_Prophage.w +is_a: SO:0000772 ! genomic_island + +[Term] +id: SO:0001008 +name: tetraloop +def: "A base-paired stem with loop of 4 non-hydrogen bonded nucleotides." [SO:ke] +xref: http://en.wikipedia.org/wiki/Tetraloop "wiki" +is_a: SO:0000313 ! stem_loop + +[Term] +id: SO:0001009 +name: DNA_constraint_sequence +def: "A double-stranded DNA used to control macromolecular structure and function." [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au\]&dispmax=50] +synonym: "DNA constraint" EXACT [] +synonym: "DNA constraint sequence" EXACT [] +is_a: SO:0000442 ! ds_oligo + +[Term] +id: SO:0001010 +name: i_motif +def: "A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH." [PMID:9753739] +synonym: "i motif" EXACT [] +synonym: "short intercalated motif" EXACT [] +is_a: SO:0000142 ! DNA_sequence_secondary_structure + +[Term] +id: SO:0001011 +name: PNA_oligo +def: "Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [SO:ke] +synonym: "peptide nucleic acid" EXACT [] +synonym: "PNA oligo" EXACT [] +xref: http://en.wikipedia.org/wiki/Peptide_nucleic_acid "wiki" +is_a: SO:0001247 ! synthetic_oligo +relationship: has_quality SO:0001184 ! PNA + +[Term] +id: SO:0001012 +name: DNAzyme +def: "A DNA sequence with catalytic activity." [SO:cb] +comment: Added by request from Colin Batchelor. +synonym: "catalytic DNA" EXACT [] +synonym: "deoxyribozyme" RELATED [] +synonym: "DNA enzyme" EXACT [] +is_a: SO:0000696 ! oligo +relationship: has_quality SO:0001185 ! enzymatic + +[Term] +id: SO:0001013 +name: MNP +def: "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431] +synonym: "multiple nucleotide polymorphism" RELATED [] +is_a: SO:0002007 ! MNV + +[Term] +id: SO:0001014 +name: intron_domain +comment: Requested by Colin Batchelor, Feb 2007. +synonym: "intron domain" EXACT [] +is_a: SO:0000835 ! primary_transcript_region +relationship: part_of SO:0000188 ! intron + +[Term] +id: SO:0001015 +name: wobble_base_pair +def: "A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C." [PMID:11256617] +synonym: "wobble base pair" EXACT [] +synonym: "wobble pair" EXACT [] +xref: http://en.wikipedia.org/wiki/Wobble_base_pair "wiki" +is_a: SO:0000028 ! base_pair + +[Term] +id: SO:0001016 +name: internal_guide_sequence +def: "A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb] +synonym: "IGS" EXACT [] +synonym: "internal guide sequence" EXACT [] +is_a: SO:0001014 ! intron_domain +relationship: part_of SO:0000587 ! group_I_intron + +[Term] +id: SO:0001017 +name: silent_mutation +def: "A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation." [SO:ke] +comment: Added in March 2007 in after meeting with PharmGKB. Although this term is in common usage, it is better to annotate with the most specific term possible, such as synonymous codon, intron variant etc. +synonym: "silent mutation" EXACT [] +xref: http://en.wikipedia.org/wiki/Silent_mutation "wiki" +xref: loinc:LA6700-4 "Silent" +is_a: SO:0001878 ! feature_variant + +[Term] +id: SO:0001018 +name: epitope +def: "A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells." [http://en.wikipedia.org/wiki/Epitope, SO:cb] +comment: Requested by Trish Whetzel. +xref: http://en.wikipedia.org/wiki/Epitope "wiki" +is_a: SO:0000409 ! binding_site + +[Term] +id: SO:0001019 +name: copy_number_variation +def: "A variation that increases or decreases the copy number of a given region." [SO:ke] +subset: SOFA +synonym: "CNP" EXACT [] +synonym: "CNV" EXACT [] +synonym: "copy number polymorphism" EXACT [] +synonym: "copy number variation" EXACT [] +xref: http://en.wikipedia.org/wiki/Copy_number_variation "wiki" +is_a: SO:0001059 ! sequence_alteration + +[Term] +id: SO:0001020 +name: sequence_variant_affecting_copy_number +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting copy number" EXACT [] +synonym: "sequence variant affecting copy number" EXACT [] +is_obsolete: true +replaced_by: SO:0001563 + +[Term] +id: SO:0001021 +name: chromosome_breakpoint +alt_id: SO:0001242 +synonym: "aberration breakpoint" EXACT [] +synonym: "aberration_junction" EXACT [] +synonym: "chromosome breakpoint" EXACT [] +is_a: SO:0000699 ! junction +relationship: part_of SO:0000340 ! chromosome + +[Term] +id: SO:0001022 +name: inversion_breakpoint +def: "The point within a chromosome where an inversion begins or ends." [SO:cb] +synonym: "inversion breakpoint" EXACT [] +is_a: SO:0001021 ! chromosome_breakpoint + +[Term] +id: SO:0001023 +name: allele +def: "An allele is one of a set of coexisting sequence variants of a gene." [SO:immuno_workshop] +synonym: "allelomorph" EXACT [] +xref: http://en.wikipedia.org/wiki/Allele "wiki" +is_a: SO:0001507 ! variant_collection +relationship: variant_of SO:0000704 ! gene + +[Term] +id: SO:0001024 +name: haplotype +def: "A haplotype is one of a set of coexisting sequence variants of a haplotype block." [SO:immuno_workshop] +xref: http://en.wikipedia.org/wiki/Haplotype "wiki" +is_a: SO:0001507 ! variant_collection +relationship: variant_of SO:0000355 ! haplotype_block + +[Term] +id: SO:0001025 +name: polymorphic_sequence_variant +def: "A sequence variant that is segregating in one or more natural populations of a species." [SO:immuno_workshop] +synonym: "polymorphic sequence variant" EXACT [] +is_a: SO:0001023 ! allele + +[Term] +id: SO:0001026 +name: genome +def: "A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop] +xref: http://en.wikipedia.org/wiki/Genome "wiki" +is_a: SO:0001260 ! sequence_collection +relationship: has_part SO:0001235 ! replicon + +[Term] +id: SO:0001027 +name: genotype +def: "A genotype is a variant genome, complete or incomplete." [SO:immuno_workshop] +xref: http://en.wikipedia.org/wiki/Genotype "wiki" +is_a: SO:0001507 ! variant_collection +relationship: variant_of SO:0001026 ! genome + +[Term] +id: SO:0001028 +name: diplotype +def: "A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known." [SO:immuno_workshop] +is_a: SO:0001507 ! variant_collection + +[Term] +id: SO:0001029 +name: direction_attribute +synonym: "direction attribute" EXACT [] +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0001030 +name: forward +def: "Forward is an attribute of the feature, where the feature is in the 5' to 3' direction." [SO:ke] +is_a: SO:0001029 ! direction_attribute + +[Term] +id: SO:0001031 +name: reverse +def: "Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer." [SO:ke] +is_a: SO:0001029 ! direction_attribute + +[Term] +id: SO:0001032 +name: mitochondrial_DNA +comment: This terms is used by MO. +synonym: "mitochondrial DNA" EXACT [] +synonym: "mtDNA" EXACT [] +xref: http://en.wikipedia.org/wiki/Mitochondrial_DNA "wiki" +is_a: SO:0000737 ! mitochondrial_sequence +relationship: has_quality SO:0000352 ! DNA + +[Term] +id: SO:0001033 +name: chloroplast_DNA +comment: This term is used by MO. +synonym: "chloroplast DNA" EXACT [] +is_a: SO:0000745 ! chloroplast_sequence +relationship: has_quality SO:0000352 ! DNA + +[Term] +id: SO:0001034 +name: miRtron +def: "A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma] +comment: Ruby et al. Nature 448:83 describe a new class of miRNAs that are derived from de-branched introns. +is_a: SO:0001014 ! intron_domain +relationship: has_part SO:0001244 ! pre_miRNA + +[Term] +id: SO:0001035 +name: piRNA +def: "A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke] +synonym: "piwi-associated RNA" EXACT [] +xref: http://en.wikipedia.org/wiki/PiRNA "wiki" +is_a: SO:0000655 ! ncRNA + +[Term] +id: SO:0001036 +name: arginyl_tRNA +def: "A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke] +synonym: "arginyl tRNA" EXACT [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0000212 ! arginine_tRNA_primary_transcript + +[Term] +id: SO:0001037 +name: mobile_genetic_element +def: "A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355] +subset: SOFA +synonym: "MGE" EXACT [] +synonym: "mobile genetic element" EXACT [] +xref: http://en.wikipedia.org/wiki/Mobile_genetic_element "wiki" +is_a: SO:0001411 ! biological_region +relationship: has_quality SO:0001234 ! mobile + +[Term] +id: SO:0001038 +name: extrachromosomal_mobile_genetic_element +def: "An MGE that is not integrated into the host chromosome." [SO:ke] +synonym: "extrachromosomal mobile genetic element" EXACT [] +is_a: SO:0001037 ! mobile_genetic_element + +[Term] +id: SO:0001039 +name: integrated_mobile_genetic_element +def: "An MGE that is integrated into the host chromosome." [SO:ke] +subset: SOFA +synonym: "integrated mobile genetic element" EXACT [] +is_a: SO:0001037 ! mobile_genetic_element + +[Term] +id: SO:0001040 +name: integrated_plasmid +def: "A plasmid sequence that is integrated within the host chromosome." [SO:ke] +synonym: "integrated plasmid" EXACT [] +is_a: SO:0001039 ! integrated_mobile_genetic_element +relationship: derives_from SO:0000155 ! plasmid + +[Term] +id: SO:0001041 +name: viral_sequence +def: "The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke] +comment: The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct. +synonym: "viral sequence" EXACT [] +synonym: "virus sequence" EXACT [] +is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element +is_a: SO:0001235 ! replicon + +[Term] +id: SO:0001042 +name: phage_sequence +def: "The nucleotide sequence of a virus that infects bacteria." [SO:ke] +synonym: "bacteriophage" EXACT [] +synonym: "phage" EXACT [] +synonym: "phage sequence" EXACT [] +xref: http://en.wikipedia.org/wiki/Bacteriophage "wiki" +is_a: SO:0001041 ! viral_sequence + +[Term] +id: SO:0001043 +name: attCtn_site +def: "An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at] +synonym: "attCtn site" EXACT [] +is_a: SO:0000946 ! integration_excision_site +relationship: part_of SO:0000371 ! conjugative_transposon + +[Term] +id: SO:0001044 +name: nuclear_mt_pseudogene +def: "A nuclear pseudogene of either coding or non-coding mitochondria derived sequence." [SO:xp] +comment: Definition change requested by Val, 3172757. +synonym: "nuclear mitochondrial pseudogene" EXACT [] +synonym: "nuclear mt pseudogene" EXACT [] +synonym: "NUMT" EXACT [] +xref: http://en.wikipedia.org/wiki/Numt "wikipedia" +is_a: SO:0001760 ! non_processed_pseudogene + +[Term] +id: SO:0001045 +name: cointegrated_plasmid +def: "A MGE region consisting of two fused plasmids resulting from a replicative transposition event." [phigo:at] +synonym: "cointegrated plasmid" EXACT [] +synonym: "cointegrated replicon" EXACT [] +is_a: SO:0001039 ! integrated_mobile_genetic_element + +[Term] +id: SO:0001046 +name: IRLinv_site +def: "Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at] +synonym: "IRLinv site" EXACT [] +is_a: SO:0001048 ! inversion_site_part +relationship: part_of SO:0000948 ! inversion_site + +[Term] +id: SO:0001047 +name: IRRinv_site +def: "Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at] +synonym: "IRRinv site" EXACT [] +is_a: SO:0001048 ! inversion_site_part +relationship: part_of SO:0000948 ! inversion_site + +[Term] +id: SO:0001048 +name: inversion_site_part +def: "A region located within an inversion site." [SO:ke] +comment: A term created to allow the parts of an inversion site have an is_a path back to the root. +synonym: "inversion site part" EXACT [] +is_a: SO:0000342 ! site_specific_recombination_target_region + +[Term] +id: SO:0001049 +name: defective_conjugative_transposon +def: "An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." [Phigo:ariane] +synonym: "defective conjugative transposon" EXACT [] +is_a: SO:0000772 ! genomic_island + +[Term] +id: SO:0001050 +name: repeat_fragment +def: "A portion of a repeat, interrupted by the insertion of another element." [SO:ke] +comment: Requested by Chris Smith, and others at Flybase to help annotate nested repeats. +synonym: "repeat fragment" EXACT [] +is_a: SO:0000840 ! repeat_component +relationship: part_of SO:0001649 ! nested_repeat + +[Term] +id: SO:0001051 +name: nested_region +is_obsolete: true + +[Term] +id: SO:0001052 +name: nested_repeat +is_obsolete: true + +[Term] +id: SO:0001053 +name: nested_transposon +is_obsolete: true + +[Term] +id: SO:0001054 +name: transposon_fragment +def: "A portion of a transposon, interrupted by the insertion of another element." [SO:ke] +synonym: "transposon fragment" EXACT [] +is_a: SO:0000840 ! repeat_component +relationship: part_of SO:0001648 ! nested_transposon + +[Term] +id: SO:0001055 +name: transcriptional_cis_regulatory_region +def: "A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative] +subset: SOFA +synonym: "transcription-control region" EXACT [] +synonym: "transcriptional cis regulatory region" EXACT [] +is_a: SO:0001679 ! transcription_regulatory_region + +[Term] +id: SO:0001056 +name: splicing_regulatory_region +def: "A regulatory_region that modulates splicing." [SO:ke] +subset: SOFA +synonym: "splicing regulatory region" EXACT [] +is_a: SO:0001679 ! transcription_regulatory_region + +[Term] +id: SO:0001057 +name: enhanceosome +is_obsolete: true + +[Term] +id: SO:0001058 +name: promoter_targeting_sequence +def: "A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." [SO:regcreative] +synonym: "promoter targeting sequence" EXACT [] +is_a: SO:0001055 ! transcriptional_cis_regulatory_region + +[Term] +id: SO:0001059 +name: sequence_alteration +alt_id: SO:1000004 +alt_id: SO:1000007 +def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke] +comment: Merged with partially characterized change in nucleotide sequence. +subset: SOFA +synonym: "partially characterised change in DNA sequence" NARROW [] +synonym: "partially_characterised_change_in_DNA_sequence" NARROW [] +synonym: "sequence alteration" EXACT [] +synonym: "sequence variation" RELATED [] +synonym: "uncharacterised_change_in_nucleotide_sequence" NARROW [] +is_a: SO:0000110 ! sequence_feature + +[Term] +id: SO:0001060 +name: sequence_variant +def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke] +synonym: "ANNOVAR:unknown" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] +synonym: "Jannovar:sequence_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "sequence variant" EXACT [] +synonym: "VAAST:sequence_variant" EXACT VAR [] +is_a: SO:0002072 ! sequence_comparison + +[Term] +id: SO:0001061 +name: propeptide_cleavage_site +alt_id: BS:00063 +def: "The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR] +comment: Discrete. +subset: biosapiens +synonym: "propeptide cleavage site" EXACT [] +is_a: SO:0100011 ! cleaved_peptide_region +relationship: part_of SO:0001062 ! propeptide + +[Term] +id: SO:0001062 +name: propeptide +alt_id: BS:00077 +def: "Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR] +comment: Range. +subset: biosapiens +synonym: "propep" RELATED [uniprot:feature_type] +xref: http://en.wikipedia.org/wiki/Propeptide "wiki" +is_a: SO:0100011 ! cleaved_peptide_region + +[Term] +id: SO:0001063 +name: immature_peptide_region +alt_id: BS:00129 +def: "An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR] +comment: Range. +subset: biosapiens +subset: SOFA +synonym: "immature peptide region" EXACT [] +is_a: SO:0000839 ! polypeptide_region + +[Term] +id: SO:0001064 +name: active_peptide +alt_id: BS:00076 +def: "Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual] +comment: Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length. +subset: biosapiens +synonym: "active peptide" EXACT [] +synonym: "peptide" BROAD [uniprot:feature_type] +xref: http://en.wikipedia.org/wiki/Peptide "wiki" +is_a: SO:0000419 ! mature_protein_region + +[Term] +id: SO:0001066 +name: compositionally_biased_region_of_peptide +alt_id: BS:00068 +def: "Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length." [EBIBS:GAR, UniProt:curation_manual] +comment: Range. +subset: biosapiens +synonym: "compbias" RELATED [uniprot:feature_type] +synonym: "compositional bias" RELATED [] +synonym: "compositionally biased" RELATED [] +synonym: "compositionally biased region of peptide" RELATED [] +synonym: "compositionally_biased_region" EXACT [] +is_a: SO:0000839 ! polypeptide_region + +[Term] +id: SO:0001067 +name: polypeptide_motif +alt_id: BS:00032 +def: "A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual] +comment: Range. +subset: biosapiens +synonym: "motif" BROAD [uniprot:feature_type] +synonym: "polypeptide motif" EXACT [] +is_a: SO:0100021 ! polypeptide_conserved_region + +[Term] +id: SO:0001068 +name: polypeptide_repeat +alt_id: BS:00070 +def: "A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR] +comment: Range. +subset: biosapiens +synonym: "polypeptide repeat" EXACT [] +synonym: "repeat" RELATED [uniprot:feature_type] +is_a: SO:0100021 ! polypeptide_conserved_region + +[Term] +id: SO:0001070 +name: polypeptide_structural_region +alt_id: BS:00337 +def: "Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb] +comment: Range. +subset: biosapiens +synonym: "polypeptide structural region" EXACT [] +synonym: "structural_region" RELATED [] +is_a: SO:0000839 ! polypeptide_region + +[Term] +id: SO:0001071 +name: membrane_structure +alt_id: BS:00128 +def: "Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR] +comment: Range. +subset: biosapiens +synonym: "membrane structure" EXACT [] +is_a: SO:0001070 ! polypeptide_structural_region + +[Term] +id: SO:0001072 +name: extramembrane_polypeptide_region +alt_id: BS:00154 +def: "Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb] +comment: Range. +subset: biosapiens +synonym: "extramembrane" RELATED BS [] +synonym: "extramembrane polypeptide region" EXACT [] +synonym: "extramembrane_region" RELATED BS [] +synonym: "topo_dom" RELATED BS [uniprot:feature_type] +is_a: SO:0001070 ! polypeptide_structural_region +relationship: part_of SO:0001071 ! membrane_structure + +[Term] +id: SO:0001073 +name: cytoplasmic_polypeptide_region +alt_id: BS:00145 +def: "Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb] +subset: biosapiens +synonym: "cytoplasm_location" EXACT BS [] +synonym: "cytoplasmic polypeptide region" EXACT [] +synonym: "inside" RELATED BS [] +is_a: SO:0001072 ! extramembrane_polypeptide_region + +[Term] +id: SO:0001074 +name: non_cytoplasmic_polypeptide_region +alt_id: BS:00144 +def: "Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb] +comment: This could be inside an organelle within the cell. +subset: biosapiens +synonym: "non cytoplasmic polypeptide region" EXACT [] +synonym: "non_cytoplasm_location" EXACT BS [] +synonym: "outside" RELATED BS [] +is_a: SO:0001072 ! extramembrane_polypeptide_region + +[Term] +id: SO:0001075 +name: intramembrane_polypeptide_region +alt_id: BS:00156 +def: "Polypeptide region present in the lipid bilayer." [EBIBS:GAR] +subset: biosapiens +synonym: "intramembrane" RELATED BS [] +synonym: "intramembrane polypeptide region" EXACT [] +is_a: SO:0001070 ! polypeptide_structural_region +relationship: part_of SO:0001071 ! membrane_structure + +[Term] +id: SO:0001076 +name: membrane_peptide_loop +alt_id: BS:00155 +def: "Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb] +subset: biosapiens +synonym: "membrane peptide loop" EXACT [] +synonym: "membrane_loop" RELATED BS [] +is_a: SO:0001075 ! intramembrane_polypeptide_region + +[Term] +id: SO:0001077 +name: transmembrane_polypeptide_region +alt_id: BS:00158 +def: "Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual] +subset: biosapiens +synonym: "transmem" RELATED BS [uniprot:feature_type] +synonym: "transmembrane" RELATED BS [] +synonym: "transmembrane polypeptide region" EXACT [] +is_a: SO:0001075 ! intramembrane_polypeptide_region + +[Term] +id: SO:0001078 +name: polypeptide_secondary_structure +alt_id: BS:00003 +def: "A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR] +comment: Biosapien term was secondary_structure. +subset: biosapiens +synonym: "2nary structure" RELATED BS [] +synonym: "polypeptide secondary structure" EXACT [] +synonym: "secondary structure" RELATED BS [] +synonym: "secondary structure region" RELATED BS [] +synonym: "secondary_structure" RELATED BS [] +xref: http://en.wikipedia.org/wiki/Secondary_structure "wiki" +is_a: SO:0001070 ! polypeptide_structural_region + +[Term] +id: SO:0001079 +name: polypeptide_structural_motif +alt_id: BS:0000338 +def: "Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR] +subset: biosapiens +synonym: "polypeptide structural motif" RELATED [] +synonym: "structural_motif" RELATED BS [] +xref: http://en.wikipedia.org/wiki/Structural_motif "wiki" +is_a: SO:0001070 ! polypeptide_structural_region + +[Term] +id: SO:0001080 +name: coiled_coil +alt_id: BS:00041 +def: "A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual] +comment: Range. +subset: biosapiens +synonym: "coiled" RELATED BS [uniprot:feature_type] +synonym: "coiled coil" EXACT [] +xref: http://en.wikipedia.org/wiki/Coiled_coil "wiki" +is_a: SO:0001079 ! polypeptide_structural_motif + +[Term] +id: SO:0001081 +name: helix_turn_helix +alt_id: BS:00147 +def: "A motif comprising two helices separated by a turn." [EBIBS:GAR] +subset: biosapiens +synonym: "helix turn helix" EXACT [] +synonym: "helix-turn-helix" EXACT [] +synonym: "HTH" RELATED BS [] +is_a: SO:0001079 ! polypeptide_structural_motif +relationship: has_part SO:0001114 ! peptide_helix +relationship: has_part SO:0001128 ! polypeptide_turn_motif + +[Term] +id: SO:0001082 +name: polypeptide_sequencing_information +alt_id: BS:00125 +def: "Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR] +comment: Range. +subset: biosapiens +synonym: "sequencing_information" EXACT [] +is_a: SO:0000700 ! remark + +[Term] +id: SO:0001083 +name: non_adjacent_residues +alt_id: BS:00182 +def: "Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them." [EBIBS:GAR, UniProt:curation_manual] +subset: biosapiens +synonym: "non consecutive" EXACT [] +synonym: "non_cons" EXACT [uniprot:feature_type] +is_a: SO:0001082 ! polypeptide_sequencing_information + +[Term] +id: SO:0001084 +name: non_terminal_residue +alt_id: BS:00072 +def: "The residue at an extremity of the sequence is not the terminal residue." [EBIBS:GAR, UniProt:curation_manual] +comment: Discrete. +subset: biosapiens +synonym: "non terminal" EXACT [] +synonym: "non_ter" EXACT [uniprot:feature_type] +is_a: SO:0001082 ! polypeptide_sequencing_information + +[Term] +id: SO:0001085 +name: sequence_conflict +alt_id: BS:00069 +def: "Different sources report differing sequences." [EBIBS:GAR, UniProt:curation_manual] +comment: Discrete. +subset: biosapiens +synonym: "conflict" EXACT [uniprot:feature_type] +is_a: SO:0001082 ! polypeptide_sequencing_information + +[Term] +id: SO:0001086 +name: sequence_uncertainty +alt_id: BS:00181 +def: "Describes the positions in a sequence where the authors are unsure about the sequence assignment." [EBIBS:GAR, UniProt:curation_manual] +subset: biosapiens +synonym: "unsure" EXACT [uniprot:feature_type] +is_a: SO:0001082 ! polypeptide_sequencing_information + +[Term] +id: SO:0001087 +name: cross_link +alt_id: BS:00178 +def: "Posttranslationally formed amino acid bonds." [EBIBS:GAR, UniProt:curation_manual] +subset: biosapiens +synonym: "cross link" EXACT [] +synonym: "crosslink" RELATED [] +is_obsolete: true + +[Term] +id: SO:0001088 +name: disulfide_bond +alt_id: BS:00028 +def: "The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules." [EBIBS:GAR, UniProt:curation_manual] +comment: 2 discreet & joined. +subset: biosapiens +synonym: "disulfid" RELATED [] +synonym: "disulfide" RELATED [] +synonym: "disulfide bond" RELATED [] +synonym: "disulphide" EXACT [] +synonym: "disulphide bond" RELATED [] +is_obsolete: true + +[Term] +id: SO:0001089 +name: post_translationally_modified_region +alt_id: BS:00052 +def: "A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual] +comment: Discrete. +subset: biosapiens +synonym: "mod_res" EXACT [uniprot:feature_type] +synonym: "modified residue" EXACT [] +synonym: "post_translational_modification" EXACT [] +xref: http://en.wikipedia.org/wiki/Post_translational_modification "wiki" +is_a: SO:0100001 ! biochemical_region_of_peptide + +[Term] +id: SO:0001090 +name: covalent_binding_site +alt_id: BS:00246 +def: "Binding involving a covalent bond." [EBIBS:GAR] +subset: biosapiens +synonym: "covalent binding site" EXACT [] +is_obsolete: true + +[Term] +id: SO:0001091 +name: non_covalent_binding_site +alt_id: BS:00029 +def: "Binding site for any chemical group (co-enzyme, prosthetic group, etc.)." [EBIBS:GAR] +comment: Discrete. +subset: biosapiens +synonym: "binding" RELATED [uniprot:curation] +synonym: "binding site" RELATED [] +synonym: "non covalent binding site" EXACT [] +is_obsolete: true + +[Term] +id: SO:0001092 +name: polypeptide_metal_contact +alt_id: BS:00027 +def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual] +comment: Residue is part of a binding site for a metal ion. +subset: biosapiens +synonym: "metal_binding" RELATED [] +is_a: SO:0001656 ! metal_binding_site +is_a: SO:0100002 ! molecular_contact_region + +[Term] +id: SO:0001093 +name: protein_protein_contact +alt_id: BS:00131 +def: "A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual] +subset: biosapiens +synonym: "protein protein contact" EXACT [] +synonym: "protein protein contact site" EXACT [] +synonym: "protein_protein_interaction" RELATED [] +xref: http://en.wikipedia.org/wiki/Protein_protein_interaction "wiki" +is_a: SO:0000410 ! protein_binding_site +is_a: SO:0100002 ! molecular_contact_region + +[Term] +id: SO:0001094 +name: polypeptide_calcium_ion_contact_site +alt_id: BS:00186 +def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR] +comment: Residue involved in contact with calcium. +subset: biosapiens +synonym: "ca bind" RELATED [] +synonym: "ca_bind" EXACT BS [uniprot:feature_type] +synonym: "Ca_contact_site" EXACT [] +synonym: "polypeptide calcium ion contact site" EXACT [] +is_a: SO:0001092 ! polypeptide_metal_contact + +[Term] +id: SO:0001095 +name: polypeptide_cobalt_ion_contact_site +alt_id: BS:00136 +def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb] +subset: biosapiens +synonym: "Co_contact_site" EXACT [] +synonym: "polypeptide cobalt ion contact site" EXACT [] +is_a: SO:0001092 ! polypeptide_metal_contact + +[Term] +id: SO:0001096 +name: polypeptide_copper_ion_contact_site +alt_id: BS:00146 +def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb] +subset: biosapiens +synonym: "Cu_contact_site" EXACT [] +synonym: "polypeptide copper ion contact site" EXACT [] +is_a: SO:0001092 ! polypeptide_metal_contact + +[Term] +id: SO:0001097 +name: polypeptide_iron_ion_contact_site +alt_id: BS:00137 +def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb] +subset: biosapiens +synonym: "Fe_contact_site" EXACT [] +synonym: "polypeptide iron ion contact site" EXACT [] +is_a: SO:0001092 ! polypeptide_metal_contact + +[Term] +id: SO:0001098 +name: polypeptide_magnesium_ion_contact_site +alt_id: BS:00187 +def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb] +subset: biosapiens +synonym: "Mg_contact_site" EXACT [] +synonym: "polypeptide magnesium ion contact site" EXACT [] +is_a: SO:0001092 ! polypeptide_metal_contact + +[Term] +id: SO:0001099 +name: polypeptide_manganese_ion_contact_site +alt_id: BS:00140 +def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb] +subset: biosapiens +synonym: "Mn_contact_site" EXACT [] +synonym: "polypeptide manganese ion contact site" EXACT [] +is_a: SO:0001092 ! polypeptide_metal_contact + +[Term] +id: SO:0001100 +name: polypeptide_molybdenum_ion_contact_site +alt_id: BS:00141 +def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb] +subset: biosapiens +synonym: "Mo_contact_site" EXACT [] +synonym: "polypeptide molybdenum ion contact site" EXACT [] +is_a: SO:0001092 ! polypeptide_metal_contact + +[Term] +id: SO:0001101 +name: polypeptide_nickel_ion_contact_site +alt_id: BS:00142 +def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR] +subset: biosapiens +synonym: "Ni_contact_site" EXACT [] +synonym: "polypeptide nickel ion contact site" EXACT [] +is_a: SO:0001092 ! polypeptide_metal_contact + +[Term] +id: SO:0001102 +name: polypeptide_tungsten_ion_contact_site +alt_id: BS:00143 +def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb] +subset: biosapiens +synonym: "polypeptide tungsten ion contact site" EXACT [] +synonym: "W_contact_site" EXACT [] +is_a: SO:0001092 ! polypeptide_metal_contact + +[Term] +id: SO:0001103 +name: polypeptide_zinc_ion_contact_site +alt_id: BS:00185 +def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb] +subset: biosapiens +synonym: "polypeptide zinc ion contact site" EXACT [] +synonym: "Zn_contact_site" EXACT [] +is_a: SO:0001092 ! polypeptide_metal_contact + +[Term] +id: SO:0001104 +name: catalytic_residue +alt_id: BS:00026 +def: "Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual] +comment: Discrete. +subset: biosapiens +synonym: "act_site" RELATED [uniprot:feature_type] +synonym: "active site residue" EXACT [] +synonym: "catalytic residue" EXACT [] +is_a: SO:0001237 ! amino_acid +relationship: part_of SO:0100019 ! polypeptide_catalytic_motif + +[Term] +id: SO:0001105 +name: polypeptide_ligand_contact +alt_id: BS:00157 +def: "Residues which interact with a ligand." [EBIBS:GAR] +subset: biosapiens +synonym: "polypeptide ligand contact" EXACT [] +synonym: "protein-ligand interaction" RELATED [] +is_a: SO:0001657 ! ligand_binding_site +is_a: SO:0100002 ! molecular_contact_region + +[Term] +id: SO:0001106 +name: asx_motif +alt_id: BS:00202 +def: "A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "asx motif" EXACT [] +is_a: SO:0001078 ! polypeptide_secondary_structure + +[Term] +id: SO:0001107 +name: beta_bulge +alt_id: BS:00208 +def: "A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "beta bulge" EXACT [] +xref: http://en.wikipedia.org/wiki/Beta_bulge "wiki" +is_a: SO:0001078 ! polypeptide_secondary_structure + +[Term] +id: SO:0001108 +name: beta_bulge_loop +alt_id: BS:00209 +def: "A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "beta bulge loop" EXACT [] +is_a: SO:0001078 ! polypeptide_secondary_structure + +[Term] +id: SO:0001109 +name: beta_bulge_loop_five +alt_id: BS:00210 +def: "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "beta bulge loop five" EXACT [] +is_a: SO:0001108 ! beta_bulge_loop + +[Term] +id: SO:0001110 +name: beta_bulge_loop_six +alt_id: BS:00211 +def: "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "beta bulge loop six" EXACT [] +is_a: SO:0001108 ! beta_bulge_loop + +[Term] +id: SO:0001111 +name: beta_strand +alt_id: BS:00042 +def: "A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual] +comment: Range. +subset: biosapiens +synonym: "strand" RELATED BS [uniprot:feature_type] +xref: http://en.wikipedia.org/wiki/Beta_sheet "wiki" +is_a: SO:0001078 ! polypeptide_secondary_structure + +[Term] +id: SO:0001112 +name: antiparallel_beta_strand +alt_id: BS:0000341 +def: "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual] +comment: Range. +subset: biosapiens +synonym: "antiparallel beta strand" EXACT [] +is_a: SO:0001111 ! beta_strand + +[Term] +id: SO:0001113 +name: parallel_beta_strand +alt_id: BS:00151 +def: "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual] +comment: Range. +subset: biosapiens +synonym: "parallel beta strand" EXACT [] +is_a: SO:0001111 ! beta_strand + +[Term] +id: SO:0001114 +name: peptide_helix +alt_id: BS:00152 +def: "A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR] +comment: Range. +subset: biosapiens +synonym: "helix" RELATED BS [] +is_a: SO:0001078 ! polypeptide_secondary_structure + +[Term] +id: SO:0001115 +name: left_handed_peptide_helix +alt_id: BS:00222 +def: "A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR] +subset: biosapiens +synonym: "helix-l" RELATED [] +synonym: "left handed helix" EXACT [] +is_a: SO:0001114 ! peptide_helix + +[Term] +id: SO:0001116 +name: right_handed_peptide_helix +alt_id: BS:0000339 +def: "A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR] +subset: biosapiens +synonym: "helix" RELATED BS [] +synonym: "right handed helix" EXACT [] +is_a: SO:0001114 ! peptide_helix + +[Term] +id: SO:0001117 +name: alpha_helix +alt_id: BS:00040 +def: "The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR] +comment: Range. +subset: biosapiens +synonym: "a-helix" RELATED BS [] +synonym: "helix" RELATED BS [uniprot:feature_type] +xref: http://en.wikipedia.org/wiki/Alpha_helix "wiki" +is_a: SO:0001116 ! right_handed_peptide_helix + +[Term] +id: SO:0001118 +name: pi_helix +alt_id: BS:00153 +def: "The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR] +comment: Range. +subset: biosapiens +synonym: "pi helix" EXACT [] +xref: http://en.wikipedia.org/wiki/Pi_helix "wiki" +is_a: SO:0001116 ! right_handed_peptide_helix + +[Term] +id: SO:0001119 +name: three_ten_helix +alt_id: BS:0000340 +def: "The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR] +comment: Range. +subset: biosapiens +synonym: "3(10) helix" EXACT [] +synonym: "3-10 helix" EXACT [] +synonym: "310 helix" EXACT [] +synonym: "three ten helix" EXACT [] +xref: http://en.wikipedia.org/wiki/310_helix "wiki" +is_a: SO:0001116 ! right_handed_peptide_helix + +[Term] +id: SO:0001120 +name: polypeptide_nest_motif +alt_id: BS:00223 +def: "A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "nest" RELATED BS [] +synonym: "nest_motif" EXACT [] +synonym: "polypeptide nest motif" RELATED [] +is_a: SO:0001078 ! polypeptide_secondary_structure + +[Term] +id: SO:0001121 +name: polypeptide_nest_left_right_motif +alt_id: BS:00224 +def: "A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "nest_left_right" EXACT [] +synonym: "nest_lr" EXACT [] +synonym: "polypeptide nest left right motif" EXACT [] +is_a: SO:0001120 ! polypeptide_nest_motif + +[Term] +id: SO:0001122 +name: polypeptide_nest_right_left_motif +alt_id: BS:00225 +def: "A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "nest_right_left" EXACT [] +synonym: "nest_rl" EXACT [] +synonym: "polypeptide nest right left motif" EXACT [] +is_a: SO:0001120 ! polypeptide_nest_motif + +[Term] +id: SO:0001123 +name: schellmann_loop +alt_id: BS:00226 +def: "A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "paperclip" RELATED BS [] +synonym: "paperclip loop" RELATED [] +synonym: "schellmann loop" EXACT [] +is_a: SO:0001078 ! polypeptide_secondary_structure + +[Term] +id: SO:0001124 +name: schellmann_loop_seven +alt_id: BS:00228 +def: "Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "schellmann loop seven" EXACT [] +synonym: "seven-residue schellmann loop" EXACT [] +is_a: SO:0001123 ! schellmann_loop + +[Term] +id: SO:0001125 +name: schellmann_loop_six +alt_id: BS:00227 +def: "Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "schellmann loop six" EXACT [] +synonym: "six-residue schellmann loop" EXACT [] +is_a: SO:0001123 ! schellmann_loop + +[Term] +id: SO:0001126 +name: serine_threonine_motif +alt_id: BS:00229 +def: "A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "serine/threonine motif" EXACT [] +synonym: "st motif" EXACT [] +synonym: "st_motif" EXACT [] +is_a: SO:0001078 ! polypeptide_secondary_structure + +[Term] +id: SO:0001127 +name: serine_threonine_staple_motif +alt_id: BS:00230 +def: "A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "serine threonine staple motif" EXACT [] +synonym: "st_staple" EXACT [] +is_a: SO:0001078 ! polypeptide_secondary_structure + +[Term] +id: SO:0001128 +name: polypeptide_turn_motif +alt_id: BS:00148 +def: "A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type] +comment: Range. +subset: biosapiens +synonym: "turn" RELATED BS [] +is_a: SO:0001078 ! polypeptide_secondary_structure + +[Term] +id: SO:0001129 +name: asx_turn_left_handed_type_one +alt_id: BS:00206 +def: "Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "asx turn left handed type one" EXACT [] +synonym: "asx_turn_il" RELATED [] +is_a: SO:0000912 ! asx_turn + +[Term] +id: SO:0001130 +name: asx_turn_left_handed_type_two +alt_id: BS:00204 +def: "Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "asx turn left handed type two" EXACT [] +synonym: "asx_turn_iil" EXACT [] +is_a: SO:0000912 ! asx_turn + +[Term] +id: SO:0001131 +name: asx_turn_right_handed_type_two +alt_id: BS:00205 +def: "Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "asx turn right handed type two" EXACT [] +synonym: "asx_turn_iir" EXACT [] +is_a: SO:0000912 ! asx_turn + +[Term] +id: SO:0001132 +name: asx_turn_right_handed_type_one +alt_id: BS:00207 +def: "Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "asx turn type right handed type one" EXACT [] +synonym: "asx_turn_ir" EXACT [] +is_a: SO:0000912 ! asx_turn + +[Term] +id: SO:0001133 +name: beta_turn +alt_id: BS:00212 +def: "A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "beta turn" EXACT [] +is_a: SO:0001128 ! polypeptide_turn_motif + +[Term] +id: SO:0001134 +name: beta_turn_left_handed_type_one +alt_id: BS:00215 +def: "Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "beta turn left handed type one" EXACT [] +synonym: "beta_turn_il" EXACT [] +synonym: "type I' beta turn" EXACT [] +synonym: "type I' turn" EXACT [] +is_a: SO:0001133 ! beta_turn + +[Term] +id: SO:0001135 +name: beta_turn_left_handed_type_two +alt_id: BS:00213 +def: "Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "beta turn left handed type two" EXACT [] +synonym: "beta_turn_iil" EXACT [] +synonym: "type II' beta turn" EXACT [] +synonym: "type II' turn" EXACT [] +is_a: SO:0001133 ! beta_turn + +[Term] +id: SO:0001136 +name: beta_turn_right_handed_type_one +alt_id: BS:00216 +def: "Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "beta turn right handed type one" EXACT [] +synonym: "beta_turn_ir" EXACT [] +synonym: "type I beta turn" EXACT [] +synonym: "type I turn" EXACT [] +is_a: SO:0001133 ! beta_turn + +[Term] +id: SO:0001137 +name: beta_turn_right_handed_type_two +alt_id: BS:00214 +def: "Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "beta turn right handed type two" EXACT [] +synonym: "beta_turn_iir" EXACT [] +synonym: "type II beta turn" EXACT [] +synonym: "type II turn" EXACT [] +is_a: SO:0001133 ! beta_turn + +[Term] +id: SO:0001138 +name: gamma_turn +alt_id: BS:00219 +def: "Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "gamma turn" EXACT [] +is_a: SO:0001128 ! polypeptide_turn_motif + +[Term] +id: SO:0001139 +name: gamma_turn_classic +alt_id: BS:00220 +def: "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "classic gamma turn" EXACT [] +synonym: "gamma turn classic" EXACT [] +is_a: SO:0001138 ! gamma_turn + +[Term] +id: SO:0001140 +name: gamma_turn_inverse +alt_id: BS:00221 +def: "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "gamma turn inverse" EXACT [] +is_a: SO:0001138 ! gamma_turn + +[Term] +id: SO:0001141 +name: serine_threonine_turn +alt_id: BS:00231 +def: "A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "serine/threonine turn" EXACT [] +synonym: "st_turn" EXACT [] +is_a: SO:0001128 ! polypeptide_turn_motif + +[Term] +id: SO:0001142 +name: st_turn_left_handed_type_one +alt_id: BS:00234 +def: "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "st turn left handed type one" EXACT [] +synonym: "st_turn_il" EXACT [] +is_a: SO:0001141 ! serine_threonine_turn + +[Term] +id: SO:0001143 +name: st_turn_left_handed_type_two +alt_id: BS:00232 +def: "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "st turn left handed type two" EXACT [] +synonym: "st_turn_iil" EXACT [] +is_a: SO:0001141 ! serine_threonine_turn + +[Term] +id: SO:0001144 +name: st_turn_right_handed_type_one +alt_id: BS:00235 +def: "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "st turn right handed type one" EXACT [] +synonym: "st_turn_ir" EXACT [] +is_a: SO:0001141 ! serine_threonine_turn + +[Term] +id: SO:0001145 +name: st_turn_right_handed_type_two +alt_id: BS:00233 +def: "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "st turn right handed type two" EXACT [] +synonym: "st_turn_iir" EXACT [] +is_a: SO:0001141 ! serine_threonine_turn + +[Term] +id: SO:0001146 +name: polypeptide_variation_site +alt_id: BS:00336 +def: "A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke] +comment: For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations. +subset: biosapiens +synonym: "sequence_variations" EXACT [] +is_a: SO:0000839 ! polypeptide_region + +[Term] +id: SO:0001147 +name: natural_variant_site +alt_id: BS:00071 +def: "Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." [EBIBS:GAR, UniProt:curation_manual] +comment: Discrete. +subset: biosapiens +synonym: "natural_variant" BROAD [] +synonym: "sequence variation" BROAD [] +synonym: "variant" BROAD [uniprot:feature_type] +is_a: SO:0001146 ! polypeptide_variation_site + +[Term] +id: SO:0001148 +name: mutated_variant_site +alt_id: BS:00036 +def: "Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual] +comment: Discrete. +subset: biosapiens +synonym: "mutagen" EXACT BS [uniprot:feature_type] +synonym: "mutagenesis" EXACT [] +synonym: "mutated_site" EXACT [] +is_a: SO:0001146 ! polypeptide_variation_site + +[Term] +id: SO:0001149 +name: alternate_sequence_site +alt_id: BS:00073 +alt_id: SO:0001065 +def: "Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual] +comment: Discrete. +subset: biosapiens +synonym: "alternative_sequence" EXACT [] +synonym: "isoform" NARROW [] +synonym: "sequence variation" NARROW [] +synonym: "var_seq" EXACT [uniprot:feature_type] +synonym: "varsplic" NARROW [] +is_a: SO:0001146 ! polypeptide_variation_site + +[Term] +id: SO:0001150 +name: beta_turn_type_six +def: "A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb] +subset: biosapiens +synonym: "beta turn type six" EXACT [] +synonym: "cis-proline loop" EXACT [] +synonym: "type VI beta turn" EXACT [] +synonym: "type VI turn" EXACT [] +is_a: SO:0001133 ! beta_turn + +[Term] +id: SO:0001151 +name: beta_turn_type_six_a +def: "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb] +subset: biosapiens +synonym: "beta turn type six a" EXACT [] +synonym: "type VIa beta turn" EXACT [] +synonym: "type VIa turn" EXACT [] +is_a: SO:0001150 ! beta_turn_type_six + +[Term] +id: SO:0001152 +name: beta_turn_type_six_a_one +subset: biosapiens +synonym: "beta turn type six a one" EXACT [] +synonym: "type VIa1 beta turn" EXACT [] +synonym: "type VIa1 turn" EXACT [] +is_a: SO:0001151 ! beta_turn_type_six_a + +[Term] +id: SO:0001153 +name: beta_turn_type_six_a_two +subset: biosapiens +synonym: "beta turn type six a two" EXACT [] +synonym: "type VIa2 beta turn" EXACT [] +synonym: "type VIa2 turn" EXACT [] +is_a: SO:0001151 ! beta_turn_type_six_a + +[Term] +id: SO:0001154 +name: beta_turn_type_six_b +def: "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb] +subset: biosapiens +synonym: "beta turn type six b" EXACT [] +synonym: "type VIb beta turn" EXACT [] +synonym: "type VIb turn" EXACT [] +is_a: SO:0001150 ! beta_turn_type_six + +[Term] +id: SO:0001155 +name: beta_turn_type_eight +def: "A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb] +subset: biosapiens +synonym: "beta turn type eight" EXACT [] +synonym: "type VIII beta turn" EXACT [] +synonym: "type VIII turn" EXACT [] +is_a: SO:0001133 ! beta_turn + +[Term] +id: SO:0001156 +name: DRE_motif +def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576] +comment: This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183. Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10. +synonym: "DRE motif" EXACT [] +synonym: "NDM4" EXACT [] +synonym: "WATCGATW_motif" EXACT [] +is_a: SO:0000713 ! DNA_motif +relationship: part_of SO:0000170 ! RNApol_II_promoter + +[Term] +id: SO:0001157 +name: DMv4_motif +def: "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014)." [PMID:16827941\:12537576] +synonym: "directional motif v4" EXACT [] +synonym: "DMv4" EXACT [] +synonym: "DMv4 motif" EXACT [] +synonym: "motif 1 element" EXACT [] +synonym: "promoter motif 1" EXACT [] +synonym: "YGGTCACATR" NARROW [] +is_a: SO:0001659 ! promoter_element + +[Term] +id: SO:0001158 +name: E_box_motif +def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576\:16827941] +synonym: "AWCAGCTGWT" NARROW [] +synonym: "E box motif" EXACT [] +synonym: "generic E box motif" EXACT [] +synonym: "NDM5" RELATED [] +is_a: SO:0000713 ! DNA_motif +relationship: part_of SO:0000170 ! RNApol_II_promoter + +[Term] +id: SO:0001159 +name: DMv5_motif +def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576\:16827941] +synonym: "directional motif v5" EXACT [] +synonym: "DMv5" EXACT [] +synonym: "DMv5 motif" EXACT [] +synonym: "KTYRGTATWTTT" NARROW [] +synonym: "promoter motif 6" RELATED [] +is_a: SO:0001659 ! promoter_element +relationship: part_of SO:0000170 ! RNApol_II_promoter + +[Term] +id: SO:0001160 +name: DMv3_motif +def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576\:16827941] +synonym: "directional motif v3" EXACT [] +synonym: "DMv3" EXACT [] +synonym: "DMv3 motif" EXACT [] +synonym: "KNNCAKCNCTRNY" NARROW [] +synonym: "promoter motif 7" EXACT [] +is_a: SO:0001659 ! promoter_element +relationship: part_of SO:0000170 ! RNApol_II_promoter + +[Term] +id: SO:0001161 +name: DMv2_motif +def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576\:16827941] +synonym: "directional motif v2" EXACT [] +synonym: "DMv2" EXACT [] +synonym: "DMv2 motif" EXACT [] +synonym: "MKSYGGCARCGSYSS" NARROW [] +synonym: "promoter motif 8" EXACT [] +is_a: SO:0001659 ! promoter_element +relationship: part_of SO:0000170 ! RNApol_II_promoter + +[Term] +id: SO:0001162 +name: MTE +def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576\:15231738, PMID:16858867] +synonym: "CSARCSSAACGS" NARROW [] +synonym: "motif ten element" EXACT [] +synonym: "motif_ten_element" EXACT [] +is_a: SO:0001660 ! core_promoter_element +relationship: part_of SO:0001669 ! RNApol_II_core_promoter + +[Term] +id: SO:0001163 +name: INR1_motif +def: "A promoter motif with consensus sequence TCATTCG." [PMID:16827941] +synonym: "directional motif p3" EXACT [] +synonym: "directional promoter motif 3" EXACT [] +synonym: "DMp3" EXACT [] +synonym: "INR1 motif" EXACT [] +is_a: SO:0000713 ! DNA_motif +relationship: part_of SO:0000170 ! RNApol_II_promoter + +[Term] +id: SO:0001164 +name: DPE1_motif +def: "A promoter motif with consensus sequence CGGACGT." [PMID:16827941] +synonym: "directional motif 5" EXACT [] +synonym: "directional promoter motif 5" RELATED [] +synonym: "DMp5" EXACT [] +synonym: "DPE1 motif" EXACT [] +is_a: SO:0001659 ! promoter_element +relationship: part_of SO:0000170 ! RNApol_II_promoter + +[Term] +id: SO:0001165 +name: DMv1_motif +def: "A promoter motif with consensus sequence CARCCCT." [PMID:16827941] +synonym: "directional promoter motif v1" RELATED [] +synonym: "DMv1" RELATED [] +synonym: "DMv1 motif" EXACT [] +is_a: SO:0001659 ! promoter_element +relationship: part_of SO:0000170 ! RNApol_II_promoter + +[Term] +id: SO:0001166 +name: GAGA_motif +def: "A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941] +synonym: "GAGA" EXACT [] +synonym: "GAGA motif" EXACT [] +synonym: "NDM1" EXACT [] +is_a: SO:0000713 ! DNA_motif +relationship: part_of SO:0000170 ! RNApol_II_promoter + +[Term] +id: SO:0001167 +name: NDM2_motif +def: "A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941] +synonym: "NDM2" EXACT [] +synonym: "NDM2 motif" EXACT [] +synonym: "non directional promoter motif 2" EXACT [] +is_a: SO:0001659 ! promoter_element +relationship: part_of SO:0000170 ! RNApol_II_promoter + +[Term] +id: SO:0001168 +name: NDM3_motif +def: "A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941] +synonym: "NDM3" EXACT [] +synonym: "NDM3 motif" EXACT [] +synonym: "non directional motif 3" EXACT [] +is_a: SO:0001659 ! promoter_element +relationship: part_of SO:0000170 ! RNApol_II_promoter + +[Term] +id: SO:0001169 +name: ds_RNA_viral_sequence +def: "A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke] +synonym: "double stranded RNA virus sequence" EXACT [] +synonym: "ds RNA viral sequence" EXACT [] +is_a: SO:0001041 ! viral_sequence + +[Term] +id: SO:0001170 +name: polinton +def: "A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396] +synonym: "maverick element" RELATED [] +is_a: SO:0000208 ! terminal_inverted_repeat_element + +[Term] +id: SO:0001171 +name: rRNA_21S +def: "A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb] +synonym: "21S LSU rRNA" EXACT [] +synonym: "21S ribosomal RNA" EXACT [] +synonym: "21S rRNA" EXACT [] +synonym: "rRNA 21S" EXACT [] +is_a: SO:0000651 ! large_subunit_rRNA + +[Term] +id: SO:0001172 +name: tRNA_region +def: "A region of a tRNA." [RSC:cb] +synonym: "tRNA region" EXACT [] +is_a: SO:0000834 ! mature_transcript_region +relationship: part_of SO:0000253 ! tRNA + +[Term] +id: SO:0001173 +name: anticodon_loop +def: "A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207] +synonym: "anti-codon loop" EXACT [] +synonym: "anticodon loop" EXACT [] +is_a: SO:0001172 ! tRNA_region + +[Term] +id: SO:0001174 +name: anticodon +def: "A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb] +synonym: "anti-codon" EXACT [] +xref: http://en.wikipedia.org/wiki/Anticodon "wiki" +is_a: SO:0001172 ! tRNA_region +relationship: part_of SO:0001173 ! anticodon_loop + +[Term] +id: SO:0001175 +name: CCA_tail +def: "Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207] +synonym: "CCA sequence" EXACT [] +synonym: "CCA tail" EXACT [] +is_a: SO:0001172 ! tRNA_region + +[Term] +id: SO:0001176 +name: DHU_loop +def: "Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920] +synonym: "D loop" RELATED [] +synonym: "DHU loop" EXACT [] +is_a: SO:0001172 ! tRNA_region + +[Term] +id: SO:0001177 +name: T_loop +def: "Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207] +synonym: "T loop" EXACT [] +synonym: "TpsiC loop" EXACT [] +is_a: SO:0001172 ! tRNA_region + +[Term] +id: SO:0001178 +name: pyrrolysine_tRNA_primary_transcript +def: "A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb] +synonym: "pyrrolysine tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0001179 +name: U3_snoRNA +def: "U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012] +comment: The definition is most of the old definition for snoRNA (SO:0000275). +synonym: "small nucleolar RNA U3" EXACT [] +synonym: "snoRNA U3" EXACT [] +synonym: "U3 small nucleolar RNA" EXACT [] +synonym: "U3 snoRNA" EXACT [] +xref: http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3 "wiki" +is_a: SO:0000593 ! C_D_box_snoRNA + +[Term] +id: SO:0001180 +name: AU_rich_element +def: "A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223] +synonym: "ARE" RELATED [] +synonym: "AU rich element" EXACT [] +synonym: "AU-rich element" EXACT [] +xref: http://en.wikipedia.org/wiki/AU-rich_element "wiki" +is_a: SO:0000837 ! UTR_region +relationship: part_of SO:0000205 ! three_prime_UTR + +[Term] +id: SO:0001181 +name: Bruno_response_element +def: "A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231] +comment: Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B. +synonym: "BRE" RELATED [] +synonym: "Bruno response element" EXACT [] +is_a: SO:0000837 ! UTR_region +relationship: part_of SO:0000205 ! three_prime_UTR + +[Term] +id: SO:0001182 +name: iron_responsive_element +def: "A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843] +synonym: "IRE" EXACT [] +synonym: "iron responsive element" EXACT [] +xref: http://en.wikipedia.org/wiki/Iron_responsive_element "wiki" +is_a: SO:0000837 ! UTR_region +relationship: part_of SO:0000203 ! UTR + +[Term] +id: SO:0001183 +name: morpholino_backbone +def: "An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages." [RSC:cb] +comment: Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead. +synonym: "morpholino backbone" EXACT [] +xref: http://en.wikipedia.org/wiki/Morpholino "wiki" +is_a: SO:0000348 ! nucleic_acid + +[Term] +id: SO:0001184 +name: PNA +def: "An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [RSC:cb] +comment: Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead. +synonym: "peptide nucleic acid" RELATED [] +is_a: SO:0000348 ! nucleic_acid + +[Term] +id: SO:0001185 +name: enzymatic +def: "An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb] +comment: Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead. +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0001186 +name: ribozymic +def: "An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein." [RSC:cb] +comment: Do not use this for feature annotation. Use ribozyme (SO:0000374) instead. +is_a: SO:0001185 ! enzymatic + +[Term] +id: SO:0001187 +name: pseudouridylation_guide_snoRNA +def: "A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565] +comment: Has RNA pseudouridylation guide activity (GO:0030558). +synonym: "pseudouridylation guide snoRNA" EXACT [] +is_a: SO:0000594 ! H_ACA_box_snoRNA + +[Term] +id: SO:0001188 +name: LNA +def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link." [CHEBI:48010] +comment: Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead. +is_a: SO:0000348 ! nucleic_acid + +[Term] +id: SO:0001189 +name: LNA_oligo +def: "An oligo composed of LNA residues." [RSC:cb] +synonym: "LNA oligo" EXACT [] +synonym: "locked nucleic acid" EXACT [] +xref: http://en.wikipedia.org/wiki/Locked_nucleic_acid "wiki" +is_a: SO:0001247 ! synthetic_oligo +relationship: has_quality SO:0001188 ! LNA + +[Term] +id: SO:0001190 +name: TNA +def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone." [CHEBI:48019] +comment: Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead. +is_a: SO:0000348 ! nucleic_acid + +[Term] +id: SO:0001191 +name: TNA_oligo +def: "An oligo composed of TNA residues." [RSC:cb] +synonym: "threose nucleic acid" EXACT [] +synonym: "TNA oligo" EXACT [] +xref: http://en.wikipedia.org/wiki/Threose_nucleic_acid "wiki" +is_a: SO:0001247 ! synthetic_oligo +relationship: has_quality SO:0001190 ! TNA + +[Term] +id: SO:0001192 +name: GNA +def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA." [CHEBI:48015] +comment: Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead. +is_a: SO:0000348 ! nucleic_acid + +[Term] +id: SO:0001193 +name: GNA_oligo +def: "An oligo composed of GNA residues." [RSC:cb] +synonym: "glycerol nucleic acid" EXACT [] +synonym: "glycol nucleic acid" EXACT [] +synonym: "GNA oligo" EXACT [] +xref: http://en.wikipedia.org/wiki/Glycerol_nucleic_acid "wiki" +is_a: SO:0001247 ! synthetic_oligo +relationship: has_quality SO:0001192 ! GNA + +[Term] +id: SO:0001194 +name: R_GNA +def: "An attribute describing a GNA sequence in the (R)-GNA enantiomer." [CHEBI:48016] +comment: Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead. +synonym: "R GNA" EXACT [] +is_a: SO:0001192 ! GNA + +[Term] +id: SO:0001195 +name: R_GNA_oligo +def: "An oligo composed of (R)-GNA residues." [RSC:cb] +synonym: "(R)-glycerol nucleic acid" EXACT [] +synonym: "(R)-glycol nucleic acid" EXACT [] +synonym: "R GNA oligo" EXACT [] +is_a: SO:0001193 ! GNA_oligo +relationship: has_quality SO:0001194 ! R_GNA + +[Term] +id: SO:0001196 +name: S_GNA +def: "An attribute describing a GNA sequence in the (S)-GNA enantiomer." [CHEBI:48017] +comment: Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead. +synonym: "S GNA" EXACT [] +is_a: SO:0001192 ! GNA + +[Term] +id: SO:0001197 +name: S_GNA_oligo +def: "An oligo composed of (S)-GNA residues." [RSC:cb] +synonym: "(S)-glycerol nucleic acid" EXACT [] +synonym: "(S)-glycol nucleic acid" EXACT [] +synonym: "S GNA oligo" EXACT [] +is_a: SO:0001193 ! GNA_oligo +relationship: has_quality SO:0001196 ! S_GNA + +[Term] +id: SO:0001198 +name: ds_DNA_viral_sequence +def: "A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke] +synonym: "double stranded DNA virus" EXACT [] +synonym: "ds DNA viral sequence" EXACT [] +is_a: SO:0001041 ! viral_sequence + +[Term] +id: SO:0001199 +name: ss_RNA_viral_sequence +def: "A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke] +synonym: "single strand RNA virus" EXACT [] +synonym: "ss RNA viral sequence" EXACT [] +is_a: SO:0001041 ! viral_sequence + +[Term] +id: SO:0001200 +name: negative_sense_ssRNA_viral_sequence +def: "A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke] +synonym: "negative sense single stranded RNA virus" RELATED [] +synonym: "negative sense ssRNA viral sequence" EXACT [] +is_a: SO:0001199 ! ss_RNA_viral_sequence + +[Term] +id: SO:0001201 +name: positive_sense_ssRNA_viral_sequence +def: "A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke] +synonym: "positive sense single stranded RNA virus" RELATED [] +synonym: "positive sense ssRNA viral sequence" EXACT [] +is_a: SO:0001199 ! ss_RNA_viral_sequence + +[Term] +id: SO:0001202 +name: ambisense_ssRNA_viral_sequence +def: "A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke] +synonym: "ambisense single stranded RNA virus" EXACT [] +synonym: "ambisense ssRNA viral sequence" EXACT [] +is_a: SO:0001199 ! ss_RNA_viral_sequence + +[Term] +id: SO:0001203 +name: RNA_polymerase_promoter +def: "A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb] +synonym: "RNA polymerase promoter" EXACT [] +is_a: SO:0000167 ! promoter + +[Term] +id: SO:0001204 +name: Phage_RNA_Polymerase_Promoter +def: "A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb] +synonym: "Phage RNA Polymerase Promoter" EXACT [] +is_a: SO:0001203 ! RNA_polymerase_promoter + +[Term] +id: SO:0001205 +name: SP6_RNA_Polymerase_Promoter +def: "A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb] +synonym: "SP6 RNA Polymerase Promoter" EXACT [] +is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter + +[Term] +id: SO:0001206 +name: T3_RNA_Polymerase_Promoter +def: "A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb] +synonym: "T3 RNA Polymerase Promoter" EXACT [] +is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter + +[Term] +id: SO:0001207 +name: T7_RNA_Polymerase_Promoter +def: "A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb] +synonym: "T7 RNA Polymerase Promoter" EXACT [] +is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter + +[Term] +id: SO:0001208 +name: five_prime_EST +def: "An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family." [http://www.ncbi.nlm.nih.gov/About/primer/est.html] +synonym: "5' EST" EXACT [] +synonym: "five prime EST" EXACT [] +is_a: SO:0000345 ! EST + +[Term] +id: SO:0001209 +name: three_prime_EST +def: "An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs)." [http://www.ncbi.nlm.nih.gov/About/primer/est.html] +synonym: "3' EST" EXACT [] +synonym: "three prime EST" EXACT [] +is_a: SO:0000345 ! EST + +[Term] +id: SO:0001210 +name: translational_frameshift +def: "The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke] +synonym: "ribosomal frameshift" EXACT [] +synonym: "translational frameshift" EXACT [] +xref: http://en.wikipedia.org/wiki/Translational_frameshift "wiki" +is_a: SO:0000836 ! mRNA_region + +[Term] +id: SO:0001211 +name: plus_1_translational_frameshift +def: "The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke] +synonym: "plus 1 ribosomal frameshift" EXACT [] +synonym: "plus 1 translational frameshift" EXACT [] +is_a: SO:0001210 ! translational_frameshift + +[Term] +id: SO:0001212 +name: plus_2_translational_frameshift +def: "The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke] +synonym: "plus 2 ribosomal frameshift" EXACT [] +synonym: "plus 2 translational frameshift" EXACT [] +is_a: SO:0001210 ! translational_frameshift + +[Term] +id: SO:0001213 +name: group_III_intron +def: "Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794] +comment: GO:0000374. +synonym: "group III intron" EXACT [] +xref: http://en.wikipedia.org/wiki/Group_III_intron "wiki" +is_a: SO:0000588 ! autocatalytically_spliced_intron + +[Term] +id: SO:0001214 +name: noncoding_region_of_exon +def: "The maximal intersection of exon and UTR." [SO:ke] +comment: An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding. +subset: SOFA +synonym: "noncoding region of exon" EXACT [] +is_a: SO:0000852 ! exon_region + +[Term] +id: SO:0001215 +name: coding_region_of_exon +def: "The region of an exon that encodes for protein sequence." [SO:ke] +comment: An exon containing either a start or stop codon will be partially coding and partially non coding. +subset: SOFA +synonym: "coding region of exon" EXACT [] +is_a: SO:0000852 ! exon_region + +[Term] +id: SO:0001216 +name: endonuclease_spliced_intron +def: "An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke] +synonym: "endonuclease spliced intron" EXACT [] +is_a: SO:0000188 ! intron + +[Term] +id: SO:0001217 +name: protein_coding_gene +synonym: "protein coding gene" EXACT [] +is_a: SO:0000704 ! gene +relationship: has_quality SO:0000010 ! protein_coding + +[Term] +id: SO:0001218 +name: transgenic_insertion +def: "An insertion that derives from another organism, via the use of recombinant DNA technology." [SO:bm] +synonym: "transgenic insertion" EXACT [] +is_a: SO:0000667 ! insertion +relationship: has_quality SO:0000781 ! transgenic + +[Term] +id: SO:0001219 +name: retrogene +is_a: SO:0000704 ! gene +relationship: has_quality SO:0000569 ! retrotransposed + +[Term] +id: SO:0001220 +name: silenced_by_RNA_interference +def: "An attribute describing an epigenetic process where a gene is inactivated by RNA interference." [RSC:cb] +comment: RNA interference is GO:0016246. +synonym: "silenced by RNA interference" EXACT [] +is_a: SO:0000893 ! silenced + +[Term] +id: SO:0001221 +name: silenced_by_histone_modification +def: "An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb] +comment: Histone modification is GO:0016570. +synonym: "silenced by histone modification" EXACT [] +is_a: SO:0000893 ! silenced + +[Term] +id: SO:0001222 +name: silenced_by_histone_methylation +def: "An attribute describing an epigenetic process where a gene is inactivated by histone methylation." [RSC:cb] +comment: Histone methylation is GO:0016571. +synonym: "silenced by histone methylation" EXACT [] +is_a: SO:0001221 ! silenced_by_histone_modification + +[Term] +id: SO:0001223 +name: silenced_by_histone_deacetylation +def: "An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." [RSC:cb] +comment: Histone deacetylation is GO:0016573. +synonym: "silenced by histone deacetylation" EXACT [] +is_a: SO:0001221 ! silenced_by_histone_modification + +[Term] +id: SO:0001224 +name: gene_silenced_by_RNA_interference +def: "A gene that is silenced by RNA interference." [SO:xp] +synonym: "gene silenced by RNA interference" EXACT [] +synonym: "RNA interference silenced gene" EXACT [] +synonym: "RNAi silenced gene" EXACT [] +is_a: SO:0000127 ! silenced_gene +relationship: has_quality SO:0001220 ! silenced_by_RNA_interference + +[Term] +id: SO:0001225 +name: gene_silenced_by_histone_modification +def: "A gene that is silenced by histone modification." [SO:xp] +synonym: "gene silenced by histone modification" EXACT [] +is_a: SO:0000127 ! silenced_gene +relationship: has_quality SO:0001221 ! silenced_by_histone_modification + +[Term] +id: SO:0001226 +name: gene_silenced_by_histone_methylation +def: "A gene that is silenced by histone methylation." [SO:xp] +synonym: "gene silenced by histone methylation" EXACT [] +is_a: SO:0001225 ! gene_silenced_by_histone_modification +relationship: has_quality SO:0001222 ! silenced_by_histone_methylation + +[Term] +id: SO:0001227 +name: gene_silenced_by_histone_deacetylation +def: "A gene that is silenced by histone deacetylation." [SO:xp] +synonym: "gene silenced by histone deacetylation" EXACT [] +is_a: SO:0001225 ! gene_silenced_by_histone_modification +relationship: has_quality SO:0001223 ! silenced_by_histone_deacetylation + +[Term] +id: SO:0001228 +name: dihydrouridine +def: "A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring." [RSC:cb] +synonym: " D" EXACT RNAMOD [] +xref: http://en.wikipedia.org/wiki/Dihydrouridine "wiki" +xref: RNAMOD:051 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001229 +name: pseudouridine +def: "A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position." [RSC:cb] +comment: The free molecule is CHEBI:17802. +synonym: " Y" EXACT RNAMOD [] +xref: http://en.wikipedia.org/wiki/Pseudouridine "wiki" +xref: RNAMOD:050 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001230 +name: inosine +def: "A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb] +comment: The free molecule is CHEBI:17596. +synonym: "I" RELATED [] +synonym: "RNAMOD:017" RELATED [] +xref: http://en.wikipedia.org/wiki/Inosine "wiki" +is_a: SO:0000250 ! modified_RNA_base_feature + +[Term] +id: SO:0001231 +name: seven_methylguanine +def: "A modified RNA base in which guanine is methylated at the 7- position." [RSC:cb] +comment: The free molecule is CHEBI:2274. +synonym: "7-methylguanine" EXACT [] +synonym: "seven methylguanine" EXACT [] +is_a: SO:0000250 ! modified_RNA_base_feature + +[Term] +id: SO:0001232 +name: ribothymidine +def: "A modified RNA base in which thymine is bound to the ribose ring." [RSC:cb] +comment: The free molecule is CHEBI:30832. +is_a: SO:0000250 ! modified_RNA_base_feature + +[Term] +id: SO:0001233 +name: methylinosine +def: "A modified RNA base in which methylhypoxanthine is bound to the ribose ring." [RSC:cb] +is_a: SO:0001274 ! modified_inosine + +[Term] +id: SO:0001234 +name: mobile +def: "An attribute describing a feature that has either intra-genome or intracellular mobility." [RSC:cb] +xref: http://en.wikipedia.org/wiki/Mobile "wiki" +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0001235 +name: replicon +def: "A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207] +subset: SOFA +xref: http://en.wikipedia.org/wiki/Replicon_(genetics) "wiki" +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0001236 +name: base +def: "A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke] +subset: SOFA +xref: http://en.wikipedia.org/wiki/Nucleobase "wiki" +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0001237 +name: amino_acid +def: "A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb] +comment: Probably in the future this will cross reference to Chebi. +synonym: "amino acid" EXACT [] +xref: http://en.wikipedia.org/wiki/Amino_acid "wiki" +is_a: SO:0001411 ! biological_region +relationship: part_of SO:0000104 ! polypeptide + +[Term] +id: SO:0001238 +name: major_TSS +synonym: "major transcription start site" EXACT [] +synonym: "major TSS" EXACT [] +is_a: SO:0000315 ! TSS + +[Term] +id: SO:0001239 +name: minor_TSS +synonym: "minor TSS" EXACT [] +is_a: SO:0000315 ! TSS + +[Term] +id: SO:0001240 +name: TSS_region +def: "The region of a gene from the 5' most TSS to the 3' TSS." [BBOP:nw] +synonym: "TSS region" EXACT [] +is_a: SO:0000842 ! gene_component_region +relationship: has_part SO:0000315 ! TSS + +[Term] +id: SO:0001241 +name: encodes_alternate_transcription_start_sites +synonym: "encodes alternate transcription start sites" EXACT [] +is_a: SO:0000401 ! gene_attribute + +[Term] +id: SO:0001243 +name: miRNA_primary_transcript_region +def: "A part of an miRNA primary_transcript." [SO:ke] +synonym: "miRNA primary transcript region" EXACT [] +is_a: SO:0000835 ! primary_transcript_region + +[Term] +id: SO:0001244 +name: pre_miRNA +def: "The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke] +synonym: "pre-miRNA" EXACT [] +is_a: SO:0001243 ! miRNA_primary_transcript_region + +[Term] +id: SO:0001245 +name: miRNA_stem +def: "The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke] +synonym: "miRNA stem" EXACT [] +is_a: SO:0001243 ! miRNA_primary_transcript_region +relationship: part_of SO:0001244 ! pre_miRNA + +[Term] +id: SO:0001246 +name: miRNA_loop +def: "The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke] +synonym: "miRNA loop" EXACT [] +is_a: SO:0001243 ! miRNA_primary_transcript_region +relationship: part_of SO:0001244 ! pre_miRNA + +[Term] +id: SO:0001247 +name: synthetic_oligo +def: "An oligo composed of synthetic nucleotides." [SO:ke] +synonym: "synthetic oligo" EXACT [] +is_a: SO:0000696 ! oligo + +[Term] +id: SO:0001248 +name: assembly +def: "A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke] +subset: SOFA +xref: http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly "wiki" +is_a: SO:0001410 ! experimental_feature + +[Term] +id: SO:0001249 +name: fragment_assembly +def: "A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths." [SO:ke] +synonym: "fragment assembly" EXACT [] +synonym: "physical map" EXACT [] +is_a: SO:0001248 ! assembly + +[Term] +id: SO:0001250 +name: fingerprint_map +def: "A fingerprint_map is a physical map composed of restriction fragments." [SO:ke] +synonym: "BACmap" EXACT [] +synonym: "fingerprint map" EXACT [] +synonym: "FPC" EXACT [] +synonym: "FPCmap" EXACT [] +synonym: "restriction map" EXACT [] +is_a: SO:0001249 ! fragment_assembly +relationship: has_part SO:0000412 ! restriction_fragment + +[Term] +id: SO:0001251 +name: STS_map +def: "An STS map is a physical map organized by the unique STS landmarks." [SO:ke] +synonym: "STS map" EXACT [] +is_a: SO:0001249 ! fragment_assembly +relationship: has_part SO:0000331 ! STS + +[Term] +id: SO:0001252 +name: RH_map +def: "A radiation hybrid map is a physical map." [SO:ke] +synonym: "radiation hybrid map" EXACT [] +synonym: "RH map" EXACT [] +is_a: SO:0001249 ! fragment_assembly +relationship: has_part SO:0000331 ! STS + +[Term] +id: SO:0001253 +name: sonicate_fragment +def: "A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments." [SO:ke] +synonym: "sonicate fragment" EXACT [] +is_a: SO:0000143 ! assembly_component + +[Term] +id: SO:0001254 +name: polyploid +def: "A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke] +xref: http://en.wikipedia.org/wiki/Polyploid "wiki" +is_a: SO:1000182 ! chromosome_number_variation + +[Term] +id: SO:0001255 +name: autopolyploid +def: "A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke] +xref: http://en.wikipedia.org/wiki/Autopolyploid "wiki" +is_a: SO:0001254 ! polyploid + +[Term] +id: SO:0001256 +name: allopolyploid +def: "A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke] +xref: http://en.wikipedia.org/wiki/Allopolyploid "wiki" +is_a: SO:0001254 ! polyploid + +[Term] +id: SO:0001257 +name: homing_endonuclease_binding_site +def: "The binding site (recognition site) of a homing endonuclease. The binding site is typically large." [SO:ke] +synonym: "homing endonuclease binding site" EXACT [] +is_a: SO:0000059 ! nuclease_binding_site + +[Term] +id: SO:0001258 +name: octamer_motif +def: "A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662] +comment: Nature. 1986 Oct 16-22;323(6089):640-3. +synonym: "octamer motif" EXACT [] +is_a: SO:0000713 ! DNA_motif +relationship: part_of SO:0000170 ! RNApol_II_promoter + +[Term] +id: SO:0001259 +name: apicoplast_chromosome +def: "A chromosome originating in an apicoplast." [SO:xp] +synonym: "apicoplast chromosome" EXACT [] +is_a: SO:0000340 ! chromosome +relationship: has_origin SO:0000743 ! apicoplast_sequence + +[Term] +id: SO:0001260 +name: sequence_collection +def: "A collection of discontinuous sequences." [SO:ke] +synonym: "sequence collection" EXACT [] + +[Term] +id: SO:0001261 +name: overlapping_feature_set +def: "A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature." [SO:ke] +comment: This feature was requested by Nicole, tracker id 1911479. It is required to gather evidence together for annotation. An example would be overlapping ESTs that support an mRNA. +synonym: "overlapping feature set" EXACT [] +is_a: SO:0000703 ! experimental_result_region + +[Term] +id: SO:0001262 +name: overlapping_EST_set +def: "A continous experimental result region extending the length of multiple overlapping EST's." [SO:ke] +synonym: "overlapping EST set" EXACT [] +is_a: SO:0001261 ! overlapping_feature_set +relationship: has_part SO:0000345 ! EST + +[Term] +id: SO:0001263 +name: ncRNA_gene +synonym: "ncRNA gen" EXACT [] +synonym: "ncRNA gene" EXACT [] +synonym: "non-coding RNA gene" RELATED [] +is_a: SO:0000704 ! gene + +[Term] +id: SO:0001264 +name: gRNA_gene +synonym: "gRNA gene" EXACT [] +is_a: SO:0001263 ! ncRNA_gene +relationship: has_quality SO:0000979 ! gRNA_encoding + +[Term] +id: SO:0001265 +name: miRNA_gene +alt_id: SO:0001270 +synonym: "miRNA gene" EXACT [] +synonym: "stRNA gene" EXACT [] +synonym: "stRNA_gene" EXACT [] +is_a: SO:0001263 ! ncRNA_gene +relationship: has_quality SO:0000571 ! miRNA_encoding +relationship: has_quality SO:0000656 ! stRNA_encoding + +[Term] +id: SO:0001266 +name: scRNA_gene +synonym: "scRNA gene" EXACT [] +is_a: SO:0001263 ! ncRNA_gene +relationship: has_quality SO:0000575 ! scRNA_encoding + +[Term] +id: SO:0001267 +name: snoRNA_gene +synonym: "snoRNA gene" EXACT [] +is_a: SO:0001263 ! ncRNA_gene +relationship: has_quality SO:0000578 ! snoRNA_encoding + +[Term] +id: SO:0001268 +name: snRNA_gene +synonym: "snRNA gene" EXACT [] +is_a: SO:0001263 ! ncRNA_gene +relationship: has_quality SO:0001263 ! ncRNA_gene + +[Term] +id: SO:0001269 +name: SRP_RNA_gene +synonym: "SRP RNA gene" EXACT [] +is_a: SO:0001263 ! ncRNA_gene +relationship: has_quality SO:0000642 ! SRP_RNA_encoding + +[Term] +id: SO:0001271 +name: tmRNA_gene +synonym: "tmRNA gene" EXACT [] +is_a: SO:0001263 ! ncRNA_gene +relationship: has_quality SO:0000659 ! tmRNA_encoding + +[Term] +id: SO:0001272 +name: tRNA_gene +synonym: "tRNA gene" EXACT [] +is_a: SO:0001263 ! ncRNA_gene +relationship: has_quality SO:0000663 ! tRNA_encoding + +[Term] +id: SO:0001273 +name: modified_adenosine +def: "A modified adenine is an adenine base feature that has been altered." [SO:ke] +synonym: "modified adenosine" EXACT [] +is_a: SO:0000250 ! modified_RNA_base_feature + +[Term] +id: SO:0001274 +name: modified_inosine +def: "A modified inosine is an inosine base feature that has been altered." [SO:ke] +synonym: "modified inosine" EXACT [] +is_a: SO:0001230 ! inosine + +[Term] +id: SO:0001275 +name: modified_cytidine +def: "A modified cytidine is a cytidine base feature which has been altered." [SO:ke] +synonym: "modified cytidine" EXACT [] +is_a: SO:0000250 ! modified_RNA_base_feature + +[Term] +id: SO:0001276 +name: modified_guanosine +synonym: "modified guanosine" EXACT [] +is_a: SO:0000250 ! modified_RNA_base_feature + +[Term] +id: SO:0001277 +name: modified_uridine +synonym: "modified uridine" EXACT [] +is_a: SO:0000250 ! modified_RNA_base_feature + +[Term] +id: SO:0001278 +name: one_methylinosine +def: "1-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/] +synonym: "1-methylinosine" EXACT [] +synonym: "m1I" EXACT RNAMOD [] +synonym: "one methylinosine" EXACT [] +xref: RNAMOD:018 +is_a: SO:0001274 ! modified_inosine + +[Term] +id: SO:0001279 +name: one_two_prime_O_dimethylinosine +def: "1,2'-O-dimethylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/] +synonym: "1,2'-O-dimethylinosine" EXACT [] +synonym: "m'Im" EXACT RNAMOD [] +synonym: "one two prime O dimethylinosine" EXACT [] +xref: RNAMOD:019 +is_a: SO:0001274 ! modified_inosine + +[Term] +id: SO:0001280 +name: two_prime_O_methylinosine +def: "2'-O-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/] +synonym: "2'-O-methylinosine" EXACT [] +synonym: "Im" EXACT RNAMOD [] +synonym: "two prime O methylinosine" EXACT [] +xref: RNAMOD:081 +is_a: SO:0001274 ! modified_inosine + +[Term] +id: SO:0001281 +name: three_methylcytidine +def: "3-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] +synonym: "3-methylcytidine" EXACT [] +synonym: "m3C" EXACT RNAMOD [] +synonym: "three methylcytidine" EXACT [] +xref: RNAMOD:020 +is_a: SO:0001275 ! modified_cytidine + +[Term] +id: SO:0001282 +name: five_methylcytidine +def: "5-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] +synonym: "5-methylcytidine" EXACT [] +synonym: "five methylcytidine" EXACT [] +synonym: "m5C" EXACT RNAMOD [] +xref: RNAMOD:021 +is_a: SO:0001275 ! modified_cytidine + +[Term] +id: SO:0001283 +name: two_prime_O_methylcytidine +def: "2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] +synonym: "2'-O-methylcytidine" EXACT [] +synonym: "Cm" EXACT RNAMOD [] +synonym: "two prime O methylcytidine" EXACT [] +xref: RNAMOD:022 +is_a: SO:0001275 ! modified_cytidine + +[Term] +id: SO:0001284 +name: two_thiocytidine +def: "2-thiocytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] +synonym: "2-thiocytidine" EXACT [] +synonym: "s2C" EXACT RNAMOD [] +synonym: "two thiocytidine" EXACT [] +xref: RNAMOD:023 +is_a: SO:0001275 ! modified_cytidine + +[Term] +id: SO:0001285 +name: N4_acetylcytidine +def: "N4-acetylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] +synonym: "ac4C" EXACT RNAMOD [] +synonym: "N4 acetylcytidine" EXACT [] +synonym: "N4-acetylcytidine" EXACT [] +xref: RNAMOD:024 +is_a: SO:0001275 ! modified_cytidine + +[Term] +id: SO:0001286 +name: five_formylcytidine +def: "5-formylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] +synonym: "5-formylcytidine" EXACT [] +synonym: "f5C" EXACT RNAMOD [] +synonym: "five formylcytidine" EXACT [] +xref: RNAMOD:025 +is_a: SO:0001275 ! modified_cytidine + +[Term] +id: SO:0001287 +name: five_two_prime_O_dimethylcytidine +def: "5,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] +synonym: "5,2'-O-dimethylcytidine" EXACT [] +synonym: "five two prime O dimethylcytidine" EXACT [] +synonym: "m5Cm" EXACT RNAMOD [] +xref: RNAMOD:026 +is_a: SO:0001275 ! modified_cytidine + +[Term] +id: SO:0001288 +name: N4_acetyl_2_prime_O_methylcytidine +def: "N4-acetyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] +synonym: "ac4Cm" EXACT RNAMOD [] +synonym: "N4 acetyl 2 prime O methylcytidine" EXACT [] +synonym: "N4-acetyl-2'-O-methylcytidine" EXACT [] +xref: RNAMOD:027 +is_a: SO:0001275 ! modified_cytidine + +[Term] +id: SO:0001289 +name: lysidine +def: "Lysidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] +synonym: "k2C" EXACT RNAMOD [] +xref: http://en.wikipedia.org/wiki/Lysidine "wiki" +xref: RNAMOD:028 +is_a: SO:0001275 ! modified_cytidine + +[Term] +id: SO:0001290 +name: N4_methylcytidine +def: "N4-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] +synonym: "m4C" EXACT RNAMOD [] +synonym: "N4 methylcytidine" EXACT [] +synonym: "N4-methylcytidine" EXACT [] +xref: RNAMOD:082 +is_a: SO:0001275 ! modified_cytidine + +[Term] +id: SO:0001291 +name: N4_2_prime_O_dimethylcytidine +def: "N4,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] +synonym: "m4Cm" EXACT RNAMOD [] +synonym: "N4 2 prime O dimethylcytidine" EXACT [] +synonym: "N4,2'-O-dimethylcytidine" EXACT [] +xref: RNAMOD:083 +is_a: SO:0001275 ! modified_cytidine + +[Term] +id: SO:0001292 +name: five_hydroxymethylcytidine +def: "5-hydroxymethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] +synonym: "5-hydroxymethylcytidine" EXACT [] +synonym: "five hydroxymethylcytidine" EXACT [] +synonym: "hm5C" EXACT RNAMOD [] +xref: RNAMOD:084 +is_a: SO:0001275 ! modified_cytidine + +[Term] +id: SO:0001293 +name: five_formyl_two_prime_O_methylcytidine +def: "5-formyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] +synonym: "5-formyl-2'-O-methylcytidine" EXACT [] +synonym: "f5Cm" EXACT RNAMOD [] +synonym: "five formyl two prime O methylcytidine" EXACT [] +xref: RNAMOD:095 +is_a: SO:0001275 ! modified_cytidine + +[Term] +id: SO:0001294 +name: N4_N4_2_prime_O_trimethylcytidine +def: "N4_N4_2_prime_O_trimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] +synonym: "m42Cm" EXACT RNAMOD [] +synonym: "N4,N4,2'-O-trimethylcytidine" EXACT [] +xref: RNAMOD:107 +is_a: SO:0001275 ! modified_cytidine + +[Term] +id: SO:0001295 +name: one_methyladenosine +def: "1_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "1-methyladenosine" EXACT [] +synonym: "m1A" EXACT RNAMOD [] +synonym: "one methyladenosine" EXACT [] +xref: RNAMOD:001 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001296 +name: two_methyladenosine +def: "2_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "2-methyladenosine" EXACT [] +synonym: "m2A" EXACT RNAMOD [] +synonym: "two methyladenosine" EXACT [] +xref: RNAMOD:002 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001297 +name: N6_methyladenosine +def: "N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "m6A" EXACT RNAMOD [] +synonym: "N6 methyladenosine" EXACT [] +synonym: "N6-methyladenosine" EXACT [] +xref: RNAMOD:003 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001298 +name: two_prime_O_methyladenosine +def: "2prime_O_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "2'-O-methyladenosine" EXACT [] +synonym: "Am" EXACT RNAMOD [] +synonym: "two prime O methyladenosine" EXACT [] +xref: RNAMOD:004 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001299 +name: two_methylthio_N6_methyladenosine +def: "2_methylthio_N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "2-methylthio-N6-methyladenosine" EXACT [] +synonym: "ms2m6A" EXACT RNAMOD [] +synonym: "two methylthio N6 methyladenosine" EXACT [] +xref: RNAMOD:005 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001300 +name: N6_isopentenyladenosine +def: "N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "i6A" EXACT RNAMOD [] +synonym: "N6 isopentenyladenosine" EXACT [] +synonym: "N6-isopentenyladenosine" EXACT [] +xref: RNAMOD:006 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001301 +name: two_methylthio_N6_isopentenyladenosine +def: "2_methylthio_N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "2-methylthio-N6-isopentenyladenosine" EXACT [] +synonym: "ms2i6A" EXACT RNAMOD [] +synonym: "two methylthio N6 isopentenyladenosine" EXACT [] +xref: RNAMOD:007 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001302 +name: N6_cis_hydroxyisopentenyl_adenosine +def: "N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "io6A" EXACT RNAMOD [] +synonym: "N6 cis hydroxyisopentenyl adenosine" EXACT [] +synonym: "N6-(cis-hydroxyisopentenyl)adenosine" EXACT [] +xref: RNAMOD:008 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001303 +name: two_methylthio_N6_cis_hydroxyisopentenyl_adenosine +def: "2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine" EXACT [] +synonym: "ms2io6A" EXACT RNAMOD [] +synonym: "two methylthio N6 cis hydroxyisopentenyl adenosine" EXACT [] +xref: RNAMOD:009 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001304 +name: N6_glycinylcarbamoyladenosine +def: "N6_glycinylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "g6A" EXACT RNAMOD [] +synonym: "N6 glycinylcarbamoyladenosine" EXACT [] +synonym: "N6-glycinylcarbamoyladenosine" EXACT [] +xref: RNAMOD:010 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001305 +name: N6_threonylcarbamoyladenosine +def: "N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "N6 threonylcarbamoyladenosine" EXACT [] +synonym: "N6-threonylcarbamoyladenosine" EXACT [] +synonym: "t6A" EXACT RNAMOD [] +xref: RNAMOD:011 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001306 +name: two_methylthio_N6_threonyl_carbamoyladenosine +def: "2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "2-methylthio-N6-threonyl carbamoyladenosine" EXACT [] +synonym: "ms2t6A" EXACT RNAMOD [] +synonym: "two methylthio N6 threonyl carbamoyladenosine" EXACT [] +xref: RNAMOD:012 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001307 +name: N6_methyl_N6_threonylcarbamoyladenosine +def: "N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "m6t6A" EXACT RNAMOD [] +synonym: "N6 methyl N6 threonylcarbamoyladenosine" EXACT [] +synonym: "N6-methyl-N6-threonylcarbamoyladenosine" EXACT [] +xref: RNAMOD:013 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001308 +name: N6_hydroxynorvalylcarbamoyladenosine +def: "N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "hn6A" EXACT RNAMOD [] +synonym: "N6 hydroxynorvalylcarbamoyladenosine" EXACT [] +synonym: "N6-hydroxynorvalylcarbamoyladenosine" EXACT [] +xref: RNAMOD:014 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001309 +name: two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine +def: "2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "2-methylthio-N6-hydroxynorvalyl carbamoyladenosine" EXACT [] +synonym: "ms2hn6A" EXACT RNAMOD [] +synonym: "two methylthio N6 hydroxynorvalyl carbamoyladenosine" EXACT [] +xref: RNAMOD:015 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001310 +name: two_prime_O_ribosyladenosine_phosphate +def: "2prime_O_ribosyladenosine_phosphate is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "2'-O-ribosyladenosine (phosphate)" EXACT [] +synonym: "Ar(p)" EXACT RNAMOD [] +synonym: "two prime O ribosyladenosine phosphate" EXACT [] +xref: RNAMOD:016 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001311 +name: N6_N6_dimethyladenosine +def: "N6_N6_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "m62A" EXACT RNAMOD [] +synonym: "N6,N6-dimethyladenosine" EXACT [] +xref: RNAMOD:080 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001312 +name: N6_2_prime_O_dimethyladenosine +def: "N6_2prime_O_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "m6Am" EXACT RNAMOD [] +synonym: "N6 2 prime O dimethyladenosine" EXACT [] +synonym: "N6,2'-O-dimethyladenosine" EXACT [] +xref: RNAMOD:088 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001313 +name: N6_N6_2_prime_O_trimethyladenosine +def: "N6_N6_2prime_O_trimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "m62Am" EXACT RNAMOD [] +synonym: "N6,N6,2'-O-trimethyladenosine" EXACT [] +xref: RNAMOD:089 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001314 +name: one_two_prime_O_dimethyladenosine +def: "1,2'-O-dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "1,2'-O-dimethyladenosine" EXACT [] +synonym: "m1Am" EXACT RNAMOD [] +synonym: "one two prime O dimethyladenosine" EXACT [] +xref: RNAMOD:097 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001315 +name: N6_acetyladenosine +def: "N6_acetyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] +synonym: "ac6A" EXACT RNAMOD [] +synonym: "N6 acetyladenosine" EXACT [] +synonym: "N6-acetyladenosine" EXACT [] +xref: RNAMOD:102 +is_a: SO:0001273 ! modified_adenosine + +[Term] +id: SO:0001316 +name: seven_deazaguanosine +def: "7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/] +synonym: "7-deazaguanosine" RELATED [] +synonym: "seven deazaguanosine" EXACT [] +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001317 +name: queuosine +def: "Queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] +synonym: " Q" EXACT RNAMOD [] +xref: http://en.wikipedia.org/wiki/Queuosine "wiki" +xref: RNAMOD:043 +is_a: SO:0001316 ! seven_deazaguanosine + +[Term] +id: SO:0001318 +name: epoxyqueuosine +def: "Epoxyqueuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] +synonym: "eQ" EXACT RNAMOD [] +xref: RNAMOD:044 +is_a: SO:0001316 ! seven_deazaguanosine + +[Term] +id: SO:0001319 +name: galactosyl_queuosine +def: "Galactosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] +synonym: "galactosyl queuosine" EXACT [] +synonym: "galactosyl-queuosine" EXACT [] +synonym: "galQ" EXACT RNAMOD [] +xref: RNAMOD:045 +is_a: SO:0001316 ! seven_deazaguanosine + +[Term] +id: SO:0001320 +name: mannosyl_queuosine +def: "Mannosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] +synonym: "mannosyl queuosine" EXACT [] +synonym: "mannosyl-queuosine" EXACT [] +synonym: "manQ" EXACT RNAMOD [] +xref: RNAMOD:046 +is_a: SO:0001316 ! seven_deazaguanosine + +[Term] +id: SO:0001321 +name: seven_cyano_seven_deazaguanosine +def: "7_cyano_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] +synonym: "7-cyano-7-deazaguanosine" EXACT [] +synonym: "preQ0" EXACT RNAMOD [] +synonym: "seven cyano seven deazaguanosine" EXACT [] +xref: RNAMOD:047 +is_a: SO:0001316 ! seven_deazaguanosine + +[Term] +id: SO:0001322 +name: seven_aminomethyl_seven_deazaguanosine +def: "7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] +synonym: "7-aminomethyl-7-deazaguanosine" EXACT [] +synonym: "preQ1" EXACT RNAMOD [] +synonym: "seven aminomethyl seven deazaguanosine" EXACT [] +xref: RNAMOD:048 +is_a: SO:0001316 ! seven_deazaguanosine + +[Term] +id: SO:0001323 +name: archaeosine +def: "Archaeosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] +synonym: "G+" EXACT RNAMOD [] +xref: RNAMOD:049 +is_a: SO:0001316 ! seven_deazaguanosine + +[Term] +id: SO:0001324 +name: one_methylguanosine +def: "1_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "1-methylguanosine" EXACT [] +synonym: "m1G" EXACT RNAMOD [] +synonym: "one methylguanosine" EXACT [] +xref: RNAMOD:029 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001325 +name: N2_methylguanosine +def: "N2_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "m2G" EXACT RNAMOD [] +synonym: "N2 methylguanosine" EXACT [] +synonym: "N2-methylguanosine" EXACT [] +xref: RNAMOD:030 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001326 +name: seven_methylguanosine +def: "7_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "7-methylguanosine" EXACT [] +synonym: "m7G" EXACT RNAMOD [] +synonym: "seven methylguanosine" EXACT [] +xref: RNAMOD:031 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001327 +name: two_prime_O_methylguanosine +def: "2prime_O_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "2'-O-methylguanosine" EXACT [] +synonym: "Gm" EXACT RNAMOD [] +synonym: "two prime O methylguanosine" EXACT [] +xref: RNAMOD:032 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001328 +name: N2_N2_dimethylguanosine +def: "N2_N2_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "m22G" EXACT RNAMOD [] +synonym: "N2,N2-dimethylguanosine" EXACT [] +xref: RNAMOD:033 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001329 +name: N2_2_prime_O_dimethylguanosine +def: "N2_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "m2Gm" EXACT RNAMOD [] +synonym: "N2 2 prime O dimethylguanosine" EXACT [] +synonym: "N2,2'-O-dimethylguanosine" EXACT [] +xref: RNAMOD:034 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001330 +name: N2_N2_2_prime_O_trimethylguanosine +def: "N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "m22Gmv" EXACT RNAMOD [] +synonym: "N2,N2,2'-O-trimethylguanosine" EXACT [] +xref: RNAMOD:035 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001331 +name: two_prime_O_ribosylguanosine_phosphate +def: "2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "2'-O-ribosylguanosine (phosphate)" EXACT [] +synonym: "Gr(p)" EXACT RNAMOD [] +synonym: "two prime O ribosylguanosine phosphate" EXACT [] +xref: RNAMOD:036 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001332 +name: wybutosine +def: "Wybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "yW" EXACT RNAMOD [] +xref: RNAMOD:037 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001333 +name: peroxywybutosine +def: "Peroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "o2yW" EXACT RNAMOD [] +xref: RNAMOD:038 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001334 +name: hydroxywybutosine +def: "Hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "OHyW" EXACT RNAMOD [] +xref: RNAMOD:039 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001335 +name: undermodified_hydroxywybutosine +def: "Undermodified_hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "OHyW*" EXACT RNAMOD [] +synonym: "undermodified hydroxywybutosine" EXACT [] +xref: RNAMOD:040 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001336 +name: wyosine +def: "Wyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "IMG" EXACT RNAMOD [] +xref: RNAMOD:041 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001337 +name: methylwyosine +def: "Methylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "mimG" EXACT RNAMOD [] +xref: RNAMOD:042 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001338 +name: N2_7_dimethylguanosine +def: "N2_7_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "m2,7G" EXACT RNAMOD [] +synonym: "N2 7 dimethylguanosine" EXACT [] +synonym: "N2,7-dimethylguanosine" EXACT [] +xref: RNAMOD:090 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001339 +name: N2_N2_7_trimethylguanosine +def: "N2_N2_7_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "m2,2,7G" EXACT RNAMOD [] +synonym: "N2,N2,7-trimethylguanosine" EXACT [] +xref: RNAMOD:091 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001340 +name: one_two_prime_O_dimethylguanosine +def: "1_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "1,2'-O-dimethylguanosine" EXACT [] +synonym: "m1Gm" EXACT RNAMOD [] +synonym: "one two prime O dimethylguanosine" EXACT [] +xref: RNAMOD:096 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001341 +name: four_demethylwyosine +def: "4_demethylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "4-demethylwyosine" EXACT [] +synonym: "four demethylwyosine" EXACT [] +synonym: "imG-14" EXACT RNAMOD [] +xref: RNAMOD:100 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001342 +name: isowyosine +def: "Isowyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "imG2" EXACT RNAMOD [] +xref: RNAMOD:101 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001343 +name: N2_7_2prirme_O_trimethylguanosine +def: "N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "m2,7Gm" EXACT RNAMOD [] +synonym: "N2 7 2prirme O trimethylguanosine" EXACT [] +synonym: "N2,7,2'-O-trimethylguanosine" EXACT [] +xref: RNAMOD:106 +is_a: SO:0001276 ! modified_guanosine + +[Term] +id: SO:0001344 +name: five_methyluridine +def: "5_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-methyluridine" EXACT [] +synonym: "five methyluridine" EXACT [] +synonym: "m5U" EXACT RNAMOD [] +xref: http://en.wikipedia.org/wiki/5-methyluridine "wiki" +xref: RNAMOD:052 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001345 +name: two_prime_O_methyluridine +def: "2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "2'-O-methyluridine" EXACT [] +synonym: "two prime O methyluridine" EXACT [] +synonym: "Um" EXACT RNAMOD [] +xref: RNAMOD:053 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001346 +name: five_two_prime_O_dimethyluridine +def: "5_2_prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5,2'-O-dimethyluridine" EXACT [] +synonym: "five two prime O dimethyluridine" EXACT [] +synonym: "m5Um" EXACT RNAMOD [] +xref: RNAMOD:054 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001347 +name: one_methylpseudouridine +def: "1_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "1-methylpseudouridine" EXACT [] +synonym: "m1Y" EXACT RNAMOD [] +synonym: "one methylpseudouridine" EXACT [] +xref: RNAMOD:055 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001348 +name: two_prime_O_methylpseudouridine +def: "2prime_O_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "2'-O-methylpseudouridine" EXACT [] +synonym: "two prime O methylpseudouridine" EXACT [] +synonym: "Ym" EXACT RNAMOD [] +xref: RNAMOD:056 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001349 +name: two_thiouridine +def: "2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "2-thiouridine" EXACT [] +synonym: "s2U" EXACT RNAMOD [] +synonym: "two thiouridine" EXACT [] +xref: RNAMOD:057 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001350 +name: four_thiouridine +def: "4_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "4-thiouridine" EXACT [] +synonym: "four thiouridine" EXACT [] +synonym: "s4U" EXACT RNAMOD [] +xref: RNAMOD:058 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001351 +name: five_methyl_2_thiouridine +def: "5_methyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-methyl-2-thiouridine" EXACT [] +synonym: "five methyl 2 thiouridine" EXACT [] +synonym: "m5s2U" EXACT RNAMOD [] +xref: RNAMOD:059 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001352 +name: two_thio_two_prime_O_methyluridine +def: "2_thio_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "2-thio-2'-O-methyluridine" EXACT [] +synonym: "s2Um" EXACT RNAMOD [] +synonym: "two thio two prime O methyluridine" EXACT [] +xref: RNAMOD:060 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001353 +name: three_three_amino_three_carboxypropyl_uridine +def: "3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "3-(3-amino-3-carboxypropyl)uridine" EXACT [] +synonym: "acp3U" EXACT RNAMOD [] +xref: RNAMOD:061 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001354 +name: five_hydroxyuridine +def: "5_hydroxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-hydroxyuridine" EXACT [] +synonym: "five hydroxyuridine" EXACT [] +synonym: "ho5U" EXACT RNAMOD [] +xref: RNAMOD:060 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001355 +name: five_methoxyuridine +def: "5_methoxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-methoxyuridine" EXACT [] +synonym: "five methoxyuridine" EXACT [] +synonym: "mo5U" EXACT RNAMOD [] +xref: RNAMOD:063 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001356 +name: uridine_five_oxyacetic_acid +def: "Uridine_5_oxyacetic_acid is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "cmo5U" EXACT RNAMOD [] +synonym: "uridine 5-oxyacetic acid" EXACT [] +synonym: "uridine five oxyacetic acid" EXACT [] +xref: RNAMOD:064 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001357 +name: uridine_five_oxyacetic_acid_methyl_ester +def: "Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "mcmo5U" EXACT RNAMOD [] +synonym: "uridine 5-oxyacetic acid methyl ester" EXACT [] +synonym: "uridine five oxyacetic acid methyl ester" EXACT [] +xref: RNAMOD:065 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001358 +name: five_carboxyhydroxymethyl_uridine +def: "5_carboxyhydroxymethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-(carboxyhydroxymethyl)uridine" EXACT [] +synonym: "chm5U" EXACT RNAMOD [] +synonym: "five carboxyhydroxymethyl uridine" EXACT [] +xref: RNAMOD:066 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001359 +name: five_carboxyhydroxymethyl_uridine_methyl_ester +def: "5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-(carboxyhydroxymethyl)uridine methyl ester" EXACT [] +synonym: "five carboxyhydroxymethyl uridine methyl ester" EXACT [] +synonym: "mchm5U" EXACT RNAMOD [] +xref: RNAMOD:067 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001360 +name: five_methoxycarbonylmethyluridine +def: "Five_methoxycarbonylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-methoxycarbonylmethyluridine" EXACT [] +synonym: "five methoxycarbonylmethyluridine" EXACT [] +synonym: "mcm5U" EXACT RNAMOD [] +xref: RNAMOD:068 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001361 +name: five_methoxycarbonylmethyl_two_prime_O_methyluridine +def: "Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-methoxycarbonylmethyl-2'-O-methyluridine" EXACT [] +synonym: "five methoxycarbonylmethyl two prime O methyluridine" EXACT [] +synonym: "mcm5Um" EXACT RNAMOD [] +xref: RNAMOD:069 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001362 +name: five_methoxycarbonylmethyl_two_thiouridine +def: "5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-methoxycarbonylmethyl-2-thiouridine" EXACT [] +synonym: "five methoxycarbonylmethyl two thiouridine" EXACT [] +synonym: "mcm5s2U" EXACT RNAMOD [] +xref: RNAMOD:070 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001363 +name: five_aminomethyl_two_thiouridine +def: "5_aminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-aminomethyl-2-thiouridine" EXACT [] +synonym: "five aminomethyl two thiouridine" EXACT [] +synonym: "nm5s2U" EXACT RNAMOD [] +xref: RNAMOD:071 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001364 +name: five_methylaminomethyluridine +def: "5_methylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-methylaminomethyluridine" EXACT [] +synonym: "five methylaminomethyluridine" EXACT [] +synonym: "mnm5U" EXACT RNAMOD [] +xref: RNAMOD:072 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001365 +name: five_methylaminomethyl_two_thiouridine +def: "5_methylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-methylaminomethyl-2-thiouridine" EXACT [] +synonym: "five methylaminomethyl two thiouridine" EXACT [] +synonym: "mnm5s2U" EXACT RNAMOD [] +xref: RNAMOD:073 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001366 +name: five_methylaminomethyl_two_selenouridine +def: "5_methylaminomethyl_2_selenouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-methylaminomethyl-2-selenouridine" EXACT [] +synonym: "five methylaminomethyl two selenouridine" EXACT [] +synonym: "mnm5se2U" EXACT RNAMOD [] +xref: RNAMOD:074 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001367 +name: five_carbamoylmethyluridine +def: "5_carbamoylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-carbamoylmethyluridine" EXACT [] +synonym: "five carbamoylmethyluridine" EXACT [] +synonym: "ncm5U" EXACT RNAMOD [] +xref: RNAMOD:075 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001368 +name: five_carbamoylmethyl_two_prime_O_methyluridine +def: "5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-carbamoylmethyl-2'-O-methyluridine" EXACT [] +synonym: "five carbamoylmethyl two prime O methyluridine" EXACT [] +synonym: "ncm5Um" EXACT RNAMOD [] +xref: RNAMOD:076 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001369 +name: five_carboxymethylaminomethyluridine +def: "5_carboxymethylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-carboxymethylaminomethyluridine" EXACT [] +synonym: "cmnm5U" EXACT RNAMOD [] +synonym: "five carboxymethylaminomethyluridine" EXACT [] +xref: RNAMOD:077 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001370 +name: five_carboxymethylaminomethyl_two_prime_O_methyluridine +def: "5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-carboxymethylaminomethyl- 2'-O-methyluridine" EXACT [] +synonym: "cmnm5Um" EXACT RNAMOD [] +synonym: "five carboxymethylaminomethyl two prime O methyluridine" EXACT [] +xref: RNAMOD:078 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001371 +name: five_carboxymethylaminomethyl_two_thiouridine +def: "5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-carboxymethylaminomethyl-2-thiouridine" EXACT [] +synonym: "cmnm5s2U" EXACT RNAMOD [] +synonym: "five carboxymethylaminomethyl two thiouridine" EXACT [] +xref: RNAMOD:079 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001372 +name: three_methyluridine +def: "3_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "3-methyluridine" EXACT [] +synonym: "m3U" EXACT RNAMOD [] +synonym: "three methyluridine" EXACT [] +xref: RNAMOD:085 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001373 +name: one_methyl_three_three_amino_three_carboxypropyl_pseudouridine +def: "1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "1-methyl-3-(3-amino-3-carboxypropyl) pseudouridine" EXACT [] +synonym: "m1acp3Y" EXACT RNAMOD [] +xref: RNAMOD:086 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001374 +name: five_carboxymethyluridine +def: "5_carboxymethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-carboxymethyluridine" EXACT [] +synonym: "cm5U" EXACT RNAMOD [] +synonym: "five carboxymethyluridine" EXACT [] +xref: RNAMOD:087 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001375 +name: three_two_prime_O_dimethyluridine +def: "3_2prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "3,2'-O-dimethyluridine" EXACT [] +synonym: "m3Um" EXACT RNAMOD [] +synonym: "three two prime O dimethyluridine" EXACT [] +xref: RNAMOD:092 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001376 +name: five_methyldihydrouridine +def: "5_methyldihydrouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-methyldihydrouridine" EXACT [] +synonym: "five methyldihydrouridine" EXACT [] +synonym: "m5D" EXACT RNAMOD [] +xref: RNAMOD:093 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001377 +name: three_methylpseudouridine +def: "3_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "3-methylpseudouridine" EXACT [] +synonym: "m3Y" EXACT RNAMOD [] +synonym: "three methylpseudouridine" EXACT [] +xref: RNAMOD:094 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001378 +name: five_taurinomethyluridine +def: "5_taurinomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-taurinomethyluridine" EXACT [] +synonym: "five taurinomethyluridine" EXACT [] +synonym: "tm5U" EXACT RNAMOD [] +xref: RNAMOD:098 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001379 +name: five_taurinomethyl_two_thiouridine +def: "5_taurinomethyl_2_thiouridineis a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-taurinomethyl-2-thiouridine" EXACT [] +synonym: "five taurinomethyl two thiouridine" EXACT [] +synonym: "tm5s2U" EXACT RNAMOD [] +xref: RNAMOD:099 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001380 +name: five_isopentenylaminomethyl_uridine +def: "5_isopentenylaminomethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-(isopentenylaminomethyl)uridine" EXACT [] +synonym: "five isopentenylaminomethyl uridine" EXACT [] +synonym: "inm5U" EXACT RNAMOD [] +xref: RNAMOD:103 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001381 +name: five_isopentenylaminomethyl_two_thiouridine +def: "5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-(isopentenylaminomethyl)- 2-thiouridine" EXACT [] +synonym: "five isopentenylaminomethyl two thiouridine" EXACT [] +synonym: "inm5s2U" EXACT RNAMOD [] +xref: RNAMOD:104 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001382 +name: five_isopentenylaminomethyl_two_prime_O_methyluridine +def: "5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] +synonym: "5-(isopentenylaminomethyl)- 2'-O-methyluridine" EXACT [] +synonym: "five isopentenylaminomethyl two prime O methyluridine" EXACT [] +synonym: "inm5Um" EXACT RNAMOD [] +xref: RNAMOD:105 +is_a: SO:0001277 ! modified_uridine + +[Term] +id: SO:0001383 +name: histone_binding_site +def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone." [SO:ke] +synonym: "histone binding site" EXACT [] +is_a: SO:0001654 ! nucleotide_to_protein_binding_site + +[Term] +id: SO:0001384 +name: CDS_fragment +synonym: "CDS fragment" EXACT [] +synonym: "incomplete CDS" EXACT [] +is_a: SO:0000316 ! CDS +relationship: has_quality SO:0000731 ! fragmentary + +[Term] +id: SO:0001385 +name: modified_amino_acid_feature +def: "A post translationally modified amino acid feature." [SO:ke] +synonym: "modified amino acid feature" EXACT [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001386 +name: modified_glycine +def: "A post translationally modified glycine amino acid feature." [SO:ke] +synonym: "ModGly" EXACT AAMOD [] +synonym: "modified glycine" EXACT [] +xref: MOD:00908 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001387 +name: modified_L_alanine +def: "A post translationally modified alanine amino acid feature." [SO:ke] +synonym: "ModAla" EXACT AAMOD [] +synonym: "modified L alanine" EXACT [] +synonym: "modified L-alanine" EXACT [] +xref: MOD:00901 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001388 +name: modified_L_asparagine +def: "A post translationally modified asparagine amino acid feature." [SO:ke] +synonym: "ModAsn" EXACT AAMOD [] +synonym: "modified L asparagine" EXACT [] +synonym: "modified L-asparagine" EXACT [] +xref: MOD:00903 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001389 +name: modified_L_aspartic_acid +def: "A post translationally modified aspartic acid amino acid feature." [SO:ke] +synonym: "ModAsp" EXACT AAMOD [] +synonym: "modified L aspartic acid" EXACT [] +synonym: "modified L-aspartic acid" EXACT [] +xref: MOD:00904 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001390 +name: modified_L_cysteine +def: "A post translationally modified cysteine amino acid feature." [SO:ke] +synonym: "ModCys" EXACT AAMOD [] +synonym: "modified L cysteine" EXACT [] +synonym: "modified L-cysteine" EXACT [] +xref: MOD:00905 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001391 +name: modified_L_glutamic_acid +synonym: "ModGlu" EXACT AAMOD [] +synonym: "modified L glutamic acid" EXACT [] +synonym: "modified L-glutamic acid" EXACT [] +xref: MOD:00906 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001392 +name: modified_L_threonine +def: "A post translationally modified threonine amino acid feature." [SO:ke] +synonym: "modified L threonine" EXACT [] +synonym: "modified L-threonine" EXACT [] +synonym: "ModThr" EXACT AAMOD [] +xref: MOD:00917 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001393 +name: modified_L_tryptophan +def: "A post translationally modified tryptophan amino acid feature." [SO:ke] +synonym: "modified L tryptophan" EXACT [] +synonym: "modified L-tryptophan" EXACT [] +synonym: "ModTrp" EXACT AAMOD [] +xref: MOD:00918 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001394 +name: modified_L_glutamine +def: "A post translationally modified glutamine amino acid feature." [SO:ke] +synonym: "ModGln" EXACT [] +synonym: "modified L glutamine" EXACT [] +synonym: "modified L-glutamine" EXACT [] +xref: MOD:00907 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001395 +name: modified_L_methionine +def: "A post translationally modified methionine amino acid feature." [SO:ke] +synonym: "modified L methionine" EXACT [] +synonym: "modified L-methionine" EXACT [] +synonym: "ModMet" EXACT AAMOD [] +xref: MOD:00913 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001396 +name: modified_L_isoleucine +def: "A post translationally modified isoleucine amino acid feature." [SO:ke] +synonym: "modified L isoleucine" EXACT [] +synonym: "modified L-isoleucine" EXACT [] +synonym: "ModIle" EXACT AAMOD [] +xref: MOD:00910 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001397 +name: modified_L_phenylalanine +def: "A post translationally modified phenylalanine amino acid feature." [SO:ke] +synonym: "modified L phenylalanine" EXACT [] +synonym: "modified L-phenylalanine" EXACT [] +synonym: "ModPhe" EXACT AAMOD [] +xref: MOD:00914 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001398 +name: modified_L_histidine +def: "A post translationally modified histidine amino acid feature." [SO:ke] +synonym: "ModHis" EXACT [] +synonym: "modified L histidine" EXACT [] +synonym: "modified L-histidine" EXACT [] +xref: MOD:00909 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001399 +name: modified_L_serine +def: "A post translationally modified serine amino acid feature." [SO:ke] +synonym: "modified L serine" EXACT [] +synonym: "modified L-serine" EXACT [] +synonym: "MosSer" EXACT AAMOD [] +xref: MOD:00916 "http://www.psidev.info/index.php?q=node/104" +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001400 +name: modified_L_lysine +def: "A post translationally modified lysine amino acid feature." [SO:ke] +synonym: "modified L lysine" EXACT [] +synonym: "modified L-lysine" EXACT [] +synonym: "ModLys" EXACT AAMOD [] +xref: MOD:00912 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001401 +name: modified_L_leucine +def: "A post translationally modified leucine amino acid feature." [SO:ke] +synonym: "modified L leucine" EXACT [] +synonym: "modified L-leucine " EXACT [] +synonym: "ModLeu" EXACT AAMOD [] +xref: MOD:00911 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001402 +name: modified_L_selenocysteine +def: "A post translationally modified selenocysteine amino acid feature." [SO:ke] +synonym: "modified L selenocysteine" EXACT [] +synonym: "modified L-selenocysteine" EXACT [] +xref: MOD:01158 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001403 +name: modified_L_valine +def: "A post translationally modified valine amino acid feature." [SO:ke] +synonym: "modified L valine" EXACT [] +synonym: "modified L-valine" EXACT [] +synonym: "ModVal" EXACT AAMOD [] +xref: MOD:00920 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001404 +name: modified_L_proline +def: "A post translationally modified proline amino acid feature." [SO:ke] +synonym: "modified L proline" EXACT [] +synonym: "modified L-proline " EXACT [] +synonym: "ModPro" EXACT AAMOD [] +xref: MOD:00915 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001405 +name: modified_L_tyrosine +def: "A post translationally modified tyrosine amino acid feature." [SO:ke] +synonym: "modified L tyrosine" EXACT [] +synonym: "modified L-tyrosine" EXACT [] +synonym: "ModTry" EXACT AAMOD [] +xref: MOD:00919 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001406 +name: modified_L_arginine +def: "A post translationally modified arginine amino acid feature." [SO:ke] +synonym: "ModArg" EXACT AAMOD [] +synonym: "modified L arginine" EXACT [] +synonym: "modified L-arginine" EXACT [] +xref: MOD:00902 +is_a: SO:0001385 ! modified_amino_acid_feature + +[Term] +id: SO:0001407 +name: peptidyl +def: "An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds." [SO:ke] +is_a: SO:0000443 ! polymer_attribute + +[Term] +id: SO:0001408 +name: cleaved_for_gpi_anchor_region +def: "The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh] +synonym: "cleaved for gpi anchor region" EXACT [] +is_a: SO:0100011 ! cleaved_peptide_region + +[Term] +id: SO:0001409 +name: biomaterial_region +def: "A region which is intended for use in an experiment." [SO:cb] +subset: SOFA +synonym: "biomaterial region" EXACT [] +is_a: SO:0000001 ! region + +[Term] +id: SO:0001410 +name: experimental_feature +def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb] +subset: SOFA +synonym: "analysis feature" RELATED [] +synonym: "experimental output artefact" EXACT [] +synonym: "experimental_output_artefact" EXACT [] +is_a: SO:0000001 ! region + +[Term] +id: SO:0001411 +name: biological_region +def: "A region defined by its disposition to be involved in a biological process." [SO:cb] +subset: SOFA +synonym: "biological region" EXACT [] +is_a: SO:0000001 ! region + +[Term] +id: SO:0001412 +name: topologically_defined_region +def: "A region that is defined according to its relations with other regions within the same sequence." [SO:cb] +subset: SOFA +synonym: "topologically defined region" EXACT [] +is_a: SO:0000001 ! region + +[Term] +id: SO:0001413 +name: translocation_breakpoint +def: "The point within a chromosome where a translocation begins or ends." [SO:cb] +synonym: "translocation breakpoint" EXACT [] +is_a: SO:0001021 ! chromosome_breakpoint + +[Term] +id: SO:0001414 +name: insertion_breakpoint +def: "The point within a chromosome where a insertion begins or ends." [SO:cb] +synonym: "insertion breakpoint" EXACT [] +is_a: SO:0001021 ! chromosome_breakpoint + +[Term] +id: SO:0001415 +name: deletion_breakpoint +def: "The point within a chromosome where a deletion begins or ends." [SO:cb] +synonym: "deletion breakpoint" EXACT [] +is_a: SO:0001021 ! chromosome_breakpoint + +[Term] +id: SO:0001416 +name: five_prime_flanking_region +def: "A flanking region located five prime of a specific region." [SO:chado] +synonym: "5' flanking region" RELATED [] +synonym: "five prime flanking region" EXACT [] +is_a: SO:0000239 ! flanking_region + +[Term] +id: SO:0001417 +name: three_prime_flanking_region +def: "A flanking region located three prime of a specific region." [SO:chado] +synonym: "3' flanking region" RELATED [] +synonym: "three prime flanking region" EXACT [] +is_a: SO:0000239 ! flanking_region + +[Term] +id: SO:0001418 +name: transcribed_fragment +def: "An experimental region, defined by a tiling array experiment to be transcribed at some level." [SO:ke] +comment: Term requested by the MODencode group. +synonym: "transcribed fragment" EXACT [] +synonym: "transfrag" RELATED [] +is_a: SO:0001410 ! experimental_feature + +[Term] +id: SO:0001419 +name: cis_splice_site +def: "Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke] +subset: SOFA +synonym: "cis splice site" EXACT [] +is_a: SO:0000162 ! splice_site + +[Term] +id: SO:0001420 +name: trans_splice_site +def: "Primary transcript region bordering trans-splice junction." [SO:ke] +subset: SOFA +synonym: "trans splice site" EXACT [] +is_a: SO:0000162 ! splice_site + +[Term] +id: SO:0001421 +name: splice_junction +def: "The boundary between an intron and an exon." [SO:ke] +synonym: "splice boundary" EXACT [] +synonym: "splice junction" EXACT [] +is_a: SO:0000699 ! junction + +[Term] +id: SO:0001422 +name: conformational_switch +def: "A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke] +comment: MM Young, K Kirshenbaum, KA Dill & S Highsmith. Predicting conformational switches in proteins. Protein Science, 1999, 8, 1752-64. K. Kirshenbaum, M.M. Young and S. Highsmith. Predicting Allosteric Switches in Myosins. Protein Science 8(9):1806-1815. 1999. +synonym: "polypeptide conformational switch" EXACT [] +is_a: SO:0100001 ! biochemical_region_of_peptide + +[Term] +id: SO:0001423 +name: dye_terminator_read +def: "A read produced by the dye terminator method of sequencing." [SO:ke] +synonym: "dye terminator read" RELATED [] +is_a: SO:0000150 ! read + +[Term] +id: SO:0001424 +name: pyrosequenced_read +def: "A read produced by pyrosequencing technology." [SO:ke] +comment: An example is a read produced by Roche 454 technology. +synonym: "pyorsequenced read" RELATED [] +is_a: SO:0000150 ! read + +[Term] +id: SO:0001425 +name: ligation_based_read +def: "A read produced by ligation based sequencing technologies." [SO:ke] +comment: An example of this kind of read is one produced by ABI SOLiD. +synonym: "ligation based read" RELATED [] +is_a: SO:0000150 ! read + +[Term] +id: SO:0001426 +name: polymerase_synthesis_read +def: "A read produced by the polymerase based sequence by synthesis method." [SO:ke] +comment: An example is a read produced by Illumina technology. +synonym: "polymerase synthesis read" RELATED [] +is_a: SO:0000150 ! read + +[Term] +id: SO:0001427 +name: cis_regulatory_frameshift_element +def: "A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence." [RFAM:jd] +synonym: "cis regulatory frameshift element" EXACT [] +is_a: SO:0001679 ! transcription_regulatory_region + +[Term] +id: SO:0001428 +name: expressed_sequence_assembly +def: "A sequence assembly derived from expressed sequences." [SO:ke] +comment: From tracker [ 2372385 ] expressed_sequence_assembly. +synonym: "expressed sequence assembly" EXACT [] +is_a: SO:0000353 ! sequence_assembly + +[Term] +id: SO:0001429 +name: DNA_binding_site +def: "A binding site that, in the molecule, interacts selectively and non-covalently with DNA." [SO:ke] +synonym: "DNA binding site" EXACT [] +is_a: SO:0001655 ! nucleotide_binding_site + +[Term] +id: SO:0001431 +name: cryptic_gene +def: "A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning." [SO:ke] +synonym: "cryptic gene" EXACT [] +is_a: SO:0000704 ! gene +relationship: has_quality SO:0000976 ! cryptic + +[Term] +id: SO:0001432 +name: sequence_variant_affecting_polyadenylation +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting polyadenylation" RELATED [] +synonym: "sequence variant affecting polyadenylation" EXACT [] +is_obsolete: true +replaced_by: SO:0001545 + +[Term] +id: SO:0001433 +name: three_prime_RACE_clone +def: "A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host." [modENCODE:nlw] +synonym: "3' RACE clone" RELATED [] +is_a: SO:0000317 ! cDNA_clone + +[Term] +id: SO:0001434 +name: cassette_pseudogene +def: "A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy." [SO:ke] +comment: Requested by the Trypanosome community. +synonym: "cassette pseudogene" EXACT [] +synonym: "cassette type psedogene" RELATED [] +is_a: SO:0001760 ! non_processed_pseudogene + +[Term] +id: SO:0001435 +name: alanine +comment: A place holder for a cross product with chebi. +synonym: "A" EXACT aa1 [] +synonym: "Ala" EXACT aa3 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001436 +name: valine +comment: A place holder for a cross product with chebi. +synonym: "V" EXACT aa1 [] +synonym: "Val" EXACT aa3 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001437 +name: leucine +comment: A place holder for a cross product with chebi. +synonym: "L" EXACT aa1 [] +synonym: "Leu" EXACT aa3 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001438 +name: isoleucine +comment: A place holder for a cross product with chebi. +synonym: "I" EXACT aa1 [] +synonym: "Ile" EXACT aa3 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001439 +name: proline +comment: A place holder for a cross product with chebi. +synonym: "P" EXACT aa1 [] +synonym: "Pro" EXACT aa3 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001440 +name: tryptophan +comment: A place holder for a cross product with chebi. +synonym: "Trp" EXACT aa3 [] +synonym: "W" EXACT aa1 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001441 +name: phenylalanine +comment: A place holder for a cross product with chebi. +synonym: "F" EXACT aa1 [] +synonym: "Phe" EXACT aa3 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001442 +name: methionine +comment: A place holder for a cross product with chebi. +synonym: "M" EXACT aa1 [] +synonym: "Met" EXACT aa3 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001443 +name: glycine +comment: A place holder for a cross product with chebi. +synonym: "G" EXACT aa1 [] +synonym: "Gly" EXACT aa3 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001444 +name: serine +comment: A place holder for a cross product with chebi. +synonym: "S" EXACT aa1 [] +synonym: "Ser" EXACT aa3 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001445 +name: threonine +comment: A place holder for a cross product with chebi. +synonym: "T" EXACT aa1 [] +synonym: "Thr" EXACT aa3 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001446 +name: tyrosine +comment: A place holder for a cross product with chebi. +synonym: "Tyr" EXACT aa3 [] +synonym: "Y" EXACT aa1 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001447 +name: cysteine +comment: A place holder for a cross product with chebi. +synonym: "C" EXACT aa1 [] +synonym: "Cys" EXACT aa3 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001448 +name: glutamine +comment: A place holder for a cross product with chebi. +synonym: "Gln" EXACT aa3 [] +synonym: "Q" EXACT aa1 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001449 +name: asparagine +comment: A place holder for a cross product with chebi. +synonym: "Asn" EXACT aa3 [] +synonym: "N" EXACT aa1 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001450 +name: lysine +comment: A place holder for a cross product with chebi. +synonym: "K" EXACT aa1 [] +synonym: "Lys" EXACT aa3 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001451 +name: arginine +comment: A place holder for a cross product with chebi. +synonym: "Arg" EXACT aa3 [] +synonym: "R" EXACT aa1 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001452 +name: histidine +comment: A place holder for a cross product with chebi. +synonym: "H" EXACT aa1 [] +synonym: "His" EXACT aa3 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001453 +name: aspartic_acid +comment: A place holder for a cross product with chebi. +synonym: "Asp" EXACT aa3 [] +synonym: "aspartic acid" EXACT [] +synonym: "D" EXACT aa1 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001454 +name: glutamic_acid +comment: A place holder for a cross product with chebi. +synonym: "E" EXACT aa1 [] +synonym: "Glu" EXACT aa3 [] +synonym: "glutamic acid" EXACT [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001455 +name: selenocysteine +comment: A place holder for a cross product with chebi. +synonym: "Sec" EXACT aa3 [] +synonym: "U" EXACT aa1 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001456 +name: pyrrolysine +comment: A place holder for a cross product with chebi. +synonym: "O" EXACT aa1 [] +synonym: "Pyl" EXACT aa3 [] +is_a: SO:0001237 ! amino_acid + +[Term] +id: SO:0001457 +name: transcribed_cluster +def: "A region defined by a set of transcribed sequences from the same gene or expressed pseudogene." [SO:ke] +comment: This term was requested by Jeff Bowes, using the tracker, ID = 2594157. +synonym: "transcribed cluster" EXACT [] +synonym: "unigene cluster" RELATED [] +is_a: SO:0001410 ! experimental_feature +relationship: has_part SO:0000695 ! reagent + +[Term] +id: SO:0001458 +name: unigene_cluster +def: "A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene." [SO:ke] +comment: This term was requested by Jeff Bowes, using the tracker, ID = 2594157. +synonym: "unigene cluster" RELATED [] +is_a: SO:0001457 ! transcribed_cluster + +[Term] +id: SO:0001459 +name: CRISPR +def: "Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences." [RFAM:jd] +synonym: "Clustered_Regularly_Interspaced_Short_Palindromic_Repeat" EXACT [] +synonym: "CRISPR element" EXACT [] +xref: http:en.wikipedia.org/wiki/CRISPR +is_a: SO:0000314 ! direct_repeat + +[Term] +id: SO:0001460 +name: insulator_binding_site +def: "A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke] +comment: See tracker ID 2060908. +synonym: "insulator binding site" RELATED [] +is_a: SO:0001654 ! nucleotide_to_protein_binding_site +relationship: part_of SO:0000627 ! insulator + +[Term] +id: SO:0001461 +name: enhancer_binding_site +def: "A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke] +synonym: "enhancer binding site" RELATED [] +is_a: SO:0001654 ! nucleotide_to_protein_binding_site +relationship: part_of SO:0000165 ! enhancer + +[Term] +id: SO:0001462 +name: contig_collection +def: "A collection of contigs." [SO:ke] +comment: See tracker ID: 2138359. +synonym: "contig collection" EXACT [] +is_a: SO:0001085 ! sequence_conflict +is_a: SO:0001260 ! sequence_collection +relationship: has_part SO:0000149 ! contig + +[Term] +id: SO:0001463 +name: lincRNA +def: "A multiexonic non-coding RNA transcribed by RNA polymerase II." [PMID:19182780, SO:ke] +synonym: "large intervening non-coding RNA" EXACT [] +synonym: "long intergenic non-coding RNA" EXACT [] +is_a: SO:0001877 ! lnc_RNA + +[Term] +id: SO:0001464 +name: UST +def: "An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw] +synonym: "UTR sequence tag" EXACT [] +is_a: SO:0000345 ! EST + +[Term] +id: SO:0001465 +name: three_prime_UST +def: "A UST located in the 3'UTR of a protein-coding transcript." [SO:nlw] +synonym: "3' UST" RELATED [] +is_a: SO:0001464 ! UST + +[Term] +id: SO:0001466 +name: five_prime_UST +def: "An UST located in the 5'UTR of a protein-coding transcript." [SO:nlw] +synonym: "5' UST" RELATED [] +is_a: SO:0001464 ! UST + +[Term] +id: SO:0001467 +name: RST +def: "A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw] +synonym: "RACE sequence tag" EXACT [] +is_a: SO:0000345 ! EST + +[Term] +id: SO:0001468 +name: three_prime_RST +def: "A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." [SO:nlw] +synonym: "3' RST" EXACT [] +is_a: SO:0001467 ! RST + +[Term] +id: SO:0001469 +name: five_prime_RST +def: "A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." [SO:nlw] +synonym: "5' RST" RELATED [] +is_a: SO:0001467 ! RST + +[Term] +id: SO:0001470 +name: UST_match +def: "A match against an UST sequence." [SO:nlw] +synonym: "UST match" EXACT [] +is_a: SO:0000102 ! expressed_sequence_match + +[Term] +id: SO:0001471 +name: RST_match +def: "A match against an RST sequence." [SO:nlw] +synonym: "RST match" EXACT [] +is_a: SO:0000102 ! expressed_sequence_match + +[Term] +id: SO:0001472 +name: primer_match +def: "A nucleotide match to a primer sequence." [SO:nlw] +synonym: "primer match" EXACT [] +is_a: SO:0000347 ! nucleotide_match + +[Term] +id: SO:0001473 +name: miRNA_antiguide +def: "A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke] +synonym: "miRNA antiguide " EXACT [] +synonym: "miRNA passenger strand" EXACT [] +synonym: "miRNA star" EXACT [] +is_a: SO:0001243 ! miRNA_primary_transcript_region +created_by: kareneilbeck +creation_date: 2009-05-27T03:35:43Z + +[Term] +id: SO:0001474 +name: trans_splice_junction +def: "The boundary between the spliced leader and the first exon of the mRNA." [SO:ke] +synonym: "trans-splice junction" EXACT [] +is_a: SO:0000699 ! junction +created_by: kareneilbeck +creation_date: 2009-07-13T04:50:49Z + +[Term] +id: SO:0001475 +name: outron +def: "A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke] +is_a: SO:0000835 ! primary_transcript_region +created_by: kareneilbeck +creation_date: 2009-07-14T11:36:08Z + +[Term] +id: SO:0001476 +name: natural_plasmid +def: "A plasmid that occurs naturally." [SO:xp] +synonym: "natural plasmid" EXACT [] +is_a: SO:0000155 ! plasmid +is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element +relationship: has_quality SO:0000782 ! natural +created_by: kareneilbeck +creation_date: 2009-09-01T03:43:06Z + +[Term] +id: SO:0001477 +name: gene_trap_construct +def: "A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh] +synonym: "gene trap construct" EXACT [] +is_a: SO:0000637 ! engineered_plasmid +created_by: kareneilbeck +creation_date: 2009-09-01T03:49:09Z + +[Term] +id: SO:0001478 +name: promoter_trap_construct +def: "A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh] +synonym: "promoter trap construct" EXACT [] +is_a: SO:0000637 ! engineered_plasmid +created_by: kareneilbeck +creation_date: 2009-09-01T03:52:01Z + +[Term] +id: SO:0001479 +name: enhancer_trap_construct +def: "An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh] +synonym: "enhancer trap construct" EXACT [] +is_a: SO:0000637 ! engineered_plasmid +created_by: kareneilbeck +creation_date: 2009-09-01T03:53:26Z + +[Term] +id: SO:0001480 +name: PAC_end +def: "A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh] +synonym: "PAC end" EXACT [] +is_a: SO:0000150 ! read +relationship: part_of SO:0000154 ! PAC +created_by: kareneilbeck +creation_date: 2009-09-09T05:18:12Z + +[Term] +id: SO:0001481 +name: RAPD +def: "RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers." [ZFIN:mh] +synonym: "Random Amplification Polymorphic DNA" EXACT [] +is_a: SO:0000006 ! PCR_product +created_by: kareneilbeck +creation_date: 2009-09-09T05:26:10Z + +[Term] +id: SO:0001482 +name: shadow_enhancer +synonym: "shadow enhancer" EXACT [] +is_a: SO:0000165 ! enhancer +created_by: kareneilbeck +creation_date: 2009-09-09T05:29:29Z + +[Term] +id: SO:0001483 +name: SNV +def: "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm] +subset: SOFA +synonym: "single nucleotide variant" EXACT [] +is_a: SO:1000002 ! substitution +created_by: kareneilbeck +creation_date: 2009-10-08T11:37:49Z + +[Term] +id: SO:0001484 +name: X_element_combinatorial_repeat +def: "An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html] +comment: X element combinatorial repeats contain Tbf1p binding sites,\nand possible functions include a role in telomerase-independent telomere\nmaintenance via recombination or as a barrier against transcriptional\nsilencing. These are usually present as a combination of one or more of\nseveral types of smaller elements (designated A, B, C, or D). This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. +synonym: "X element combinatorial repeat" EXACT [] +is_a: SO:0000657 ! repeat_region +relationship: part_of SO:0000624 ! telomere +created_by: kareneilbeck +creation_date: 2009-11-10T11:03:37Z + +[Term] +id: SO:0001485 +name: Y_prime_element +def: "A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http\://www.yeastgenome.org/help/glossary.html] +comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. +synonym: "Y' element" EXACT [] +is_a: SO:0000657 ! repeat_region +relationship: part_of SO:0000624 ! telomere +created_by: kareneilbeck +creation_date: 2009-11-10T12:08:57Z + +[Term] +id: SO:0001486 +name: standard_draft +def: "The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete." [DOI:10.1126] +synonym: "standard draft" EXACT [] +is_a: SO:0001499 ! whole_genome_sequence_status +created_by: kareneilbeck +creation_date: 2009-10-23T12:48:32Z + +[Term] +id: SO:0001487 +name: high_quality_draft +def: "The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome." [DOI:10.1126] +synonym: "high quality draft" EXACT [] +is_a: SO:0001499 ! whole_genome_sequence_status +created_by: kareneilbeck +creation_date: 2009-10-23T12:52:36Z + +[Term] +id: SO:0001488 +name: improved_high_quality_draft +def: "The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution." [DOI:10.1126] +synonym: "improved high quality draft" EXACT [] +is_a: SO:0001499 ! whole_genome_sequence_status +created_by: kareneilbeck +creation_date: 2009-10-23T12:54:35Z + +[Term] +id: SO:0001489 +name: annotation_directed_improved_draft +def: "The status of a whole genome sequence,where annotation, and verification of coding regions has occurred." [DOI:10.1126] +synonym: "annotation directed improvement" EXACT [] +is_a: SO:0001499 ! whole_genome_sequence_status +created_by: kareneilbeck +creation_date: 2009-10-23T12:57:10Z + +[Term] +id: SO:0001490 +name: noncontiguous_finished +def: "The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions." [DOI:10.1126] +synonym: "non contiguous finished" EXACT [] +is_a: SO:0001499 ! whole_genome_sequence_status +created_by: kareneilbeck +creation_date: 2009-10-23T01:01:07Z + +[Term] +id: SO:0001491 +name: finished_genome +def: "The status of a whole genome sequence, with less than 1 error per 100,000 base pairs." [DOI:10.1126] +synonym: "finished" EXACT [] +synonym: "finished genome" EXACT [] +is_a: SO:0001499 ! whole_genome_sequence_status +created_by: kareneilbeck +creation_date: 2009-10-23T01:04:43Z + +[Term] +id: SO:0001492 +name: intronic_regulatory_region +def: "A regulatory region that is part of an intron." [SO:ke] +synonym: "intronic regulatory region" EXACT [] +is_a: SO:0001679 ! transcription_regulatory_region +relationship: part_of SO:0000188 ! intron +created_by: kareneilbeck +creation_date: 2009-11-08T02:48:02Z + +[Term] +id: SO:0001493 +name: centromere_DNA_Element_I +def: "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754] +comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699. +synonym: "CDEI" EXACT [] +synonym: "Centromere DNA Element I" EXACT [] +is_a: SO:0000330 ! conserved_region +relationship: part_of SO:0001794 ! point_centromere +created_by: kareneilbeck +creation_date: 2009-11-09T05:47:23Z + +[Term] +id: SO:0001494 +name: centromere_DNA_Element_II +def: "A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754] +comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699. +synonym: "CDEII" EXACT [] +synonym: "centromere DNA Element II" EXACT [] +is_a: SO:0000330 ! conserved_region +relationship: part_of SO:0001794 ! point_centromere +created_by: kareneilbeck +creation_date: 2009-11-09T05:51:26Z + +[Term] +id: SO:0001495 +name: centromere_DNA_Element_III +def: "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754] +comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699. +synonym: "CDEIII" EXACT [] +synonym: "centromere DNA Element III" EXACT [] +is_a: SO:0000330 ! conserved_region +relationship: part_of SO:0001794 ! point_centromere +created_by: kareneilbeck +creation_date: 2009-11-09T05:54:47Z + +[Term] +id: SO:0001496 +name: telomeric_repeat +def: "The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065] +comment: The repeats are maintained by telomerase and there is generally 300 (+/-) 75 bp of TG(1-3) at a given end. Telomeric repeats function in completing chromosome replication and protecting the ends from degradation and end-to-end fusions. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880739. +synonym: "telomeric repeat" EXACT [] +is_a: SO:0000657 ! repeat_region +relationship: part_of SO:0000624 ! telomere +created_by: kareneilbeck +creation_date: 2009-11-09T06:00:42Z + +[Term] +id: SO:0001497 +name: X_element +def: "The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434] +comment: Possible functions include roles in chromosomal segregation,\nmaintenance of chromosome stability, recombinational sequestering, or as a\nbarrier to transcriptional silencing. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. \n\nFrom Janos Demeter: The only region shared by all chromosome ends, the X element core sequence is a small conserved element (~475 bp) that contains an ARS sequence and in most cases an Abf1p binding site. Between these is a GC-rich region nearly identical to the meiosis-specific regulatory sequence URS1. +synonym: "X element" RELATED [] +synonym: "X element core sequence" EXACT [] +is_a: SO:0000330 ! conserved_region +relationship: part_of SO:0000624 ! telomere +created_by: kareneilbeck +creation_date: 2009-11-10T10:56:54Z + +[Term] +id: SO:0001498 +name: YAC_end +def: "A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke] +synonym: "YAC end" EXACT [] +is_a: SO:0000150 ! read +relationship: part_of SO:0000152 ! YAC +created_by: kareneilbeck +creation_date: 2009-11-19T11:07:18Z + +[Term] +id: SO:0001499 +name: whole_genome_sequence_status +def: "The status of whole genome sequence." [DOI:10.1126] +comment: This terms and children were added to SO in response to tracker request by Patrick Chain. The paper Genome Project Standards in a New Era of Sequencing. Science October 9th 2009, addresses these terms. +synonym: "whole genome sequence status" EXACT [] +is_a: SO:0000905 ! status +created_by: kareneilbeck +creation_date: 2009-10-23T12:47:47Z + +[Term] +id: SO:0001500 +name: heritable_phenotypic_marker +def: "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." [JAX:hdene] +synonym: "heritable phenotypic marker" EXACT [] +synonym: "phenotypic marker" EXACT [] +is_a: SO:0001645 ! genetic_marker +created_by: kareneilbeck +creation_date: 2009-12-07T01:50:55Z + +[Term] +id: SO:0001501 +name: peptide_collection +def: "A collection of peptide sequences." [BBOP:nlw] +comment: Term requested via tracker ID: 2910829. +synonym: "peptide collection" EXACT [] +synonym: "peptide set" EXACT [] +is_a: SO:0001260 ! sequence_collection +relationship: has_part SO:0000104 ! polypeptide +created_by: kareneilbeck +creation_date: 2009-12-11T10:58:58Z + +[Term] +id: SO:0001502 +name: high_identity_region +def: "An experimental feature with high sequence identity to another sequence." [SO:ke] +comment: Requested by tracker ID: 2902685. +synonym: "high identity region" EXACT [] +is_a: SO:0001410 ! experimental_feature +created_by: kareneilbeck +creation_date: 2009-12-11T11:06:05Z + +[Term] +id: SO:0001503 +name: processed_transcript +def: "A transcript for which no open reading frame has been identified and for which no other function has been determined." [MGI:hdeen] +comment: Ensembl and Vega also use this term name. Requested by Howard Deen of MGI. +synonym: "processed transcript" EXACT [] +is_a: SO:0000673 ! transcript +created_by: kareneilbeck +creation_date: 2009-12-21T05:37:14Z + +[Term] +id: SO:0001504 +name: assortment_derived_variation +def: "A chromosome variation derived from an event during meiosis." [SO:ke] +synonym: "assortment derived variation" RELATED [] +is_a: SO:0000240 ! chromosome_variation +created_by: kareneilbeck +creation_date: 2010-03-02T05:03:18Z + +[Term] +id: SO:0001505 +name: reference_genome +def: "A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly." [SO:ke] +synonym: "reference genome" RELATED [] +is_a: SO:0001026 ! genome +created_by: kareneilbeck +creation_date: 2010-03-03T02:10:03Z + +[Term] +id: SO:0001506 +name: variant_genome +def: "A collection of sequences (often chromosomes) of an individual." [SO:ke] +synonym: "variant genome" RELATED [] +is_a: SO:0001026 ! genome +created_by: kareneilbeck +creation_date: 2010-03-03T02:11:25Z + +[Term] +id: SO:0001507 +name: variant_collection +def: "A collection of one or more sequences of an individual." [SO:ke] +synonym: "variant collection" RELATED [] +is_a: SO:0001260 ! sequence_collection +relationship: has_part SO:0001059 ! sequence_alteration +created_by: kareneilbeck +creation_date: 2010-03-03T02:13:28Z + +[Term] +id: SO:0001508 +name: alteration_attribute +synonym: "alteration attribute" EXACT [] +is_a: SO:0000733 ! feature_attribute +created_by: kareneilbeck +creation_date: 2010-03-04T02:53:23Z + +[Term] +id: SO:0001509 +name: chromosomal_variation_attribute +synonym: "chromosomal variation attribute" EXACT [] +is_a: SO:0001508 ! alteration_attribute +created_by: kareneilbeck +creation_date: 2010-03-04T02:54:30Z + +[Term] +id: SO:0001510 +name: intrachromosomal +is_a: SO:0001509 ! chromosomal_variation_attribute +created_by: kareneilbeck +creation_date: 2010-03-04T02:55:25Z + +[Term] +id: SO:0001511 +name: interchromosomal +is_a: SO:0001509 ! chromosomal_variation_attribute +created_by: kareneilbeck +creation_date: 2010-03-04T02:55:43Z + +[Term] +id: SO:0001512 +name: insertion_attribute +def: "A quality of a chromosomal insertion,." [SO:ke] +synonym: "insertion attribute" EXACT [] +is_a: SO:0001508 ! alteration_attribute +created_by: kareneilbeck +creation_date: 2010-03-04T02:55:56Z + +[Term] +id: SO:0001513 +name: tandem +is_a: SO:0001512 ! insertion_attribute +created_by: kareneilbeck +creation_date: 2010-03-04T02:56:37Z + +[Term] +id: SO:0001514 +name: direct +def: "A quality of an insertion where the insert is not in a cytologically inverted orientation." [SO:ke] +is_a: SO:0001512 ! insertion_attribute +created_by: kareneilbeck +creation_date: 2010-03-04T02:56:49Z + +[Term] +id: SO:0001515 +name: inverted +def: "A quality of an insertion where the insert is in a cytologically inverted orientation." [SO:ke] +is_a: SO:0001512 ! insertion_attribute +created_by: kareneilbeck +creation_date: 2010-03-04T02:57:40Z + +[Term] +id: SO:0001516 +name: free +def: "The quality of a duplication where the new region exists independently of the original." [SO:ke] +is_a: SO:0001523 ! duplication_attribute +created_by: kareneilbeck +creation_date: 2010-03-04T02:57:51Z + +[Term] +id: SO:0001517 +name: inversion_attribute +synonym: "inversion attribute" EXACT [] +is_a: SO:0001508 ! alteration_attribute +created_by: kareneilbeck +creation_date: 2010-03-04T02:58:10Z + +[Term] +id: SO:0001518 +name: pericentric +is_a: SO:0001517 ! inversion_attribute +created_by: kareneilbeck +creation_date: 2010-03-04T02:58:24Z + +[Term] +id: SO:0001519 +name: paracentric +is_a: SO:0001517 ! inversion_attribute +created_by: kareneilbeck +creation_date: 2010-03-04T02:58:35Z + +[Term] +id: SO:0001520 +name: translocaton_attribute +synonym: "translocation attribute" EXACT [] +is_a: SO:0001508 ! alteration_attribute +created_by: kareneilbeck +creation_date: 2010-03-04T02:58:47Z + +[Term] +id: SO:0001521 +name: reciprocal +is_a: SO:0001520 ! translocaton_attribute +created_by: kareneilbeck +creation_date: 2010-03-04T02:59:34Z + +[Term] +id: SO:0001522 +name: insertional +is_a: SO:0001520 ! translocaton_attribute +created_by: kareneilbeck +creation_date: 2010-03-04T02:59:51Z + +[Term] +id: SO:0001523 +name: duplication_attribute +synonym: "duplication attribute" RELATED [] +is_a: SO:0001508 ! alteration_attribute +created_by: kareneilbeck +creation_date: 2010-03-05T01:56:33Z + +[Term] +id: SO:0001524 +name: chromosomally_aberrant_genome +synonym: "chromosomally aberrant genome" RELATED [] +is_a: SO:0001506 ! variant_genome +created_by: kareneilbeck +creation_date: 2010-03-05T02:21:00Z + +[Term] +id: SO:0001525 +name: assembly_error_correction +def: "A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake." [SO:ke] +synonym: "assembly error correction" RELATED [] +is_a: SO:0000413 ! sequence_difference +created_by: kareneilbeck +creation_date: 2010-03-09T02:16:31Z + +[Term] +id: SO:0001526 +name: base_call_error_correction +def: "A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake." [SO:ke] +synonym: "base call error correction" RELATED [] +is_a: SO:0000413 ! sequence_difference +created_by: kareneilbeck +creation_date: 2010-03-09T02:18:07Z + +[Term] +id: SO:0001527 +name: peptide_localization_signal +def: "A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke] +subset: SOFA +synonym: "localization signal" RELATED [] +synonym: "peptide localization signal" EXACT [] +is_a: SO:0000839 ! polypeptide_region +created_by: kareneilbeck +creation_date: 2010-03-11T02:15:05Z + +[Term] +id: SO:0001528 +name: nuclear_localization_signal +def: "A polypeptide region that targets a polypeptide to the nucleus." [SO:ke] +synonym: "NLS" EXACT [] +xref: http://en.wikipedia.org/wiki/Nuclear_localization_signal "wikipedia" +is_a: SO:0001527 ! peptide_localization_signal +created_by: kareneilbeck +creation_date: 2010-03-11T02:16:38Z + +[Term] +id: SO:0001529 +name: endosomal_localization_signal +def: "A polypeptide region that targets a polypeptide to the endosome." [SO:ke] +synonym: "endosomal localization signal" EXACT [] +is_a: SO:0001527 ! peptide_localization_signal +created_by: kareneilbeck +creation_date: 2010-03-11T02:20:58Z + +[Term] +id: SO:0001530 +name: lysosomal_localization_signal +def: "A polypeptide region that targets a polypeptide to the lysosome." [SO:ke] +synonym: "lysosomal localization signal" EXACT [] +is_a: SO:0001527 ! peptide_localization_signal +created_by: kareneilbeck +creation_date: 2010-03-11T02:24:10Z + +[Term] +id: SO:0001531 +name: nuclear_export_signal +def: "A polypeptide region that targets a polypeptide to he cytoplasm." [SO:ke] +synonym: "NES" EXACT [] +synonym: "nuclear export signal" EXACT [] +xref: http://en.wikipedia.org/wiki/Nuclear_export_signal +is_a: SO:0001527 ! peptide_localization_signal +created_by: kareneilbeck +creation_date: 2010-03-11T02:25:25Z + +[Term] +id: SO:0001532 +name: recombination_signal_sequence +def: "A region recognized by a recombinase." [SO:ke] +synonym: "recombination signal sequence" RELATED [] +xref: http://en.wikipedia.org/wiki/Recombination_Signal_Sequences "wikipedia" +is_a: SO:0000299 ! specific_recombination_site +created_by: kareneilbeck +creation_date: 2010-03-11T03:16:47Z + +[Term] +id: SO:0001533 +name: cryptic_splice_site +def: "A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke] +synonym: "cryptic splice signal" RELATED [] +synonym: "cryptic splice site" EXACT [] +is_a: SO:0000162 ! splice_site +created_by: kareneilbeck +creation_date: 2010-03-11T03:25:06Z + +[Term] +id: SO:0001534 +name: nuclear_rim_localization_signal +def: "A polypeptide region that targets a polypeptide to the nuclear rim." [SO:ke] +synonym: "nuclear rim localization signal" RELATED [] +xref: PMID:16027110 +is_a: SO:0001527 ! peptide_localization_signal +created_by: kareneilbeck +creation_date: 2010-03-11T03:31:30Z + +[Term] +id: SO:0001535 +name: p_element +def: "A P_element is a DNA transposon responsible for hybrid dysgenesis." [SO:ke] +synonym: "P element" RELATED [] +is_a: SO:0000182 ! DNA_transposon +created_by: kareneilbeck +creation_date: 2010-03-12T03:40:33Z + +[Term] +id: SO:0001536 +name: functional_variant +def: "A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke] +synonym: "functional variant" EXACT [] +is_a: SO:0001060 ! sequence_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:30:25Z + +[Term] +id: SO:0001537 +name: structural_variant +def: "A sequence variant that changes one or more sequence features." [SO:ke] +synonym: "Jannovar:structural_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "structural variant" RELATED [] +synonym: "VAT:svOverlap" EXACT VAR [] +xref: http://vat.gersteinlab.org/formats.php "VAT" +is_a: SO:0001060 ! sequence_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:31:01Z + +[Term] +id: SO:0001538 +name: transcript_function_variant +def: "A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke] +synonym: "transcript function variant" EXACT [] +is_a: SO:0001536 ! functional_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:32:58Z + +[Term] +id: SO:0001539 +name: translational_product_function_variant +def: "A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke] +synonym: "translational product variant" EXACT [] +is_a: SO:0001536 ! functional_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:46:15Z + +[Term] +id: SO:0001540 +name: level_of_transcript_variant +def: "A sequence variant which alters the level of a transcript." [SO:ke] +synonym: "level of transcript variant" EXACT [] +is_a: SO:0001538 ! transcript_function_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:47:07Z + +[Term] +id: SO:0001541 +name: decreased_transcript_level_variant +def: "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke] +synonym: "decreased transcript level" EXACT [] +is_a: SO:0001540 ! level_of_transcript_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:47:47Z + +[Term] +id: SO:0001542 +name: increased_transcript_level_variant +def: "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke] +synonym: "increased transcript level variant" EXACT [] +is_a: SO:0001540 ! level_of_transcript_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:48:17Z + +[Term] +id: SO:0001543 +name: transcript_processing_variant +def: "A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence." [SO:ke] +synonym: "transcript processing variant" EXACT [] +is_a: SO:0001538 ! transcript_function_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:48:48Z + +[Term] +id: SO:0001544 +name: editing_variant +def: "A transcript processing variant whereby the process of editing is disrupted with respect to the reference." [SO:ke] +synonym: "editing variant" EXACT [] +is_a: SO:0001543 ! transcript_processing_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:49:25Z + +[Term] +id: SO:0001545 +name: polyadenylation_variant +def: "A sequence variant that changes polyadenylation with respect to a reference sequence." [SO:ke] +synonym: "polyadenylation variant" EXACT [] +is_a: SO:0001543 ! transcript_processing_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:49:40Z + +[Term] +id: SO:0001546 +name: transcript_stability_variant +def: "A variant that changes the stability of a transcript with respect to a reference sequence." [SO:ke] +synonym: "transcript stability variant" EXACT [] +is_a: SO:0001538 ! transcript_function_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:50:01Z + +[Term] +id: SO:0001547 +name: decreased_transcript_stability_variant +def: "A sequence variant that decreases transcript stability with respect to a reference sequence." [SO:ke] +synonym: "decrease transcript stability variant" EXACT [] +is_a: SO:0001546 ! transcript_stability_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:50:23Z + +[Term] +id: SO:0001548 +name: increased_transcript_stability_variant +def: "A sequence variant that increases transcript stability with respect to a reference sequence." [SO:ke] +synonym: "increased transcript stability variant" EXACT [] +is_a: SO:0001546 ! transcript_stability_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:50:39Z + +[Term] +id: SO:0001549 +name: transcription_variant +def: "A variant that changes alters the transcription of a transcript with respect to a reference sequence." [SO:ke] +synonym: "transcription variant" EXACT [] +is_a: SO:0001538 ! transcript_function_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:51:26Z + +[Term] +id: SO:0001550 +name: rate_of_transcription_variant +def: "A sequence variant that changes the rate of transcription with respect to a reference sequence." [SO:ke] +synonym: "rate of transcription variant" EXACT [] +is_a: SO:0001549 ! transcription_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:51:50Z + +[Term] +id: SO:0001551 +name: increased_transcription_rate_variant +def: "A sequence variant that increases the rate of transcription with respect to a reference sequence." [SO:ke] +synonym: "increased transcription rate variant" EXACT [] +is_a: SO:0001550 ! rate_of_transcription_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:52:17Z + +[Term] +id: SO:0001552 +name: decreased_transcription_rate_variant +def: "A sequence variant that decreases the rate of transcription with respect to a reference sequence." [SO:ke] +synonym: "decreased transcription rate variant" EXACT [] +is_a: SO:0001550 ! rate_of_transcription_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:52:43Z + +[Term] +id: SO:0001553 +name: translational_product_level_variant +def: "A functional variant that changes the translational product level with respect to a reference sequence." [SO:ke] +synonym: "translational product level variant" EXACT [] +is_a: SO:0001539 ! translational_product_function_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:53:32Z + +[Term] +id: SO:0001554 +name: polypeptide_function_variant +def: "A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke] +synonym: "polypeptide function variant" EXACT [] +is_a: SO:0001539 ! translational_product_function_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:53:54Z + +[Term] +id: SO:0001555 +name: decreased_translational_product_level +def: "A sequence variant which decreases the translational product level with respect to a reference sequence." [SO:ke] +synonym: "decrease translational product level" EXACT [] +is_a: SO:0001553 ! translational_product_level_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:54:25Z + +[Term] +id: SO:0001556 +name: increased_translational_product_level +def: "A sequence variant which increases the translational product level with respect to a reference sequence." [SO:ke] +synonym: "increase translational product level" EXACT [] +is_a: SO:0001553 ! translational_product_level_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:55:25Z + +[Term] +id: SO:0001557 +name: polypeptide_gain_of_function_variant +def: "A sequence variant which causes gain of polypeptide function with respect to a reference sequence." [SO:ke] +synonym: "polypeptide gain of function variant" EXACT [] +is_a: SO:0001554 ! polypeptide_function_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:56:12Z + +[Term] +id: SO:0001558 +name: polypeptide_localization_variant +def: "A sequence variant which changes the localization of a polypeptide with respect to a reference sequence." [SO:ke] +synonym: "polypeptide localization variant" EXACT [] +is_a: SO:0001554 ! polypeptide_function_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:56:37Z + +[Term] +id: SO:0001559 +name: polypeptide_loss_of_function_variant +def: "A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence." [SO:ke] +synonym: "polypeptide loss of function variant" EXACT [] +is_a: SO:0001554 ! polypeptide_function_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:56:58Z + +[Term] +id: SO:0001560 +name: inactive_ligand_binding_site +def: "A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence." [SO:ke] +synonym: "inactive ligand binding site" EXACT [] +is_a: SO:0001559 ! polypeptide_loss_of_function_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:58:00Z + +[Term] +id: SO:0001561 +name: polypeptide_partial_loss_of_function +def: "A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence." [SO:ke] +synonym: "polypeptide partial loss of function" EXACT [] +is_a: SO:0001559 ! polypeptide_loss_of_function_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:58:32Z + +[Term] +id: SO:0001562 +name: polypeptide_post_translational_processing_variant +def: "A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence." [SO:ke] +synonym: "polypeptide post translational processing variant" EXACT [] +is_a: SO:0001554 ! polypeptide_function_variant +created_by: kareneilbeck +creation_date: 2010-03-22T11:59:06Z + +[Term] +id: SO:0001563 +name: copy_number_change +def: "A sequence variant where copies of a feature (CNV) are either increased or decreased." [SO:ke] +synonym: "copy number change" EXACT [] +is_a: SO:0001537 ! structural_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:27:33Z + +[Term] +id: SO:0001564 +name: gene_variant +def: "A sequence variant where the structure of the gene is changed." [SO:ke] +synonym: "gene structure variant" EXACT [] +synonym: "Jannovar:gene_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "snpEff:GENE" EXACT VAR [] +synonym: "VAAST:gene_variant" EXACT VAR [] +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +is_a: SO:0001878 ! feature_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:28:01Z + +[Term] +id: SO:0001565 +name: gene_fusion +def: "A sequence variant whereby a two genes have become joined." [SO:ke] +synonym: "gene fusion" EXACT [] +is_a: SO:0001564 ! gene_variant +is_a: SO:0001882 ! feature_fusion +created_by: kareneilbeck +creation_date: 2010-03-22T02:28:28Z + +[Term] +id: SO:0001566 +name: regulatory_region_variant +def: "A sequence variant located within a regulatory region." [SO:ke] +comment: EBI term: Regulatory region variations - In regulatory region annotated by Ensembl. +synonym: "Jannovar:regulatory_region_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "regulatory region variant" EXACT [] +synonym: "regulatory_region_" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] +synonym: "snpEff:REGULATION" EXACT VAR [] +synonym: "VEP:regulatory_region_variant" EXACT VAR [] +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +is_a: SO:0001878 ! feature_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:28:48Z + +[Term] +id: SO:0001567 +name: stop_retained_variant +def: "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke] +synonym: "Jannovar:stop_retained_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "snpEff:NON_SYNONYMOUS_STOP" EXACT VAR [] +synonym: "snpEff:SYNONYMOUS_STOP" EXACT VAR [] +synonym: "stop retained variant" EXACT [] +synonym: "VAAST:stop_retained" EXACT VAR [] +synonym: "VAAST:stop_retained_variant" EXACT VAR [] +synonym: "VEP:stop_retained_variant" EXACT VAR [] +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +is_a: SO:0001590 ! terminator_codon_variant +is_a: SO:0001819 ! synonymous_variant +created_by: kareneilbeck +creation_date: 2010-04-19T05:02:30Z + +[Term] +id: SO:0001568 +name: splicing_variant +def: "A sequence variant that changes the process of splicing." [SO:ke] +synonym: "Jannovar:splicing_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "splicing variant" EXACT [] +xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html +is_a: SO:0001576 ! transcript_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:29:22Z + +[Term] +id: SO:0001569 +name: cryptic_splice_site_variant +def: "A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +synonym: "cryptic splice site activation" EXACT [] +xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html +is_a: SO:0001568 ! splicing_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:29:41Z + +[Term] +id: SO:0001570 +name: cryptic_splice_acceptor +def: "A sequence variant whereby a new splice site is created due to the activation of a new acceptor." [SO:ke] +synonym: "cryptic splice acceptor" EXACT [] +is_a: SO:0001569 ! cryptic_splice_site_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:30:11Z + +[Term] +id: SO:0001571 +name: cryptic_splice_donor +def: "A sequence variant whereby a new splice site is created due to the activation of a new donor." [SO:ke] +synonym: "cryptic splice donor" EXACT [] +is_a: SO:0001569 ! cryptic_splice_site_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:30:35Z + +[Term] +id: SO:0001572 +name: exon_loss_variant +def: "A sequence variant whereby an exon is lost from the transcript." [SO:ke] +synonym: "exon loss" EXACT [] +synonym: "Jannovar:exon_loss_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "snpEff:EXON_DELETED" EXACT VAR [] +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +is_a: SO:0001568 ! splicing_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:31:09Z + +[Term] +id: SO:0001573 +name: intron_gain_variant +def: "A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +synonym: "intron gain" EXACT [] +synonym: "intron gain variant" EXACT [] +xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html +is_a: SO:0001568 ! splicing_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:31:25Z + +[Term] +id: SO:0001574 +name: splice_acceptor_variant +def: "A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke] +synonym: "Jannovar:splice_acceptor_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "Seattleseq:splice-acceptor" EXACT VAR [] +synonym: "snpEff:SPLICE_SITE_ACCEPTOR" EXACT VAR [] +synonym: "splice acceptor variant" EXACT [] +synonym: "VAAST:splice_acceptor_variant" EXACT VAR [] +synonym: "VEP:splice_acceptor_variant" EXACT VAR [] +xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +is_a: SO:0001629 ! splice_site_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:31:52Z + +[Term] +id: SO:0001575 +name: splice_donor_variant +def: "A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke] +synonym: "Jannovar:splice_donor_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "Seattleseq:splice-donor" EXACT VAR [] +synonym: "snpEff:SPLICE_SITE_DONOR" EXACT VAR [] +synonym: "splice donor variant" EXACT [] +synonym: "VAAST:splice_donor_variant" EXACT VAR [] +synonym: "VEP:splice_donor_variant" EXACT VAR [] +xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +is_a: SO:0001629 ! splice_site_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:32:10Z + +[Term] +id: SO:0001576 +name: transcript_variant +def: "A sequence variant that changes the structure of the transcript." [SO:ke] +synonym: "Jannovar:transcript_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "snpEff:TRANSCRIPT" EXACT VAR [] +synonym: "transcript variant" EXACT [] +synonym: "VAAST:transcript_variant" EXACT VAR [] +xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +is_a: SO:0001564 ! gene_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:32:41Z + +[Term] +id: SO:0001577 +name: complex_transcript_variant +def: "A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border." [http://ensembl.org/info/docs/variation/index.html] +comment: EBI term: Complex InDel - Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border. +synonym: "complex change in transcript" EXACT [] +synonym: "complex transcript variant" EXACT [] +synonym: "complex_indel" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] +synonym: "Seattleseq:codingComplex" RELATED VAR [] +synonym: "Seattleseq:codingComplex-near-splice" RELATED VAR [] +xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" +is_a: SO:0001576 ! transcript_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:33:03Z + +[Term] +id: SO:0001578 +name: stop_lost +def: "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke] +comment: EBI term: Stop lost - In coding sequence, resulting in the loss of a stop codon. +synonym: "ANNOVAR:stoploss" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] +synonym: "Jannovar:stop_lost" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "Seattleseq:stop-lost" EXACT VAR [] +synonym: "Seattleseq:stop-lost-near-splice" RELATED VAR [] +synonym: "snpEff:STOP_LOST" EXACT VAR [] +synonym: "stop codon lost" EXACT [] +synonym: "stop lost" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] +synonym: "VAAST:stop_lost" EXACT VAR [] +synonym: "VAT:removedStop" EXACT VAR [] +synonym: "VEP:stop_lost" EXACT VAR [] +xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +xref: http://vat.gersteinlab.org/formats.php "VAT" +xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +is_a: SO:0001590 ! terminator_codon_variant +is_a: SO:0001907 ! feature_elongation +is_a: SO:0001992 ! nonsynonymous_variant +created_by: kareneilbeck +creation_date: 2010-03-23T03:46:42Z + +[Term] +id: SO:0001579 +name: transcript_sequence_variant +synonym: "transcript sequence variant" EXACT [] +is_obsolete: true + +[Term] +id: SO:0001580 +name: coding_sequence_variant +alt_id: SO:0001581 +def: "A sequence variant that changes the coding sequence." [SO:ke] +synonym: "coding sequence variant" EXACT [] +synonym: "coding variant" EXACT [] +synonym: "codon variant" EXACT [] +synonym: "codon_variant" EXACT [] +synonym: "Jannovar:coding_sequence_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "Seattleseq:coding" EXACT VAR [] +synonym: "snpEff:CDS" EXACT VAR [] +synonym: "snpEff:CODON_CHANGE" RELATED VAR [] +synonym: "VAAST:coding_sequence_variant" EXACT VAR [] +synonym: "VEP:coding_sequence_variant" EXACT VAR [] +xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html +xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +is_a: SO:0001791 ! exon_variant +is_a: SO:0001968 ! coding_transcript_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:34:36Z + +[Term] +id: SO:0001582 +name: initiator_codon_variant +def: "A codon variant that changes at least one base of the first codon of a transcript." [SO:ke] +comment: This is being used to annotate changes to the first codon of a transcript, when the first annotated codon is not to methionine. A variant is predicted to change the first amino acid of a translation irrespective of the fact that the underlying codon is an AUG. As such for transcripts with an incomplete CDS (sequence does not start with an AUG), it is still called. +synonym: "initiatior codon variant" EXACT [] +synonym: "initiator codon change" EXACT [] +synonym: "Jannovar:initiator_codon_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "snpEff:NON_SYNONYMOUS_START" RELATED VAR [] +synonym: "VAT:startOverlap" EXACT VAR [] +xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +xref: http://vat.gersteinlab.org/formats.php "VAT" +xref: loinc:LA6695-6 "Initiating Methionine" +is_a: SO:0001580 ! coding_sequence_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:35:18Z + +[Term] +id: SO:0001583 +name: missense_variant +alt_id: SO:0001584 +alt_id: SO:0001783 +def: "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke] +comment: EBI term: Non-synonymous SNPs. SNPs that are located in the coding sequence and result in an amino acid change in the encoded peptide sequence. A change that causes a non_synonymous_codon can be more than 3 bases - for example 4 base substitution. +synonym: "ANNOVAR:nonsynonymous SNV" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] +synonym: "Jannovar:missense_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "missense" EXACT [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] +synonym: "missense codon" EXACT [] +synonym: "Seattleseq:missense" EXACT VAR [] +synonym: "Seattleseq:missense-near-splice" RELATED VAR [] +synonym: "snpEff:NON_SYNONYMOUS_CODING" EXACT VAR [] +synonym: "VAAST:missense_variant" EXACT VAR [] +synonym: "VAAST:non_synonymous_codon" RELATED VAR [] +synonym: "VAT:nonsynonymous" EXACT VAR [] +synonym: "VEP:missense_variant" EXACT VAR [] +xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html +xref: http://en.wikipedia.org/wiki/Missense_mutation +xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +xref: http://vat.gersteinlab.org/formats.php "VAT" +xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +xref: loinc:LA6698-0 "Missense" +is_a: SO:0001992 ! nonsynonymous_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:35:49Z + +[Term] +id: SO:0001585 +name: conservative_missense_variant +def: "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke] +synonym: "conservative missense codon" EXACT [] +synonym: "conservative missense variant" EXACT [] +synonym: "neutral missense codon" RELATED [] +synonym: "quiet missense codon" RELATED [] +xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html +is_a: SO:0001583 ! missense_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:36:40Z + +[Term] +id: SO:0001586 +name: non_conservative_missense_variant +def: "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke] +synonym: "non conservative missense codon" EXACT [] +synonym: "non conservative missense variant" EXACT [] +xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html +is_a: SO:0001583 ! missense_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:37:16Z + +[Term] +id: SO:0001587 +name: stop_gained +def: "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke] +comment: EBI term: Stop gained - In coding sequence, resulting in the gain of a stop codon (i.e. leading to a shortened peptide sequence). +synonym: "ANNOVAR:stopgain" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] +synonym: "Jannovar:stop_gained" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "nonsense" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] +synonym: "nonsense codon" EXACT [] +synonym: "Seattleseq:stop-gained" EXACT VAR [] +synonym: "Seattleseq:stop-gained-near-splice" RELATED VAR [] +synonym: "snpEff:STOP_GAINED" EXACT VAR [] +synonym: "stop codon gained" RELATED [] +synonym: "stop gained" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] +synonym: "VAAST:stop_gained" EXACT VAR [] +synonym: "VAT:prematureStop" EXACT VAR [] +synonym: "VEP:stop_gained" EXACT VAR [] +xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +xref: http://vat.gersteinlab.org/formats.php "VAT" +xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +xref: loinc:LA6699-8 "Nonsense" +is_a: SO:0001906 ! feature_truncation +is_a: SO:0001992 ! nonsynonymous_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:37:52Z + +[Term] +id: SO:0001589 +name: frameshift_variant +def: "A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke] +comment: EBI term:Frameshift variations - In coding sequence, resulting in a frameshift. +synonym: "ANNOVAR:frameshift block substitution" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] +synonym: "ANNOVAR:frameshift substitution" RELATED [] +synonym: "frameshift variant" EXACT [] +synonym: "frameshift_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] +synonym: "frameshift_coding" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] +synonym: "Jannovar:frameshift_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "Seattleseq:frameshift" EXACT VAR [] +synonym: "Seattleseq:frameshift-near-splice" RELATED VAR [] +synonym: "snpEff:FRAME_SHIFT" EXACT VAR [] +synonym: "VAAST:frameshift_variant" EXACT VAR [] +synonym: "VAT:deletionFS" NARROW VAR [] +synonym: "VAT:insertionFS" NARROW VAR [] +synonym: "VEP:frameshift_variant" EXACT VAR [] +xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +xref: http://vat.gersteinlab.org/formats.php "VAT" +xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +xref: loinc:LA6694-9 "Frameshift" +is_a: SO:0001818 ! protein_altering_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:40:19Z + +[Term] +id: SO:0001590 +name: terminator_codon_variant +alt_id: SO:0001625 +def: "A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke] +comment: The terminal codon may be the terminator, or in an incomplete transcript the last available codon. +synonym: "terminal codon variant" EXACT [] +synonym: "terminal_codon_variant" EXACT [] +synonym: "terminator codon variant" EXACT [] +synonym: "VAT:endOverlap" EXACT VAR [] +xref: http://vat.gersteinlab.org/formats.php "VAT" +xref: loinc:LA6700-2 "Stop Codon Mutation" +is_a: SO:0001580 ! coding_sequence_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:40:37Z + +[Term] +id: SO:0001591 +name: frame_restoring_variant +def: "A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke] +synonym: "frame restoring variant" EXACT [] +is_a: SO:0001589 ! frameshift_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:41:09Z + +[Term] +id: SO:0001592 +name: minus_1_frameshift_variant +def: "A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535] +synonym: "-1 frameshift variant" EXACT [] +synonym: "minus 1 frameshift variant" EXACT [] +is_a: SO:0001589 ! frameshift_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:41:30Z + +[Term] +id: SO:0001593 +name: minus_2_frameshift_variant +synonym: "-2 frameshift variant" EXACT [] +synonym: "minus 2 frameshift variant" EXACT [] +is_a: SO:0001589 ! frameshift_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:41:52Z + +[Term] +id: SO:0001594 +name: plus_1_frameshift_variant +def: "A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535] +synonym: "+1 frameshift variant" EXACT [] +synonym: "plus 1 frameshift variant" EXACT [] +is_a: SO:0001589 ! frameshift_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:42:06Z + +[Term] +id: SO:0001595 +name: plus_2_frameshift_variant +synonym: "+2 frameshift variant" EXACT [] +synonym: "plus 2 frameshift variant" EXACT [] +is_a: SO:0001589 ! frameshift_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:42:23Z + +[Term] +id: SO:0001596 +name: transcript_secondary_structure_variant +def: "A sequence variant within a transcript that changes the secondary structure of the RNA product." [SO:ke] +synonym: "transcript secondary structure variant" EXACT [] +is_a: SO:0001576 ! transcript_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:43:18Z + +[Term] +id: SO:0001597 +name: compensatory_transcript_secondary_structure_variant +def: "A secondary structure variant that compensate for the change made by a previous variant." [SO:ke] +synonym: "compensatory transcript secondary structure variant" EXACT [] +is_a: SO:0001596 ! transcript_secondary_structure_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:43:54Z + +[Term] +id: SO:0001598 +name: translational_product_structure_variant +def: "A sequence variant within the transcript that changes the structure of the translational product." [SO:ke] +synonym: "translational product structure variant" EXACT [] +xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html +is_a: SO:0001564 ! gene_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:44:17Z + +[Term] +id: SO:0001599 +name: 3D_polypeptide_structure_variant +def: "A sequence variant that changes the resulting polypeptide structure." [SO:ke] +synonym: "3D polypeptide structure variant" EXACT [] +is_a: SO:0001539 ! translational_product_function_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:44:46Z + +[Term] +id: SO:0001600 +name: complex_3D_structural_variant +def: "A sequence variant that changes the resulting polypeptide structure." [SO:ke] +synonym: "complex 3D structural variant" EXACT [] +is_a: SO:0001599 ! 3D_polypeptide_structure_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:45:13Z + +[Term] +id: SO:0001601 +name: conformational_change_variant +def: "A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence." [SO:ke] +synonym: "conformational change variant" EXACT [] +is_a: SO:0001599 ! 3D_polypeptide_structure_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:45:48Z + +[Term] +id: SO:0001602 +name: complex_change_of_translational_product_variant +synonym: "complex change of translational product variant" EXACT [] +is_a: SO:0001539 ! translational_product_function_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:46:54Z + +[Term] +id: SO:0001603 +name: polypeptide_sequence_variant +def: "A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke] +synonym: "polypeptide sequence variant" EXACT [] +is_a: SO:0001598 ! translational_product_structure_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:47:13Z + +[Term] +id: SO:0001604 +name: amino_acid_deletion +def: "A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide." [SO:ke] +synonym: "amino acid deletion" EXACT [] +xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html +is_a: SO:0001603 ! polypeptide_sequence_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:47:36Z + +[Term] +id: SO:0001605 +name: amino_acid_insertion +def: "A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide." [SO:ke] +synonym: "amino acid insertion" EXACT [] +xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html +is_a: SO:0001603 ! polypeptide_sequence_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:47:56Z + +[Term] +id: SO:0001606 +name: amino_acid_substitution +def: "A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." [SO:ke] +synonym: "amino acid substitution" EXACT [] +synonym: "VAAST:amino_acid_substitution" EXACT VAR [] +xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html +is_a: SO:0001603 ! polypeptide_sequence_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:48:17Z + +[Term] +id: SO:0001607 +name: conservative_amino_acid_substitution +def: "A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide." [SO:ke] +synonym: "conservative amino acid substitution" EXACT [] +is_a: SO:0001606 ! amino_acid_substitution +created_by: kareneilbeck +creation_date: 2010-03-22T02:48:57Z + +[Term] +id: SO:0001608 +name: non_conservative_amino_acid_substitution +def: "A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide." [SO:ke] +synonym: "non conservative amino acid substitution" EXACT [] +is_a: SO:0001606 ! amino_acid_substitution +created_by: kareneilbeck +creation_date: 2010-03-22T02:49:23Z + +[Term] +id: SO:0001609 +name: elongated_polypeptide +def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke] +synonym: "elongated polypeptide" EXACT [] +xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html +is_a: SO:0001603 ! polypeptide_sequence_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:49:52Z + +[Term] +id: SO:0001610 +name: elongated_polypeptide_C_terminal +def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus." [SO:ke] +synonym: "elongated polypeptide C terminal" EXACT [] +is_a: SO:0001609 ! elongated_polypeptide +created_by: kareneilbeck +creation_date: 2010-03-22T02:50:20Z + +[Term] +id: SO:0001611 +name: elongated_polypeptide_N_terminal +def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus." [SO:ke] +synonym: "elongated polypeptide N terminal" EXACT [] +is_a: SO:0001609 ! elongated_polypeptide +created_by: kareneilbeck +creation_date: 2010-03-22T02:50:31Z + +[Term] +id: SO:0001612 +name: elongated_in_frame_polypeptide_C_terminal +def: "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke] +synonym: "elongated in frame polypeptide C terminal" EXACT [] +is_a: SO:0001610 ! elongated_polypeptide_C_terminal +created_by: kareneilbeck +creation_date: 2010-03-22T02:51:05Z + +[Term] +id: SO:0001613 +name: elongated_out_of_frame_polypeptide_C_terminal +def: "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke] +synonym: "elongated polypeptide out of frame C terminal" EXACT [] +is_a: SO:0001610 ! elongated_polypeptide_C_terminal +created_by: kareneilbeck +creation_date: 2010-03-22T02:51:20Z + +[Term] +id: SO:0001614 +name: elongated_in_frame_polypeptide_N_terminal_elongation +def: "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke] +synonym: "elongated in frame polypeptide N terminal" EXACT [] +is_a: SO:0001611 ! elongated_polypeptide_N_terminal +created_by: kareneilbeck +creation_date: 2010-03-22T02:51:49Z + +[Term] +id: SO:0001615 +name: elongated_out_of_frame_polypeptide_N_terminal +def: "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke] +synonym: "elongated out of frame N terminal" EXACT [] +is_a: SO:0001611 ! elongated_polypeptide_N_terminal +created_by: kareneilbeck +creation_date: 2010-03-22T02:52:05Z + +[Term] +id: SO:0001616 +name: polypeptide_fusion +def: "A sequence variant that causes a fusion of two polypeptide sequences." [SO:ke] +synonym: "polypeptide fusion" EXACT [] +is_a: SO:0001603 ! polypeptide_sequence_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:52:43Z + +[Term] +id: SO:0001617 +name: polypeptide_truncation +def: "A sequence variant of the CD that causes a truncation of the resulting polypeptide." [SO:ke] +synonym: "polypeptide truncation" EXACT [] +xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html +is_a: SO:0001603 ! polypeptide_sequence_variant +created_by: kareneilbeck +creation_date: 2010-03-22T02:53:07Z + +[Term] +id: SO:0001618 +name: inactive_catalytic_site +def: "A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence." [SO:ke] +synonym: "inactive catalytic site" EXACT [] +is_a: SO:0001560 ! inactive_ligand_binding_site +created_by: kareneilbeck +creation_date: 2010-03-22T03:06:14Z + +[Term] +id: SO:0001619 +name: non_coding_transcript_variant +def: "A transcript variant of a non coding RNA gene." [SO:ke] +comment: Within non-coding gene - Located within a gene that does not code for a protein. +synonym: "ANNOVAR:ncRNA" NARROW VAR [http://annovar.openbioinformatics.org/en/latest/user-guide/gene/] +synonym: "Jannovar:non_coding_transcript_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "nc transcript variant" EXACT [] +synonym: "non coding transcript variant" EXACT [] +synonym: "VEP:non_coding_transcript_variant" EXACT VAR [] +synonym: "within_non_coding_gene" EXACT dbsnp [http://ensembl.org/info/docs/variation/index.html] +xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +is_a: SO:0001576 ! transcript_variant +created_by: kareneilbeck +creation_date: 2010-03-23T11:16:23Z + +[Term] +id: SO:0001620 +name: mature_miRNA_variant +def: "A transcript variant located with the sequence of the mature miRNA." [SO:ke] +comment: EBI term: Within mature miRNA - Located within a microRNA. +synonym: "mature miRNA variant" EXACT [] +synonym: "snpEff:MICRO_RNA" EXACT VAR [] +synonym: "VEP:mature_miRNA_variant" EXACT VAR [] +synonym: "within_mature_miRNA" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +xref: XX:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +is_a: SO:0001619 ! non_coding_transcript_variant +created_by: kareneilbeck +creation_date: 2010-03-23T11:16:58Z + +[Term] +id: SO:0001621 +name: NMD_transcript_variant +def: "A variant in a transcript that is the target of NMD." [SO:ke] +synonym: "NMD transcript variant" EXACT [] +synonym: "NMD_transcript" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] +synonym: "VEP:NMD_transcript_variant" EXACT VAR [] +xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +is_a: SO:0001576 ! transcript_variant +created_by: kareneilbeck +creation_date: 2010-03-23T11:20:40Z + +[Term] +id: SO:0001622 +name: UTR_variant +def: "A transcript variant that is located within the UTR." [SO:ke] +synonym: "UTR variant" EXACT [] +synonym: "UTR_" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] +is_a: SO:0001791 ! exon_variant +is_a: SO:0001968 ! coding_transcript_variant +created_by: kareneilbeck +creation_date: 2010-03-23T11:22:58Z + +[Term] +id: SO:0001623 +name: 5_prime_UTR_variant +def: "A UTR variant of the 5' UTR." [SO:ke] +comment: EBI term: 5prime UTR variations - In 5prime UTR (untranslated region). +synonym: "5'UTR variant" EXACT [] +synonym: "5PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] +synonym: "ANNOVAR:UTR5" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] +synonym: "five prime UTR variant" EXACT [] +synonym: "Jannovar:5_prime_utr_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "Seattleseq:5-prime-UTR" EXACT VAR [] +synonym: "snpEff:UTR_5_PRIME" EXACT VAR [] +synonym: "untranslated-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] +synonym: "VAAST:5_prime_UTR_variant" EXACT VAR [] +synonym: "VAAST:five_prime_UTR_variant" EXACT VAR [] +synonym: "VEP:5_prime_UTR_variant" EXACT VAR [] +xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +is_a: SO:0001622 ! UTR_variant +created_by: kareneilbeck +creation_date: 2010-03-23T11:23:29Z + +[Term] +id: SO:0001624 +name: 3_prime_UTR_variant +def: "A UTR variant of the 3' UTR." [SO:ke] +comment: EBI term 3prime UTR variations - In 3prime UTR. +synonym: "3'UTR variant" EXACT [] +synonym: "3PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] +synonym: "ANNOVAR:UTR3" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] +synonym: "Jannovar:3_prime_utr_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "Seattleseq:3-prime-UTR" EXACT VAR [] +synonym: "snpEff:UTR_3_PRIME" EXACT VAR [] +synonym: "three prime UTR variant" EXACT [] +synonym: "untranslated-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] +synonym: "VAAST:3_prime_UTR_variant" EXACT VAR [] +synonym: "VAAST:three_prime_UTR_variant" EXACT VAR [] +synonym: "VEP:3_prime_UTR_variant" EXACT VAR [] +xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +is_a: SO:0001622 ! UTR_variant +created_by: kareneilbeck +creation_date: 2010-03-23T11:23:54Z + +[Term] +id: SO:0001626 +name: incomplete_terminal_codon_variant +def: "A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke] +comment: EBI term: Partial codon - Located within the final, incomplete codon of a transcript with a shortened coding sequence where the end is unknown. +synonym: "incomplete terminal codon variant" EXACT [] +synonym: "partial_codon" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] +synonym: "VEP:incomplete_terminal_codon_variant" EXACT VAR [] +xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +is_a: SO:0001590 ! terminator_codon_variant +is_a: SO:0001650 ! inframe_variant +created_by: kareneilbeck +creation_date: 2010-03-23T03:51:15Z + +[Term] +id: SO:0001627 +name: intron_variant +def: "A transcript variant occurring within an intron." [SO:ke] +comment: EBI term: Intronic variations - In intron. +synonym: "ANNOVAR:intronic" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] +synonym: "intron variant" EXACT [] +synonym: "intron_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] +synonym: "intronic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] +synonym: "Jannovar:intron_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "Seattleseq:intron" EXACT VAR [] +synonym: "Seattleseq:intron-near-splice" RELATED VAR [] +synonym: "snpEff:INTRON" EXACT VAR [] +synonym: "VAAST:intron_variant" EXACT VAR [] +synonym: "VEP:intron_variant" EXACT VAR [] +xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +is_a: SO:0001576 ! transcript_variant +created_by: kareneilbeck +creation_date: 2010-03-23T03:52:38Z + +[Term] +id: SO:0001628 +name: intergenic_variant +def: "A sequence variant located in the intergenic region, between genes." [SO:ke] +comment: EBI term Intergenic variations - More than 5 kb either upstream or downstream of a transcript. +synonym: "ANNOVAR:intergenic" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] +synonym: "intergenic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] +synonym: "intergenic variant" EXACT [] +synonym: "Jannovar:intergenic_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "Seattleseq:intergenic" EXACT VAR [] +synonym: "snpEff:INTERGENIC" EXACT VAR [] +synonym: "VEP:intergenic_variant" EXACT VAR [] +xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +is_a: SO:0001878 ! feature_variant +created_by: kareneilbeck +creation_date: 2010-03-23T05:07:37Z + +[Term] +id: SO:0001629 +name: splice_site_variant +def: "A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html] +comment: EBI term - essential splice site - In the first 2 or the last 2 base pairs of an intron. The 5th base is on the donor (5') side of the intron. Updated to b in line with Cancer Genome Project at the Sanger. +synonym: "essential_splice_site" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] +synonym: "splice site variant" EXACT [] +synonym: "VAT:spliceOverlap" EXACT VAR [] +xref: http://vat.gersteinlab.org/formats.php "VAT" +is_a: SO:0001568 ! splicing_variant +is_a: SO:0001627 ! intron_variant +created_by: kareneilbeck +creation_date: 2010-03-24T09:42:00Z + +[Term] +id: SO:0001630 +name: splice_region_variant +def: "A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [http://ensembl.org/info/docs/variation/index.html] +comment: EBI term: splice site - 1-3 bps into an exon or 3-8 bps into an intron. +synonym: "ANNOVAR:splicing" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] +synonym: "Jannovar:splice_region_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "snpEff:SPLICE_SITE_BRANCH" RELATED VAR [] +synonym: "snpEff:SPLICE_SITE_BRANCH_U12" RELATED VAR [] +synonym: "snpEff:SPLICE_SITE_REGION" EXACT VAR [] +synonym: "splice region variant" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] +synonym: "VAAST:splice_region_variant" EXACT VAR [] +synonym: "VEP:splice_region_variant" EXACT VAR [] +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +is_a: SO:0001568 ! splicing_variant +created_by: kareneilbeck +creation_date: 2010-03-24T09:46:02Z + +[Term] +id: SO:0001631 +name: upstream_gene_variant +def: "A sequence variant located 5' of a gene." [SO:ke] +comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references. +synonym: "ANNOVAR:upstream" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] +synonym: "Jannovar:upstream_gene_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "snpEff:UPSTREAM" EXACT VAR [] +synonym: "upstream gene variant" EXACT [] +synonym: "VEP:upstream_gene_variant" EXACT VAR [] +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +is_a: SO:0001628 ! intergenic_variant +created_by: kareneilbeck +creation_date: 2010-03-24T09:49:13Z + +[Term] +id: SO:0001632 +name: downstream_gene_variant +def: "A sequence variant located 3' of a gene." [SO:ke] +comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references. +synonym: "ANNOVAR:downstream" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] +synonym: "downstream gene variant" EXACT [] +synonym: "Jannovar:downstream_gene_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +synonym: "snpEff:DOWNSTREAM" EXACT VAR [] +synonym: "VEP:downstream_gene_variant" EXACT VAR [] +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences +is_a: SO:0001628 ! intergenic_variant +created_by: kareneilbeck +creation_date: 2010-03-24T09:49:38Z + +[Term] +id: SO:0001633 +name: 5KB_downstream_variant +def: "A sequence variant located within 5 KB of the end of a gene." [SO:ke] +comment: EBI term Downstream variations - Within 5 kb downstream of the 3prime end of a transcript. +synonym: "5KB downstream variant" EXACT [] +synonym: "downstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] +synonym: "Seattleseq:downstream-gene" EXACT VAR [] +synonym: "within 5KB downstream" RELATED [] +xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" +is_a: SO:0001632 ! downstream_gene_variant +created_by: kareneilbeck +creation_date: 2010-03-24T09:50:16Z + +[Term] +id: SO:0001634 +name: 500B_downstream_variant +def: "A sequence variant located within a half KB of the end of a gene." [SO:ke] +synonym: "500B downstream variant" EXACT [] +synonym: "near-gene-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] +is_a: SO:0001632 ! downstream_gene_variant +created_by: kareneilbeck +creation_date: 2010-03-24T09:50:42Z + +[Term] +id: SO:0001635 +name: 5KB_upstream_variant +def: "A sequence variant located within 5KB 5' of a gene." [SO:ke] +comment: EBI term Upstream variations - Within 5 kb upstream of the 5prime end of a transcript. +synonym: "5kb upstream variant" EXACT [] +synonym: "Seattleseq:upstream-gene" EXACT VAR [] +synonym: "upstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] +xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" +is_a: SO:0001631 ! upstream_gene_variant +created_by: kareneilbeck +creation_date: 2010-03-24T09:51:06Z + +[Term] +id: SO:0001636 +name: 2KB_upstream_variant +def: "A sequence variant located within 2KB 5' of a gene." [SO:ke] +synonym: "2KB upstream variant" EXACT [] +synonym: "near-gene-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] +is_a: SO:0001631 ! upstream_gene_variant +created_by: kareneilbeck +creation_date: 2010-03-24T09:51:22Z + +[Term] +id: SO:0001637 +name: rRNA_gene +def: "A gene that encodes for ribosomal RNA." [SO:ke] +synonym: "rDNA" EXACT [] +synonym: "rRNA gene" EXACT [] +is_a: SO:0001263 ! ncRNA_gene +created_by: kareneilbeck +creation_date: 2010-04-21T10:10:32Z + +[Term] +id: SO:0001638 +name: piRNA_gene +def: "A gene that encodes for an piwi associated RNA." [SO:ke] +synonym: "piRNA gene" EXACT [] +is_a: SO:0001263 ! ncRNA_gene +created_by: kareneilbeck +creation_date: 2010-04-21T10:11:36Z + +[Term] +id: SO:0001639 +name: RNase_P_RNA_gene +def: "A gene that encodes an RNase P RNA." [SO:ke] +synonym: "RNase P RNA gene" EXACT [] +is_a: SO:0001263 ! ncRNA_gene +created_by: kareneilbeck +creation_date: 2010-04-21T10:13:23Z + +[Term] +id: SO:0001640 +name: RNase_MRP_RNA_gene +def: "A gene that encodes a RNase_MRP_RNA." [SO:ke] +synonym: "RNase MRP RNA gene" RELATED [] +is_a: SO:0001263 ! ncRNA_gene +created_by: kareneilbeck +creation_date: 2010-04-21T10:13:58Z + +[Term] +id: SO:0001641 +name: lincRNA_gene +def: "A gene that encodes large intervening non-coding RNA." [SO:ke] +synonym: "lincRNA gene" EXACT [] +is_a: SO:0001263 ! ncRNA_gene +created_by: kareneilbeck +creation_date: 2010-04-21T10:14:24Z + +[Term] +id: SO:0001642 +name: mathematically_defined_repeat +def: "A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness." [SO:jestill] +comment: Mathematically defined repeat regions are determined without regard to the biological origin of the repetitive region. The repeat units of a MDR are the overlapping oligomers of size k that were used to for the query. Tools that can annotate mathematically defined repeats include Tallymer (Kurtz et al 2008, BMC Genomics: 517) and RePS (Wang et al, Genome Res 12(5): 824-831.). +synonym: "mathematically defined repeat" EXACT [] +is_a: SO:0001410 ! experimental_feature +created_by: kareneilbeck +creation_date: 2010-05-03T11:50:14Z + +[Term] +id: SO:0001643 +name: telomerase_RNA_gene +def: "A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase." [SO:ke] +synonym: "Telomerase RNA component" EXACT [] +synonym: "telomerase RNA gene" EXACT [] +synonym: "TERC" EXACT [] +xref: http:http\://en.wikipedia.org/wiki/Telomerase_RNA_component "wikipedia" +is_a: SO:0001263 ! ncRNA_gene +created_by: kareneilbeck +creation_date: 2010-05-18T05:26:38Z + +[Term] +id: SO:0001644 +name: targeting_vector +def: "An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467] +synonym: "targeting vector" RELATED [] +is_a: SO:0000440 ! vector_replicon +is_a: SO:0000804 ! engineered_region +relationship: has_part SO:0000853 ! homologous_region +relationship: has_quality SO:0000783 ! engineered +created_by: kareneilbeck +creation_date: 2010-05-28T02:05:25Z + +[Term] +id: SO:0001645 +name: genetic_marker +def: "A measurable sequence feature that varies within a population." [SO:db] +synonym: "genetic marker" RELATED [] +is_a: SO:0001411 ! biological_region +created_by: kareneilbeck +creation_date: 2010-05-28T02:33:07Z + +[Term] +id: SO:0001646 +name: DArT_marker +def: "A genetic marker, discovered using Diversity Arrays Technology (DArT) technology." [SO:ke] +synonym: "DArT marker" EXACT [] +is_a: SO:0001645 ! genetic_marker +created_by: kareneilbeck +creation_date: 2010-05-28T02:34:43Z + +[Term] +id: SO:0001647 +name: kozak_sequence +def: "A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke] +subset: SOFA +synonym: "kozak consensus" EXACT [] +synonym: "kozak consensus sequence" EXACT [] +synonym: "kozak sequence" EXACT [] +xref: http://en.wikipedia.org/wiki/Kozak_consensus_sequence "wikipedia" +is_a: SO:0000139 ! ribosome_entry_site +created_by: kareneilbeck +creation_date: 2010-06-07T03:12:20Z + +[Term] +id: SO:0001648 +name: nested_transposon +def: "A transposon that is disrupted by the insertion of another element." [SO:ke] +synonym: "nested transposon" EXACT [] +is_a: SO:0000101 ! transposable_element +created_by: kareneilbeck +creation_date: 2010-06-23T03:22:57Z + +[Term] +id: SO:0001649 +name: nested_repeat +def: "A repeat that is disrupted by the insertion of another element." [SO:ke] +synonym: "nested repeat" RELATED [] +is_a: SO:0000657 ! repeat_region +created_by: kareneilbeck +creation_date: 2010-06-23T03:24:55Z + +[Term] +id: SO:0001650 +name: inframe_variant +def: "A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke] +synonym: "ANNOVAR:nonframeshift block substitution" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] +synonym: "ANNOVAR:nonframeshift substitution" RELATED VAR [] +synonym: "cds-indel" EXACT dbsnp [] +synonym: "inframe variant" EXACT [] +synonym: "VAAST:inframe_variant" EXACT VAR [] +is_a: SO:0001818 ! protein_altering_variant +created_by: kareneilbeck +creation_date: 2010-07-19T01:24:44Z + +[Term] +id: SO:0001653 +name: retinoic_acid_responsive_element +def: "A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671] +synonym: "RARE" EXACT [] +synonym: "retinoic acid responsive element" EXACT [] +is_a: SO:0000713 ! DNA_motif +relationship: part_of SO:0000167 ! promoter +created_by: kareneilbeck +creation_date: 2010-08-03T10:46:12Z + +[Term] +id: SO:0001654 +name: nucleotide_to_protein_binding_site +def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke] +subset: SOFA +synonym: "nucleotide to protein binding site" RELATED [] +is_a: SO:0000410 ! protein_binding_site +created_by: kareneilbeck +creation_date: 2010-08-03T12:26:05Z + +[Term] +id: SO:0001655 +name: nucleotide_binding_site +def: "A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb] +comment: See GO:0000166 : nucleotide binding. +synonym: "np_bind" EXACT BS [uniprot:feature] +synonym: "nucleotide binding site" EXACT [] +is_a: SO:0000409 ! binding_site +created_by: kareneilbeck +creation_date: 2010-08-03T12:30:04Z + +[Term] +id: SO:0001656 +name: metal_binding_site +def: "A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb] +comment: See GO:0046872 : metal ion binding. +synonym: "metal binding site" RELATED [] +is_a: SO:0000409 ! binding_site +created_by: kareneilbeck +creation_date: 2010-08-03T12:31:42Z + +[Term] +id: SO:0001657 +name: ligand_binding_site +def: "A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone." [SO:ke] +synonym: "ligand binding site" EXACT [] +is_a: SO:0000409 ! binding_site +created_by: kareneilbeck +creation_date: 2010-08-03T12:32:58Z + +[Term] +id: SO:0001658 +name: nested_tandem_repeat +def: "An NTR is a nested repeat of two distinct tandem motifs interspersed with each other." [SO:AF] +comment: Tracker ID: 3052459. +synonym: "nested tandem repeat" EXACT [] +synonym: "NTR" EXACT [] +is_a: SO:0001649 ! nested_repeat +created_by: kareneilbeck +creation_date: 2010-08-26T09:36:16Z + +[Term] +id: SO:0001659 +name: promoter_element +synonym: "promoter element" EXACT [] +is_a: SO:0000713 ! DNA_motif +relationship: overlaps SO:0000235 ! TF_binding_site +created_by: kareneilbeck +creation_date: 2010-10-01T11:48:32Z + +[Term] +id: SO:0001660 +name: core_promoter_element +synonym: "core promoter element" EXACT [] +synonym: "general transcription factor binding site" RELATED [] +is_a: SO:0001659 ! promoter_element +created_by: kareneilbeck +creation_date: 2010-10-01T11:49:03Z + +[Term] +id: SO:0001661 +name: RNA_polymerase_II_TATA_box +def: "A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867] +synonym: "RNA polymerase II TATA box" EXACT [] +is_a: SO:0000174 ! TATA_box +relationship: part_of SO:0001669 ! RNApol_II_core_promoter +created_by: kareneilbeck +creation_date: 2010-10-01T02:42:12Z + +[Term] +id: SO:0001662 +name: RNA_polymerase_III_TATA_box +def: "A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke] +synonym: "RNA polymerase III TATA box" EXACT [] +is_a: SO:0000174 ! TATA_box +relationship: part_of SO:0000171 ! RNApol_III_promoter +created_by: kareneilbeck +creation_date: 2010-10-01T02:43:16Z + +[Term] +id: SO:0001663 +name: BREd_motif +def: "A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867] +synonym: "BREd" EXACT [] +synonym: "BREd motif" RELATED [] +is_a: SO:0001660 ! core_promoter_element +relationship: part_of SO:0001669 ! RNApol_II_core_promoter +created_by: kareneilbeck +creation_date: 2010-10-01T02:49:55Z + +[Term] +id: SO:0001664 +name: DCE +def: "A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867] +synonym: "downstream core element" RELATED [] +is_a: SO:0001660 ! core_promoter_element +relationship: part_of SO:0001669 ! RNApol_II_core_promoter +created_by: kareneilbeck +creation_date: 2010-10-01T02:56:41Z + +[Term] +id: SO:0001665 +name: DCE_SI +def: "A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke] +synonym: "DCE SI" RELATED [] +is_a: SO:0000713 ! DNA_motif +relationship: part_of SO:0001664 ! DCE +created_by: kareneilbeck +creation_date: 2010-10-01T03:00:10Z + +[Term] +id: SO:0001666 +name: DCE_SII +def: "A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke] +synonym: "DCE SII" EXACT [] +is_a: SO:0000713 ! DNA_motif +relationship: part_of SO:0001664 ! DCE +created_by: kareneilbeck +creation_date: 2010-10-01T03:00:30Z + +[Term] +id: SO:0001667 +name: DCE_SIII +def: "A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke] +synonym: "DCE SIII" EXACT [] +is_a: SO:0000713 ! DNA_motif +relationship: part_of SO:0001664 ! DCE +created_by: kareneilbeck +creation_date: 2010-10-01T03:00:44Z + +[Term] +id: SO:0001668 +name: proximal_promoter_element +def: "DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor)." [PMID:12515390, PMID:9679020, SO:ml] +synonym: "proximal promoter element" RELATED [] +synonym: "specific transcription factor binding site" RELATED [] +is_a: SO:0001678 ! regulatory_promoter_element +created_by: kareneilbeck +creation_date: 2010-10-01T03:10:23Z + +[Term] +id: SO:0001669 +name: RNApol_II_core_promoter +def: "The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867] +synonym: "RNApol II core promoter" EXACT [] +is_a: SO:0000170 ! RNApol_II_promoter +created_by: kareneilbeck +creation_date: 2010-10-01T03:13:41Z + +[Term] +id: SO:0001670 +name: distal_promoter_element +synonym: "distal promoter element" RELATED [] +is_a: SO:0001678 ! regulatory_promoter_element +created_by: kareneilbeck +creation_date: 2010-10-01T03:21:08Z + +[Term] +id: SO:0001671 +name: bacterial_RNApol_promoter_sigma_70 +synonym: "bacterial RNA polymerase promoter sigma 70" EXACT [] +is_a: SO:0000613 ! bacterial_RNApol_promoter +created_by: kareneilbeck +creation_date: 2010-10-06T01:41:34Z + +[Term] +id: SO:0001672 +name: bacterial_RNApol_promoter_sigma54 +synonym: "bacterial RNA polymerase promoter sigma54" EXACT [] +is_a: SO:0000613 ! bacterial_RNApol_promoter +created_by: kareneilbeck +creation_date: 2010-10-06T01:42:37Z + +[Term] +id: SO:0001673 +name: minus_12_signal +def: "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472] +synonym: "minus 12 signal" EXACT [] +is_a: SO:0000713 ! DNA_motif +relationship: part_of SO:0001672 ! bacterial_RNApol_promoter_sigma54 +created_by: kareneilbeck +creation_date: 2010-10-06T01:44:57Z + +[Term] +id: SO:0001674 +name: minus_24_signal +def: "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472] +synonym: "minus 24 signal" RELATED [] +is_a: SO:0000713 ! DNA_motif +relationship: part_of SO:0001672 ! bacterial_RNApol_promoter_sigma54 +created_by: kareneilbeck +creation_date: 2010-10-06T01:45:24Z + +[Term] +id: SO:0001675 +name: A_box_type_1 +def: "An A box within an RNA polymerase III type 1 promoter." [SO:ke] +comment: The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true. +synonym: "A box type 1" RELATED [] +is_a: SO:0000619 ! A_box +relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1 +created_by: kareneilbeck +creation_date: 2010-10-06T05:43:43Z + +[Term] +id: SO:0001676 +name: A_box_type_2 +def: "An A box within an RNA polymerase III type 2 promoter." [SO:ke] +comment: The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true. +synonym: "A box type 2" RELATED [] +is_a: SO:0000619 ! A_box +relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2 +created_by: kareneilbeck +creation_date: 2010-10-06T05:44:18Z + +[Term] +id: SO:0001677 +name: intermediate_element +def: "A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659] +synonym: "IE" EXACT [] +synonym: "intermediate element" RELATED [] +is_a: SO:0001660 ! core_promoter_element +relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1 +created_by: kareneilbeck +creation_date: 2010-10-06T05:52:03Z + +[Term] +id: SO:0001678 +name: regulatory_promoter_element +def: "A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659] +synonym: "regulatory promoter element" RELATED [] +is_a: SO:0001659 ! promoter_element +created_by: kareneilbeck +creation_date: 2010-10-07T04:39:48Z + +[Term] +id: SO:0001679 +name: transcription_regulatory_region +def: "A regulatory region that is involved in the control of the process of transcription." [SO:ke] +subset: SOFA +synonym: "transcription regulatory region" EXACT [] +is_a: SO:0005836 ! regulatory_region +created_by: kareneilbeck +creation_date: 2010-10-12T03:49:35Z + +[Term] +id: SO:0001680 +name: translation_regulatory_region +def: "A regulatory region that is involved in the control of the process of translation." [SO:ke] +synonym: "translation regulatory region" EXACT [] +is_a: SO:0005836 ! regulatory_region +created_by: kareneilbeck +creation_date: 2010-10-12T03:52:45Z + +[Term] +id: SO:0001681 +name: recombination_regulatory_region +def: "A regulatory region that is involved in the control of the process of recombination." [SO:ke] +synonym: "recombination regulatory region" EXACT [] +is_a: SO:0005836 ! regulatory_region +created_by: kareneilbeck +creation_date: 2010-10-12T03:53:35Z + +[Term] +id: SO:0001682 +name: replication_regulatory_region +def: "A regulatory region that is involved in the control of the process of nucleotide replication." [SO:ke] +synonym: "replication regulatory region" RELATED [] +is_a: SO:0005836 ! regulatory_region +created_by: kareneilbeck +creation_date: 2010-10-12T03:54:09Z + +[Term] +id: SO:0001683 +name: sequence_motif +def: "A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif] +subset: SOFA +synonym: "sequence motif" RELATED [] +xref: http://en.wikipedia.org/wiki/Sequence_motif "wikipedia" +is_a: SO:0001411 ! biological_region +created_by: kareneilbeck +creation_date: 2010-10-14T04:13:22Z + +[Term] +id: SO:0001684 +name: experimental_feature_attribute +def: "An attribute of an experimentally derived feature." [SO:ke] +synonym: "experimental feature attribute" RELATED [] +is_a: SO:0000733 ! feature_attribute +created_by: kareneilbeck +creation_date: 2010-10-28T02:22:23Z + +[Term] +id: SO:0001685 +name: score +def: "The score of an experimentally derived feature such as a p-value." [SO:ke] +is_a: SO:0001684 ! experimental_feature_attribute +created_by: kareneilbeck +creation_date: 2010-10-28T02:23:16Z + +[Term] +id: SO:0001686 +name: quality_value +def: "An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score." [SO:ke] +synonym: "quality value" RELATED [] +is_a: SO:0001684 ! experimental_feature_attribute +created_by: kareneilbeck +creation_date: 2010-10-28T02:24:11Z + +[Term] +id: SO:0001687 +name: restriction_enzyme_recognition_site +def: "The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke] +synonym: "restriction endonuclease recognition site" EXACT [] +synonym: "restriction enzyme recognition site" EXACT [] +is_a: SO:0001954 ! restriction_enzyme_region +created_by: kareneilbeck +creation_date: 2010-10-29T12:29:57Z + +[Term] +id: SO:0001688 +name: restriction_enzyme_cleavage_junction +def: "The boundary at which a restriction enzyme breaks the nucleotide sequence." [SO:ke] +synonym: "restriction enzyme cleavage junction" EXACT [] +is_a: SO:0000699 ! junction +created_by: kareneilbeck +creation_date: 2010-10-29T12:35:02Z + +[Term] +id: SO:0001689 +name: five_prime_restriction_enzyme_junction +def: "The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke] +synonym: "5' restriction enzyme junction" EXACT [] +is_a: SO:0001694 ! single_strand_restriction_enzyme_cleavage_site +relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site +created_by: kareneilbeck +creation_date: 2010-10-29T12:36:24Z + +[Term] +id: SO:0001690 +name: three_prime_restriction_enzyme_junction +synonym: "3' restriction enzyme junction" EXACT [] +is_a: SO:0001694 ! single_strand_restriction_enzyme_cleavage_site +relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site +created_by: kareneilbeck +creation_date: 2010-10-29T12:37:52Z + +[Term] +id: SO:0001691 +name: blunt_end_restriction_enzyme_cleavage_site +def: "A restriction enzyme recognition site that, when cleaved, results in no overhangs." [SBOL:jgquinn, SO:ke] +synonym: "blunt end restriction enzyme cleavage site" EXACT [] +is_a: SO:0001687 ! restriction_enzyme_recognition_site +created_by: kareneilbeck +creation_date: 2010-10-29T12:39:53Z + +[Term] +id: SO:0001692 +name: sticky_end_restriction_enzyme_cleavage_site +synonym: "sticky end restriction enzyme cleavage site" RELATED [] +is_a: SO:0001687 ! restriction_enzyme_recognition_site +created_by: kareneilbeck +creation_date: 2010-10-29T12:40:50Z + +[Term] +id: SO:0001693 +name: blunt_end_restriction_enzyme_cleavage_junction +def: "A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke] +synonym: "blunt end restriction enzyme cleavage site" RELATED [] +is_a: SO:0001688 ! restriction_enzyme_cleavage_junction +relationship: part_of SO:0001691 ! blunt_end_restriction_enzyme_cleavage_site +created_by: kareneilbeck +creation_date: 2010-10-29T12:43:14Z + +[Term] +id: SO:0001694 +name: single_strand_restriction_enzyme_cleavage_site +def: "A restriction enzyme cleavage site whereby only one strand is cut." [SO:ke] +synonym: "single strand restriction enzyme cleavage site" RELATED [] +is_a: SO:0001688 ! restriction_enzyme_cleavage_junction +created_by: kareneilbeck +creation_date: 2010-10-29T12:44:48Z + +[Term] +id: SO:0001695 +name: restriction_enzyme_single_strand_overhang +def: "A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke] +synonym: "single strand overhang" EXACT [] +synonym: "sticky end" RELATED [] +is_a: SO:0001954 ! restriction_enzyme_region +relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site +created_by: kareneilbeck +creation_date: 2010-10-29T12:48:35Z + +[Term] +id: SO:0001696 +name: experimentally_defined_binding_region +def: "A region that has been implicated in binding although the exact coordinates of binding may be unknown." [SO:ke] +synonym: "experimentally defined binding region" RELATED [] +is_a: SO:0001410 ! experimental_feature +created_by: kareneilbeck +creation_date: 2010-11-02T11:39:59Z + +[Term] +id: SO:0001697 +name: ChIP_seq_region +def: "A region of sequence identified by CHiP seq technology to contain a protein binding site." [SO:ke] +synonym: "ChIP seq region" RELATED [] +is_a: SO:0001696 ! experimentally_defined_binding_region +relationship: contains SO:0000410 ! protein_binding_site +created_by: kareneilbeck +creation_date: 2010-11-02T11:43:07Z + +[Term] +id: SO:0001698 +name: ASPE_primer +def: "\"A primer containing an SNV at the 3' end for accurate genotyping." [http://www.ncbi.nlm.nih.gov/pubmed/11252801] +synonym: "allele specific primer extension primer" EXACT [] +synonym: "ASPE primer" EXACT [] +is_a: SO:0000112 ! primer +created_by: kareneilbeck +creation_date: 2010-11-11T03:25:21Z + +[Term] +id: SO:0001699 +name: dCAPS_primer +def: "A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site." [http://www.ncbi.nlm.nih.gov/pubmed/9628033] +synonym: "dCAPS primer" EXACT [] +synonym: "derived cleaved amplified polymorphic primer" EXACT [] +is_a: SO:0000112 ! primer +created_by: kareneilbeck +creation_date: 2010-11-11T03:27:09Z + +[Term] +id: SO:0001700 +name: histone_modification +def: "Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone] +synonym: "histone modification" EXACT [] +synonym: "histone modification site" RELATED [] +is_a: SO:0001089 ! post_translationally_modified_region +is_a: SO:0001720 ! epigenetically_modified_region +relationship: has_quality SO:0000133 ! epigenetically_modified +created_by: kareneilbeck +creation_date: 2010-03-31T10:22:08Z + +[Term] +id: SO:0001701 +name: histone_methylation_site +def: "A histone modification site where the modification is the methylation of the residue." [SO:ke] +synonym: "histone methylation" EXACT [] +synonym: "histone methylation site" EXACT [] +is_a: SO:0001700 ! histone_modification +created_by: kareneilbeck +creation_date: 2010-03-31T10:23:02Z + +[Term] +id: SO:0001702 +name: histone_acetylation_site +def: "A histone modification where the modification is the acylation of the residue." [SO:ke] +synonym: "histone acetylation" EXACT [] +synonym: "histone acetylation site" EXACT [] +is_a: SO:0001700 ! histone_modification +created_by: kareneilbeck +creation_date: 2010-03-31T10:23:27Z + +[Term] +id: SO:0001703 +name: H3K9_acetylation_site +def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone] +synonym: "H3K9 acetylation site" EXACT [] +synonym: "H3K9Ac" RELATED [] +is_a: SO:0001973 ! histone_3_acetylation_site +created_by: kareneilbeck +creation_date: 2010-03-31T10:25:05Z + +[Term] +id: SO:0001704 +name: H3K14_acetylation_site +def: "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone] +synonym: "H3K14 acetylation site" EXACT [] +synonym: "H3K14Ac" RELATED [] +is_a: SO:0001973 ! histone_3_acetylation_site +created_by: kareneilbeck +creation_date: 2010-03-31T10:25:53Z + +[Term] +id: SO:0001705 +name: H3K4_monomethylation_site +def: "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone] +synonym: "H3K4 mono-methylation site" EXACT [] +synonym: "H3K4me1" RELATED [] +is_a: SO:0001734 ! H3K4_methylation_site +created_by: kareneilbeck +creation_date: 2010-03-31T10:28:14Z + +[Term] +id: SO:0001706 +name: H3K4_trimethylation +def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] +synonym: "H3K4 tri-methylation" EXACT [] +synonym: "H3K4me3" RELATED [] +is_a: SO:0001734 ! H3K4_methylation_site +created_by: kareneilbeck +creation_date: 2010-03-31T10:29:12Z + +[Term] +id: SO:0001707 +name: H3K9_trimethylation_site +def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] +synonym: "H3K9 tri-methylation site" EXACT [] +synonym: "H3K9Me3" RELATED [] +is_a: SO:0001736 ! H3K9_methylation_site +created_by: kareneilbeck +creation_date: 2010-03-31T10:30:34Z + +[Term] +id: SO:0001708 +name: H3K27_monomethylation_site +def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone] +synonym: "H2K27 mono-methylation site" EXACT [] +synonym: "H2K27Me1" RELATED [] +is_a: SO:0001732 ! H3K27_methylation_site +created_by: kareneilbeck +creation_date: 2010-03-31T10:31:54Z + +[Term] +id: SO:0001709 +name: H3K27_trimethylation_site +def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] +synonym: "H3K27 tri-methylation site" EXACT [] +synonym: "H3K27Me3" RELATED [] +is_a: SO:0001732 ! H3K27_methylation_site +created_by: kareneilbeck +creation_date: 2010-03-31T10:32:41Z + +[Term] +id: SO:0001710 +name: H3K79_monomethylation_site +def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone] +synonym: "H3K79 mono-methylation site" EXACT [] +synonym: "H3K79me1" RELATED [] +is_a: SO:0001735 ! H3K79_methylation_site +created_by: kareneilbeck +creation_date: 2010-03-31T10:33:42Z + +[Term] +id: SO:0001711 +name: H3K79_dimethylation_site +def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone] +synonym: "H3K79 di-methylation site" EXACT [] +synonym: "H3K79Me2" RELATED [] +is_a: SO:0001735 ! H3K79_methylation_site +created_by: kareneilbeck +creation_date: 2010-03-31T10:34:39Z + +[Term] +id: SO:0001712 +name: H3K79_trimethylation_site +def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] +synonym: "H3K79 tri-methylation site" EXACT [] +synonym: "H3K79Me3" RELATED [] +is_a: SO:0001735 ! H3K79_methylation_site +created_by: kareneilbeck +creation_date: 2010-03-31T10:35:30Z + +[Term] +id: SO:0001713 +name: H4K20_monomethylation_site +def: "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone] +synonym: "H4K20 mono-methylation site" EXACT [] +synonym: "H4K20Me1" RELATED [] +is_a: SO:0001701 ! histone_methylation_site +created_by: kareneilbeck +creation_date: 2010-03-31T10:36:43Z + +[Term] +id: SO:0001714 +name: H2BK5_monomethylation_site +def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone] +synonym: "H2BK5 mono-methylation site" EXACT [] +is_a: SO:0001701 ! histone_methylation_site +created_by: kareneilbeck +creation_date: 2010-03-31T10:38:12Z + +[Term] +id: SO:0001715 +name: ISRE +def: "An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding." [http://genesdev.cshlp.org/content/2/4/383.abstrac] +comment: Term requested via tracker (2981725) by Alan Ruttenberg, April 2010. It has been described as both an enhancer and a promoter, so the parent is the more general term. +synonym: "interferon stimulated response element" EXACT [] +is_a: SO:0001055 ! transcriptional_cis_regulatory_region +created_by: kareneilbeck +creation_date: 2010-04-05T11:15:08Z + +[Term] +id: SO:0001716 +name: histone_ubiqitination_site +def: "A histone modification site where ubiquitin may be added." [SO:ke] +synonym: "histone ubiquitination site" RELATED [] +is_a: SO:0001700 ! histone_modification +created_by: kareneilbeck +creation_date: 2010-04-13T10:12:18Z + +[Term] +id: SO:0001717 +name: H2B_ubiquitination_site +def: "A histone modification site on H2B where ubiquitin may be added." [SO:ke] +synonym: "H2BUbiq" RELATED [] +is_a: SO:0001716 ! histone_ubiqitination_site +created_by: kareneilbeck +creation_date: 2010-04-13T10:13:28Z + +[Term] +id: SO:0001718 +name: H3K18_acetylation_site +def: "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke] +synonym: "H3K18 acetylation site" EXACT [] +synonym: "H3K18Ac" RELATED [] +is_a: SO:0001973 ! histone_3_acetylation_site +created_by: kareneilbeck +creation_date: 2010-04-13T10:39:35Z + +[Term] +id: SO:0001719 +name: H3K23_acylation_site +def: "A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke] +synonym: "H3K23 acylation site" RELATED [] +synonym: "H3K23Ac" RELATED [] +is_a: SO:0001973 ! histone_3_acetylation_site +created_by: kareneilbeck +creation_date: 2010-04-13T10:42:45Z + +[Term] +id: SO:0001720 +name: epigenetically_modified_region +def: "A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke] +subset: SOFA +synonym: "epigenetically modified region" RELATED [] +is_a: SO:0001411 ! biological_region +relationship: has_quality SO:0000133 ! epigenetically_modified +created_by: kareneilbeck +creation_date: 2010-03-27T12:02:29Z + +[Term] +id: SO:0001721 +name: H3K27_acylation_site +def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke] +synonym: "H3K27 acylation site" EXACT [] +synonym: "H3K27Ac" RELATED [] +is_a: SO:0001973 ! histone_3_acetylation_site +created_by: kareneilbeck +creation_date: 2010-04-13T10:44:09Z + +[Term] +id: SO:0001722 +name: H3K36_monomethylation_site +def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke] +synonym: "H3K36 mono-methylation site" EXACT [] +synonym: "H3K36" RELATED [] +synonym: "unidirectional gene fusion" EXACT [] +is_a: SO:0001565 ! gene_fusion +created_by: kareneilbeck +creation_date: 2016-02-23T12:16:48Z + +[Term] +id: SO:0002086 +name: bidirectional_gene_fusion +def: "A sequence variant whereby a two genes, on alternate strands have become joined." [SO:ke] +comment: Requested by SNPEFF team. Feb 2016. +synonym: "bidirectional gene fusion" EXACT [] +is_a: SO:0001565 ! gene_fusion +created_by: kareneilbeck +creation_date: 2016-02-23T12:17:18Z + +[Term] +id: SO:0002087 +name: pseudogenic_CDS +def: "A non functional descendant of the coding portion of a coding transcript, part of a pseudogene." [SO:ke] +synonym: "pseudogenic CDS" EXACT [] +is_a: SO:0000462 ! pseudogenic_region +relationship: part_of SO:0000516 ! pseudogenic_transcript +created_by: kareneilbeck +creation_date: 2016-02-29T12:58:52Z + +[Term] +id: SO:0002088 +name: non_coding_transcript_splice_region_variant +def: "A transcript variant occurring within the splice region (1-3 bases of the exon or 3-8 bases of the intron) of a non coding transcript." [SO:ke] +synonym: "ANNOVAR:ncRNA_splicing" NARROW [] +is_a: SO:0001619 ! non_coding_transcript_variant +is_a: SO:0001630 ! splice_region_variant +created_by: kareneilbeck +creation_date: 2016-03-07T09:40:46Z + +[Term] +id: SO:0002089 +name: 3_prime_UTR_exon_variant +def: "A UTR variant of exonic sequence of the 3' UTR." [SO:ke] +comment: Requested by visze github tracker ID 346. +synonym: "3 prime UTR exon variant" EXACT [] +is_a: SO:0001624 ! 3_prime_UTR_variant +created_by: kareneilbeck +creation_date: 2016-03-07T10:37:04Z + +[Term] +id: SO:0002090 +name: 3_prime_UTR_intron_variant +def: "A UTR variant of intronic sequence of the 3' UTR." [SO:ke] +comment: Requested by visze github tracker ID 346. +synonym: "3 prime UTR intron variant" EXACT [] +is_a: SO:0001624 ! 3_prime_UTR_variant +is_a: SO:0001969 ! coding_transcript_intron_variant +created_by: kareneilbeck +creation_date: 2016-03-07T10:37:41Z + +[Term] +id: SO:0002091 +name: 5_prime_UTR_intron_variant +def: "A UTR variant of intronic sequence of the 5' UTR." [SO:ke] +comment: Requested by visze github tracker ID 346. +synonym: "5 prime UTR intron variant" EXACT [] +is_a: SO:0001623 ! 5_prime_UTR_variant +is_a: SO:0001969 ! coding_transcript_intron_variant +created_by: kareneilbeck +creation_date: 2016-03-07T10:38:04Z + +[Term] +id: SO:0002092 +name: 5_prime_UTR_exon_variant +def: "A UTR variant of exonic sequence of the 5' UTR." [SO:ke] +comment: Requested by visze github tracker ID 346. +synonym: "5 prime UTR exon variant" EXACT [] +is_a: SO:0001623 ! 5_prime_UTR_variant +created_by: kareneilbeck +creation_date: 2016-03-07T10:38:26Z + +[Term] +id: SO:0002093 +name: structural_interaction_variant +def: "A variant that impacts the internal interactions of the resulting polypeptide structure." [SO:ke] +comment: Requested by Pablo Cingolani. The way I calculate this is simply by looking at the PDB entry of one protein and then marking those AA that are within 3 Angstrom of each other (and far away in the AA sequence, e.g. over 20 AA distance). The assumption is that, since they are very close in distance, they must be "interacting" and thus important for protein structure. +synonym: "structural interaction variant" EXACT [] +is_a: SO:0001599 ! 3D_polypeptide_structure_variant +created_by: kareneilbeck +creation_date: 2016-03-07T11:43:55Z + +[Term] +id: SO:0005836 +name: regulatory_region +def: "A region of sequence that is involved in the control of a biological process." [SO:ke] +subset: SOFA +synonym: "regulatory region" EXACT [] +xref: http://en.wikipedia.org/wiki/Regulatory_region "wiki" +is_a: SO:0000831 ! gene_member_region + +[Term] +id: SO:0005837 +name: U14_snoRNA_primary_transcript +def: "The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." [PMID:2251119] +synonym: "4.5S snRNA primary transcript" EXACT [] +synonym: "U14 snoRNA primary transcript" EXACT [] +is_a: SO:0000232 ! snoRNA_primary_transcript + +[Term] +id: SO:0005841 +name: methylation_guide_snoRNA +def: "A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565] +comment: Has RNA 2'-O-ribose methylation guide activity (GO:0030561). +synonym: "methylation guide snoRNA" EXACT [] +is_a: SO:0000593 ! C_D_box_snoRNA +relationship: derives_from SO:0000580 ! methylation_guide_snoRNA_primary_transcript + +[Term] +id: SO:0005843 +name: rRNA_cleavage_RNA +def: "An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules." [GOC:kgc] +synonym: "rRNA cleavage RNA" EXACT [] +is_a: SO:0000655 ! ncRNA +relationship: derives_from SO:0000582 ! rRNA_cleavage_snoRNA_primary_transcript + +[Term] +id: SO:0005845 +name: exon_of_single_exon_gene +def: "An exon that is the only exon in a gene." [RSC:cb] +synonym: "exon of single exon gene" EXACT [] +synonym: "single_exon" RELATED [] +synonym: "singleton exon" EXACT [] +is_a: SO:0000147 ! exon + +[Term] +id: SO:0005847 +name: cassette_array_member +synonym: "cassette array member" EXACT [] +is_a: SO:0005848 ! gene_cassette_member + +[Term] +id: SO:0005848 +name: gene_cassette_member +synonym: "gene cassette member" EXACT [] +is_a: SO:0000081 ! gene_array_member + +[Term] +id: SO:0005849 +name: gene_subarray_member +synonym: "gene subarray member" EXACT [] +is_a: SO:0000081 ! gene_array_member + +[Term] +id: SO:0005850 +name: primer_binding_site +def: "Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +synonym: "primer binding site" EXACT [] +xref: http://en.wikipedia.org/wiki/Primer_binding_site "wiki" +is_a: SO:0001655 ! nucleotide_binding_site +relationship: part_of SO:0000186 ! LTR_retrotransposon + +[Term] +id: SO:0005851 +name: gene_array +def: "An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so." [SO:ma] +comment: This would include, for example, a cluster of genes each encoding the major ribosomal RNAs and a cluster of histone gene subarrays. +synonym: "gene array" EXACT [] +is_a: SO:0005855 ! gene_group + +[Term] +id: SO:0005852 +name: gene_subarray +def: "A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function." [SO:ma] +comment: This would include, for example, a cluster of genes encoding different histones. +synonym: "gene subarray" EXACT [] +is_a: SO:0005855 ! gene_group + +[Term] +id: SO:0005853 +name: gene_cassette +def: "A gene that can be substituted for a related gene at a different site in the genome." [SGD:se] +comment: This would include, for example, the mating type gene cassettes of S. cerevisiae. Gene cassettes usually exist as linear sequences as part of a larger DNA molecule, such as a chromosome or plasmid. +synonym: "gene cassette" EXACT [] +xref: http://en.wikipedia.org/wiki/Gene_cassette "wiki" +is_a: SO:0000704 ! gene + +[Term] +id: SO:0005854 +name: gene_cassette_array +def: "An array of non-functional genes whose members, when captured by recombination form functional genes." [SO:ma] +comment: This would include, for example, the arrays of non-functional VSG genes of Trypanosomes. +synonym: "gene cassette array" EXACT [] +is_a: SO:0005855 ! gene_group +relationship: has_part SO:0005853 ! gene_cassette + +[Term] +id: SO:0005855 +name: gene_group +def: "A collection of related genes." [SO:ma] +subset: SOFA +synonym: "gene group" EXACT [] +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0005856 +name: selenocysteine_tRNA_primary_transcript +def: "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke] +synonym: "selenocysteine tRNA primary transcript" EXACT [] +is_a: SO:0000210 ! tRNA_primary_transcript + +[Term] +id: SO:0005857 +name: selenocysteinyl_tRNA +def: "A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." [SO:ke] +synonym: "selenocysteinyl tRNA" EXACT [] +synonym: "selenocysteinyl-transfer ribonucleic acid" EXACT [] +synonym: "selenocysteinyl-transfer RNA" EXACT [] +is_a: SO:0000253 ! tRNA +relationship: derives_from SO:0005856 ! selenocysteine_tRNA_primary_transcript + +[Term] +id: SO:0005858 +name: syntenic_region +def: "A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species." [http://www.informatics.jax.org/silverbook/glossary.shtml] +synonym: "syntenic region" EXACT [] +is_a: SO:0000330 ! conserved_region +relationship: has_quality SO:0000860 ! syntenic + +[Term] +id: SO:0100001 +name: biochemical_region_of_peptide +def: "A region of a peptide that is involved in a biochemical function." [EBIBS:GAR] +comment: Range. +subset: biosapiens +synonym: "biochemical motif" EXACT [] +synonym: "biochemical region of peptide" EXACT [] +synonym: "biochemical_region" RELATED [] +is_a: SO:0001067 ! polypeptide_motif + +[Term] +id: SO:0100002 +name: molecular_contact_region +def: "A region that is involved a contact with another molecule." [EBIBS:GAR] +comment: Range. +subset: biosapiens +synonym: "molecular contact region" RELATED [] +is_a: SO:0100001 ! biochemical_region_of_peptide + +[Term] +id: SO:0100003 +name: intrinsically_unstructured_polypeptide_region +def: "A region of polypeptide chain with high conformational flexibility." [EBIBS:GAR] +subset: biosapiens +synonym: "disordered region" RELATED BS [] +synonym: "intrinsically unstructured polypeptide region" EXACT [] +is_a: SO:0001070 ! polypeptide_structural_region + +[Term] +id: SO:0100004 +name: catmat_left_handed_three +def: "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "catmat-3l" EXACT [] +is_a: SO:0001078 ! polypeptide_secondary_structure + +[Term] +id: SO:0100005 +name: catmat_left_handed_four +def: "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "catmat-4l" EXACT [] +is_a: SO:0001078 ! polypeptide_secondary_structure + +[Term] +id: SO:0100006 +name: catmat_right_handed_three +def: "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "catmat-3r" EXACT [] +is_a: SO:0001078 ! polypeptide_secondary_structure + +[Term] +id: SO:0100007 +name: catmat_right_handed_four +def: "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "catmat-4r" EXACT [] +is_a: SO:0001078 ! polypeptide_secondary_structure + +[Term] +id: SO:0100008 +name: alpha_beta_motif +def: "A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] +subset: biosapiens +synonym: "alpha beta motif" EXACT [] +is_a: SO:0001078 ! polypeptide_secondary_structure + +[Term] +id: SO:0100009 +name: lipoprotein_signal_peptide +def: "A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." [EBIBS:GAR] +subset: biosapiens +synonym: "lipoprotein signal peptide" EXACT [] +synonym: "prokaryotic membrane lipoprotein lipid attachment site" EXACT [] +is_a: SO:0100011 ! cleaved_peptide_region + +[Term] +id: SO:0100010 +name: no_output +def: "An experimental region wherean analysis has been run and not produced any annotation." [EBIBS:GAR] +subset: biosapiens +synonym: "no output" EXACT BS [] +is_a: SO:0000703 ! experimental_result_region + +[Term] +id: SO:0100011 +name: cleaved_peptide_region +def: "The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR] +comment: Range. +subset: biosapiens +subset: SOFA +synonym: "cleaved peptide region" EXACT [] +is_a: SO:0000839 ! polypeptide_region +relationship: part_of SO:0001063 ! immature_peptide_region + +[Term] +id: SO:0100012 +name: peptide_coil +def: "Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds)." [EBIBS:GAR] +subset: biosapiens +synonym: "coil" RELATED BS [] +synonym: "peptide coil" EXACT [] +synonym: "random coil" RELATED BS [] +is_a: SO:0001078 ! polypeptide_secondary_structure + +[Term] +id: SO:0100013 +name: hydrophobic_region_of_peptide +def: "Hydrophobic regions are regions with a low affinity for water." [EBIBS:GAR] +comment: Range. +subset: biosapiens +synonym: "hydropathic" RELATED [] +synonym: "hydrophobic region of peptide" RELATED [] +synonym: "hydrophobic_region" EXACT [] +synonym: "hydrophobicity" RELATED [] +is_a: SO:0000839 ! polypeptide_region + +[Term] +id: SO:0100014 +name: n_terminal_region +def: "The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR] +subset: biosapiens +synonym: "N-region" RELATED [] +is_a: SO:0100011 ! cleaved_peptide_region +relationship: part_of SO:0000418 ! signal_peptide + +[Term] +id: SO:0100015 +name: c_terminal_region +def: "The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR] +subset: biosapiens +synonym: "C-region" RELATED [] +is_a: SO:0100011 ! cleaved_peptide_region +relationship: part_of SO:0000418 ! signal_peptide + +[Term] +id: SO:0100016 +name: central_hydrophobic_region_of_signal_peptide +def: "The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR] +subset: biosapiens +synonym: "central hydrophobic region of signal peptide" EXACT [] +synonym: "central_hydrophobic_region" RELATED [] +synonym: "H-region" RELATED [] +is_a: SO:0100011 ! cleaved_peptide_region +relationship: part_of SO:0000418 ! signal_peptide + +[Term] +id: SO:0100017 +name: polypeptide_conserved_motif +def: "A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR] +subset: biosapiens +synonym: "motif" RELATED [] +is_a: SO:0001067 ! polypeptide_motif + +[Term] +id: SO:0100018 +name: polypeptide_binding_motif +def: "A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." [EBIBS:GAR] +subset: biosapiens +synonym: "binding" RELATED [uniprot:feature_type] +synonym: "polypeptide binding motif" EXACT [] +is_a: SO:0100001 ! biochemical_region_of_peptide + +[Term] +id: SO:0100019 +name: polypeptide_catalytic_motif +def: "A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR] +subset: biosapiens +synonym: "catalytic_motif" RELATED [] +synonym: "polypeptide catalytic motif" EXACT [] +is_a: SO:0100001 ! biochemical_region_of_peptide + +[Term] +id: SO:0100020 +name: polypeptide_DNA_contact +def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke] +subset: biosapiens +synonym: "DNA_bind" EXACT BS [uniprot:feature] +synonym: "polypeptide DNA contact" EXACT [] +is_a: SO:0001429 ! DNA_binding_site +is_a: SO:0100002 ! molecular_contact_region + +[Term] +id: SO:0100021 +name: polypeptide_conserved_region +def: "A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR] +subset: biosapiens +synonym: "polypeptide conserved region" EXACT [] +is_a: SO:0000839 ! polypeptide_region + +[Term] +id: SO:1000002 +name: substitution +def: "A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke] +subset: SOFA +xref: loinc:LA6690-7 "Substitution" +is_a: SO:0001059 ! sequence_alteration +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:1000005 +name: complex_substitution +def: "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +subset: SOFA +synonym: "complex substitution" EXACT [] +is_a: SO:1000002 ! substitution + +[Term] +id: SO:1000008 +name: point_mutation +def: "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop] +subset: SOFA +synonym: "point mutation" EXACT [] +xref: http://en.wikipedia.org/wiki/Point_mutation "wiki" +is_a: SO:0001483 ! SNV + +[Term] +id: SO:1000009 +name: transition +def: "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +is_a: SO:0001483 ! SNV + +[Term] +id: SO:1000010 +name: pyrimidine_transition +def: "A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke] +synonym: "pyrimidine transition" EXACT [] +is_a: SO:1000009 ! transition + +[Term] +id: SO:1000011 +name: C_to_T_transition +def: "A transition of a cytidine to a thymine." [SO:ke] +synonym: "C to T transition" EXACT [] +is_a: SO:1000010 ! pyrimidine_transition + +[Term] +id: SO:1000012 +name: C_to_T_transition_at_pCpG_site +def: "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +synonym: "C to T transition at pCpG site" EXACT [] +is_a: SO:1000011 ! C_to_T_transition + +[Term] +id: SO:1000013 +name: T_to_C_transition +synonym: "T to C transition" EXACT [] +is_a: SO:1000010 ! pyrimidine_transition + +[Term] +id: SO:1000014 +name: purine_transition +def: "A substitution of a purine, A or G, for another purine." [SO:ke] +synonym: "purine transition" EXACT [] +is_a: SO:1000009 ! transition + +[Term] +id: SO:1000015 +name: A_to_G_transition +def: "A transition of an adenine to a guanine." [SO:ke] +synonym: "A to G transition" EXACT [] +is_a: SO:1000014 ! purine_transition + +[Term] +id: SO:1000016 +name: G_to_A_transition +def: "A transition of a guanine to an adenine." [SO:ke] +synonym: "G to A transition" EXACT [] +is_a: SO:1000014 ! purine_transition + +[Term] +id: SO:1000017 +name: transversion +def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +xref: http://en.wikipedia.org/wiki/Transversion "wiki" +is_a: SO:0001483 ! SNV + +[Term] +id: SO:1000018 +name: pyrimidine_to_purine_transversion +def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke] +synonym: "pyrimidine to purine transversion" EXACT [] +is_a: SO:1000017 ! transversion + +[Term] +id: SO:1000019 +name: C_to_A_transversion +def: "A transversion from cytidine to adenine." [SO:ke] +synonym: "C to A transversion" EXACT [] +is_a: SO:1000018 ! pyrimidine_to_purine_transversion + +[Term] +id: SO:1000020 +name: C_to_G_transversion +synonym: "C to G transversion" EXACT [] +is_a: SO:1000018 ! pyrimidine_to_purine_transversion + +[Term] +id: SO:1000021 +name: T_to_A_transversion +def: "A transversion from T to A." [SO:ke] +synonym: "T to A transversion" EXACT [] +is_a: SO:1000018 ! pyrimidine_to_purine_transversion + +[Term] +id: SO:1000022 +name: T_to_G_transversion +def: "A transversion from T to G." [SO:ke] +synonym: "T to G transversion" EXACT [] +is_a: SO:1000018 ! pyrimidine_to_purine_transversion + +[Term] +id: SO:1000023 +name: purine_to_pyrimidine_transversion +def: "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke] +synonym: "purine to pyrimidine transversion" EXACT [] +is_a: SO:1000017 ! transversion + +[Term] +id: SO:1000024 +name: A_to_C_transversion +def: "A transversion from adenine to cytidine." [SO:ke] +synonym: "A to C transversion" EXACT [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion + +[Term] +id: SO:1000025 +name: A_to_T_transversion +def: "A transversion from adenine to thymine." [SO:ke] +synonym: "A to T transversion" EXACT [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion + +[Term] +id: SO:1000026 +name: G_to_C_transversion +def: "A transversion from guanine to cytidine." [SO:ke] +synonym: "G to C transversion" EXACT [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion + +[Term] +id: SO:1000027 +name: G_to_T_transversion +def: "A transversion from guanine to thymine." [SO:ke] +synonym: "G to T transversion" EXACT [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion + +[Term] +id: SO:1000028 +name: intrachromosomal_mutation +def: "A chromosomal structure variation within a single chromosome." [SO:ke] +synonym: "intrachromosomal mutation" EXACT [] +is_a: SO:1000183 ! chromosome_structure_variation +relationship: has_quality SO:0001510 ! intrachromosomal + +[Term] +id: SO:1000029 +name: chromosomal_deletion +def: "An incomplete chromosome." [SO:ke] +synonym: "(bacteria)&Dgr;" RELATED [] +synonym: "(Drosophila)Df" RELATED [] +synonym: "(fungi)D" RELATED [] +synonym: "chromosomal deletion" EXACT [] +synonym: "deficiency" EXACT [] +xref: http://en.wikipedia.org/wiki/Chromosomal_deletion "wiki" +is_a: SO:1000028 ! intrachromosomal_mutation +relationship: has_part SO:0000159 ! deletion + +[Term] +id: SO:1000030 +name: chromosomal_inversion +def: "An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke] +synonym: "(bacteria)IN" RELATED [] +synonym: "(Drosophila)In" RELATED [] +synonym: "(fungi)In" RELATED [] +synonym: "chromosomal inversion" EXACT [] +xref: http://en.wikipedia.org/wiki/Chromosomal_inversion "wiki" +is_a: SO:1000028 ! intrachromosomal_mutation +relationship: has_part SO:1000036 ! inversion + +[Term] +id: SO:1000031 +name: interchromosomal_mutation +def: "A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke] +synonym: "interchromosomal mutation" EXACT [] +is_a: SO:1000183 ! chromosome_structure_variation +relationship: has_quality SO:0001511 ! interchromosomal + +[Term] +id: SO:1000032 +name: indel +def: "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, http:http\://www.hgvs.org/mutnomen/recs-DNA.html#indel] +comment: Indels can have a different number of bases than the corresponding reference sequence. +xref: http://en.wikipedia.org/wiki/Indel "wiki" +xref: loinc:LA9659-9 "Insertion and Deletion" +is_a: SO:0001059 ! sequence_alteration + +[Term] +id: SO:1000035 +name: duplication +def: "An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th] +synonym: "nucleotide duplication" EXACT [] +synonym: "nucleotide_duplication" RELATED [] +xref: loinc:LA6686-5 "Duplication" +is_a: SO:0000667 ! insertion + +[Term] +id: SO:1000036 +name: inversion +def: "A continuous nucleotide sequence is inverted in the same position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +subset: DBVAR +subset: SOFA +synonym: "inversion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] +xref: loinc:LA6689-9 "Inversion" +is_a: SO:0001059 ! sequence_alteration +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:1000037 +name: chromosomal_duplication +def: "An extra chromosome." [SO:ke] +synonym: "(Drosophila)Dp" RELATED [] +synonym: "(fungi)Dp" RELATED [] +synonym: "chromosomal duplication" EXACT [] +xref: http://en.wikipedia.org/wiki/Chromosomal_duplication "wiki" +is_a: SO:1000183 ! chromosome_structure_variation + +[Term] +id: SO:1000038 +name: intrachromosomal_duplication +def: "A duplication that occurred within a chromosome." [SO:ke] +synonym: "intrachromosomal duplication" EXACT [] +is_a: SO:1000028 ! intrachromosomal_mutation +is_a: SO:1000037 ! chromosomal_duplication +relationship: has_part SO:1000035 ! duplication + +[Term] +id: SO:1000039 +name: direct_tandem_duplication +def: "A tandem duplication where the individual regions are in the same orientation." [SO:ke] +synonym: "direct tandem duplication" EXACT [] +is_a: SO:1000173 ! tandem_duplication + +[Term] +id: SO:1000040 +name: inverted_tandem_duplication +def: "A tandem duplication where the individual regions are not in the same orientation." [SO:ke] +synonym: "inverted tandem duplication" EXACT [] +synonym: "mirror duplication" RELATED [] +is_a: SO:1000173 ! tandem_duplication + +[Term] +id: SO:1000041 +name: intrachromosomal_transposition +def: "A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke] +synonym: "(Drosophila)Tp" RELATED [] +synonym: "intrachromosomal transposition" EXACT [] +is_a: SO:0000453 ! chromosomal_transposition +is_a: SO:1000038 ! intrachromosomal_duplication +relationship: has_part SO:0000199 ! translocation +relationship: has_part SO:1000035 ! duplication + +[Term] +id: SO:1000042 +name: compound_chromosome +def: "A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke] +synonym: "compound chromosome" EXACT [] +is_a: SO:1000183 ! chromosome_structure_variation + +[Term] +id: SO:1000043 +name: Robertsonian_fusion +def: "A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere." [http://en.wikipedia.org/wiki/Robertsonian_translocation] +synonym: "centric-fusion translocations" EXACT [] +synonym: "Robertsonian fusion" EXACT [] +synonym: "whole-arm translocations" EXACT [] +xref: http://en.wikipedia.org/wiki/Robertsonian_fusion "wiki" +is_a: SO:1000044 ! chromosomal_translocation + +[Term] +id: SO:1000044 +name: chromosomal_translocation +def: "A chromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual] +synonym: "(Drosophila)T" RELATED [] +synonym: "(fungi)T" RELATED [] +synonym: "chromosomal translocation" EXACT [] +xref: http://en.wikipedia.org/wiki/Chromosomal_translocation "wiki" +is_a: SO:0000199 ! translocation +is_a: SO:1000031 ! interchromosomal_mutation + +[Term] +id: SO:1000045 +name: ring_chromosome +def: "A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." [http://en.wikipedia.org/wiki/Ring_chromosome] +synonym: "(Drosophila)R" RELATED [] +synonym: "(fungi)C" RELATED [] +synonym: "ring chromosome" EXACT [] +xref: http://en.wikipedia.org/wiki/Ring_chromosome "wiki" +is_a: SO:1000028 ! intrachromosomal_mutation +relationship: has_quality SO:0000988 ! circular + +[Term] +id: SO:1000046 +name: pericentric_inversion +def: "A chromosomal inversion that includes the centromere." [FB:reference_manual] +synonym: "pericentric inversion" EXACT [] +is_a: SO:1000030 ! chromosomal_inversion +relationship: has_quality SO:0001518 ! pericentric + +[Term] +id: SO:1000047 +name: paracentric_inversion +def: "A chromosomal inversion that does not include the centromere." [FB:reference_manual] +synonym: "paracentric inversion" EXACT [] +is_a: SO:1000030 ! chromosomal_inversion +relationship: has_quality SO:0001519 ! paracentric + +[Term] +id: SO:1000048 +name: reciprocal_chromosomal_translocation +def: "A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." [FB:reference_manual] +synonym: "reciprocal chromosomal translocation" EXACT [] +is_a: SO:1000044 ! chromosomal_translocation + +[Term] +id: SO:1000049 +name: sequence_variation_affecting_transcript +alt_id: SO:1000177 +alt_id: SO:1000179 +def: "Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting transcript" EXACT [] +synonym: "mutation causing partially characterised change in transcript" RELATED [] +synonym: "mutation causing uncharacterised change in transcript" RELATED [] +synonym: "sequence variant causing partially characterised change in transcript" EXACT [] +synonym: "sequence variant causing uncharacterised change in transcript" EXACT [] +synonym: "sequence variation affecting transcript" EXACT [] +synonym: "sequence_variant_causing_partially_characterised_change_in_transcript" EXACT [] +synonym: "sequence_variant_causing_uncharacterised_change_in_transcript" EXACT [] +is_obsolete: true +replaced_by: SO:0001576 + +[Term] +id: SO:1000050 +name: sequence_variant_causing_no_change_in_transcript +def: "No effect on the state of the RNA." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is not change, it is not a good ontological term. +synonym: "mutation causing no change in transcript" RELATED [] +synonym: "sequence variant causing no change in transcript" EXACT [] +is_obsolete: true + +[Term] +id: SO:1000054 +name: sequence_variation_affecting_coding_sequence +def: "Any of the amino acid coding triplets of a gene are affected by the DNA mutation." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting coding sequence" EXACT [] +synonym: "sequence variation affecting coding sequence" RELATED [] +is_obsolete: true +replaced_by: SO:0001580 + +[Term] +id: SO:1000055 +name: sequence_variant_causing_initiator_codon_change_in_transcript +def: "The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing initiator codon change in transcript" RELATED [] +synonym: "sequence variant causing initiator codon change in transcript" EXACT [] +is_obsolete: true +replaced_by: SO:0001582 + +[Term] +id: SO:1000056 +name: sequence_variant_causing_amino_acid_coding_codon_change_in_transcript +def: "The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutaton causing amino acid coding codon change in transcript" RELATED [] +synonym: "sequence variant causing amino acid coding codon change in transcript" EXACT [] +is_obsolete: true +consider: SO:0001606 + +[Term] +id: SO:1000057 +name: sequence_variant_causing_synonymous_codon_change_in_transcript +def: "The changed codon has the same translation product as the original codon." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing synonymous codon change in transcript" RELATED [] +synonym: "sequence variant causing synonymous codon change in transcript" EXACT [] +is_obsolete: true +replaced_by: SO:0001819 + +[Term] +id: SO:1000058 +name: sequence_variant_causing_non_synonymous_codon_change_in_transcript +def: "A DNA point mutation that causes a substitution of an amino acid by an other." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing non synonymous codon change in transcript" RELATED [] +synonym: "non-synonymous codon change in transcript" EXACT [] +synonym: "sequence variant causing non synonymous codon change in transcript" EXACT [] +is_obsolete: true +consider: SO:0001583 + +[Term] +id: SO:1000059 +name: sequence_variant_causing_missense_codon_change_in_transcript +def: "The nucleotide change in the codon leads to a new codon coding for a new amino acid." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing missense codon change in transcript" RELATED [] +synonym: "sequence variant causing missense codon change in transcript" EXACT [] +is_obsolete: true +consider: SO:0001583 + +[Term] +id: SO:1000060 +name: sequence_variant_causing_conservative_missense_codon_change_in_transcript +def: "The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix. +synonym: "mutation causing conservative missense codon change in transcript" RELATED [] +synonym: "sequence variant causing conservative missense codon change in transcript" EXACT [] +is_obsolete: true +replaced_by: SO:0001585 + +[Term] +id: SO:1000061 +name: sequence_variant_causing_nonconservative_missense_codon_change_in_transcript +def: "The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix. +synonym: "mutation causing nonconservative missense codon change in transcript" RELATED [] +synonym: "sequence variant causing nonconservative missense codon change in transcript" EXACT [] +is_obsolete: true +consider: SO:0001586 + +[Term] +id: SO:1000062 +name: sequence_variant_causing_nonsense_codon_change_in_transcript +def: "The nucleotide change in the codon triplet creates a terminator codon." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing nonsense codon change in transcript" RELATED [] +synonym: "sequence variant causing nonsense codon change in transcript" EXACT [] +is_obsolete: true +consider: SO:0001587 + +[Term] +id: SO:1000063 +name: sequence_variant_causing_terminator_codon_change_in_transcript +def: "The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence." [SO:ke] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing terminator codon change in transcript" RELATED [] +synonym: "sequence variant causing terminator codon change in transcript" EXACT [] +is_obsolete: true +consider: SO:0001590 + +[Term] +id: SO:1000064 +name: sequence_variation_affecting_reading_frame +def: "An umbrella term for terms describing an effect of a sequence variation on the frame of translation." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting reading frame" EXACT [] +synonym: "sequence variation affecting reading frame" RELATED [] +is_obsolete: true + +[Term] +id: SO:1000065 +name: frameshift_sequence_variation +def: "A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke] +synonym: "frameshift mutation" EXACT [] +synonym: "frameshift sequence variation" RELATED [] +synonym: "out of frame mutation" RELATED [] +xref: http://en.wikipedia.org/wiki/Frameshift_mutation "wiki" +is_obsolete: true + +[Term] +id: SO:1000066 +name: sequence_variant_causing_plus_1_frameshift_mutation +def: "A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide." [SO:ke] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "plus 1 frameshift mutation" EXACT [] +synonym: "sequence variant causing plus 1 frameshift mutation" EXACT [] +is_obsolete: true +replaced_by: SO:0001594 + +[Term] +id: SO:1000067 +name: sequence_variant_causing_minus_1_frameshift +def: "A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide." [SO:ke] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "minus 1 frameshift mutation" EXACT [] +synonym: "sequence variant causing minus 1 frameshift" EXACT [] +is_obsolete: true +replaced_by: SO:0001592 + +[Term] +id: SO:1000068 +name: sequence_variant_causing_plus_2_frameshift +def: "A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides." [SO:ke] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "plus 2 frameshift mutation" EXACT [] +synonym: "sequence variant causing plus 2 frameshift" EXACT [] +is_obsolete: true +replaced_by: SO:0001595 + +[Term] +id: SO:1000069 +name: sequence_variant_causing_minus_2_frameshift +def: "A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides." [SO:ke] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "minus 2 frameshift mutation" EXACT [] +synonym: "sequence variant causing minus 2 frameshift" EXACT [] +is_obsolete: true +replaced_by: SO:0001593 + +[Term] +id: SO:1000070 +name: sequence_variant_affecting_transcript_processing +def: "Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting transcript processing" RELATED [] +synonym: "sequence variant affecting transcript processing" EXACT [] +is_obsolete: true +replaced_by: SO:0001543 + +[Term] +id: SO:1000071 +name: sequence_variant_affecting_splicing +def: "A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting splicing" RELATED [] +synonym: "sequence variant affecting splicing" EXACT [] +is_obsolete: true +replaced_by: SO:0001568 + +[Term] +id: SO:1000072 +name: sequence_variant_affecting_splice_donor +def: "A sequence_variant_effect that changes the splice donor sequence." [SO:ke] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting splice donor" RELATED [] +synonym: "sequence variant affecting splice donor" RELATED [] +synonym: "splice donor mutation" EXACT [] +is_obsolete: true +replaced_by: SO:0001575 + +[Term] +id: SO:1000073 +name: sequence_variant_affecting_splice_acceptor +def: "A sequence_variant_effect that changes the splice acceptor sequence." [SO:ke] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting splicing" RELATED [] +synonym: "sequence variant affecting splice acceptor" RELATED [] +synonym: "splice acceptor mutation" EXACT [] +is_obsolete: true +replaced_by: SO:0001574 + +[Term] +id: SO:1000074 +name: sequence_variant_causing_cryptic_splice_activation +def: "A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: A cryptic splice site is only used when the natural splice site has been disrupted by a sequence alteration. +synonym: "cryptic splice activator sequence variant" EXACT [] +synonym: "mutation causing cryptic splice activator" RELATED [] +synonym: "sequence variant causing cryptic splice activator" EXACT [] +is_obsolete: true +replaced_by: SO:0001569 + +[Term] +id: SO:1000075 +name: sequence_variant_affecting_editing +def: "Sequence variant affects the editing of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting editing" RELATED [] +synonym: "sequence variant affecting editing" EXACT [] +is_obsolete: true +replaced_by: SO:0001544 + +[Term] +id: SO:1000076 +name: sequence_variant_affecting_transcription +def: "Mutation affects the process of transcription, its initiation, progression or termination." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting transcription" RELATED [] +synonym: "sequence variant affecting transcription" EXACT [] +is_obsolete: true +replaced_by: SO:0001549 + +[Term] +id: SO:1000078 +name: sequence_variant_decreasing_rate_of_transcription +def: "A sequence variation that decreases the rate a which transcription of the sequence occurs." [SO:ke] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation decreasing rate of transcription" RELATED [] +synonym: "sequence variation decreasing rate of transcription" EXACT [] +is_obsolete: true + +[Term] +id: SO:1000079 +name: sequence_variation_affecting_transcript_sequence +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting transcript sequence" EXACT [] +synonym: "sequence variation affecting transcript sequence" EXACT [] +is_obsolete: true + +[Term] +id: SO:1000080 +name: sequence_variant_increasing_rate_of_transcription +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation increasing rate of transcription" RELATED [] +synonym: "sequence variation increasing rate of transcription" EXACT [] +is_obsolete: true + +[Term] +id: SO:1000081 +name: sequence_variant_affecting_rate_of_transcription +def: "A mutation that alters the rate a which transcription of the sequence occurs." [SO:ke] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting rate of transcription" RELATED [] +synonym: "sequence variant affecting rate of transcription" EXACT [] +is_obsolete: true +replaced_by: SO:0001550 + +[Term] +id: SO:1000082 +name: sequence variant_affecting_transcript_stability +def: "Sequence variant affects the stability of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting transcript stability" RELATED [] +synonym: "sequence variant affecting transcript stability" EXACT [] +is_obsolete: true +replaced_by: SO:0001546 + +[Term] +id: SO:1000083 +name: sequence_variant_increasing_transcript_stability +def: "Sequence variant increases the stability (half-life) of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation increasing transcript stability" RELATED [] +synonym: "sequence variant increasing transcript stability" EXACT [] +is_obsolete: true + +[Term] +id: SO:1000084 +name: sequence_variant_decreasing_transcript_stability +def: "Sequence variant decreases the stability (half-life) of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation decreasing transcript stability" RELATED [] +synonym: "sequence variant decreasing transcript stability" EXACT [] +is_obsolete: true + +[Term] +id: SO:1000085 +name: sequence_variation_affecting_level_of_transcript +def: "A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting level of transcript" RELATED [] +synonym: "sequence variation affecting level of transcript" EXACT [] +is_obsolete: true +replaced_by: SO:0001540 + +[Term] +id: SO:1000086 +name: sequence_variation_decreasing_level_of_transcript +def: "A sequence variation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation decreasing level of transcript" EXACT [] +synonym: "sequence variation decreasing level of transcript" RELATED [] +is_obsolete: true + +[Term] +id: SO:1000087 +name: sequence_variation_increasing_level_of_transcript +def: "A sequence_variation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation increasing level of transcript" EXACT [] +synonym: "sequence variation increasing level of transcript" EXACT [] +is_obsolete: true + +[Term] +id: SO:1000088 +name: sequence_variant_affecting_translational_product +alt_id: SO:1000090 +alt_id: SO:1000091 +def: "A sequence variant causing a change in primary translation product of a transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting translational product" RELATED [] +synonym: "mutation causing partially characterised change of translational product" RELATED [] +synonym: "mutation causing uncharacterised change of translational product" RELATED [] +synonym: "sequence variant affecting translational product" EXACT [] +synonym: "sequence variant causing partially characterised change of translational product" EXACT [] +synonym: "sequence variant causing uncharacterised change of translational product" EXACT [] +synonym: "sequence_variant_causing_partially_characterised_change_of_translational_product" EXACT [] +synonym: "sequence_variant_causing_uncharacterised_change_of_translational_product" EXACT [] +is_obsolete: true +replaced_by: SO:0001553 + +[Term] +id: SO:1000089 +name: sequence_variant_causing_no_change_of_translational_product +def: "The sequence variant at RNA level does not lead to any change in polypeptide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also, as there is no change, this is not a good ontological term. +synonym: "mutation causing no change of translational product" RELATED [] +synonym: "sequence variant causing no change of translational product" EXACT [] +is_obsolete: true + +[Term] +id: SO:1000092 +name: sequence_variant_causing_complex_change_of_translational_product +def: "Any sequence variant effect that is known at nucleotide level but cannot be explained by using other key terms." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing complex change of translational product" RELATED [] +synonym: "sequence variant causing complex change of translational product" EXACT [] +is_obsolete: true +consider: SO:0001539 + +[Term] +id: SO:1000093 +name: sequence_variant_causing_amino_acid_substitution +def: "The replacement of a single amino acid by another." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing amino acid substitution" RELATED [] +synonym: "sequence variant causing amino acid substitution" EXACT [] +is_obsolete: true +replaced_by: SO:0001606 + +[Term] +id: SO:1000094 +name: sequence_variant_causing_conservative_amino_acid_substitution +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing conservative amino acid substitution" RELATED [] +synonym: "sequence variant causing conservative amino acid substitution" EXACT [] +is_obsolete: true +replaced_by: SO:0001607 + +[Term] +id: SO:1000095 +name: sequence_variant_causing_nonconservative_amino_acid_substitution +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing nonconservative amino acid substitution" RELATED [] +synonym: "sequence variant causing nonconservative amino acid substitution" EXACT [] +is_obsolete: true +replaced_by: SO:0001607 + +[Term] +id: SO:1000096 +name: sequence_variant_causing_amino_acid_insertion +def: "The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing amino acid insertion" RELATED [] +synonym: "sequence variant causing amino acid insertion" EXACT [] +is_obsolete: true +replaced_by: SO:0001605 + +[Term] +id: SO:1000097 +name: sequence_variant_causing_amino_acid_deletion +def: "The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing amino acid deletion" RELATED [] +synonym: "sequence variant causing amino acid deletion" EXACT [] +is_obsolete: true +consider: SO:0001825 + +[Term] +id: SO:1000098 +name: sequence_variant_causing_polypeptide_truncation +def: "The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062)." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing polypeptide truncation" RELATED [] +synonym: "sequence variant causing polypeptide truncation" EXACT [] +is_obsolete: true +replaced_by: SO:0001587 + +[Term] +id: SO:1000099 +name: sequence_variant_causing_polypeptide_elongation +def: "The extension of the translational product at either (or both) the N-terminus and/or the C-terminus." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing polypeptide elongation" RELATED [] +synonym: "sequence variant causing polypeptide elongation" EXACT [] +is_obsolete: true +replaced_by: SO:0001609 + +[Term] +id: SO:1000100 +name: mutation_causing_polypeptide_N_terminal_elongation +def: "." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing polypeptide N terminal elongation" EXACT [] +synonym: "polypeptide N-terminal elongation" EXACT [] +is_obsolete: true +replaced_by: SO:0001611 + +[Term] +id: SO:1000101 +name: mutation_causing_polypeptide_C_terminal_elongation +def: "." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing polypeptide C terminal elongation" EXACT [] +synonym: "polypeptide C-terminal elongation" EXACT [] +is_obsolete: true +replaced_by: SO:0001610 + +[Term] +id: SO:1000102 +name: sequence_variant_affecting_level_of_translational_product +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting level of translational product" RELATED [] +synonym: "sequence variant affecting level of translational product" EXACT [] +is_obsolete: true +replaced_by: SO:0001553 + +[Term] +id: SO:1000103 +name: sequence_variant_decreasing_level_of_translation_product +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutationdecreasing level of translation product" RELATED [] +synonym: "sequence variant decreasing level of translation product" EXACT [] +is_obsolete: true +replaced_by: SO:0001555 + +[Term] +id: SO:1000104 +name: sequence_variant_increasing_level_of_translation_product +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutationt increasing level of translation product" RELATED [] +synonym: "sequence variant increasing level of translation product" EXACT [] +is_obsolete: true + +[Term] +id: SO:1000105 +name: sequence_variant_affecting_polypeptide_amino_acid_sequence +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting polypeptide amino acid sequence" RELATED [] +synonym: "sequence variant affecting polypeptide amino acid sequence" EXACT [] +is_obsolete: true +replaced_by: SO:0001603 + +[Term] +id: SO:1000106 +name: mutation_causing_inframe_polypeptide_N_terminal_elongation +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "inframe polypeptide N-terminal elongation" EXACT [] +synonym: "mutation causing inframe polypeptide N terminal elongation" EXACT [] +is_obsolete: true +replaced_by: SO:0001614 + +[Term] +id: SO:1000107 +name: mutation_causing_out_of_frame_polypeptide_N_terminal_elongation +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing out of frame polypeptide N terminal elongation" EXACT [] +synonym: "out of frame polypeptide N-terminal elongation" EXACT [] +is_obsolete: true +replaced_by: SO:0001615 + +[Term] +id: SO:1000108 +name: mutaton_causing_inframe_polypeptide_C_terminal_elongation +synonym: "inframe_polypeptide C-terminal elongation" EXACT [] +synonym: "mutaton causing inframe polypeptide C terminal elongation" EXACT [] +is_obsolete: true +replaced_by: SO:0001612 + +[Term] +id: SO:1000109 +name: mutation_causing_out_of_frame_polypeptide_C_terminal_elongation +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing out of frame polypeptide C terminal elongation" EXACT [] +synonym: "out of frame polypeptide C-terminal elongation" EXACT [] +is_obsolete: true +replaced_by: SO:0001613 + +[Term] +id: SO:1000110 +name: frame_restoring_sequence_variant +def: "A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke] +synonym: "frame restoring mutation" EXACT [] +synonym: "frame restoring sequence variant" EXACT [] +is_obsolete: true + +[Term] +id: SO:1000111 +name: sequence_variant_affecting_3D_structure_of_polypeptide +alt_id: SO:1000113 +alt_id: SO:1000114 +def: "A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule." [SO:ke] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting 3D structure of polypeptide" RELATED [] +synonym: "mutation causing partially characterised 3D structural change" RELATED [] +synonym: "mutation causing uncharacterised 3D structural change" RELATED [] +synonym: "sequence variant affecting 3D structure of polypeptide" EXACT [] +synonym: "sequence variant affecting 3D-structure of polypeptide" EXACT [] +synonym: "sequence variant causing partially characterised 3D structural change" EXACT [] +synonym: "sequence variant causing uncharacterised 3D structural change" EXACT [] +synonym: "sequence_variant_causing_partially_characterised_3D_structural_change" EXACT [] +synonym: "sequence_variant_causing_uncharacterised_3D_structural_change" EXACT [] +is_obsolete: true +replaced_by: SO:0001599 + +[Term] +id: SO:1000112 +name: sequence_variant_causing_no_3D_structural_change +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is no effect, it is not a good term. +synonym: "mutation causing no 3D structural change" RELATED [] +synonym: "sequence variant causing no 3D structural change" EXACT [] +is_obsolete: true + +[Term] +id: SO:1000115 +name: sequence_variant_causing_complex_3D_structural_change +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing complex 3D structural change" RELATED [] +synonym: "sequence variant causing complex 3D structural change" EXACT [] +is_obsolete: true +replaced_by: SO:0001600 + +[Term] +id: SO:1000116 +name: sequence_variant_causing_conformational_change +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing conformational change" RELATED [] +synonym: "sequence variant causing conformational change" EXACT [] +is_obsolete: true +replaced_by: SO:0001601 + +[Term] +id: SO:1000117 +name: sequence_variant_affecting_polypeptide_function +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting polypeptide function" RELATED [] +synonym: "sequence variant affecting polypeptide function" EXACT [] +is_obsolete: true +replaced_by: SO:0001554 + +[Term] +id: SO:1000118 +name: sequence_variant_causing_loss_of_function_of_polypeptide +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "loss of function of polypeptide" RELATED [] +synonym: "mutation causing loss of function of polypeptide" RELATED [] +synonym: "sequence variant causing loss of function of polypeptide" EXACT [] +is_obsolete: true +replaced_by: SO:0001559 + +[Term] +id: SO:1000119 +name: sequence_variant_causing_inactive_ligand_binding_site +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing inactive ligand binding site" RELATED [] +synonym: "sequence variant causing inactive ligand binding site" EXACT [] +is_obsolete: true +replaced_by: SO:0001560 + +[Term] +id: SO:1000120 +name: sequence_variant_causing_inactive_catalytic_site +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing inactive catalytic site" RELATED [] +synonym: "sequence variant causing inactive catalytic site" EXACT [] +is_obsolete: true +replaced_by: SO:0001618 + +[Term] +id: SO:1000121 +name: sequence_variant_causing_polypeptide_localization_change +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing polypeptide localization change" RELATED [] +synonym: "sequence variant causing polypeptide localization change" EXACT [] +is_obsolete: true +replaced_by: SO:0001558 + +[Term] +id: SO:1000122 +name: sequence_variant_causing_polypeptide_post_translational_processing_change +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing polypeptide post translational processing change" RELATED [] +synonym: "polypeptide post-translational processing affected" EXACT [] +synonym: "sequence variant causing polypeptide post translational processing change" EXACT [] +is_obsolete: true +replaced_by: SO:0001562 + +[Term] +id: SO:1000123 +name: polypeptide_post_translational_processing_affected +synonym: "polypeptide_post-translational_processing_affected" RELATED [] +is_obsolete: true + +[Term] +id: SO:1000124 +name: sequence_variant_causing_partial_loss_of_function_of_polypeptide +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing partial loss of function of polypeptide" RELATED [] +synonym: "partial loss of function of polypeptide" EXACT [] +synonym: "sequence variant causing partial loss of function of polypeptide" EXACT [] +is_obsolete: true +replaced_by: SO:0001561 + +[Term] +id: SO:1000125 +name: sequence_variant_causing_gain_of_function_of_polypeptide +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "gain of function of polypeptide" EXACT [] +synonym: "mutation causing gain of function of polypeptide" RELATED [] +synonym: "sequence variant causing gain of function of polypeptide" EXACT [] +is_obsolete: true +replaced_by: SO:0001557 + +[Term] +id: SO:1000126 +name: sequence_variant_affecting_transcript_secondary_structure +def: "A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule." [SO:ke] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting transcript secondary structure" RELATED [] +synonym: "sequence variant affecting transcript secondary structure" EXACT [] +is_obsolete: true +replaced_by: SO:0001596 + +[Term] +id: SO:1000127 +name: sequence_variant_causing_compensatory_transcript_secondary_structure_mutation +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing compensatory transcript secondary structure mutation" RELATED [] +synonym: "sequence variant causing compensatory transcript secondary structure mutation" EXACT [] +is_obsolete: true +replaced_by: SO:0001597 + +[Term] +id: SO:1000132 +name: sequence_variant_effect +def: "The effect of a change in nucleotide sequence." [SO:ke] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.\nUpdated after discussion with Peter Taschner - Feb 09. +synonym: "sequence variant effect" RELATED [] +is_obsolete: true + +[Term] +id: SO:1000134 +name: sequence_variant_causing_polypeptide_fusion +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing polypeptide fusion" RELATED [] +synonym: "sequence variant causing polypeptide fusion" EXACT [] +is_obsolete: true +replaced_by: SO:0001616 + +[Term] +id: SO:1000136 +name: autosynaptic_chromosome +def: "An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." [PMID:6804304] +synonym: "(Drosophila)A" RELATED [] +synonym: "autosynaptic chromosome" EXACT [] +is_a: SO:1000183 ! chromosome_structure_variation + +[Term] +id: SO:1000138 +name: homo_compound_chromosome +def: "A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved." [SO:ke] +synonym: "homo compound chromosome" EXACT [] +synonym: "homo-compound chromosome" EXACT [] +is_a: SO:1000042 ! compound_chromosome + +[Term] +id: SO:1000140 +name: hetero_compound_chromosome +def: "A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them." [FB:reference_manual, SO:ke] +synonym: "hetero compound chromosome" EXACT [] +synonym: "hetero-compound chromosome" EXACT [] +is_a: SO:1000042 ! compound_chromosome + +[Term] +id: SO:1000141 +name: chromosome_fission +def: "A chromosome that occurred by the division of a larger chromosome." [SO:ke] +synonym: "chromosome fission" EXACT [] +is_a: SO:1000028 ! intrachromosomal_mutation + +[Term] +id: SO:1000142 +name: dexstrosynaptic_chromosome +def: "An autosynaptic chromosome carrying the two right (D = dextro) telomeres." [FB:manual] +synonym: "dexstrosynaptic chromosome" EXACT [] +is_a: SO:1000136 ! autosynaptic_chromosome + +[Term] +id: SO:1000143 +name: laevosynaptic_chromosome +def: "LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres." [FB:manual] +synonym: "laevosynaptic chromosome" EXACT [] +is_a: SO:1000136 ! autosynaptic_chromosome + +[Term] +id: SO:1000144 +name: free_duplication +def: "A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." [FB:reference_manual] +synonym: "free duplication" EXACT [] +is_a: SO:1000037 ! chromosomal_duplication + +[Term] +id: SO:1000145 +name: free_ring_duplication +def: "A ring chromosome which is a copy of another chromosome." [SO:ke] +synonym: "(Drosophila)R" RELATED [] +synonym: "free ring duplication" EXACT [] +is_a: SO:1000045 ! ring_chromosome +is_a: SO:1000144 ! free_duplication +relationship: has_quality SO:0001516 ! free + +[Term] +id: SO:1000147 +name: deficient_translocation +def: "A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual] +synonym: "(Drosophila)Df" RELATED [] +synonym: "(Drosophila)DfT" RELATED [] +synonym: "deficient translocation" EXACT [] +is_a: SO:1000029 ! chromosomal_deletion +is_a: SO:1000044 ! chromosomal_translocation +relationship: has_part SO:0000159 ! deletion + +[Term] +id: SO:1000148 +name: inversion_cum_translocation +def: "A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual] +synonym: "(Drosophila)InT" RELATED [] +synonym: "(Drosophila)T" RELATED [] +synonym: "inversion cum translocation" EXACT [] +is_a: SO:1000030 ! chromosomal_inversion +is_a: SO:1000044 ! chromosomal_translocation +relationship: has_part SO:1000036 ! inversion + +[Term] +id: SO:1000149 +name: bipartite_duplication +def: "An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual] +synonym: "(Drosophila)bDp" RELATED [] +synonym: "bipartite duplication" EXACT [] +is_a: SO:1000031 ! interchromosomal_mutation +is_a: SO:1000038 ! intrachromosomal_duplication + +[Term] +id: SO:1000150 +name: cyclic_translocation +def: "A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [FB:reference_manual] +synonym: "cyclic translocation" EXACT [] +is_a: SO:0002060 ! interchromosomal_translocation + +[Term] +id: SO:1000151 +name: bipartite_inversion +def: "A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [FB:reference_manual] +synonym: "(Drosophila)bIn" RELATED [] +synonym: "bipartite inversion" EXACT [] +is_a: SO:1000030 ! chromosomal_inversion + +[Term] +id: SO:1000152 +name: uninverted_insertional_duplication +def: "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual] +synonym: "(Drosophila)eDp" RELATED [] +synonym: "uninverted insertional duplication" EXACT [] +is_a: SO:1000154 ! insertional_duplication + +[Term] +id: SO:1000153 +name: inverted_insertional_duplication +def: "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual] +synonym: "(Drosophila)iDp" RELATED [] +synonym: "inverted insertional duplication" EXACT [] +is_a: SO:1000154 ! insertional_duplication + +[Term] +id: SO:1000154 +name: insertional_duplication +def: "A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke] +synonym: "(Drosophila)Dpp" RELATED [] +synonym: "insertional duplication" EXACT [] +is_a: SO:1000037 ! chromosomal_duplication + +[Term] +id: SO:1000155 +name: interchromosomal_transposition +def: "A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke] +synonym: "(Drosophila)Tp" RELATED [] +synonym: "interchromosomal transposition" EXACT [] +is_a: SO:0000453 ! chromosomal_transposition +is_a: SO:1000031 ! interchromosomal_mutation + +[Term] +id: SO:1000156 +name: inverted_interchromosomal_transposition +def: "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual] +synonym: "(Drosophila)iTp" RELATED [] +synonym: "inverted interchromosomal transposition" EXACT [] +is_a: SO:1000155 ! interchromosomal_transposition + +[Term] +id: SO:1000157 +name: uninverted_interchromosomal_transposition +def: "An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual] +synonym: "(Drosophila)eTp" RELATED [] +synonym: "uninverted interchromosomal transposition" EXACT [] +is_a: SO:1000155 ! interchromosomal_transposition + +[Term] +id: SO:1000158 +name: inverted_intrachromosomal_transposition +def: "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual] +synonym: "(Drosophila)iTp" RELATED [] +synonym: "inverted intrachromosomal transposition" EXACT [] +is_a: SO:1000148 ! inversion_cum_translocation +relationship: has_part SO:1000036 ! inversion + +[Term] +id: SO:1000159 +name: uninverted_intrachromosomal_transposition +def: "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual] +synonym: "(Drosophila)eTp" RELATED [] +synonym: "uninverted intrachromosomal transposition" EXACT [] +is_a: SO:1000041 ! intrachromosomal_transposition +relationship: has_part SO:0001514 ! direct + +[Term] +id: SO:1000160 +name: unoriented_insertional_duplication +def: "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual] +comment: Flag - unknown in the definition. +synonym: "(Drosophila)uDp" RELATED [] +synonym: "unoriented insertional duplication" EXACT [] +is_a: SO:1000154 ! insertional_duplication + +[Term] +id: SO:1000161 +name: unoriented_interchromosomal_transposition +def: "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual] +comment: FLAG - term describes an unknown. +synonym: "(Drosophila)uTp" RELATED [] +synonym: "unorientated interchromosomal transposition" EXACT [] +is_a: SO:1000155 ! interchromosomal_transposition + +[Term] +id: SO:1000162 +name: unoriented_intrachromosomal_transposition +def: "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual] +comment: FLAG - definition describes an unknown. +synonym: "(Drosophila)uTp" RELATED [] +synonym: "unorientated intrachromosomal transposition" EXACT [] +is_a: SO:1000041 ! intrachromosomal_transposition + +[Term] +id: SO:1000170 +name: uncharacterized_chromosomal_mutation +synonym: "uncharacterized chromosomal mutation" EXACT [] +is_a: SO:1000183 ! chromosome_structure_variation + +[Term] +id: SO:1000171 +name: deficient_inversion +def: "A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke] +synonym: "(Drosophila)Df" RELATED [] +synonym: "(Drosophila)DfIn" RELATED [] +synonym: "deficient inversion" EXACT [] +is_a: SO:1000029 ! chromosomal_deletion +is_a: SO:1000030 ! chromosomal_inversion +relationship: has_part SO:0000159 ! deletion +relationship: has_part SO:1000036 ! inversion + +[Term] +id: SO:1000173 +name: tandem_duplication +def: "A duplication consisting of 2 identical adjacent regions." [SO:ke] +subset: DBVAR +synonym: "erverted" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] +synonym: "tandem duplication" EXACT [] +is_a: SO:1000035 ! duplication + +[Term] +id: SO:1000175 +name: partially_characterized_chromosomal_mutation +synonym: "partially characterized chromosomal mutation" EXACT [] +is_a: SO:1000170 ! uncharacterized_chromosomal_mutation + +[Term] +id: SO:1000180 +name: sequence_variant_affecting_gene_structure +def: "A sequence_variant_effect that changes the gene structure." [SO:ke] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation affecting gene structure" RELATED [] +synonym: "sequence variant affecting gene structure" EXACT [] +is_obsolete: true +replaced_by: SO:0001564 + +[Term] +id: SO:1000181 +name: sequence_variant_causing_gene_fusion +def: "A sequence_variant_effect that changes the gene structure by causing a fusion to another gene." [SO:ke] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causing gene fusion" RELATED [] +synonym: "sequence variant causing gene fusion" EXACT [] +is_obsolete: true +replaced_by: SO:0001565 + +[Term] +id: SO:1000182 +name: chromosome_number_variation +def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke] +synonym: "chromosome number variation" EXACT [] +synonym: "Jannovar:chromosome_number_variation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] +is_a: SO:0000240 ! chromosome_variation + +[Term] +id: SO:1000183 +name: chromosome_structure_variation +synonym: "chromosome structure variation" EXACT [] +synonym: "snpEff:CHROMOSOME_LARGE_DELETION" EXACT VAR [] +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +is_a: SO:0000240 ! chromosome_variation + +[Term] +id: SO:1000184 +name: sequence_variant_causes_exon_loss +def: "A sequence variant affecting splicing and causes an exon loss." [SO:ke] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causes exon loss" RELATED [] +synonym: "sequence variant causes exon loss" EXACT [] +is_obsolete: true + +[Term] +id: SO:1000185 +name: sequence_variant_causes_intron_gain +def: "A sequence variant effect, causing an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072)." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "mutation causes intron gain" RELATED [] +synonym: "sequence variant causes intron gain" EXACT [] +is_obsolete: true + +[Term] +id: SO:1000186 +name: sequence_variant_causing_cryptic_splice_donor_activation +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "sequence variant causing cryptic splice donor activation" EXACT [] +is_obsolete: true +replaced_by: SO:0001571 + +[Term] +id: SO:1001186 +name: sequence_variant_causing_cryptic_splice_acceptor_activation +comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. +synonym: "sequence variant causing cryptic splice acceptor activation" EXACT [] +is_obsolete: true +replaced_by: SO:0001570 + +[Term] +id: SO:1001187 +name: alternatively_spliced_transcript +def: "A transcript that is alternatively spliced." [SO:xp] +synonym: "alternatively spliced transcript" EXACT [] +is_a: SO:0000673 ! transcript +relationship: has_quality SO:0000877 ! alternatively_spliced + +[Term] +id: SO:1001188 +name: encodes_1_polypeptide +def: "A gene that is alternately spliced, but encodes only one polypeptide." [SO:ke] +synonym: "encodes 1 polypeptide" EXACT [] +is_a: SO:0000463 ! encodes_alternately_spliced_transcripts + +[Term] +id: SO:1001189 +name: encodes_greater_than_1_polypeptide +def: "A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke] +synonym: "encodes greater than 1 polypeptide" EXACT [] +is_a: SO:0000463 ! encodes_alternately_spliced_transcripts + +[Term] +id: SO:1001190 +name: encodes_different_polypeptides_different_stop +def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons." [SO:ke] +synonym: "encodes different polypeptides different stop" EXACT [] +is_a: SO:1001195 ! encodes_overlapping_peptides + +[Term] +id: SO:1001191 +name: encodes_overlapping_peptides_different_start +def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons." [SO:ke] +synonym: "encodes overlapping peptides different start" EXACT [] +is_a: SO:1001195 ! encodes_overlapping_peptides + +[Term] +id: SO:1001192 +name: encodes_disjoint_polypeptides +def: "A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences." [SO:ke] +synonym: "encodes disjoint polypeptides" EXACT [] +is_a: SO:1001189 ! encodes_greater_than_1_polypeptide + +[Term] +id: SO:1001193 +name: encodes_overlapping_polypeptides_different_start_and_stop +def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons." [SO:ke] +synonym: "encodes overlapping polypeptides different start and stop" EXACT [] +is_a: SO:1001195 ! encodes_overlapping_peptides + +[Term] +id: SO:1001194 +name: alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping +is_obsolete: true + +[Term] +id: SO:1001195 +name: encodes_overlapping_peptides +def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." [SO:ke] +synonym: "encodes overlapping peptides" EXACT [] +is_a: SO:1001189 ! encodes_greater_than_1_polypeptide + +[Term] +id: SO:1001196 +name: cryptogene +def: "A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma] +is_a: SO:0000654 ! maxicircle_gene +is_a: SO:0001431 ! cryptic_gene +relationship: has_quality SO:0000976 ! cryptic + +[Term] +id: SO:1001197 +name: dicistronic_primary_transcript +def: "A primary transcript that has the quality dicistronic." [SO:xp] +synonym: "dicistronic primary transcript" EXACT [] +is_a: SO:0000079 ! dicistronic_transcript +is_a: SO:0000631 ! polycistronic_primary_transcript +relationship: has_quality SO:0000879 ! dicistronic + +[Term] +id: SO:1001217 +name: member_of_regulon +synonym: "member of regulon" EXACT [] +is_a: SO:0000081 ! gene_array_member + +[Term] +id: SO:1001244 +name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping +synonym: "alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non-overlapping" RELATED [] +is_obsolete: true + +[Term] +id: SO:1001246 +name: CDS_independently_known +def: "A CDS with the evidence status of being independently known." [SO:xp] +synonym: "CDS independently known" EXACT [] +is_a: SO:0000316 ! CDS +relationship: has_quality SO:0000906 ! independently_known + +[Term] +id: SO:1001247 +name: orphan_CDS +def: "A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma] +synonym: "orphan CDS" EXACT [] +is_a: SO:1001254 ! CDS_predicted +relationship: has_origin SO:0000910 ! orphan + +[Term] +id: SO:1001249 +name: CDS_supported_by_domain_match_data +def: "A CDS that is supported by domain similarity." [SO:xp] +synonym: "CDS supported by domain match data" EXACT [] +is_a: SO:1001251 ! CDS_supported_by_sequence_similarity_data +relationship: has_quality SO:0000908 ! supported_by_domain_match + +[Term] +id: SO:1001251 +name: CDS_supported_by_sequence_similarity_data +def: "A CDS that is supported by sequence similarity data." [SO:xp] +synonym: "CDS supported by sequence similarity data" EXACT [] +is_a: SO:1001254 ! CDS_predicted +relationship: has_quality SO:0000907 ! supported_by_sequence_similarity + +[Term] +id: SO:1001254 +name: CDS_predicted +def: "A CDS that is predicted." [SO:ke] +synonym: "CDS predicted" EXACT [] +is_a: SO:0000316 ! CDS +relationship: has_quality SO:0000732 ! predicted + +[Term] +id: SO:1001255 +name: status_of_coding_sequence +is_obsolete: true + +[Term] +id: SO:1001259 +name: CDS_supported_by_EST_or_cDNA_data +def: "A CDS that is supported by similarity to EST or cDNA data." [SO:xp] +synonym: "CDS supported by EST or cDNA data" EXACT [] +is_a: SO:1001251 ! CDS_supported_by_sequence_similarity_data +relationship: has_quality SO:0000909 ! supported_by_EST_or_cDNA + +[Term] +id: SO:1001260 +name: internal_Shine_Dalgarno_sequence +def: "A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke] +synonym: "internal Shine Dalgarno sequence" EXACT [] +synonym: "internal Shine-Dalgarno sequence" EXACT [] +is_a: SO:0000243 ! internal_ribosome_entry_site +is_a: SO:1001268 ! recoding_stimulatory_region + +[Term] +id: SO:1001261 +name: recoded_mRNA +def: "The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract] +synonym: "recoded mRNA" EXACT [] +is_a: SO:0000234 ! mRNA +relationship: has_quality SO:0000881 ! recoded + +[Term] +id: SO:1001262 +name: minus_1_translationally_frameshifted +def: "An attribute describing a translational frameshift of -1." [SO:ke] +synonym: "minus 1 translationally frameshifted" EXACT [] +is_a: SO:0000887 ! translationally_frameshifted + +[Term] +id: SO:1001263 +name: plus_1_translationally_frameshifted +def: "An attribute describing a translational frameshift of +1." [SO:ke] +synonym: "plus 1 translationally frameshifted" EXACT [] +is_a: SO:0000887 ! translationally_frameshifted + +[Term] +id: SO:1001264 +name: mRNA_recoded_by_translational_bypass +def: "A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract] +synonym: "mRNA recoded by translational bypass" EXACT [] +is_a: SO:1001261 ! recoded_mRNA +relationship: has_quality SO:0000886 ! recoded_by_translational_bypass + +[Term] +id: SO:1001265 +name: mRNA_recoded_by_codon_redefinition +def: "A recoded_mRNA that was modified by an alteration of codon meaning." [SO:ma] +synonym: "mRNA recoded by codon redefinition" EXACT [] +is_a: SO:1001261 ! recoded_mRNA +relationship: has_quality SO:0000882 ! codon_redefined + +[Term] +id: SO:1001266 +name: stop_codon_redefinition_as_selenocysteine +is_obsolete: true + +[Term] +id: SO:1001267 +name: stop_codon_readthrough +is_obsolete: true + +[Term] +id: SO:1001268 +name: recoding_stimulatory_region +def: "A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract] +synonym: "recoding stimulatory region" EXACT [] +synonym: "recoding stimulatory signal" EXACT [] +is_a: SO:0000836 ! mRNA_region + +[Term] +id: SO:1001269 +name: four_bp_start_codon +def: "A non-canonical start codon with 4 base pairs." [SO:ke] +synonym: "4bp start codon" EXACT [] +synonym: "four bp start codon" EXACT [] +is_a: SO:0000680 ! non_canonical_start_codon + +[Term] +id: SO:1001270 +name: stop_codon_redefinition_as_pyrrolysine +is_obsolete: true + +[Term] +id: SO:1001271 +name: archaeal_intron +def: "An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma] +comment: Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism. +synonym: "archaeal intron" EXACT [] +is_a: SO:0001216 ! endonuclease_spliced_intron + +[Term] +id: SO:1001272 +name: tRNA_intron +def: "An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke] +comment: Could be a cross product with Gene ontology, GO:0006388. +synonym: "pre-tRNA intron" EXACT [] +synonym: "tRNA intron" EXACT [] +is_a: SO:0001216 ! endonuclease_spliced_intron + +[Term] +id: SO:1001273 +name: CTG_start_codon +def: "A non-canonical start codon of sequence CTG." [SO:ke] +synonym: "CTG start codon" EXACT [] +is_a: SO:0000680 ! non_canonical_start_codon + +[Term] +id: SO:1001274 +name: SECIS_element +def: "The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031] +synonym: "SECIS element" EXACT [] +xref: http://en.wikipedia.org/wiki/SECIS_element "wiki" +is_a: SO:1001268 ! recoding_stimulatory_region + +[Term] +id: SO:1001275 +name: retron +def: "Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes." [SO:ma] +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:1001277 +name: three_prime_recoding_site +def: "The recoding stimulatory signal located downstream of the recoding site." [SO:ke] +synonym: "three prime recoding site" EXACT [] +is_a: SO:1001268 ! recoding_stimulatory_region + +[Term] +id: SO:1001279 +name: three_prime_stem_loop_structure +def: "A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke] +synonym: "three prime stem loop structure" EXACT [] +is_a: SO:1001277 ! three_prime_recoding_site + +[Term] +id: SO:1001280 +name: five_prime_recoding_site +def: "The recoding stimulatory signal located upstream of the recoding site." [SO:ke] +synonym: "five prime recoding site" EXACT [] +is_a: SO:1001268 ! recoding_stimulatory_region + +[Term] +id: SO:1001281 +name: flanking_three_prime_quadruplet_recoding_signal +def: "Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke] +synonym: "flanking three prime quadruplet recoding signal" EXACT [] +is_a: SO:1001277 ! three_prime_recoding_site + +[Term] +id: SO:1001282 +name: UAG_stop_codon_signal +def: "A stop codon signal for a UAG stop codon redefinition." [SO:ke] +synonym: "UAG stop codon signal" EXACT [] +is_a: SO:1001288 ! stop_codon_signal + +[Term] +id: SO:1001283 +name: UAA_stop_codon_signal +def: "A stop codon signal for a UAA stop codon redefinition." [SO:ke] +synonym: "UAA stop codon signal" EXACT [] +is_a: SO:1001288 ! stop_codon_signal + +[Term] +id: SO:1001284 +name: regulon +def: "A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732] +subset: SOFA +xref: http://en.wikipedia.org/wiki/Regulon "wiki" +is_a: SO:0005855 ! gene_group + +[Term] +id: SO:1001285 +name: UGA_stop_codon_signal +def: "A stop codon signal for a UGA stop codon redefinition." [SO:ke] +synonym: "UGA stop codon signal" EXACT [] +is_a: SO:1001288 ! stop_codon_signal + +[Term] +id: SO:1001286 +name: three_prime_repeat_recoding_signal +def: "A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke] +synonym: "three prime repeat recoding signal" EXACT [] +is_a: SO:1001277 ! three_prime_recoding_site + +[Term] +id: SO:1001287 +name: distant_three_prime_recoding_signal +def: "A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov\:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract] +synonym: "distant three prime recoding signal" EXACT [] +is_a: SO:1001277 ! three_prime_recoding_site + +[Term] +id: SO:1001288 +name: stop_codon_signal +def: "A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke] +comment: This term does not include the stop codons that are redefined. An example would be a stop codon that partially overlapped a frame shifting site would be an example stimulatory signal. +synonym: "stop codon signal" EXACT [] +is_a: SO:1001268 ! recoding_stimulatory_region + +[Term] +id: SO:2000061 +name: databank_entry +def: "The sequence referred to by an entry in a databank such as GenBank or SwissProt." [SO:ke] +subset: SOFA +synonym: "accession" RELATED [] +synonym: "databank entry" EXACT [] +is_a: SO:0000695 ! reagent + +[Term] +id: SO:3000000 +name: gene_segment +def: "A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination." [GOC:add] +comment: Requested by tracker 2021594, July 2008, by Alex. +synonym: "gene segment" EXACT [] +is_a: SO:0000842 ! gene_component_region + +[Typedef] +id: adjacent_to +name: adjacent_to +def: "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap." [PMID:20226267, SO:ke] +subset: SOFA + +[Typedef] +id: associated_with +name: associated_with +comment: This relationship is vague and up for discussion. + +[Typedef] +id: complete_evidence_for_feature +name: complete_evidence_for_feature +def: "B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A." [SO:ke] +comment: If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222. +is_transitive: true +is_a: evidence_for_feature ! evidence_for_feature + +[Typedef] +id: connects_on +name: connects_on +def: "X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z." [PMID:20226267] +comment: Example: A splice_junction connects_on exon, exon, mature_transcript. +created_by: kareneilbeck +creation_date: 2010-10-14T01:38:51Z + +[Typedef] +id: contained_by +name: contained_by +def: "X contained_by Y iff X starts after start of Y and X ends before end of Y." [PMID:20226267] +comment: The inverse is contains. Example: intein contained_by immature_peptide_region. +is_transitive: true +created_by: kareneilbeck +creation_date: 2010-10-14T01:26:16Z + +[Typedef] +id: contains +name: contains +def: "The inverse of contained_by." [PMID:20226267] +comment: Example: pre_miRNA contains miRNA_loop. +is_transitive: true +created_by: kareneilbeck +creation_date: 2010-10-14T01:32:15Z + +[Typedef] +id: derives_from +name: derives_from +subset: SOFA +is_transitive: true + +[Typedef] +id: disconnected_from +name: disconnected_from +def: "X is disconnected_from Y iff it is not the case that X overlaps Y." [PMID:20226267] +created_by: kareneilbeck +creation_date: 2010-10-14T01:42:10Z + +[Typedef] +id: edited_from +name: edited_from +created_by: kareneilbeck +creation_date: 2009-08-19T02:19:45Z + +[Typedef] +id: edited_to +name: edited_to +created_by: kareneilbeck +creation_date: 2009-08-19T02:19:11Z + +[Typedef] +id: evidence_for_feature +name: evidence_for_feature +def: "B is evidence_for_feature A, if an instance of B supports the existence of A." [SO:ke] +comment: This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222. +is_transitive: true + +[Typedef] +id: exemplar_of +name: exemplar_of +def: "X is exemplar of Y if X is the best evidence for Y." [SO:ke] +comment: Tracker id: 2594157. + +[Typedef] +id: finished_by +name: finished_by +def: "Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary." [PMID:20226267] +comment: Example CDS finished_by stop_codon. +created_by: kareneilbeck +creation_date: 2010-10-14T01:45:45Z + +[Typedef] +id: finishes +name: finishes +def: "X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary." [PMID:20226267] +comment: Example: stop_codon finishes CDS. +created_by: kareneilbeck +creation_date: 2010-10-14T02:17:53Z + +[Typedef] +id: gained +name: gained +def: "X gained Y if X is a variant_of X' and Y part of X but not X'." [SO:ke] +comment: A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may gain a stop codon not present in the reference sequence. +created_by: kareneilbeck +creation_date: 2011-06-28T12:51:10Z + +[Typedef] +id: genome_of +name: genome_of + +[Typedef] +id: guided_by +name: guided_by +created_by: kareneilbeck +creation_date: 2009-08-19T02:27:04Z + +[Typedef] +id: guides +name: guides +created_by: kareneilbeck +creation_date: 2009-08-19T02:27:24Z + +[Typedef] +id: has_integral_part +name: has_integral_part +def: "X has_integral_part Y if and only if: X has_part Y and Y part_of X." [http://precedings.nature.com/documents/3495/version/1] +comment: Example: mRNA has_integral_part CDS. +is_a: has_part ! has_part +created_by: kareneilbeck +creation_date: 2009-08-19T12:01:46Z + +[Typedef] +id: has_origin +name: has_origin + +[Typedef] +id: has_part +name: has_part +def: "Inverse of part_of." [http://precedings.nature.com/documents/3495/version/1] +comment: Example: operon has_part gene. + +[Typedef] +id: has_quality +name: has_quality +comment: The relationship between a feature and an attribute. + +[Typedef] +id: homologous_to +name: homologous_to +subset: SOFA +is_symmetric: true +is_a: similar_to ! similar_to + +[Typedef] +id: integral_part_of +name: integral_part_of +def: "X integral_part_of Y if and only if: X part_of Y and Y has_part X." [http://precedings.nature.com/documents/3495/version/1] +comment: Example: exon integral_part_of transcript. +is_a: part_of ! part_of +created_by: kareneilbeck +creation_date: 2009-08-19T12:03:28Z + +[Typedef] +id: is_consecutive_sequence_of +name: is_consecutive_sequence_of +def: "R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical)." [PMID:20226267] +comment: Example: region is consecutive_sequence of base. +created_by: kareneilbeck +creation_date: 2010-10-14T02:19:48Z + +[Typedef] +id: lost +name: lost +def: "X lost Y if X is a variant_of X' and Y part of X' but not X." [SO:ke] +comment: A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may have lost a stop codon present in the reference sequence. +created_by: kareneilbeck +creation_date: 2011-06-28T12:53:16Z + +[Typedef] +id: maximally_overlaps +name: maximally_overlaps +def: "A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y." [PMID:20226267] +comment: Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR. +created_by: kareneilbeck +creation_date: 2010-10-14T01:34:48Z + +[Typedef] +id: member_of +name: member_of +comment: A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444. +subset: SOFA +is_transitive: true +is_a: part_of ! part_of + +[Typedef] +id: non_functional_homolog_of +name: non_functional_homolog_of +def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke] +subset: SOFA +is_a: homologous_to ! homologous_to + +[Typedef] +id: orthologous_to +name: orthologous_to +subset: SOFA +is_symmetric: true +is_a: homologous_to ! homologous_to + +[Typedef] +id: overlaps +name: overlaps +def: "X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y." [PMID:20226267] +comment: Example: coding_exon overlaps CDS. +created_by: kareneilbeck +creation_date: 2010-10-14T01:33:15Z + +[Typedef] +id: paralogous_to +name: paralogous_to +subset: SOFA +is_symmetric: true +is_a: homologous_to ! homologous_to + +[Typedef] +id: part_of +name: part_of +def: "X part_of Y if X is a subregion of Y." [http://precedings.nature.com/documents/3495/version/1] +comment: Example: amino_acid part_of polypeptide. +subset: SOFA +is_transitive: true + +[Typedef] +id: partial_evidence_for_feature +name: partial_evidence_for_feature +def: "B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A." [SO:ke] +is_a: evidence_for_feature ! evidence_for_feature + +[Typedef] +id: position_of +name: position_of + +[Typedef] +id: processed_from +name: processed_from +def: "Inverse of processed_into." [http://precedings.nature.com/documents/3495/version/1] +comment: Example: miRNA processed_from miRNA_primary_transcript. +created_by: kareneilbeck +creation_date: 2009-08-19T12:14:00Z + +[Typedef] +id: processed_into +name: processed_into +def: "X is processed_into Y if a region X is modified to create Y." [http://precedings.nature.com/documents/3495/version/1] +comment: Example: miRNA_primary_transcript processed into miRNA. +created_by: kareneilbeck +creation_date: 2009-08-19T12:15:02Z + +[Typedef] +id: recombined_from +name: recombined_from +created_by: kareneilbeck +creation_date: 2009-08-19T02:21:03Z + +[Typedef] +id: recombined_to +name: recombined_to +created_by: kareneilbeck +creation_date: 2009-08-19T02:20:07Z + +[Typedef] +id: sequence_of +name: sequence_of + +[Typedef] +id: similar_to +name: similar_to +subset: SOFA +is_symmetric: true + +[Typedef] +id: started_by +name: started_by +def: "X is strted_by Y if Y is part_of X and X and Y share a 5' boundary." [PMID:20226267] +comment: Example: CDS started_by start_codon. +created_by: kareneilbeck +creation_date: 2010-10-14T01:43:55Z + +[Typedef] +id: starts +name: starts +def: "X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary." [PMID:20226267] +comment: Example: start_codon starts CDS. +created_by: kareneilbeck +creation_date: 2010-10-14T01:47:53Z + +[Typedef] +id: trans_spliced_from +name: trans_spliced_from +created_by: kareneilbeck +creation_date: 2009-08-19T02:22:14Z + +[Typedef] +id: trans_spliced_to +name: trans_spliced_to +created_by: kareneilbeck +creation_date: 2009-08-19T02:22:00Z + +[Typedef] +id: transcribed_from +name: transcribed_from +def: "X is transcribed_from Y if X is synthesized from template Y." [http://precedings.nature.com/documents/3495/version/1] +comment: Example: primary_transcript transcribed_from gene. +created_by: kareneilbeck +creation_date: 2009-08-19T12:05:39Z + +[Typedef] +id: transcribed_to +name: transcribed_to +def: "Inverse of transcribed_from." [http://precedings.nature.com/documents/3495/version/1] +comment: Example: gene transcribed_to primary_transcript. +created_by: kareneilbeck +creation_date: 2009-08-19T12:08:24Z + +[Typedef] +id: translates_to +name: translates_to +def: "Inverse of translation _of." [http://precedings.nature.com/documents/3495/version/1] +comment: Example: codon translates_to amino_acid. +created_by: kareneilbeck +creation_date: 2009-08-19T12:11:53Z + +[Typedef] +id: translation_of +name: translation_of +def: "X is translation of Y if Y is translated by ribosome to create X." [http://precedings.nature.com/documents/3495/version/1] +comment: Example: Polypeptide translation_of CDS. +created_by: kareneilbeck +creation_date: 2009-08-19T12:09:59Z + +[Typedef] +id: variant_of +name: variant_of +def: "A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A." [SO:immuno_workshop] +comment: Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith. + diff --git a/tests/data/ontologymaps/sequence_ontology/sequence_ontology.txt b/tests/data/ontologymaps/sequence_ontology/sequence_ontology.txt deleted file mode 100644 index f40f2b9f2..000000000 --- a/tests/data/ontologymaps/sequence_ontology/sequence_ontology.txt +++ /dev/null @@ -1,2284 +0,0 @@ -SO:0000000 Sequence_Ontology -SO:0000001 region -SO:0000002 sequence_secondary_structure -SO:0000003 G_quartet -SO:0000004 interior_coding_exon -SO:0000005 satellite_DNA -SO:0000006 PCR_product -SO:0000007 read_pair -SO:0000008 gene_sensu_your_favorite_organism -SO:0000009 gene_class -SO:0000010 protein_coding -SO:0000011 non_protein_coding -SO:0000012 scRNA_primary_transcript -SO:0000013 scRNA -SO:0000014 INR_motif -SO:0000015 DPE_motif -SO:0000016 BREu_motif -SO:0000017 PSE_motif -SO:0000018 linkage_group -SO:0000020 RNA_internal_loop -SO:0000021 asymmetric_RNA_internal_loop -SO:0000022 A_minor_RNA_motif -SO:0000023 K_turn_RNA_motif -SO:0000024 sarcin_like_RNA_motif -SO:0000025 symmetric_RNA_internal_loop -SO:0000026 RNA_junction_loop -SO:0000027 RNA_hook_turn -SO:0000028 base_pair -SO:0000029 WC_base_pair -SO:0000030 sugar_edge_base_pair -SO:0000031 aptamer -SO:0000032 DNA_aptamer -SO:0000033 RNA_aptamer -SO:0000034 morpholino_oligo -SO:0000035 riboswitch -SO:0000036 matrix_attachment_site -SO:0000037 locus_control_region -SO:0000038 match_set -SO:0000039 match_part -SO:0000040 genomic_clone -SO:0000041 sequence_operation -SO:0000042 pseudogene_attribute -SO:0000043 processed_pseudogene -SO:0000044 pseudogene_by_unequal_crossing_over -SO:0000045 delete -SO:0000046 insert -SO:0000047 invert -SO:0000048 substitute -SO:0000049 translocate -SO:0000050 gene_part -SO:0000051 probe -SO:0000052 assortment_derived_deficiency -SO:0000053 sequence_variant_affecting_regulatory_region -SO:0000054 aneuploid -SO:0000055 hyperploid -SO:0000056 hypoploid -SO:0000057 operator -SO:0000058 assortment_derived_aneuploid -SO:0000059 nuclease_binding_site -SO:0000060 compound_chromosome_arm -SO:0000061 restriction_enzyme_binding_site -SO:0000062 deficient_intrachromosomal_transposition -SO:0000063 deficient_interchromosomal_transposition -SO:0000064 gene_by_transcript_attribute -SO:0000065 free_chromosome_arm -SO:0000066 gene_by_polyadenylation_attribute -SO:0000067 gene_to_gene_feature -SO:0000068 overlapping -SO:0000069 inside_intron -SO:0000070 inside_intron_antiparallel -SO:0000071 inside_intron_parallel -SO:0000072 end_overlapping_gene -SO:0000073 five_prime_three_prime_overlap -SO:0000074 five_prime_five_prime_overlap -SO:0000075 three_prime_three_prime_overlap -SO:0000076 three_prime_five_prime_overlap -SO:0000077 antisense -SO:0000078 polycistronic_transcript -SO:0000079 dicistronic_transcript -SO:0000080 operon_member -SO:0000081 gene_array_member -SO:0000082 processed_transcript_attribute -SO:0000083 macronuclear_sequence -SO:0000084 micronuclear_sequence -SO:0000085 gene_by_genome_location -SO:0000086 gene_by_organelle_of_genome -SO:0000087 nuclear_gene -SO:0000088 mt_gene -SO:0000089 kinetoplast_gene -SO:0000090 plastid_gene -SO:0000091 apicoplast_gene -SO:0000092 ct_gene -SO:0000093 chromoplast_gene -SO:0000094 cyanelle_gene -SO:0000095 leucoplast_gene -SO:0000096 proplastid_gene -SO:0000097 nucleomorph_gene -SO:0000098 plasmid_gene -SO:0000099 proviral_gene -SO:0000100 endogenous_retroviral_gene -SO:0000101 transposable_element -SO:0000102 expressed_sequence_match -SO:0000103 clone_insert_end -SO:0000104 polypeptide -SO:0000105 chromosome_arm -SO:0000106 non_capped_primary_transcript -SO:0000107 sequencing_primer -SO:0000108 mRNA_with_frameshift -SO:0000109 sequence_variant_obs -SO:0000110 sequence_feature -SO:0000111 transposable_element_gene -SO:0000112 primer -SO:0000113 proviral_region -SO:0000114 methylated_cytosine -SO:0000115 transcript_feature -SO:0000116 edited -SO:0000117 transcript_with_readthrough_stop_codon -SO:0000118 transcript_with_translational_frameshift -SO:0000119 regulated -SO:0000120 protein_coding_primary_transcript -SO:0000121 forward_primer -SO:0000122 RNA_sequence_secondary_structure -SO:0000123 transcriptionally_regulated -SO:0000124 transcriptionally_constitutive -SO:0000125 transcriptionally_induced -SO:0000126 transcriptionally_repressed -SO:0000127 silenced_gene -SO:0000128 gene_silenced_by_DNA_modification -SO:0000129 gene_silenced_by_DNA_methylation -SO:0000130 post_translationally_regulated -SO:0000131 translationally_regulated -SO:0000132 reverse_primer -SO:0000133 epigenetically_modified -SO:0000134 genomically_imprinted -SO:0000135 maternally_imprinted -SO:0000136 paternally_imprinted -SO:0000137 allelically_excluded -SO:0000138 gene_rearranged_at_DNA_level -SO:0000139 ribosome_entry_site -SO:0000140 attenuator -SO:0000141 terminator -SO:0000142 DNA_sequence_secondary_structure -SO:0000143 assembly_component -SO:0000144 primary_transcript_attribute -SO:0000145 recoded_codon -SO:0000146 capped -SO:0000147 exon -SO:0000148 supercontig -SO:0000149 contig -SO:0000150 read -SO:0000151 clone -SO:0000152 YAC -SO:0000153 BAC -SO:0000154 PAC -SO:0000155 plasmid -SO:0000156 cosmid -SO:0000157 phagemid -SO:0000158 fosmid -SO:0000159 deletion -SO:0000160 lambda_clone -SO:0000161 methylated_adenine -SO:0000162 splice_site -SO:0000163 five_prime_cis_splice_site -SO:0000164 three_prime_cis_splice_site -SO:0000165 enhancer -SO:0000166 enhancer_bound_by_factor -SO:0000167 promoter -SO:0000168 restriction_enzyme_cut_site -SO:0000169 RNApol_I_promoter -SO:0000170 RNApol_II_promoter -SO:0000171 RNApol_III_promoter -SO:0000172 CAAT_signal -SO:0000173 GC_rich_promoter_region -SO:0000174 TATA_box -SO:0000175 minus_10_signal -SO:0000176 minus_35_signal -SO:0000177 cross_genome_match -SO:0000178 operon -SO:0000179 clone_insert_start -SO:0000180 retrotransposon -SO:0000181 translated_nucleotide_match -SO:0000182 DNA_transposon -SO:0000183 non_transcribed_region -SO:0000184 U2_intron -SO:0000185 primary_transcript -SO:0000186 LTR_retrotransposon -SO:0000187 repeat_family -SO:0000188 intron -SO:0000189 non_LTR_retrotransposon -SO:0000190 five_prime_intron -SO:0000191 interior_intron -SO:0000192 three_prime_intron -SO:0000193 RFLP_fragment -SO:0000194 LINE_element -SO:0000195 coding_exon -SO:0000196 five_prime_coding_exon_coding_region -SO:0000197 three_prime_coding_exon_coding_region -SO:0000198 noncoding_exon -SO:0000199 translocation -SO:0000200 five_prime_coding_exon -SO:0000201 interior_exon -SO:0000202 three_prime_coding_exon -SO:0000203 UTR -SO:0000204 five_prime_UTR -SO:0000205 three_prime_UTR -SO:0000206 SINE_element -SO:0000207 simple_sequence_length_variation -SO:0000208 terminal_inverted_repeat_element -SO:0000209 rRNA_primary_transcript -SO:0000210 tRNA_primary_transcript -SO:0000211 alanine_tRNA_primary_transcript -SO:0000212 arginine_tRNA_primary_transcript -SO:0000213 asparagine_tRNA_primary_transcript -SO:0000214 aspartic_acid_tRNA_primary_transcript -SO:0000215 cysteine_tRNA_primary_transcript -SO:0000216 glutamic_acid_tRNA_primary_transcript -SO:0000217 glutamine_tRNA_primary_transcript -SO:0000218 glycine_tRNA_primary_transcript -SO:0000219 histidine_tRNA_primary_transcript -SO:0000220 isoleucine_tRNA_primary_transcript -SO:0000221 leucine_tRNA_primary_transcript -SO:0000222 lysine_tRNA_primary_transcript -SO:0000223 methionine_tRNA_primary_transcript -SO:0000224 phenylalanine_tRNA_primary_transcript -SO:0000225 proline_tRNA_primary_transcript -SO:0000226 serine_tRNA_primary_transcript -SO:0000227 threonine_tRNA_primary_transcript -SO:0000228 tryptophan_tRNA_primary_transcript -SO:0000229 tyrosine_tRNA_primary_transcript -SO:0000230 valine_tRNA_primary_transcript -SO:0000231 snRNA_primary_transcript -SO:0000232 snoRNA_primary_transcript -SO:0000233 mature_transcript -SO:0000234 mRNA -SO:0000235 TF_binding_site -SO:0000236 ORF -SO:0000237 transcript_attribute -SO:0000238 foldback_element -SO:0000239 flanking_region -SO:0000240 chromosome_variation -SO:0000241 internal_UTR -SO:0000242 untranslated_region_polycistronic_mRNA -SO:0000243 internal_ribosome_entry_site -SO:0000244 four_cutter_restriction_site -SO:0000245 mRNA_by_polyadenylation_status -SO:0000246 polyadenylated -SO:0000247 mRNA_not_polyadenylated -SO:0000248 sequence_length_variation -SO:0000249 six_cutter_restriction_site -SO:0000250 modified_RNA_base_feature -SO:0000251 eight_cutter_restriction_site -SO:0000252 rRNA -SO:0000253 tRNA -SO:0000254 alanyl_tRNA -SO:0000255 rRNA_small_subunit_primary_transcript -SO:0000256 asparaginyl_tRNA -SO:0000257 aspartyl_tRNA -SO:0000258 cysteinyl_tRNA -SO:0000259 glutaminyl_tRNA -SO:0000260 glutamyl_tRNA -SO:0000261 glycyl_tRNA -SO:0000262 histidyl_tRNA -SO:0000263 isoleucyl_tRNA -SO:0000264 leucyl_tRNA -SO:0000265 lysyl_tRNA -SO:0000266 methionyl_tRNA -SO:0000267 phenylalanyl_tRNA -SO:0000268 prolyl_tRNA -SO:0000269 seryl_tRNA -SO:0000270 threonyl_tRNA -SO:0000271 tryptophanyl_tRNA -SO:0000272 tyrosyl_tRNA -SO:0000273 valyl_tRNA -SO:0000274 snRNA -SO:0000275 snoRNA -SO:0000276 miRNA -SO:0000277 bound_by_factor -SO:0000278 transcript_bound_by_nucleic_acid -SO:0000279 transcript_bound_by_protein -SO:0000280 engineered_gene -SO:0000281 engineered_foreign_gene -SO:0000282 mRNA_with_minus_1_frameshift -SO:0000283 engineered_foreign_transposable_element_gene -SO:0000284 type_I_enzyme_restriction_site -SO:0000285 foreign_gene -SO:0000286 long_terminal_repeat -SO:0000287 fusion_gene -SO:0000288 engineered_fusion_gene -SO:0000289 microsatellite -SO:0000290 dinucleotide_repeat_microsatellite_feature -SO:0000291 trinucleotide_repeat_microsatellite_feature -SO:0000292 repetitive_element -SO:0000293 engineered_foreign_repetitive_element -SO:0000294 inverted_repeat -SO:0000295 U12_intron -SO:0000296 origin_of_replication -SO:0000297 D_loop -SO:0000298 recombination_feature -SO:0000299 specific_recombination_site -SO:0000300 recombination_feature_of_rearranged_gene -SO:0000301 vertebrate_immune_system_gene_recombination_feature -SO:0000302 J_gene_recombination_feature -SO:0000303 clip -SO:0000304 type_II_enzyme_restriction_site -SO:0000305 modified_DNA_base -SO:0000306 methylated_DNA_base_feature -SO:0000307 CpG_island -SO:0000308 sequence_feature_locating_method -SO:0000309 computed_feature -SO:0000310 predicted_ab_initio_computation -SO:0000311 computed_feature_by_similarity -SO:0000312 experimentally_determined -SO:0000313 stem_loop -SO:0000314 direct_repeat -SO:0000315 TSS -SO:0000316 CDS -SO:0000317 cDNA_clone -SO:0000318 start_codon -SO:0000319 stop_codon -SO:0000320 intronic_splice_enhancer -SO:0000321 mRNA_with_plus_1_frameshift -SO:0000322 nuclease_hypersensitive_site -SO:0000323 coding_start -SO:0000324 tag -SO:0000325 rRNA_large_subunit_primary_transcript -SO:0000326 SAGE_tag -SO:0000327 coding_end -SO:0000328 microarray_oligo -SO:0000329 mRNA_with_plus_2_frameshift -SO:0000330 conserved_region -SO:0000331 STS -SO:0000332 coding_conserved_region -SO:0000333 exon_junction -SO:0000334 nc_conserved_region -SO:0000335 mRNA_with_minus_2_frameshift -SO:0000336 pseudogene -SO:0000337 RNAi_reagent -SO:0000338 MITE -SO:0000339 recombination_hotspot -SO:0000340 chromosome -SO:0000341 chromosome_band -SO:0000342 site_specific_recombination_target_region -SO:0000343 match -SO:0000344 splice_enhancer -SO:0000345 EST -SO:0000346 loxP_site -SO:0000347 nucleotide_match -SO:0000348 nucleic_acid -SO:0000349 protein_match -SO:0000350 FRT_site -SO:0000351 synthetic_sequence -SO:0000352 DNA -SO:0000353 sequence_assembly -SO:0000354 group_1_intron_homing_endonuclease_target_region -SO:0000355 haplotype_block -SO:0000356 RNA -SO:0000357 flanked -SO:0000359 floxed -SO:0000360 codon -SO:0000361 FRT_flanked -SO:0000362 invalidated_by_chimeric_cDNA -SO:0000363 floxed_gene -SO:0000364 transposable_element_flanking_region -SO:0000365 integron -SO:0000366 insertion_site -SO:0000367 attI_site -SO:0000368 transposable_element_insertion_site -SO:0000369 integrase_coding_region -SO:0000370 small_regulatory_ncRNA -SO:0000371 conjugative_transposon -SO:0000372 enzymatic_RNA -SO:0000373 recombinationally_inverted_gene -SO:0000374 ribozyme -SO:0000375 rRNA_5_8S -SO:0000376 RNA_6S -SO:0000377 CsrB_RsmB_RNA -SO:0000378 DsrA_RNA -SO:0000379 GcvB_RNA -SO:0000380 hammerhead_ribozyme -SO:0000381 group_IIA_intron -SO:0000382 group_IIB_intron -SO:0000383 MicF_RNA -SO:0000384 OxyS_RNA -SO:0000385 RNase_MRP_RNA -SO:0000386 RNase_P_RNA -SO:0000387 RprA_RNA -SO:0000388 RRE_RNA -SO:0000389 spot_42_RNA -SO:0000390 telomerase_RNA -SO:0000391 U1_snRNA -SO:0000392 U2_snRNA -SO:0000393 U4_snRNA -SO:0000394 U4atac_snRNA -SO:0000395 U5_snRNA -SO:0000396 U6_snRNA -SO:0000397 U6atac_snRNA -SO:0000398 U11_snRNA -SO:0000399 U12_snRNA -SO:0000400 sequence_attribute -SO:0000401 gene_attribute -SO:0000402 enhancer_attribute -SO:0000403 U14_snoRNA -SO:0000404 vault_RNA -SO:0000405 Y_RNA -SO:0000406 twintron -SO:0000407 rRNA_18S -SO:0000408 site -SO:0000409 binding_site -SO:0000410 protein_binding_site -SO:0000411 rescue_region -SO:0000412 restriction_fragment -SO:0000413 sequence_difference -SO:0000414 invalidated_by_genomic_contamination -SO:0000415 invalidated_by_genomic_polyA_primed_cDNA -SO:0000416 invalidated_by_partial_processing -SO:0000417 polypeptide_domain -SO:0000418 signal_peptide -SO:0000419 mature_protein_region -SO:0000420 five_prime_terminal_inverted_repeat -SO:0000421 three_prime_terminal_inverted_repeat -SO:0000422 U5_LTR_region -SO:0000423 R_LTR_region -SO:0000424 U3_LTR_region -SO:0000425 five_prime_LTR -SO:0000426 three_prime_LTR -SO:0000427 R_five_prime_LTR_region -SO:0000428 U5_five_prime_LTR_region -SO:0000429 U3_five_prime_LTR_region -SO:0000430 R_three_prime_LTR_region -SO:0000431 U3_three_prime_LTR_region -SO:0000432 U5_three_prime_LTR_region -SO:0000433 non_LTR_retrotransposon_polymeric_tract -SO:0000434 target_site_duplication -SO:0000435 RR_tract -SO:0000436 ARS -SO:0000437 assortment_derived_duplication -SO:0000438 gene_not_polyadenylated -SO:0000439 inverted_ring_chromosome -SO:0000440 vector_replicon -SO:0000441 ss_oligo -SO:0000442 ds_oligo -SO:0000443 polymer_attribute -SO:0000444 three_prime_noncoding_exon -SO:0000445 five_prime_noncoding_exon -SO:0000446 UTR_intron -SO:0000447 five_prime_UTR_intron -SO:0000448 three_prime_UTR_intron -SO:0000449 random_sequence -SO:0000450 interband -SO:0000451 gene_with_polyadenylated_mRNA -SO:0000452 transgene_attribute -SO:0000453 chromosomal_transposition -SO:0000454 rasiRNA -SO:0000455 gene_with_mRNA_with_frameshift -SO:0000456 recombinationally_rearranged_gene -SO:0000457 interchromosomal_duplication -SO:0000458 D_gene_segment -SO:0000459 gene_with_trans_spliced_transcript -SO:0000460 vertebrate_immunoglobulin_T_cell_receptor_segment -SO:0000461 inversion_derived_bipartite_deficiency -SO:0000462 pseudogenic_region -SO:0000463 encodes_alternately_spliced_transcripts -SO:0000464 decayed_exon -SO:0000465 inversion_derived_deficiency_plus_duplication -SO:0000466 V_gene_segment -SO:0000467 post_translationally_regulated_by_protein_stability -SO:0000468 golden_path_fragment -SO:0000469 post_translationally_regulated_by_protein_modification -SO:0000470 J_gene_segment -SO:0000471 autoregulated -SO:0000472 tiling_path -SO:0000473 negatively_autoregulated -SO:0000474 tiling_path_fragment -SO:0000475 positively_autoregulated -SO:0000476 contig_read -SO:0000477 polycistronic_gene -SO:0000478 C_gene_segment -SO:0000479 trans_spliced_transcript -SO:0000480 tiling_path_clone -SO:0000481 terminal_inverted_repeat -SO:0000482 vertebrate_immunoglobulin_T_cell_receptor_gene_cluster -SO:0000483 nc_primary_transcript -SO:0000484 three_prime_coding_exon_noncoding_region -SO:0000485 DJ_J_cluster -SO:0000486 five_prime_coding_exon_noncoding_region -SO:0000487 VDJ_J_C_cluster -SO:0000488 VDJ_J_cluster -SO:0000489 VJ_C_cluster -SO:0000490 VJ_J_C_cluster -SO:0000491 VJ_J_cluster -SO:0000492 D_gene_recombination_feature -SO:0000493 three_prime_D_heptamer -SO:0000494 three_prime_D_nonamer -SO:0000495 three_prime_D_spacer -SO:0000496 five_prime_D_heptamer -SO:0000497 five_prime_D_nonamer -SO:0000498 five_prime_D_spacer -SO:0000499 virtual_sequence -SO:0000500 Hoogsteen_base_pair -SO:0000501 reverse_Hoogsteen_base_pair -SO:0000502 transcribed_region -SO:0000503 alternately_spliced_gene_encodeing_one_transcript -SO:0000504 D_DJ_C_cluster -SO:0000505 D_DJ_cluster -SO:0000506 D_DJ_J_C_cluster -SO:0000507 pseudogenic_exon -SO:0000508 D_DJ_J_cluster -SO:0000509 D_J_C_cluster -SO:0000510 VD_gene_segment -SO:0000511 J_C_cluster -SO:0000512 inversion_derived_deficiency_plus_aneuploid -SO:0000513 J_cluster -SO:0000514 J_nonamer -SO:0000515 J_heptamer -SO:0000516 pseudogenic_transcript -SO:0000517 J_spacer -SO:0000518 V_DJ_cluster -SO:0000519 V_DJ_J_cluster -SO:0000520 V_VDJ_C_cluster -SO:0000521 V_VDJ_cluster -SO:0000522 V_VDJ_J_cluster -SO:0000523 V_VJ_C_cluster -SO:0000524 V_VJ_cluster -SO:0000525 V_VJ_J_cluster -SO:0000526 V_cluster -SO:0000527 V_D_DJ_C_cluster -SO:0000528 V_D_DJ_cluster -SO:0000529 V_D_DJ_J_C_cluster -SO:0000530 V_D_DJ_J_cluster -SO:0000531 V_D_J_C_cluster -SO:0000532 V_D_J_cluster -SO:0000533 V_heptamer -SO:0000534 V_J_cluster -SO:0000535 V_J_C_cluster -SO:0000536 V_nonamer -SO:0000537 V_spacer -SO:0000538 V_gene_recombination_feature -SO:0000539 DJ_C_cluster -SO:0000540 DJ_J_C_cluster -SO:0000541 VDJ_C_cluster -SO:0000542 V_DJ_C_cluster -SO:0000543 alternately_spliced_gene_encoding_greater_than_one_transcript -SO:0000544 helitron -SO:0000545 recoding_pseudoknot -SO:0000546 designed_sequence -SO:0000547 inversion_derived_bipartite_duplication -SO:0000548 gene_with_edited_transcript -SO:0000549 inversion_derived_duplication_plus_aneuploid -SO:0000550 aneuploid_chromosome -SO:0000551 polyA_signal_sequence -SO:0000552 Shine_Dalgarno_sequence -SO:0000553 polyA_site -SO:0000554 assortment_derived_deficiency_plus_duplication -SO:0000555 five_prime_clip -SO:0000556 five_prime_D_recombination_signal_sequence -SO:0000557 three_prime_clip -SO:0000558 C_cluster -SO:0000559 D_cluster -SO:0000560 D_J_cluster -SO:0000561 heptamer_of_recombination_feature_of_vertebrate_immune_system_gene -SO:0000562 nonamer_of_recombination_feature_of_vertebrate_immune_system_gene -SO:0000563 vertebrate_immune_system_gene_recombination_spacer -SO:0000564 V_DJ_J_C_cluster -SO:0000565 V_VDJ_J_C_cluster -SO:0000566 V_VJ_J_C_cluster -SO:0000567 inversion_derived_aneuploid_chromosome -SO:0000568 bidirectional_promoter -SO:0000569 retrotransposed -SO:0000570 three_prime_D_recombination_signal_sequence -SO:0000571 miRNA_encoding -SO:0000572 DJ_gene_segment -SO:0000573 rRNA_encoding -SO:0000574 VDJ_gene_segment -SO:0000575 scRNA_encoding -SO:0000576 VJ_gene_segment -SO:0000577 centromere -SO:0000578 snoRNA_encoding -SO:0000579 edited_transcript_feature -SO:0000580 methylation_guide_snoRNA_primary_transcript -SO:0000581 cap -SO:0000582 rRNA_cleavage_snoRNA_primary_transcript -SO:0000583 pre_edited_region -SO:0000584 tmRNA -SO:0000585 C_D_box_snoRNA_encoding -SO:0000586 tmRNA_primary_transcript -SO:0000587 group_I_intron -SO:0000588 autocatalytically_spliced_intron -SO:0000589 SRP_RNA_primary_transcript -SO:0000590 SRP_RNA -SO:0000591 pseudoknot -SO:0000592 H_pseudoknot -SO:0000593 C_D_box_snoRNA -SO:0000594 H_ACA_box_snoRNA -SO:0000595 C_D_box_snoRNA_primary_transcript -SO:0000596 H_ACA_box_snoRNA_primary_transcript -SO:0000597 transcript_edited_by_U_insertion/deletion -SO:0000598 edited_by_C_insertion_and_dinucleotide_insertion -SO:0000599 edited_by_C_to_U_substitution -SO:0000600 edited_by_A_to_I_substitution -SO:0000601 edited_by_G_addition -SO:0000602 guide_RNA -SO:0000603 group_II_intron -SO:0000604 editing_block -SO:0000605 intergenic_region -SO:0000606 editing_domain -SO:0000607 unedited_region -SO:0000608 H_ACA_box_snoRNA_encoding -SO:0000609 oligo_U_tail -SO:0000610 polyA_sequence -SO:0000611 branch_site -SO:0000612 polypyrimidine_tract -SO:0000613 bacterial_RNApol_promoter -SO:0000614 bacterial_terminator -SO:0000615 terminator_of_type_2_RNApol_III_promoter -SO:0000616 transcription_end_site -SO:0000617 RNApol_III_promoter_type_1 -SO:0000618 RNApol_III_promoter_type_2 -SO:0000619 A_box -SO:0000620 B_box -SO:0000621 RNApol_III_promoter_type_3 -SO:0000622 C_box -SO:0000623 snRNA_encoding -SO:0000624 telomere -SO:0000625 silencer -SO:0000626 chromosomal_regulatory_element -SO:0000627 insulator -SO:0000628 chromosomal_structural_element -SO:0000629 five_prime_open_reading_frame -SO:0000630 upstream_AUG_codon -SO:0000631 polycistronic_primary_transcript -SO:0000632 monocistronic_primary_transcript -SO:0000633 monocistronic_mRNA -SO:0000634 polycistronic_mRNA -SO:0000635 mini_exon_donor_RNA -SO:0000636 spliced_leader_RNA -SO:0000637 engineered_plasmid -SO:0000638 transcribed_spacer_region -SO:0000639 internal_transcribed_spacer_region -SO:0000640 external_transcribed_spacer_region -SO:0000641 tetranucleotide_repeat_microsatellite_feature -SO:0000642 SRP_RNA_encoding -SO:0000643 minisatellite -SO:0000644 antisense_RNA -SO:0000645 antisense_primary_transcript -SO:0000646 siRNA -SO:0000647 miRNA_primary_transcript -SO:0000650 small_subunit_rRNA -SO:0000651 large_subunit_rRNA -SO:0000652 rRNA_5S -SO:0000653 rRNA_28S -SO:0000654 maxicircle_gene -SO:0000655 ncRNA -SO:0000656 stRNA_encoding -SO:0000657 repeat_region -SO:0000658 dispersed_repeat -SO:0000659 tmRNA_encoding -SO:0000660 DNA_invertase_target_sequence -SO:0000661 intron_attribute -SO:0000662 spliceosomal_intron -SO:0000663 tRNA_encoding -SO:0000664 introgressed_chromosome_region -SO:0000665 monocistronic_transcript -SO:0000666 mobile_intron -SO:0000667 insertion -SO:0000668 EST_match -SO:0000669 sequence_rearrangement_feature -SO:0000670 chromosome_breakage_sequence -SO:0000671 internal_eliminated_sequence -SO:0000672 macronucleus_destined_segment -SO:0000673 transcript -SO:0000674 non_canonical_splice_site -SO:0000675 canonical_splice_site -SO:0000676 canonical_three_prime_splice_site -SO:0000677 canonical_five_prime_splice_site -SO:0000678 non_canonical_three_prime_splice_site -SO:0000679 non_canonical_five_prime_splice_site -SO:0000680 non_canonical_start_codon -SO:0000681 aberrant_processed_transcript -SO:0000682 splicing_feature -SO:0000683 exonic_splice_enhancer -SO:0000684 nuclease_sensitive_site -SO:0000685 DNAseI_hypersensitive_site -SO:0000686 translocation_element -SO:0000687 deletion_junction -SO:0000688 golden_path -SO:0000689 cDNA_match -SO:0000690 gene_with_polycistronic_transcript -SO:0000691 cleaved_initiator_methionine -SO:0000692 gene_with_dicistronic_transcript -SO:0000693 gene_with_recoded_mRNA -SO:0000694 SNP -SO:0000695 reagent -SO:0000696 oligo -SO:0000697 gene_with_stop_codon_read_through -SO:0000698 gene_with_stop_codon_redefined_as_pyrrolysine -SO:0000699 junction -SO:0000700 remark -SO:0000701 possible_base_call_error -SO:0000702 possible_assembly_error -SO:0000703 experimental_result_region -SO:0000704 gene -SO:0000705 tandem_repeat -SO:0000706 trans_splice_acceptor_site -SO:0000707 trans_splice_donor_site -SO:0000708 SL1_acceptor_site -SO:0000709 SL2_acceptor_site -SO:0000710 gene_with_stop_codon_redefined_as_selenocysteine -SO:0000711 gene_with_mRNA_recoded_by_translational_bypass -SO:0000712 gene_with_transcript_with_translational_frameshift -SO:0000713 DNA_motif -SO:0000714 nucleotide_motif -SO:0000715 RNA_motif -SO:0000716 dicistronic_mRNA -SO:0000717 reading_frame -SO:0000718 blocked_reading_frame -SO:0000719 ultracontig -SO:0000720 foreign_transposable_element -SO:0000721 gene_with_dicistronic_primary_transcript -SO:0000722 gene_with_dicistronic_mRNA -SO:0000723 iDNA -SO:0000724 oriT -SO:0000725 transit_peptide -SO:0000726 repeat_unit -SO:0000727 CRM -SO:0000728 intein -SO:0000729 intein_containing -SO:0000730 gap -SO:0000731 fragmentary -SO:0000732 predicted -SO:0000733 feature_attribute -SO:0000734 exemplar_mRNA -SO:0000735 sequence_location -SO:0000736 organelle_sequence -SO:0000737 mitochondrial_sequence -SO:0000738 nuclear_sequence -SO:0000739 nucleomorphic_sequence -SO:0000740 plastid_sequence -SO:0000741 kinetoplast -SO:0000742 maxicircle -SO:0000743 apicoplast_sequence -SO:0000744 chromoplast_sequence -SO:0000745 chloroplast_sequence -SO:0000746 cyanelle_sequence -SO:0000747 leucoplast_sequence -SO:0000748 proplastid_sequence -SO:0000749 plasmid_location -SO:0000750 amplification_origin -SO:0000751 proviral_location -SO:0000752 gene_group_regulatory_region -SO:0000753 clone_insert -SO:0000754 lambda_vector -SO:0000755 plasmid_vector -SO:0000756 cDNA -SO:0000757 single_stranded_cDNA -SO:0000758 double_stranded_cDNA -SO:0000759 plasmid_clone -SO:0000760 YAC_clone -SO:0000761 phagemid_clone -SO:0000762 PAC_clone -SO:0000763 fosmid_clone -SO:0000764 BAC_clone -SO:0000765 cosmid_clone -SO:0000766 pyrrolysyl_tRNA -SO:0000767 clone_insert_start -SO:0000768 episome -SO:0000769 tmRNA_coding_piece -SO:0000770 tmRNA_acceptor_piece -SO:0000771 QTL -SO:0000772 genomic_island -SO:0000773 pathogenic_island -SO:0000774 metabolic_island -SO:0000775 adaptive_island -SO:0000776 symbiosis_island -SO:0000777 pseudogenic_rRNA -SO:0000778 pseudogenic_tRNA -SO:0000779 engineered_episome -SO:0000780 transposable_element_attribute -SO:0000781 transgenic -SO:0000782 natural -SO:0000783 engineered -SO:0000784 foreign -SO:0000785 cloned_region -SO:0000786 reagent_attribute -SO:0000787 clone_attribute -SO:0000788 cloned -SO:0000789 validated -SO:0000790 invalidated -SO:0000791 cloned_genomic -SO:0000792 cloned_cDNA -SO:0000793 engineered_DNA -SO:0000794 engineered_rescue_region -SO:0000795 rescue_mini_gene -SO:0000796 transgenic_transposable_element -SO:0000797 natural_transposable_element -SO:0000798 engineered_transposable_element -SO:0000799 engineered_foreign_transposable_element -SO:0000800 assortment_derived_duplication -SO:0000801 assortment_derived_deficiency_plus_duplication -SO:0000802 assortment_derived_deficiency -SO:0000803 assortment_derived_aneuploid -SO:0000804 engineered_region -SO:0000805 engineered_foreign_region -SO:0000806 fusion -SO:0000807 engineered_tag -SO:0000808 validated_cDNA_clone -SO:0000809 invalidated_cDNA_clone -SO:0000810 chimeric_cDNA_clone -SO:0000811 genomically_contaminated_cDNA_clone -SO:0000812 polyA_primed_cDNA_clone -SO:0000813 partially_processed_cDNA_clone -SO:0000814 rescue -SO:0000815 mini_gene -SO:0000816 rescue_gene -SO:0000817 wild_type -SO:0000818 wild_type_rescue_gene -SO:0000819 mitochondrial_chromosome -SO:0000820 chloroplast_chromosome -SO:0000821 chromoplast_chromosome -SO:0000822 cyanelle_chromosome -SO:0000823 leucoplast_chromosome -SO:0000824 macronuclear_chromosome -SO:0000825 micronuclear_chromosome -SO:0000828 nuclear_chromosome -SO:0000829 nucleomorphic_chromosome -SO:0000830 chromosome_part -SO:0000831 gene_member_region -SO:0000832 promoter_region -SO:0000833 transcript_region -SO:0000834 mature_transcript_region -SO:0000835 primary_transcript_region -SO:0000836 mRNA_region -SO:0000837 UTR_region -SO:0000838 rRNA_primary_transcript_region -SO:0000839 polypeptide_region -SO:0000840 repeat_component -SO:0000841 spliceosomal_intron_region -SO:0000842 gene_component_region -SO:0000843 bacterial_RNApol_promoter_region -SO:0000844 RNApol_II_promoter_region -SO:0000845 RNApol_III_promoter_type_1_region -SO:0000846 RNApol_III_promoter_type_2_region -SO:0000847 tmRNA_region -SO:0000848 LTR_component -SO:0000849 three_prime_LTR_component -SO:0000850 five_prime_LTR_component -SO:0000851 CDS_region -SO:0000852 exon_region -SO:0000853 homologous_region -SO:0000854 paralogous_region -SO:0000855 orthologous_region -SO:0000856 conserved -SO:0000857 homologous -SO:0000858 orthologous -SO:0000859 paralogous -SO:0000860 syntenic -SO:0000861 capped_primary_transcript -SO:0000862 capped_mRNA -SO:0000863 mRNA_attribute -SO:0000864 exemplar -SO:0000865 frameshift -SO:0000866 minus_1_frameshift -SO:0000867 minus_2_frameshift -SO:0000868 plus_1_frameshift -SO:0000869 plus_2_framshift -SO:0000870 trans_spliced -SO:0000871 polyadenylated_mRNA -SO:0000872 trans_spliced_mRNA -SO:0000873 edited_transcript -SO:0000874 edited_transcript_by_A_to_I_substitution -SO:0000875 bound_by_protein -SO:0000876 bound_by_nucleic_acid -SO:0000877 alternatively_spliced -SO:0000878 monocistronic -SO:0000879 dicistronic -SO:0000880 polycistronic -SO:0000881 recoded -SO:0000882 codon_redefined -SO:0000883 stop_codon_read_through -SO:0000884 stop_codon_redefined_as_pyrrolysine -SO:0000885 stop_codon_redefined_as_selenocysteine -SO:0000886 recoded_by_translational_bypass -SO:0000887 translationally_frameshifted -SO:0000888 maternally_imprinted_gene -SO:0000889 paternally_imprinted_gene -SO:0000890 post_translationally_regulated_gene -SO:0000891 negatively_autoregulated_gene -SO:0000892 positively_autoregulated_gene -SO:0000893 silenced -SO:0000894 silenced_by_DNA_modification -SO:0000895 silenced_by_DNA_methylation -SO:0000896 translationally_regulated_gene -SO:0000897 allelically_excluded_gene -SO:0000898 epigenetically_modified_gene -SO:0000899 nuclear_mitochondrial -SO:0000900 processed -SO:0000901 unequally_crossed_over -SO:0000902 transgene -SO:0000903 endogenous_retroviral_sequence -SO:0000904 rearranged_at_DNA_level -SO:0000905 status -SO:0000906 independently_known -SO:0000907 supported_by_sequence_similarity -SO:0000908 supported_by_domain_match -SO:0000909 supported_by_EST_or_cDNA -SO:0000910 orphan -SO:0000911 predicted_by_ab_initio_computation -SO:0000912 asx_turn -SO:0000913 cloned_cDNA_insert -SO:0000914 cloned_genomic_insert -SO:0000915 engineered_insert -SO:0000916 edit_operation -SO:0000917 insert_U -SO:0000918 delete_U -SO:0000919 substitute_A_to_I -SO:0000920 insert_C -SO:0000921 insert_dinucleotide -SO:0000922 substitute_C_to_U -SO:0000923 insert_G -SO:0000924 insert_GC -SO:0000925 insert_GU -SO:0000926 insert_CU -SO:0000927 insert_AU -SO:0000928 insert_AA -SO:0000929 edited_mRNA -SO:0000930 guide_RNA_region -SO:0000931 anchor_region -SO:0000932 pre_edited_mRNA -SO:0000933 intermediate -SO:0000934 miRNA_target_site -SO:0000935 edited_CDS -SO:0000936 vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment -SO:0000937 vertebrate_immune_system_feature -SO:0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster -SO:0000939 vertebrate_immune_system_gene_recombination_signal_feature -SO:0000940 recombinationally_rearranged -SO:0000941 recombinationally_rearranged_vertebrate_immune_system_gene -SO:0000942 attP_site -SO:0000943 attB_site -SO:0000944 attL_site -SO:0000945 attR_site -SO:0000946 integration_excision_site -SO:0000947 resolution_site -SO:0000948 inversion_site -SO:0000949 dif_site -SO:0000950 attC_site -SO:0000951 eukaryotic_terminator -SO:0000952 oriV -SO:0000953 oriC -SO:0000954 DNA_chromosome -SO:0000955 double_stranded_DNA_chromosome -SO:0000956 single_stranded_DNA_chromosome -SO:0000957 linear_double_stranded_DNA_chromosome -SO:0000958 circular_double_stranded_DNA_chromosome -SO:0000959 linear_single_stranded_DNA_chromosome -SO:0000960 circular_single_stranded_DNA_chromosome -SO:0000961 RNA_chromosome -SO:0000962 single_stranded_RNA_chromosome -SO:0000963 linear_single_stranded_RNA_chromosome -SO:0000964 linear_double_stranded_RNA_chromosome -SO:0000965 double_stranded_RNA_chromosome -SO:0000966 circular_single_stranded_RNA_chromosome -SO:0000967 circular_double_stranded_RNA_chromosome -SO:0000968 sequence_replication_mode -SO:0000969 rolling_circle -SO:0000970 theta_replication -SO:0000971 DNA_replication_mode -SO:0000972 RNA_replication_mode -SO:0000973 insertion_sequence -SO:0000975 minicircle_gene -SO:0000976 cryptic -SO:0000977 anchor_binding_site -SO:0000978 template_region -SO:0000979 gRNA_encoding -SO:0000980 minicircle -SO:0000981 rho_dependent_bacterial_terminator -SO:0000982 rho_independent_bacterial_terminator -SO:0000983 strand_attribute -SO:0000984 single -SO:0000985 double -SO:0000986 topology_attribute -SO:0000987 linear -SO:0000988 circular -SO:0000989 class_II_RNA -SO:0000990 class_I_RNA -SO:0000991 genomic_DNA -SO:0000992 BAC_cloned_genomic_insert -SO:0000993 consensus -SO:0000994 consensus_region -SO:0000995 consensus_mRNA -SO:0000996 predicted_gene -SO:0000997 gene_fragment -SO:0000998 recursive_splice_site -SO:0000999 BAC_end -SO:0001000 rRNA_16S -SO:0001001 rRNA_23S -SO:0001002 rRNA_25S -SO:0001003 solo_LTR -SO:0001004 low_complexity -SO:0001005 low_complexity_region -SO:0001006 prophage -SO:0001007 cryptic_prophage -SO:0001008 tetraloop -SO:0001009 DNA_constraint_sequence -SO:0001010 i_motif -SO:0001011 PNA_oligo -SO:0001012 DNAzyme -SO:0001013 MNP -SO:0001014 intron_domain -SO:0001015 wobble_base_pair -SO:0001016 internal_guide_sequence -SO:0001017 silent_mutation -SO:0001018 epitope -SO:0001019 copy_number_variation -SO:0001020 sequence_variant_affecting_copy_number -SO:0001021 chromosome_breakpoint -SO:0001022 inversion_breakpoint -SO:0001023 allele -SO:0001024 haplotype -SO:0001025 polymorphic_sequence_variant -SO:0001026 genome -SO:0001027 genotype -SO:0001028 diplotype -SO:0001029 direction_attribute -SO:0001030 forward -SO:0001031 reverse -SO:0001032 mitochondrial_DNA -SO:0001033 chloroplast_DNA -SO:0001034 miRtron -SO:0001035 piRNA -SO:0001036 arginyl_tRNA -SO:0001037 mobile_genetic_element -SO:0001038 extrachromosomal_mobile_genetic_element -SO:0001039 integrated_mobile_genetic_element -SO:0001040 integrated_plasmid -SO:0001041 viral_sequence -SO:0001042 phage_sequence -SO:0001043 attCtn_site -SO:0001044 nuclear_mt_pseudogene -SO:0001045 cointegrated_plasmid -SO:0001046 IRLinv_site -SO:0001047 IRRinv_site -SO:0001048 inversion_site_part -SO:0001049 defective_conjugative_transposon -SO:0001050 repeat_fragment -SO:0001051 nested_region -SO:0001052 nested_repeat -SO:0001053 nested_transposon -SO:0001054 transposon_fragment -SO:0001055 transcriptional_cis_regulatory_region -SO:0001056 splicing_regulatory_region -SO:0001057 enhanceosome -SO:0001058 promoter_targeting_sequence -SO:0001059 sequence_alteration -SO:0001060 sequence_variant -SO:0001061 propeptide_cleavage_site -SO:0001062 propeptide -SO:0001063 immature_peptide_region -SO:0001064 active_peptide -SO:0001066 compositionally_biased_region_of_peptide -SO:0001067 polypeptide_motif -SO:0001068 polypeptide_repeat -SO:0001070 polypeptide_structural_region -SO:0001071 membrane_structure -SO:0001072 extramembrane_polypeptide_region -SO:0001073 cytoplasmic_polypeptide_region -SO:0001074 non_cytoplasmic_polypeptide_region -SO:0001075 intramembrane_polypeptide_region -SO:0001076 membrane_peptide_loop -SO:0001077 transmembrane_polypeptide_region -SO:0001078 polypeptide_secondary_structure -SO:0001079 polypeptide_structural_motif -SO:0001080 coiled_coil -SO:0001081 helix_turn_helix -SO:0001082 polypeptide_sequencing_information -SO:0001083 non_adjacent_residues -SO:0001084 non_terminal_residue -SO:0001085 sequence_conflict -SO:0001086 sequence_uncertainty -SO:0001087 cross_link -SO:0001088 disulfide_bond -SO:0001089 post_translationally_modified_region -SO:0001090 covalent_binding_site -SO:0001091 non_covalent_binding_site -SO:0001092 polypeptide_metal_contact -SO:0001093 protein_protein_contact -SO:0001094 polypeptide_calcium_ion_contact_site -SO:0001095 polypeptide_cobalt_ion_contact_site -SO:0001096 polypeptide_copper_ion_contact_site -SO:0001097 polypeptide_iron_ion_contact_site -SO:0001098 polypeptide_magnesium_ion_contact_site -SO:0001099 polypeptide_manganese_ion_contact_site -SO:0001100 polypeptide_molybdenum_ion_contact_site -SO:0001101 polypeptide_nickel_ion_contact_site -SO:0001102 polypeptide_tungsten_ion_contact_site -SO:0001103 polypeptide_zinc_ion_contact_site -SO:0001104 catalytic_residue -SO:0001105 polypeptide_ligand_contact -SO:0001106 asx_motif -SO:0001107 beta_bulge -SO:0001108 beta_bulge_loop -SO:0001109 beta_bulge_loop_five -SO:0001110 beta_bulge_loop_six -SO:0001111 beta_strand -SO:0001112 antiparallel_beta_strand -SO:0001113 parallel_beta_strand -SO:0001114 peptide_helix -SO:0001115 left_handed_peptide_helix -SO:0001116 right_handed_peptide_helix -SO:0001117 alpha_helix -SO:0001118 pi_helix -SO:0001119 three_ten_helix -SO:0001120 polypeptide_nest_motif -SO:0001121 polypeptide_nest_left_right_motif -SO:0001122 polypeptide_nest_right_left_motif -SO:0001123 schellmann_loop -SO:0001124 schellmann_loop_seven -SO:0001125 schellmann_loop_six -SO:0001126 serine_threonine_motif -SO:0001127 serine_threonine_staple_motif -SO:0001128 polypeptide_turn_motif -SO:0001129 asx_turn_left_handed_type_one -SO:0001130 asx_turn_left_handed_type_two -SO:0001131 asx_turn_right_handed_type_two -SO:0001132 asx_turn_right_handed_type_one -SO:0001133 beta_turn -SO:0001134 beta_turn_left_handed_type_one -SO:0001135 beta_turn_left_handed_type_two -SO:0001136 beta_turn_right_handed_type_one -SO:0001137 beta_turn_right_handed_type_two -SO:0001138 gamma_turn -SO:0001139 gamma_turn_classic -SO:0001140 gamma_turn_inverse -SO:0001141 serine_threonine_turn -SO:0001142 st_turn_left_handed_type_one -SO:0001143 st_turn_left_handed_type_two -SO:0001144 st_turn_right_handed_type_one -SO:0001145 st_turn_right_handed_type_two -SO:0001146 polypeptide_variation_site -SO:0001147 natural_variant_site -SO:0001148 mutated_variant_site -SO:0001149 alternate_sequence_site -SO:0001150 beta_turn_type_six -SO:0001151 beta_turn_type_six_a -SO:0001152 beta_turn_type_six_a_one -SO:0001153 beta_turn_type_six_a_two -SO:0001154 beta_turn_type_six_b -SO:0001155 beta_turn_type_eight -SO:0001156 DRE_motif -SO:0001157 DMv4_motif -SO:0001158 E_box_motif -SO:0001159 DMv5_motif -SO:0001160 DMv3_motif -SO:0001161 DMv2_motif -SO:0001162 MTE -SO:0001163 INR1_motif -SO:0001164 DPE1_motif -SO:0001165 DMv1_motif -SO:0001166 GAGA_motif -SO:0001167 NDM2_motif -SO:0001168 NDM3_motif -SO:0001169 ds_RNA_viral_sequence -SO:0001170 polinton -SO:0001171 rRNA_21S -SO:0001172 tRNA_region -SO:0001173 anticodon_loop -SO:0001174 anticodon -SO:0001175 CCA_tail -SO:0001176 DHU_loop -SO:0001177 T_loop -SO:0001178 pyrrolysine_tRNA_primary_transcript -SO:0001179 U3_snoRNA -SO:0001180 AU_rich_element -SO:0001181 Bruno_response_element -SO:0001182 iron_responsive_element -SO:0001183 morpholino_backbone -SO:0001184 PNA -SO:0001185 enzymatic -SO:0001186 ribozymic -SO:0001187 pseudouridylation_guide_snoRNA -SO:0001188 LNA -SO:0001189 LNA_oligo -SO:0001190 TNA -SO:0001191 TNA_oligo -SO:0001192 GNA -SO:0001193 GNA_oligo -SO:0001194 R_GNA -SO:0001195 R_GNA_oligo -SO:0001196 S_GNA -SO:0001197 S_GNA_oligo -SO:0001198 ds_DNA_viral_sequence -SO:0001199 ss_RNA_viral_sequence -SO:0001200 negative_sense_ssRNA_viral_sequence -SO:0001201 positive_sense_ssRNA_viral_sequence -SO:0001202 ambisense_ssRNA_viral_sequence -SO:0001203 RNA_polymerase_promoter -SO:0001204 Phage_RNA_Polymerase_Promoter -SO:0001205 SP6_RNA_Polymerase_Promoter -SO:0001206 T3_RNA_Polymerase_Promoter -SO:0001207 T7_RNA_Polymerase_Promoter -SO:0001208 five_prime_EST -SO:0001209 three_prime_EST -SO:0001210 translational_frameshift -SO:0001211 plus_1_translational_frameshift -SO:0001212 plus_2_translational_frameshift -SO:0001213 group_III_intron -SO:0001214 noncoding_region_of_exon -SO:0001215 coding_region_of_exon -SO:0001216 endonuclease_spliced_intron -SO:0001217 protein_coding_gene -SO:0001218 transgenic_insertion -SO:0001219 retrogene -SO:0001220 silenced_by_RNA_interference -SO:0001221 silenced_by_histone_modification -SO:0001222 silenced_by_histone_methylation -SO:0001223 silenced_by_histone_deacetylation -SO:0001224 gene_silenced_by_RNA_interference -SO:0001225 gene_silenced_by_histone_modification -SO:0001226 gene_silenced_by_histone_methylation -SO:0001227 gene_silenced_by_histone_deacetylation -SO:0001228 dihydrouridine -SO:0001229 pseudouridine -SO:0001230 inosine -SO:0001231 seven_methylguanine -SO:0001232 ribothymidine -SO:0001233 methylinosine -SO:0001234 mobile -SO:0001235 replicon -SO:0001236 base -SO:0001237 amino_acid -SO:0001238 major_TSS -SO:0001239 minor_TSS -SO:0001240 TSS_region -SO:0001241 encodes_alternate_transcription_start_sites -SO:0001243 miRNA_primary_transcript_region -SO:0001244 pre_miRNA -SO:0001245 miRNA_stem -SO:0001246 miRNA_loop -SO:0001247 synthetic_oligo -SO:0001248 assembly -SO:0001249 fragment_assembly -SO:0001250 fingerprint_map -SO:0001251 STS_map -SO:0001252 RH_map -SO:0001253 sonicate_fragment -SO:0001254 polyploid -SO:0001255 autopolyploid -SO:0001256 allopolyploid -SO:0001257 homing_endonuclease_binding_site -SO:0001258 octamer_motif -SO:0001259 apicoplast_chromosome -SO:0001260 sequence_collection -SO:0001261 overlapping_feature_set -SO:0001262 overlapping_EST_set -SO:0001263 ncRNA_gene -SO:0001264 gRNA_gene -SO:0001265 miRNA_gene -SO:0001266 scRNA_gene -SO:0001267 snoRNA_gene -SO:0001268 snRNA_gene -SO:0001269 SRP_RNA_gene -SO:0001271 tmRNA_gene -SO:0001272 tRNA_gene -SO:0001273 modified_adenosine -SO:0001274 modified_inosine -SO:0001275 modified_cytidine -SO:0001276 modified_guanosine -SO:0001277 modified_uridine -SO:0001278 one_methylinosine -SO:0001279 one_two_prime_O_dimethylinosine -SO:0001280 two_prime_O_methylinosine -SO:0001281 three_methylcytidine -SO:0001282 five_methylcytidine -SO:0001283 two_prime_O_methylcytidine -SO:0001284 two_thiocytidine -SO:0001285 N4_acetylcytidine -SO:0001286 five_formylcytidine -SO:0001287 five_two_prime_O_dimethylcytidine -SO:0001288 N4_acetyl_2_prime_O_methylcytidine -SO:0001289 lysidine -SO:0001290 N4_methylcytidine -SO:0001291 N4_2_prime_O_dimethylcytidine -SO:0001292 five_hydroxymethylcytidine -SO:0001293 five_formyl_two_prime_O_methylcytidine -SO:0001294 N4_N4_2_prime_O_trimethylcytidine -SO:0001295 one_methyladenosine -SO:0001296 two_methyladenosine -SO:0001297 N6_methyladenosine -SO:0001298 two_prime_O_methyladenosine -SO:0001299 two_methylthio_N6_methyladenosine -SO:0001300 N6_isopentenyladenosine -SO:0001301 two_methylthio_N6_isopentenyladenosine -SO:0001302 N6_cis_hydroxyisopentenyl_adenosine -SO:0001303 two_methylthio_N6_cis_hydroxyisopentenyl_adenosine -SO:0001304 N6_glycinylcarbamoyladenosine -SO:0001305 N6_threonylcarbamoyladenosine -SO:0001306 two_methylthio_N6_threonyl_carbamoyladenosine -SO:0001307 N6_methyl_N6_threonylcarbamoyladenosine -SO:0001308 N6_hydroxynorvalylcarbamoyladenosine -SO:0001309 two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine -SO:0001310 two_prime_O_ribosyladenosine_phosphate -SO:0001311 N6_N6_dimethyladenosine -SO:0001312 N6_2_prime_O_dimethyladenosine -SO:0001313 N6_N6_2_prime_O_trimethyladenosine -SO:0001314 one_two_prime_O_dimethyladenosine -SO:0001315 N6_acetyladenosine -SO:0001316 seven_deazaguanosine -SO:0001317 queuosine -SO:0001318 epoxyqueuosine -SO:0001319 galactosyl_queuosine -SO:0001320 mannosyl_queuosine -SO:0001321 seven_cyano_seven_deazaguanosine -SO:0001322 seven_aminomethyl_seven_deazaguanosine -SO:0001323 archaeosine -SO:0001324 one_methylguanosine -SO:0001325 N2_methylguanosine -SO:0001326 seven_methylguanosine -SO:0001327 two_prime_O_methylguanosine -SO:0001328 N2_N2_dimethylguanosine -SO:0001329 N2_2_prime_O_dimethylguanosine -SO:0001330 N2_N2_2_prime_O_trimethylguanosine -SO:0001331 two_prime_O_ribosylguanosine_phosphate -SO:0001332 wybutosine -SO:0001333 peroxywybutosine -SO:0001334 hydroxywybutosine -SO:0001335 undermodified_hydroxywybutosine -SO:0001336 wyosine -SO:0001337 methylwyosine -SO:0001338 N2_7_dimethylguanosine -SO:0001339 N2_N2_7_trimethylguanosine -SO:0001340 one_two_prime_O_dimethylguanosine -SO:0001341 four_demethylwyosine -SO:0001342 isowyosine -SO:0001343 N2_7_2prirme_O_trimethylguanosine -SO:0001344 five_methyluridine -SO:0001345 two_prime_O_methyluridine -SO:0001346 five_two_prime_O_dimethyluridine -SO:0001347 one_methylpseudouridine -SO:0001348 two_prime_O_methylpseudouridine -SO:0001349 two_thiouridine -SO:0001350 four_thiouridine -SO:0001351 five_methyl_2_thiouridine -SO:0001352 two_thio_two_prime_O_methyluridine -SO:0001353 three_three_amino_three_carboxypropyl_uridine -SO:0001354 five_hydroxyuridine -SO:0001355 five_methoxyuridine -SO:0001356 uridine_five_oxyacetic_acid -SO:0001357 uridine_five_oxyacetic_acid_methyl_ester -SO:0001358 five_carboxyhydroxymethyl_uridine -SO:0001359 five_carboxyhydroxymethyl_uridine_methyl_ester -SO:0001360 five_methoxycarbonylmethyluridine -SO:0001361 five_methoxycarbonylmethyl_two_prime_O_methyluridine -SO:0001362 five_methoxycarbonylmethyl_two_thiouridine -SO:0001363 five_aminomethyl_two_thiouridine -SO:0001364 five_methylaminomethyluridine -SO:0001365 five_methylaminomethyl_two_thiouridine -SO:0001366 five_methylaminomethyl_two_selenouridine -SO:0001367 five_carbamoylmethyluridine -SO:0001368 five_carbamoylmethyl_two_prime_O_methyluridine -SO:0001369 five_carboxymethylaminomethyluridine -SO:0001370 five_carboxymethylaminomethyl_two_prime_O_methyluridine -SO:0001371 five_carboxymethylaminomethyl_two_thiouridine -SO:0001372 three_methyluridine -SO:0001373 one_methyl_three_three_amino_three_carboxypropyl_pseudouridine -SO:0001374 five_carboxymethyluridine -SO:0001375 three_two_prime_O_dimethyluridine -SO:0001376 five_methyldihydrouridine -SO:0001377 three_methylpseudouridine -SO:0001378 five_taurinomethyluridine -SO:0001379 five_taurinomethyl_two_thiouridine -SO:0001380 five_isopentenylaminomethyl_uridine -SO:0001381 five_isopentenylaminomethyl_two_thiouridine -SO:0001382 five_isopentenylaminomethyl_two_prime_O_methyluridine -SO:0001383 histone_binding_site -SO:0001384 CDS_fragment -SO:0001385 modified_amino_acid_feature -SO:0001386 modified_glycine -SO:0001387 modified_L_alanine -SO:0001388 modified_L_asparagine -SO:0001389 modified_L_aspartic_acid -SO:0001390 modified_L_cysteine -SO:0001391 modified_L_glutamic_acid -SO:0001392 modified_L_threonine -SO:0001393 modified_L_tryptophan -SO:0001394 modified_L_glutamine -SO:0001395 modified_L_methionine -SO:0001396 modified_L_isoleucine -SO:0001397 modified_L_phenylalanine -SO:0001398 modified_L_histidine -SO:0001399 modified_L_serine -SO:0001400 modified_L_lysine -SO:0001401 modified_L_leucine -SO:0001402 modified_L_selenocysteine -SO:0001403 modified_L_valine -SO:0001404 modified_L_proline -SO:0001405 modified_L_tyrosine -SO:0001406 modified_L_arginine -SO:0001407 peptidyl -SO:0001408 cleaved_for_gpi_anchor_region -SO:0001409 biomaterial_region -SO:0001410 experimental_feature -SO:0001411 biological_region -SO:0001412 topologically_defined_region -SO:0001413 translocation_breakpoint -SO:0001414 insertion_breakpoint -SO:0001415 deletion_breakpoint -SO:0001416 five_prime_flanking_region -SO:0001417 three_prime_flanking_region -SO:0001418 transcribed_fragment -SO:0001419 cis_splice_site -SO:0001420 trans_splice_site -SO:0001421 splice_junction -SO:0001422 conformational_switch -SO:0001423 dye_terminator_read -SO:0001424 pyrosequenced_read -SO:0001425 ligation_based_read -SO:0001426 polymerase_synthesis_read -SO:0001427 cis_regulatory_frameshift_element -SO:0001428 expressed_sequence_assembly -SO:0001429 DNA_binding_site -SO:0001431 cryptic_gene -SO:0001432 sequence_variant_affecting_polyadenylation -SO:0001433 three_prime_RACE_clone -SO:0001434 cassette_pseudogene -SO:0001435 alanine -SO:0001436 valine -SO:0001437 leucine -SO:0001438 isoleucine -SO:0001439 proline -SO:0001440 tryptophan -SO:0001441 phenylalanine -SO:0001442 methionine -SO:0001443 glycine -SO:0001444 serine -SO:0001445 threonine -SO:0001446 tyrosine -SO:0001447 cysteine -SO:0001448 glutamine -SO:0001449 asparagine -SO:0001450 lysine -SO:0001451 arginine -SO:0001452 histidine -SO:0001453 aspartic_acid -SO:0001454 glutamic_acid -SO:0001455 selenocysteine -SO:0001456 pyrrolysine -SO:0001457 transcribed_cluster -SO:0001458 unigene_cluster -SO:0001459 CRISPR -SO:0001460 insulator_binding_site -SO:0001461 enhancer_binding_site -SO:0001462 contig_collection -SO:0001463 lincRNA -SO:0001464 UST -SO:0001465 three_prime_UST -SO:0001466 five_prime_UST -SO:0001467 RST -SO:0001468 three_prime_RST -SO:0001469 five_prime_RST -SO:0001470 UST_match -SO:0001471 RST_match -SO:0001472 primer_match -SO:0001473 miRNA_antiguide -SO:0001474 trans_splice_junction -SO:0001475 outron -SO:0001476 natural_plasmid -SO:0001477 gene_trap_construct -SO:0001478 promoter_trap_construct -SO:0001479 enhancer_trap_construct -SO:0001480 PAC_end -SO:0001481 RAPD -SO:0001482 shadow_enhancer -SO:0001483 SNV -SO:0001484 X_element_combinatorial_repeat -SO:0001485 Y_prime_element -SO:0001486 standard_draft -SO:0001487 high_quality_draft -SO:0001488 improved_high_quality_draft -SO:0001489 annotation_directed_improved_draft -SO:0001490 noncontiguous_finished -SO:0001491 finished_genome -SO:0001492 intronic_regulatory_region -SO:0001493 centromere_DNA_Element_I -SO:0001494 centromere_DNA_Element_II -SO:0001495 centromere_DNA_Element_III -SO:0001496 telomeric_repeat -SO:0001497 X_element -SO:0001498 YAC_end -SO:0001499 whole_genome_sequence_status -SO:0001500 heritable_phenotypic_marker -SO:0001501 peptide_collection -SO:0001502 high_identity_region -SO:0001503 processed_transcript -SO:0001504 assortment_derived_variation -SO:0001505 reference_genome -SO:0001506 variant_genome -SO:0001507 variant_collection -SO:0001508 alteration_attribute -SO:0001509 chromosomal_variation_attribute -SO:0001510 intrachromosomal -SO:0001511 interchromosomal -SO:0001512 insertion_attribute -SO:0001513 tandem -SO:0001514 direct -SO:0001515 inverted -SO:0001516 free -SO:0001517 inversion_attribute -SO:0001518 pericentric -SO:0001519 paracentric -SO:0001520 translocaton_attribute -SO:0001521 reciprocal -SO:0001522 insertional -SO:0001523 duplication_attribute -SO:0001524 chromosomally_aberrant_genome -SO:0001525 assembly_error_correction -SO:0001526 base_call_error_correction -SO:0001527 peptide_localization_signal -SO:0001528 nuclear_localization_signal -SO:0001529 endosomal_localization_signal -SO:0001530 lysosomal_localization_signal -SO:0001531 nuclear_export_signal -SO:0001532 recombination_signal_sequence -SO:0001533 cryptic_splice_site -SO:0001534 nuclear_rim_localization_signal -SO:0001535 p_element -SO:0001536 functional_variant -SO:0001537 structural_variant -SO:0001538 transcript_function_variant -SO:0001539 translational_product_function_variant -SO:0001540 level_of_transcript_variant -SO:0001541 decreased_transcript_level_variant -SO:0001542 increased_transcript_level_variant -SO:0001543 transcript_processing_variant -SO:0001544 editing_variant -SO:0001545 polyadenylation_variant -SO:0001546 transcript_stability_variant -SO:0001547 decreased_transcript_stability_variant -SO:0001548 increased_transcript_stability_variant -SO:0001549 transcription_variant -SO:0001550 rate_of_transcription_variant -SO:0001551 increased_transcription_rate_variant -SO:0001552 decreased_transcription_rate_variant -SO:0001553 translational_product_level_variant -SO:0001554 polypeptide_function_variant -SO:0001555 decreased_translational_product_level -SO:0001556 increased_translational_product_level -SO:0001557 polypeptide_gain_of_function_variant -SO:0001558 polypeptide_localization_variant -SO:0001559 polypeptide_loss_of_function_variant -SO:0001560 inactive_ligand_binding_site -SO:0001561 polypeptide_partial_loss_of_function -SO:0001562 polypeptide_post_translational_processing_variant -SO:0001563 copy_number_change -SO:0001564 gene_variant -SO:0001565 gene_fusion -SO:0001566 regulatory_region_variant -SO:0001567 stop_retained_variant -SO:0001568 splicing_variant -SO:0001569 cryptic_splice_site_variant -SO:0001570 cryptic_splice_acceptor -SO:0001571 cryptic_splice_donor -SO:0001572 exon_loss_variant -SO:0001573 intron_gain_variant -SO:0001574 splice_acceptor_variant -SO:0001575 splice_donor_variant -SO:0001576 transcript_variant -SO:0001577 complex_transcript_variant -SO:0001578 stop_lost -SO:0001579 transcript_sequence_variant -SO:0001580 coding_sequence_variant -SO:0001582 initiator_codon_variant -SO:0001583 missense_variant -SO:0001585 conservative_missense_variant -SO:0001586 non_conservative_missense_variant -SO:0001587 stop_gained -SO:0001589 frameshift_variant -SO:0001590 terminator_codon_variant -SO:0001591 frame_restoring_variant -SO:0001592 minus_1_frameshift_variant -SO:0001593 minus_2_frameshift_variant -SO:0001594 plus_1_frameshift_variant -SO:0001595 plus_2_frameshift_variant -SO:0001596 transcript_secondary_structure_variant -SO:0001597 compensatory_transcript_secondary_structure_variant -SO:0001598 translational_product_structure_variant -SO:0001599 3D_polypeptide_structure_variant -SO:0001600 complex_3D_structural_variant -SO:0001601 conformational_change_variant -SO:0001602 complex_change_of_translational_product_variant -SO:0001603 polypeptide_sequence_variant -SO:0001604 amino_acid_deletion -SO:0001605 amino_acid_insertion -SO:0001606 amino_acid_substitution -SO:0001607 conservative_amino_acid_substitution -SO:0001608 non_conservative_amino_acid_substitution -SO:0001609 elongated_polypeptide -SO:0001610 elongated_polypeptide_C_terminal -SO:0001611 elongated_polypeptide_N_terminal -SO:0001612 elongated_in_frame_polypeptide_C_terminal -SO:0001613 elongated_out_of_frame_polypeptide_C_terminal -SO:0001614 elongated_in_frame_polypeptide_N_terminal_elongation -SO:0001615 elongated_out_of_frame_polypeptide_N_terminal -SO:0001616 polypeptide_fusion -SO:0001617 polypeptide_truncation -SO:0001618 inactive_catalytic_site -SO:0001619 non_coding_transcript_variant -SO:0001620 mature_miRNA_variant -SO:0001621 NMD_transcript_variant -SO:0001622 UTR_variant -SO:0001623 5_prime_UTR_variant -SO:0001624 3_prime_UTR_variant -SO:0001626 incomplete_terminal_codon_variant -SO:0001627 intron_variant -SO:0001628 intergenic_variant -SO:0001629 splice_site_variant -SO:0001630 splice_region_variant -SO:0001631 upstream_gene_variant -SO:0001632 downstream_gene_variant -SO:0001633 5KB_downstream_variant -SO:0001634 500B_downstream_variant -SO:0001635 5KB_upstream_variant -SO:0001636 2KB_upstream_variant -SO:0001637 rRNA_gene -SO:0001638 piRNA_gene -SO:0001639 RNase_P_RNA_gene -SO:0001640 RNase_MRP_RNA_gene -SO:0001641 lincRNA_gene -SO:0001642 mathematically_defined_repeat -SO:0001643 telomerase_RNA_gene -SO:0001644 targeting_vector -SO:0001645 genetic_marker -SO:0001646 DArT_marker -SO:0001647 kozak_sequence -SO:0001648 nested_transposon -SO:0001649 nested_repeat -SO:0001650 inframe_variant -SO:0001653 retinoic_acid_responsive_element -SO:0001654 nucleotide_to_protein_binding_site -SO:0001655 nucleotide_binding_site -SO:0001656 metal_binding_site -SO:0001657 ligand_binding_site -SO:0001658 nested_tandem_repeat -SO:0001659 promoter_element -SO:0001660 core_promoter_element -SO:0001661 RNA_polymerase_II_TATA_box -SO:0001662 RNA_polymerase_III_TATA_box -SO:0001663 BREd_motif -SO:0001664 DCE -SO:0001665 DCE_SI -SO:0001666 DCE_SII -SO:0001667 DCE_SIII -SO:0001668 proximal_promoter_element -SO:0001669 RNApol_II_core_promoter -SO:0001670 distal_promoter_element -SO:0001671 bacterial_RNApol_promoter_sigma_70 -SO:0001672 bacterial_RNApol_promoter_sigma54 -SO:0001673 minus_12_signal -SO:0001674 minus_24_signal -SO:0001675 A_box_type_1 -SO:0001676 A_box_type_2 -SO:0001677 intermediate_element -SO:0001678 regulatory_promoter_element -SO:0001679 transcription_regulatory_region -SO:0001680 translation_regulatory_region -SO:0001681 recombination_regulatory_region -SO:0001682 replication_regulatory_region -SO:0001683 sequence_motif -SO:0001684 experimental_feature_attribute -SO:0001685 score -SO:0001686 quality_value -SO:0001687 restriction_enzyme_recognition_site -SO:0001688 restriction_enzyme_cleavage_junction -SO:0001689 five_prime_restriction_enzyme_junction -SO:0001690 three_prime_restriction_enzyme_junction -SO:0001691 blunt_end_restriction_enzyme_cleavage_site -SO:0001692 sticky_end_restriction_enzyme_cleavage_site -SO:0001693 blunt_end_restriction_enzyme_cleavage_junction -SO:0001694 single_strand_restriction_enzyme_cleavage_site -SO:0001695 restriction_enzyme_single_strand_overhang -SO:0001696 experimentally_defined_binding_region -SO:0001697 ChIP_seq_region -SO:0001698 ASPE_primer -SO:0001699 dCAPS_primer -SO:0001700 histone_modification -SO:0001701 histone_methylation_site -SO:0001702 histone_acetylation_site -SO:0001703 H3K9_acetylation_site -SO:0001704 H3K14_acetylation_site -SO:0001705 H3K4_monomethylation_site -SO:0001706 H3K4_trimethylation -SO:0001707 H3K9_trimethylation_site -SO:0001708 H3K27_monomethylation_site -SO:0001709 H3K27_trimethylation_site -SO:0001710 H3K79_monomethylation_site -SO:0001711 H3K79_dimethylation_site -SO:0001712 H3K79_trimethylation_site -SO:0001713 H4K20_monomethylation_site -SO:0001714 H2BK5_monomethylation_site -SO:0001715 ISRE -SO:0001716 histone_ubiqitination_site -SO:0001717 H2B_ubiquitination_site -SO:0001718 H3K18_acetylation_site -SO:0001719 H3K23_acylation_site -SO:0001720 epigenetically_modified_region -SO:0001721 H3K27_acylation_site -SO:0001722 H3K36_monomethylation_site -SO:0001723 H3K36_dimethylation_site -SO:0001724 H3K36_trimethylation_site -SO:0001725 H3K4_dimethylation_site -SO:0001726 H3K27_dimethylation_site -SO:0001727 H3K9_monomethylation_site -SO:0001728 H3K9_dimethylation_site -SO:0001729 H4K16_acylation_site -SO:0001730 H4K5_acylation_site -SO:0001731 H4K8_acylation_site -SO:0001732 H3K27_methylation_site -SO:0001733 H3K36_methylation_site -SO:0001734 H3K4_methylation_site -SO:0001735 H3K79_methylation_site -SO:0001736 H3K9_methylation_site -SO:0001737 histone_acylation_region -SO:0001738 H4K_acylation_region -SO:0001739 gene_with_non_canonical_start_codon -SO:0001740 gene_with_start_codon_CUG -SO:0001741 pseudogenic_gene_segment -SO:0001742 copy_number_gain -SO:0001743 copy_number_loss -SO:0001744 UPD -SO:0001745 maternal_uniparental_disomy -SO:0001746 paternal_uniparental_disomy -SO:0001747 open_chromatin_region -SO:0001748 SL3_acceptor_site -SO:0001749 SL4_acceptor_site -SO:0001750 SL5_acceptor_site -SO:0001751 SL6_acceptor_site -SO:0001752 SL7_acceptor_site -SO:0001753 SL8_acceptor_site -SO:0001754 SL9_acceptor_site -SO:0001755 SL10_acceptor_site -SO:0001756 SL11_acceptor_site -SO:0001757 SL12_acceptor_site -SO:0001758 duplicated_pseudogene -SO:0001759 unitary_pseudogene -SO:0001760 non_processed_pseudogene -SO:0001761 variant_quality -SO:0001762 variant_origin -SO:0001763 variant_frequency -SO:0001764 unique_variant -SO:0001765 rare_variant -SO:0001766 polymorphic_variant -SO:0001767 common_variant -SO:0001768 fixed_variant -SO:0001769 variant_phenotype -SO:0001770 benign_variant -SO:0001771 disease_associated_variant -SO:0001772 disease_causing_variant -SO:0001773 lethal_variant -SO:0001774 quantitative_variant -SO:0001775 maternal_variant -SO:0001776 paternal_variant -SO:0001777 somatic_variant -SO:0001778 germline_variant -SO:0001779 pedigree_specific_variant -SO:0001780 population_specific_variant -SO:0001781 de_novo_variant -SO:0001782 TF_binding_site_variant -SO:0001784 complex_structural_alteration -SO:0001785 structural_alteration -SO:0001786 loss_of_heterozygosity -SO:0001787 splice_donor_5th_base_variant -SO:0001788 U_box -SO:0001789 mating_type_region -SO:0001790 paired_end_fragment -SO:0001791 exon_variant -SO:0001792 non_coding_transcript_exon_variant -SO:0001793 clone_end -SO:0001794 point_centromere -SO:0001795 regional_centromere -SO:0001796 regional_centromere_central_core -SO:0001797 centromeric_repeat -SO:0001798 regional_centromere_inner_repeat_region -SO:0001799 regional_centromere_outer_repeat_region -SO:0001800 tasiRNA -SO:0001801 tasiRNA_primary_transcript -SO:0001802 increased_polyadenylation_variant -SO:0001803 decreased_polyadenylation_variant -SO:0001804 DDB_box -SO:0001805 destruction_box -SO:0001806 ER_retention_signal -SO:0001807 KEN_box -SO:0001808 mitochondrial_targeting_signal -SO:0001809 signal_anchor -SO:0001810 PIP_box -SO:0001811 phosphorylation_site -SO:0001812 transmembrane_helix -SO:0001813 vacuolar_sorting_signal -SO:0001814 coding_variant_quality -SO:0001815 synonymous -SO:0001816 non_synonymous -SO:0001817 inframe -SO:0001818 protein_altering_variant -SO:0001819 synonymous_variant -SO:0001820 inframe_indel -SO:0001821 inframe_insertion -SO:0001822 inframe_deletion -SO:0001823 conservative_inframe_insertion -SO:0001824 disruptive_inframe_insertion -SO:0001825 conservative_inframe_deletion -SO:0001826 disruptive_inframe_deletion -SO:0001827 mRNA_read -SO:0001828 genomic_DNA_read -SO:0001829 mRNA_contig -SO:0001830 AFLP_fragment -SO:0001831 protein_hmm_match -SO:0001832 immunoglobulin_region -SO:0001833 V_region -SO:0001834 C_region -SO:0001835 N_region -SO:0001836 S_region -SO:0001837 mobile_element_insertion -SO:0001838 novel_sequence_insertion -SO:0001839 CSL_response_element -SO:0001840 GATA_box -SO:0001841 polymorphic_pseudogene -SO:0001842 AP_1_binding_site -SO:0001843 CRE -SO:0001844 CuRE -SO:0001845 DRE -SO:0001846 FLEX_element -SO:0001847 forkhead_motif -SO:0001848 homol_D_box -SO:0001849 homol_E_box -SO:0001850 HSE -SO:0001851 iron_repressed_GATA_element -SO:0001852 mating_type_M_box -SO:0001853 androgen_response_element -SO:0001854 smFISH_probe -SO:0001855 MCB -SO:0001856 CCAAT_motif -SO:0001857 Ace2_UAS -SO:0001858 TR_box -SO:0001859 STREP_motif -SO:0001860 rDNA_intergenic_spacer_element -SO:0001861 sterol_regulatory_element -SO:0001862 GT_dinucleotide_repeat -SO:0001863 GTT_trinucleotide_repeat -SO:0001864 Sap1_recognition_motif -SO:0001865 CDRE_motif -SO:0001866 BAC_read_contig -SO:0001867 candidate_gene -SO:0001868 positional_candidate_gene -SO:0001869 functional_candidate_gene -SO:0001870 enhancerRNA -SO:0001871 PCB -SO:0001872 rearrangement_region -SO:0001873 interchromosomal_breakpoint -SO:0001874 intrachromosomal_breakpoint -SO:0001875 unassigned_supercontig -SO:0001876 partial_genomic_sequence_assembly -SO:0001877 lnc_RNA -SO:0001878 feature_variant -SO:0001879 feature_ablation -SO:0001880 feature_amplification -SO:0001881 feature_translocation -SO:0001882 feature_fusion -SO:0001883 transcript_translocation -SO:0001884 regulatory_region_translocation -SO:0001885 TFBS_translocation -SO:0001886 transcript_fusion -SO:0001887 regulatory_region_fusion -SO:0001888 TFBS_fusion -SO:0001889 transcript_amplification -SO:0001890 transcript_regulatory_region_fusion -SO:0001891 regulatory_region_amplification -SO:0001892 TFBS_amplification -SO:0001893 transcript_ablation -SO:0001894 regulatory_region_ablation -SO:0001895 TFBS_ablation -SO:0001896 transposable_element_CDS -SO:0001897 transposable_element_pseudogene -SO:0001898 dg_repeat -SO:0001899 dh_repeat -SO:0001900 M26_binding_site -SO:0001901 AACCCT_box -SO:0001902 splice_region -SO:0001903 intronic_lncRNA -SO:0001904 antisense_lncRNA -SO:0001905 regional_centromere_outer_repeat_transcript -SO:0001906 feature_truncation -SO:0001907 feature_elongation -SO:0001908 internal_feature_elongation -SO:0001909 frameshift_elongation -SO:0001910 frameshift_truncation -SO:0001911 copy_number_increase -SO:0001912 copy_number_decrease -SO:0001913 bacterial_RNApol_promoter_sigma_ecf -SO:0001914 rDNA_replication_fork_barrier -SO:0001915 transcription_start_cluster -SO:0001916 CAGE_tag -SO:0001917 CAGE_cluster -SO:0001918 5_methylcytosine -SO:0001919 4_methylcytosine -SO:0001920 N6_methyladenine -SO:0001921 mitochondrial_contig -SO:0001922 mitochondrial_supercontig -SO:0001923 TERRA -SO:0001924 ARRET -SO:0001925 ARIA -SO:0001926 anti_ARRET -SO:0001927 telomeric_transcript -SO:0001928 distal_duplication -SO:0001929 mitochondrial_DNA_read -SO:0001930 chloroplast_DNA_read -SO:0001931 consensus_gDNA -SO:0001932 restriction_enzyme_five_prime_single_strand_overhang -SO:0001933 restriction_enzyme_three_prime_single_strand_overhang -SO:0001934 monomeric_repeat -SO:0001935 H3K20_trimethylation_site -SO:0001936 H3K36_acetylation_site -SO:0001937 H2BK12_acetylation_site -SO:0001938 H2AK5_acetylation_site -SO:0001939 H4K12_acetylation_site -SO:0001940 H2BK120_acetylation_site -SO:0001941 H4K91_acetylation_site -SO:0001942 H2BK20_acetylation_site -SO:0001943 H3K4ac_acetylation_site -SO:0001944 H2AK9_acetylation_site -SO:0001945 H3K56_acetylation_site -SO:0001946 H2BK15_acetylation_site -SO:0001947 H3R2_monomethylation_site -SO:0001948 H3R2_dimethylation_site -SO:0001949 H4R3_dimethylation_site -SO:0001950 H4K4_trimethylation_site -SO:0001951 H3K23_dimethylation_site -SO:0001952 promoter_flanking_region -SO:0001953 restriction_enzyme_assembly_scar -SO:0001954 restriction_enzyme_region -SO:0001955 protein_stability_element -SO:0001956 protease_site -SO:0001957 RNA_stability_element -SO:0001958 lariat_intron -SO:0001959 TCT_motif -SO:0001960 5_hydroxymethylcytosine -SO:0001961 5_formylcytosine -SO:0001962 modified_adenine -SO:0001963 modified_cytosine -SO:0001964 modified_guanine -SO:0001965 8_oxoguanine -SO:0001966 5_carboxylcytosine -SO:0001967 8_oxoadenine -SO:0001968 coding_transcript_variant -SO:0001969 coding_transcript_intron_variant -SO:0001970 non_coding_transcript_intron_variant -SO:0001971 zinc_finger_binding_site -SO:0001972 histone_4_acylation_site -SO:0001973 histone_3_acetylation_site -SO:0001974 CTCF_binding_site -SO:0001975 five_prime_sticky_end_restriction_enzyme_cleavage_site -SO:0001976 three_prime_sticky_end_restriction_enzyme_cleavage_site -SO:0001977 ribonuclease_site -SO:0001978 signature -SO:0001979 RNA_stability_element -SO:0001980 G_box -SO:0001981 L_box -SO:0001982 I-box -SO:0001983 5_prime_UTR_premature_start_codon_variant -SO:0001984 silent_mating_type_cassette_array -SO:0001985 Okazaki_fragment -SO:0001986 upstream_transcript_variant -SO:0001987 downstream_transcript_variant -SO:0001988 5_prime_UTR_premature_start_codon_gain_variant -SO:0001989 5_prime_UTR_premature_start_codon_loss_variant -SO:0001990 five_prime_UTR_premature_start_codon_location_variant -SO:0001991 consensus_AFLP_fragment -SO:0001992 nonsynonymous_variant -SO:0001993 extended_cis_splice_site -SO:0001994 intron_base_5 -SO:0001995 extended_intronic_splice_region_variant -SO:0001996 extended_intronic_splice_region -SO:0001997 subtelomere -SO:0001998 sgRNA -SO:0001999 mating_type_region_motif -SO:0002001 Y_region -SO:0002002 Z1_region -SO:0002003 Z2_region -SO:0002004 ARS_consensus_sequence -SO:0002005 DSR_motif -SO:0002006 zinc_repressed_element -SO:0002007 MNV -SO:0002008 rare_amino_acid_variant -SO:0002009 selenocysteine_loss -SO:0002010 pyrrolysine_loss -SO:0002011 intragenic_variant -SO:0002012 start_lost -SO:0002013 5_prime_UTR_truncation -SO:0002014 5_prime_UTR_elongation -SO:0002015 3_prime_UTR_truncation -SO:0002016 3_prime_UTR_elongation -SO:0002017 conserved_intergenic_variant -SO:0002018 conserved_intron_variant -SO:0002019 start_retained_variant -SO:0002020 boundary_element -SO:0002021 mating_type_region_replication_fork_barrier -SO:0002022 priRNA -SO:0002023 multiplexing_sequence_identifier -SO:0002024 W_region -SO:0002025 cis_acting_homologous_chromosome_pairing_region -SO:0002026 intein_encoding_region -SO:0002027 uORF -SO:0002028 sORF -SO:0002029 tnaORF -SO:0002030 X_region -SO:0002031 shRNA -SO:0002032 moR -SO:0002033 loR -SO:0002034 miR_encoding_snoRNA_primary_transcript -SO:0002035 lncRNA_primary_transcript -SO:0002036 miR_encoding_lncRNA_primary_transcript -SO:0002037 miR_encoding_tRNA_primary_transcript -SO:0002038 shRNA_primary_transcript -SO:0002039 miR_encoding_shRNA_primary_transcript -SO:0002040 vaultRNA_primary_transcript -SO:0002041 miR_encoding_vaultRNA_primary_transcript -SO:0002042 Y_RNA_primary_transcript -SO:0002043 miR_encoding_Y_RNA_primary_transcript -SO:0002044 TCS_element -SO:0002045 pheromone_response_element -SO:0002046 FRE -SO:0002047 transcription_pause_site -SO:0002048 disabled_reading_frame -SO:0002049 H3K27_acetylation_site -SO:0002050 constitutive_promoter -SO:0002051 inducible_promoter -SO:0002052 dominant_negative_variant -SO:0002053 gain_of_function_variant -SO:0002054 loss_of_function_variant -SO:0002055 null_mutation -SO:0002056 intronic_splicing_silencer -SO:0002057 intronic_splicing_enhancer -SO:0002058 exonic_splicing_silencer -SO:0002059 recombination_enhancer -SO:0002060 interchomosomal_translocation -SO:0002061 intrachomosomal_translocation -SO:0002062 complex_chromosomal_rearrangement -SO:0002063 alu_insertion -SO:0002064 LINE1_insertion -SO:0002065 SVA_insertion -SO:0005836 regulatory_region -SO:0005837 U14_snoRNA_primary_transcript -SO:0005841 methylation_guide_snoRNA -SO:0005843 rRNA_cleavage_RNA -SO:0005845 exon_of_single_exon_gene -SO:0005847 cassette_array_member -SO:0005848 gene_cassette_member -SO:0005849 gene_subarray_member -SO:0005850 primer_binding_site -SO:0005851 gene_array -SO:0005852 gene_subarray -SO:0005853 gene_cassette -SO:0005854 gene_cassette_array -SO:0005855 gene_group -SO:0005856 selenocysteine_tRNA_primary_transcript -SO:0005857 selenocysteinyl_tRNA -SO:0005858 syntenic_region -SO:0100001 biochemical_region_of_peptide -SO:0100002 molecular_contact_region -SO:0100003 intrinsically_unstructured_polypeptide_region -SO:0100004 catmat_left_handed_three -SO:0100005 catmat_left_handed_four -SO:0100006 catmat_right_handed_three -SO:0100007 catmat_right_handed_four -SO:0100008 alpha_beta_motif -SO:0100009 lipoprotein_signal_peptide -SO:0100010 no_output -SO:0100011 cleaved_peptide_region -SO:0100012 peptide_coil -SO:0100013 hydrophobic_region_of_peptide -SO:0100014 n_terminal_region -SO:0100015 c_terminal_region -SO:0100016 central_hydrophobic_region_of_signal_peptide -SO:0100017 polypeptide_conserved_motif -SO:0100018 polypeptide_binding_motif -SO:0100019 polypeptide_catalytic_motif -SO:0100020 polypeptide_DNA_contact -SO:0100021 polypeptide_conserved_region -SO:1000002 substitution -SO:1000005 complex_substitution -SO:1000008 point_mutation -SO:1000009 transition -SO:1000010 pyrimidine_transition -SO:1000011 C_to_T_transition -SO:1000012 C_to_T_transition_at_pCpG_site -SO:1000013 T_to_C_transition -SO:1000014 purine_transition -SO:1000015 A_to_G_transition -SO:1000016 G_to_A_transition -SO:1000017 transversion -SO:1000018 pyrimidine_to_purine_transversion -SO:1000019 C_to_A_transversion -SO:1000020 C_to_G_transversion -SO:1000021 T_to_A_transversion -SO:1000022 T_to_G_transversion -SO:1000023 purine_to_pyrimidine_transversion -SO:1000024 A_to_C_transversion -SO:1000025 A_to_T_transversion -SO:1000026 G_to_C_transversion -SO:1000027 G_to_T_transversion -SO:1000028 intrachromosomal_mutation -SO:1000029 chromosomal_deletion -SO:1000030 chromosomal_inversion -SO:1000031 interchromosomal_mutation -SO:1000032 indel -SO:1000035 duplication -SO:1000036 inversion -SO:1000037 chromosomal_duplication -SO:1000038 intrachromosomal_duplication -SO:1000039 direct_tandem_duplication -SO:1000040 inverted_tandem_duplication -SO:1000041 intrachromosomal_transposition -SO:1000042 compound_chromosome -SO:1000043 Robertsonian_fusion -SO:1000044 chromosomal_translocation -SO:1000045 ring_chromosome -SO:1000046 pericentric_inversion -SO:1000047 paracentric_inversion -SO:1000048 reciprocal_chromosomal_translocation -SO:1000049 sequence_variation_affecting_transcript -SO:1000050 sequence_variant_causing_no_change_in_transcript -SO:1000054 sequence_variation_affecting_coding_sequence -SO:1000055 sequence_variant_causing_initiator_codon_change_in_transcript -SO:1000056 sequence_variant_causing_amino_acid_coding_codon_change_in_transcript -SO:1000057 sequence_variant_causing_synonymous_codon_change_in_transcript -SO:1000058 sequence_variant_causing_non_synonymous_codon_change_in_transcript -SO:1000059 sequence_variant_causing_missense_codon_change_in_transcript -SO:1000060 sequence_variant_causing_conservative_missense_codon_change_in_transcript -SO:1000061 sequence_variant_causing_nonconservative_missense_codon_change_in_transcript -SO:1000062 sequence_variant_causing_nonsense_codon_change_in_transcript -SO:1000063 sequence_variant_causing_terminator_codon_change_in_transcript -SO:1000064 sequence_variation_affecting_reading_frame -SO:1000065 frameshift_sequence_variation -SO:1000066 sequence_variant_causing_plus_1_frameshift_mutation -SO:1000067 sequence_variant_causing_minus_1_frameshift -SO:1000068 sequence_variant_causing_plus_2_frameshift -SO:1000069 sequence_variant_causing_minus_2_frameshift -SO:1000070 sequence_variant_affecting_transcript_processing -SO:1000071 sequence_variant_affecting_splicing -SO:1000072 sequence_variant_affecting_splice_donor -SO:1000073 sequence_variant_affecting_splice_acceptor -SO:1000074 sequence_variant_causing_cryptic_splice_activation -SO:1000075 sequence_variant_affecting_editing -SO:1000076 sequence_variant_affecting_transcription -SO:1000078 sequence_variant_decreasing_rate_of_transcription -SO:1000079 sequence_variation_affecting_transcript_sequence -SO:1000080 sequence_variant_increasing_rate_of_transcription -SO:1000081 sequence_variant_affecting_rate_of_transcription -SO:1000082 sequence variant_affecting_transcript_stability -SO:1000083 sequence_variant_increasing_transcript_stability -SO:1000084 sequence_variant_decreasing_transcript_stability -SO:1000085 sequence_variation_affecting_level_of_transcript -SO:1000086 sequence_variation_decreasing_level_of_transcript -SO:1000087 sequence_variation_increasing_level_of_transcript -SO:1000088 sequence_variant_affecting_translational_product -SO:1000089 sequence_variant_causing_no_change_of_translational_product -SO:1000092 sequence_variant_causing_complex_change_of_translational_product -SO:1000093 sequence_variant_causing_amino_acid_substitution -SO:1000094 sequence_variant_causing_conservative_amino_acid_substitution -SO:1000095 sequence_variant_causing_nonconservative_amino_acid_substitution -SO:1000096 sequence_variant_causing_amino_acid_insertion -SO:1000097 sequence_variant_causing_amino_acid_deletion -SO:1000098 sequence_variant_causing_polypeptide_truncation -SO:1000099 sequence_variant_causing_polypeptide_elongation -SO:1000100 mutation_causing_polypeptide_N_terminal_elongation -SO:1000101 mutation_causing_polypeptide_C_terminal_elongation -SO:1000102 sequence_variant_affecting_level_of_translational_product -SO:1000103 sequence_variant_decreasing_level_of_translation_product -SO:1000104 sequence_variant_increasing_level_of_translation_product -SO:1000105 sequence_variant_affecting_polypeptide_amino_acid_sequence -SO:1000106 mutation_causing_inframe_polypeptide_N_terminal_elongation -SO:1000107 mutation_causing_out_of_frame_polypeptide_N_terminal_elongation -SO:1000108 mutaton_causing_inframe_polypeptide_C_terminal_elongation -SO:1000109 mutation_causing_out_of_frame_polypeptide_C_terminal_elongation -SO:1000110 frame_restoring_sequence_variant -SO:1000111 sequence_variant_affecting_3D_structure_of_polypeptide -SO:1000112 sequence_variant_causing_no_3D_structural_change -SO:1000115 sequence_variant_causing_complex_3D_structural_change -SO:1000116 sequence_variant_causing_conformational_change -SO:1000117 sequence_variant_affecting_polypeptide_function -SO:1000118 sequence_variant_causing_loss_of_function_of_polypeptide -SO:1000119 sequence_variant_causing_inactive_ligand_binding_site -SO:1000120 sequence_variant_causing_inactive_catalytic_site -SO:1000121 sequence_variant_causing_polypeptide_localization_change -SO:1000122 sequence_variant_causing_polypeptide_post_translational_processing_change -SO:1000123 polypeptide_post_translational_processing_affected -SO:1000124 sequence_variant_causing_partial_loss_of_function_of_polypeptide -SO:1000125 sequence_variant_causing_gain_of_function_of_polypeptide -SO:1000126 sequence_variant_affecting_transcript_secondary_structure -SO:1000127 sequence_variant_causing_compensatory_transcript_secondary_structure_mutation -SO:1000132 sequence_variant_effect -SO:1000134 sequence_variant_causing_polypeptide_fusion -SO:1000136 autosynaptic_chromosome -SO:1000138 homo_compound_chromosome -SO:1000140 hetero_compound_chromosome -SO:1000141 chromosome_fission -SO:1000142 dexstrosynaptic_chromosome -SO:1000143 laevosynaptic_chromosome -SO:1000144 free_duplication -SO:1000145 free_ring_duplication -SO:1000147 deficient_translocation -SO:1000148 inversion_cum_translocation -SO:1000149 bipartite_duplication -SO:1000150 cyclic_translocation -SO:1000151 bipartite_inversion -SO:1000152 uninverted_insertional_duplication -SO:1000153 inverted_insertional_duplication -SO:1000154 insertional_duplication -SO:1000155 interchromosomal_transposition -SO:1000156 inverted_interchromosomal_transposition -SO:1000157 uninverted_interchromosomal_transposition -SO:1000158 inverted_intrachromosomal_transposition -SO:1000159 uninverted_intrachromosomal_transposition -SO:1000160 unoriented_insertional_duplication -SO:1000161 unoriented_interchromosomal_transposition -SO:1000162 unoriented_intrachromosomal_transposition -SO:1000170 uncharacterized_chromosomal_mutation -SO:1000171 deficient_inversion -SO:1000173 tandem_duplication -SO:1000175 partially_characterized_chromosomal_mutation -SO:1000180 sequence_variant_affecting_gene_structure -SO:1000181 sequence_variant_causing_gene_fusion -SO:1000182 chromosome_number_variation -SO:1000183 chromosome_structure_variation -SO:1000184 sequence_variant_causes_exon_loss -SO:1000185 sequence_variant_causes_intron_gain -SO:1000186 sequence_variant_causing_cryptic_splice_donor_activation -SO:1001186 sequence_variant_causing_cryptic_splice_acceptor_activation -SO:1001187 alternatively_spliced_transcript -SO:1001188 encodes_1_polypeptide -SO:1001189 encodes_greater_than_1_polypeptide -SO:1001190 encodes_different_polypeptides_different_stop -SO:1001191 encodes_overlapping_peptides_different_start -SO:1001192 encodes_disjoint_polypeptides -SO:1001193 encodes_overlapping_polypeptides_different_start_and_stop -SO:1001194 alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping -SO:1001195 encodes_overlapping_peptides -SO:1001196 cryptogene -SO:1001197 dicistronic_primary_transcript -SO:1001217 member_of_regulon -SO:1001244 alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping -SO:1001246 CDS_independently_known -SO:1001247 orphan_CDS -SO:1001249 CDS_supported_by_domain_match_data -SO:1001251 CDS_supported_by_sequence_similarity_data -SO:1001254 CDS_predicted -SO:1001255 status_of_coding_sequence -SO:1001259 CDS_supported_by_EST_or_cDNA_data -SO:1001260 internal_Shine_Dalgarno_sequence -SO:1001261 recoded_mRNA -SO:1001262 minus_1_translationally_frameshifted -SO:1001263 plus_1_translationally_frameshifted -SO:1001264 mRNA_recoded_by_translational_bypass -SO:1001265 mRNA_recoded_by_codon_redefinition -SO:1001266 stop_codon_redefinition_as_selenocysteine -SO:1001267 stop_codon_readthrough -SO:1001268 recoding_stimulatory_region -SO:1001269 four_bp_start_codon -SO:1001270 stop_codon_redefinition_as_pyrrolysine -SO:1001271 archaeal_intron -SO:1001272 tRNA_intron -SO:1001273 CTG_start_codon -SO:1001274 SECIS_element -SO:1001275 retron -SO:1001277 three_prime_recoding_site -SO:1001279 three_prime_stem_loop_structure -SO:1001280 five_prime_recoding_site -SO:1001281 flanking_three_prime_quadruplet_recoding_signal -SO:1001282 UAG_stop_codon_signal -SO:1001283 UAA_stop_codon_signal -SO:1001284 regulon -SO:1001285 UGA_stop_codon_signal -SO:1001286 three_prime_repeat_recoding_signal -SO:1001287 distant_three_prime_recoding_signal -SO:1001288 stop_codon_signal -SO:2000061 databank_entry -SO:3000000 gene_segment -SO:3000001 non_coding_exon_variant diff --git a/tests/data/repo.db b/tests/data/repo.db index cfda9535a59c1e22ea1d40868063e9120733f856..676a66e691ac238d9a1f1cc6b20406eb335a7876 100644 GIT binary patch delta 17957 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zL0{j|tb&r1+YOgK;D@wV0ahKm#XL76-0jN?+{8!8*c!|fp8pQ}eVgM~;Me%o69eDP zU$}gH<>r%LeD9`_O=zh)GwyIIxlo92c*4zGdDgwTk*MW7zS7G4aw;Xxh2_LNGU~0i zu@P@^&8AC4nd(P|xz_eAg%?IjqhPYJn!LzlYHm>+S&ce|oGjFyq@@i31vl)!wb8># z)GmR-H2m^+A2}}{GdFjCanTgpeaR65gp*ZnhU%^ji0*TOXTb6=;(~vU=Rd5l6PEaU zP-J6kBeAmuT7b<|Z8^2OwYIW*utw#A-CDe-kV~1Ok{5$`~Sv5CIIzIVFCx3QcT`8MzLDG~O~pa#Z6zs-5JHkOZw z(vu<-z*xG`OE(rap8@54$~jbys_-h+m73O3)xl>0z5f-Y`RAtZ*O diff --git a/tests/datadriven/test_ontologies.py b/tests/datadriven/test_ontologies.py new file mode 100644 index 000000000..eb5c33680 --- /dev/null +++ b/tests/datadriven/test_ontologies.py @@ -0,0 +1,62 @@ +""" +Data-driven tests for ontologies. +""" +from __future__ import division +from __future__ import print_function +from __future__ import unicode_literals + +import os.path + +# TODO it may be a bit circular to use obo_parser as our method of +# accessing ontology information, since this is the method we use +# in the main code. However, other libraries have very heavy dependencies. +import goatools.obo_parser as obo_parser + +import ga4gh.protocol as protocol +import ga4gh.datamodel.ontologies as ontologies + +import tests.datadriven as datadriven +import tests.paths as paths + + +def testReferenceSets(): + testDataDir = os.path.join(paths.testDataDir, "ontologies") + pattern = "*.obo" + for test in datadriven.makeTests( + testDataDir, OntologyTest, pattern): + yield test + + +class OntologyTest(datadriven.DataDrivenTest): + """ + Data driven test class for ontologies. + """ + def __init__(self, localId, oboFile): + super(OntologyTest, self).__init__(localId, oboFile) + self._oboReader = obo_parser.OBOReader(obo_file=oboFile) + + def getDataModelInstance(self, localId, dataPath): + ontology = ontologies.Ontology(localId) + ontology.populateFromFile(dataPath) + return ontology + + def testProtocolElementValid(self): + # We don't have a protocol element here so this isn't meaningful. + pass + + def testGoodMappings(self): + ontology = self._gaObject + for term in self._oboReader: + self.assertIn(term.id, ontology.getTermIds(term.name)) + gaTerm = ontology.getGaTermByName(term.name) + self.assertValid( + protocol.OntologyTerm, gaTerm.toJsonDict()) + self.assertEqual(gaTerm.term, term.name) + self.assertIn(gaTerm.id, ontology.getTermIds(term.name)) + self.assertEqual( + gaTerm.sourceVersion, ontology.getSourceVersion()) + self.assertEqual(gaTerm.sourceName, ontology.getName()) + + def testBadMappings(self): + for badName in ["Not a term", None, 1234]: + self.assertEqual(0, len(self._gaObject.getTermIds(badName))) diff --git a/tests/datadriven/test_sequenceAnnotations.py b/tests/datadriven/test_sequenceAnnotations.py index b4ff655cc..e9f18327f 100644 --- a/tests/datadriven/test_sequenceAnnotations.py +++ b/tests/datadriven/test_sequenceAnnotations.py @@ -112,8 +112,7 @@ def __init__(self, featureSetLocalName, dataPath): self._dataset = datasets.Dataset(_datasetName) self._repo = datarepo.SqlDataRepository(paths.testDataRepo) self._repo.open(datarepo.MODE_READ) - self._sequenceOntologyTermMap = self._repo.getOntologyTermMapByName( - "sequence_ontology") + self._ontology = self._repo.getOntologyByName(paths.ontologyName) self._referenceSet = references.AbstractReferenceSet("test_rs") featureSetLocalName = featureSetLocalName[:-3] # remove '.db' self._testData = _testDataForFeatureSetName[featureSetLocalName] @@ -125,7 +124,7 @@ def getProtocolClass(self): def getDataModelInstance(self, localId, dataPath): featureSet = sequenceAnnotations.Gff3DbFeatureSet( self._dataset, localId) - featureSet.setSequenceOntologyTermMap(self._sequenceOntologyTermMap) + featureSet.setOntology(self._ontology) featureSet.setReferenceSet(self._referenceSet) featureSet.populateFromFile(dataPath) return featureSet diff --git a/tests/datadriven/test_variant_annotations.py b/tests/datadriven/test_variant_annotations.py index 4065a0ca4..45490dc23 100644 --- a/tests/datadriven/test_variant_annotations.py +++ b/tests/datadriven/test_variant_annotations.py @@ -17,6 +17,7 @@ import ga4gh.datamodel.ontologies as ontologies import ga4gh.protocol as protocol import tests.datadriven as datadriven +import tests.paths as paths def testVariantAnnotationSets(): @@ -116,10 +117,10 @@ def getDataModelInstance(self, localId, dataPath): referenceSet = references.AbstractReferenceSet("rs") variantSet.setReferenceSet(referenceSet) if variantSet.isAnnotated(): - sequenceOntology = ontologies.OntologyTermMap( - "sequence_ontology") + sequenceOntology = ontologies.Ontology(paths.ontologyName) + sequenceOntology.populateFromFile(paths.ontologyPath) annotationSet = variantSet.getVariantAnnotationSets()[0] - annotationSet.setSequenceOntologyTermMap(sequenceOntology) + annotationSet.setOntology(sequenceOntology) return annotationSet else: return variantSet diff --git a/tests/end_to_end/test_repo_manager.py b/tests/end_to_end/test_repo_manager.py index 67b01e0db..5565d48a7 100644 --- a/tests/end_to_end/test_repo_manager.py +++ b/tests/end_to_end/test_repo_manager.py @@ -44,16 +44,24 @@ def testEndToEnd(self): '-R', paths.referenceSetName, '-n', paths.readGroupSetName) self._runCmd( "add-featureset", self.datasetName, paths.featuresPath, - '-R', paths.referenceSetName) + '-R', paths.referenceSetName, '-O', paths.ontologyName) # ensure we can handle trailing slashes vcfPath = paths.vcfDirPath + '/' self._runCmd( "add-variantset", self.datasetName, vcfPath, '-R', paths.referenceSetName) + variantAnnotationSetName = "vas" + self._runCmd( + "add-variantset", self.datasetName, + paths.annotatedVcfPath, '-R', paths.referenceSetName, + "-aO", paths.ontologyName, "-n", variantAnnotationSetName) + self._runCmd("verify") self._runCmd("list") self._runCmd( - "remove-variantset", self.datasetName, paths.variantSetName, + "remove-variantset", self.datasetName, paths.variantSetName, "-f") + self._runCmd( + "remove-variantset", self.datasetName, variantAnnotationSetName, "-f") self._runCmd( "remove-readgroupset", self.datasetName, diff --git a/tests/paths.py b/tests/paths.py index 11e3e54c1..275edd1df 100644 --- a/tests/paths.py +++ b/tests/paths.py @@ -25,19 +25,19 @@ testDataDir, 'datasets/dataset1/variants/1kgPhase1') vcfDirPath2 = os.path.join( testDataDir, 'datasets/dataset1/variants/1kgPhase3') -vcfPath1 = os.path.join( - vcfDirPath, 'chr1.vcf.gz') +vcfPath1 = os.path.join(vcfDirPath, 'chr1.vcf.gz') vcfPath2 = os.path.join( vcfDirPath, 'chr2.vcf.gz') vcfIndexPath1 = os.path.join( vcfDirPath, 'chr1.vcf.gz.tbi') vcfIndexPath2 = os.path.join( vcfDirPath, 'chr2.vcf.gz.tbi') +annotatedVcfPath = os.path.join( + testDataDir, 'datasets/dataset1/variants/1kg.3.annotations') - -ontologyName = "sequence_ontology" -ontologyPath = os.path.join( - testDataDir, 'ontologymaps/sequence_ontology/sequence_ontology.txt') +# Ontologies +ontologyName = "so-xp-simple" +ontologyPath = os.path.join(testDataDir, 'ontologies/so-xp-simple.obo') # reads readGroupSetName = 'chr17.1-250' diff --git a/tests/unit/test_repo_manager.py b/tests/unit/test_repo_manager.py index adb2c0b04..7b0a25de5 100644 --- a/tests/unit/test_repo_manager.py +++ b/tests/unit/test_repo_manager.py @@ -115,9 +115,11 @@ def addVariantSet(self): def addFeatureSet(self): featuresPath = paths.featuresPath self._featureSetName = paths.featureSetName - cmd = "add-featureset {} {} {} --referenceSetName={}".format( + cmd = ( + "add-featureset {} {} {} --referenceSetName={} " + "--ontologyName={}").format( self._repoPath, self._datasetName, featuresPath, - self._referenceSetName) + self._referenceSetName, self._ontologyName) self.runCommand(cmd) def getFeatureSet(self): @@ -135,9 +137,9 @@ def setUp(self): self.addDataset() self.addOntology() self.addReferenceSet() - self.addFeatureSet() def testAddFeatureSet(self): + self.addFeatureSet() featureSet = self.getFeatureSet() self.assertEqual(featureSet.getLocalId(), self._featureSetName) self.assertEqual( @@ -149,6 +151,41 @@ def testAddFeatureSet(self): # self.assertEqual(featureSet.getInfo(), "TODO") # self.assertEqual(featureSet.getSourceUrl(), "TODO") + def testAddFeatureSetNoReferenceSet(self): + featuresPath = paths.featuresPath + cmd = "add-featureset {} {} {} --ontologyName={}".format( + self._repoPath, self._datasetName, featuresPath, + self._ontologyName) + self.assertRaises( + exceptions.RepoManagerException, self.runCommand, cmd) + + def testAddFeatureSetBadReferenceSet(self): + featuresPath = paths.featuresPath + cmd = ( + "add-featureset {} {} {} --referenceSetName=notafefset " + "--ontologyName={}").format( + self._repoPath, self._datasetName, featuresPath, + self._ontologyName) + self.assertRaises( + exceptions.ReferenceSetNameNotFoundException, + self.runCommand, cmd) + + def testAddFeatureSetNoOntology(self): + featuresPath = paths.featuresPath + cmd = "add-featureset {} {} {} --referenceSetName={} ".format( + self._repoPath, self._datasetName, featuresPath, + self._referenceSetName) + self.assertRaises( + exceptions.RepoManagerException, self.runCommand, cmd) + + def testAddFeatureSetBadOntology(self): + featuresPath = paths.featuresPath + cmd = "add-featureset {} {} {} --referenceSetName={} ".format( + self._repoPath, self._datasetName, featuresPath, + self._referenceSetName) + self.assertRaises( + exceptions.RepoManagerException, self.runCommand, cmd) + class TestRemoveFeatureSet(AbstractRepoManagerTest): @@ -240,38 +277,55 @@ def setUp(self): self.init() def testDefaults(self): - mapFile = paths.ontologyPath - name = os.path.split(mapFile)[1].split(".")[0] - self.runCommand("add-ontology {} {}".format(self._repoPath, mapFile)) + ontologyFile = paths.ontologyPath + name = os.path.split(ontologyFile)[1].split(".")[0] + self.runCommand("add-ontology {} {}".format( + self._repoPath, ontologyFile)) repo = self.readRepo() - ontologyTermMap = repo.getOntologyTermMapByName(name) - self.assertEqual(ontologyTermMap.getLocalId(), name) - self.assertEqual(ontologyTermMap.getDataUrl(), mapFile) + ontology = repo.getOntologyByName(name) + self.assertEqual(ontology.getName(), name) + self.assertEqual(ontology.getDataUrl(), ontologyFile) def testWithName(self): - mapFile = paths.ontologyPath + ontologyFile = paths.ontologyPath name = "test_name" self.runCommand("add-ontology {} {} --name={}".format( - self._repoPath, mapFile, name)) + self._repoPath, ontologyFile, name)) repo = self.readRepo() - ontologyTermMap = repo.getOntologyTermMapByName(name) - self.assertEqual(ontologyTermMap.getLocalId(), name) - self.assertEqual(ontologyTermMap.getDataUrl(), mapFile) + ontology = repo.getOntologyByName(name) + self.assertEqual(ontology.getName(), name) + self.assertEqual(ontology.getDataUrl(), ontologyFile) def testWithSameName(self): - mapFile = paths.ontologyPath + ontologyFile = paths.ontologyPath # Default name - cmd = "add-ontology {} {}".format(self._repoPath, mapFile) + cmd = "add-ontology {} {}".format(self._repoPath, ontologyFile) self.runCommand(cmd) self.assertRaises( exceptions.RepoManagerException, self.runCommand, cmd) # Specified name cmd = "add-ontology {} {} --name=testname".format( - self._repoPath, mapFile) + self._repoPath, ontologyFile) self.runCommand(cmd) self.assertRaises( exceptions.DuplicateNameException, self.runCommand, cmd) + def testMissingFile(self): + cmd = "add-ontology {} {}".format(self._repoPath, "/no/such/file") + self.assertRaises( + exceptions.FileOpenFailedException, self.runCommand, cmd) + + def testNonOboTextFile(self): + cmd = "add-ontology {} {}".format( + self._repoPath, paths.landingMessageHtml) + self.assertRaises( + exceptions.OntologyFileFormatException, self.runCommand, cmd) + + def testNonOboBinaryFile(self): + cmd = "add-ontology {} {}".format(self._repoPath, paths.bamPath) + self.assertRaises( + exceptions.OntologyFileFormatException, self.runCommand, cmd) + class TestRemoveDataset(AbstractRepoManagerTest): @@ -393,7 +447,7 @@ def assertOntologyRemoved(self): repo = self.readRepo() self.assertRaises( exceptions.OntologyNameNotFoundException, - repo.getOntologyTermMapByName, self._ontologyName) + repo.getOntologyByName, self._ontologyName) def testDefaults(self): self.runCommand("remove-ontology {} {} -f".format( @@ -607,6 +661,55 @@ def testMissingReferenceSet(self): # for the dataFiles argument, and other common error cases in the UI. +class TestAddAnnotatedVariantSet(AbstractRepoManagerTest): + + def setUp(self): + super(TestAddAnnotatedVariantSet, self).setUp() + self.init() + self.addDataset() + self.addReferenceSet() + self.addOntology() + self.vcfDir = paths.annotatedVcfPath + + def testNoAnnotations(self): + name = "test_vs_no_annotations" + cmd = "add-variantset {} {} {} -R {} -n {}".format( + self._repoPath, self._datasetName, self.vcfDir, + self._referenceSetName, name) + self.runCommand(cmd) + repo = self.readRepo() + dataset = repo.getDatasetByName(self._datasetName) + variantSet = dataset.getVariantSetByName(name) + self.assertEqual(len(variantSet.getVariantAnnotationSets()), 0) + + def testAnnotations(self): + name = "test_vs_annotations" + cmd = "add-variantset {} {} {} -R {} -n {} -aO {}".format( + self._repoPath, self._datasetName, self.vcfDir, + self._referenceSetName, name, self._ontologyName) + self.runCommand(cmd) + repo = self.readRepo() + dataset = repo.getDatasetByName(self._datasetName) + variantSet = dataset.getVariantSetByName(name) + self.assertEqual(len(variantSet.getVariantAnnotationSets()), 1) + + def testAnnotationsNoOntology(self): + name = "test_vs_annotations" + cmd = "add-variantset {} {} {} -R {} -n {} -a".format( + self._repoPath, self._datasetName, self.vcfDir, + self._referenceSetName, name) + self.assertRaises( + exceptions.RepoManagerException, self.runCommand, cmd) + + def testAnnotationsBadOntology(self): + name = "test_vs_annotations" + cmd = "add-variantset {} {} {} -R {} -n {} -aO {}".format( + self._repoPath, self._datasetName, self.vcfDir, + self._referenceSetName, name, "not_an_ontology") + self.assertRaises( + exceptions.OntologyNameNotFoundException, self.runCommand, cmd) + + class TestDuplicateNameDelete(AbstractRepoManagerTest): """ If two objects exist with the same name in different datasets, @@ -667,14 +770,14 @@ def testVariantSetDelete(self): self.assertEqual(len(self.dataset2.getVariantSets()), 1) def testFeatureSetDelete(self): - cmdString = "add-featureset {} {} {} --referenceSetName={}" + cmdString = "add-featureset {} {} {} -R {} -O {}" addFeatureSetCmd1 = cmdString.format( self._repoPath, self.dataset1Name, paths.featuresPath, - self._referenceSetName) + self._referenceSetName, self._ontologyName) self.runCommand(addFeatureSetCmd1) addFeatureSetCmd2 = cmdString.format( self._repoPath, self.dataset2Name, paths.featuresPath, - self._referenceSetName) + self._referenceSetName, self._ontologyName) self.runCommand(addFeatureSetCmd2) removeCmd = "remove-featureset {} {} {} -f".format( self._repoPath, self.dataset1Name, paths.featureSetName) diff --git a/tests/unit/test_variant_annotations.py b/tests/unit/test_variant_annotations.py index abfb93493..f94f12a1b 100644 --- a/tests/unit/test_variant_annotations.py +++ b/tests/unit/test_variant_annotations.py @@ -34,8 +34,8 @@ def _createVariantAnnotationSet(self, vcfDir): self._variantSet.populateFromDirectory(vcfDir) self._variantAnnotationSet = variants.HtslibVariantAnnotationSet( self._variantSet, "testVAs") - self._variantAnnotationSet.setSequenceOntologyTermMap( - self._repo.getOntologyTermMapByName("sequence_ontology")) + self._variantAnnotationSet.setOntology( + self._repo.getOntologyByName(paths.ontologyName)) def setUp(self): vcfDir = "tests/data/datasets/dataset1/variants/WASH7P_annotation" From 13ec0c25d608671ffad421d79879c1a71110e7db Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Wed, 18 May 2016 17:57:46 +0100 Subject: [PATCH 10/13] Copied obo_parser.py from goatools into source. --- .travis.yml | 3 +- ga4gh/datamodel/obo_parser.py | 690 ++++++++++++++++++++++++++++ ga4gh/datamodel/ontologies.py | 2 +- requirements.txt | 1 - tests/datadriven/test_ontologies.py | 2 +- tests/unit/test_imports.py | 1 + 6 files changed, 695 insertions(+), 4 deletions(-) create mode 100644 ga4gh/datamodel/obo_parser.py diff --git a/.travis.yml b/.travis.yml index 15521cafa..9980fe778 100644 --- a/.travis.yml +++ b/.travis.yml @@ -30,7 +30,8 @@ before_script: # run_tests.py runs everything under the script: tag so only put commands # under it that we want to run (and want to be able to run) as local tests script: - - flake8 *.py tests ga4gh scripts --exclude=ez_setup.py + - flake8 *.py tests ga4gh scripts + --exclude=ez_setup.py,ga4gh/datamodel/obo_parser.py - nosetests --with-coverage --cover-package ga4gh --cover-inclusive --cover-min-percentage 80 --cover-branches --cover-erase diff --git a/ga4gh/datamodel/obo_parser.py b/ga4gh/datamodel/obo_parser.py new file mode 100644 index 000000000..ba3642d7c --- /dev/null +++ b/ga4gh/datamodel/obo_parser.py @@ -0,0 +1,690 @@ +# Copyright 2010-2016 by Haibao Tang et al. All rights reserved. +# +# This code is part of the goatools distribution and goverend by its +# license. Please see the LICENSE file included with goatools. + +# This file was copied from https://github.com/tanghaibao/goatools on +# 2016-05-18. The file is unaltered other than adding this notice and +# by including the text of the LICENSE file here: + +# Copyright (c) 2010-2014, Haibao Tang +# All rights reserved. +# +# Redistribution and use in source and binary forms, with or without modification, +# are permitted provided that the following conditions are met: +# +# Redistributions of source code must retain the above copyright notice, this list +# of conditions and the following disclaimer. +# +# Redistributions in binary form must reproduce the above copyright notice, this +# list of conditions and the following disclaimer in the documentation and/or +# other materials provided with the distribution. +# +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR +# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +"""Read and store Gene Ontology's obo file.""" +# -*- coding: UTF-8 -*- +from __future__ import print_function +from collections import defaultdict +import sys +import os +import re + +GraphEngines = ("pygraphviz", "pydot") + +__copyright__ = "Copyright (C) 2010-2016, H Tang et al., All rights reserved." +__author__ = "various" + +class OBOReader(object): + """Read goatools.org's obo file. Load into this iterable class. + + Download obo from: http://geneontology.org/ontology/go-basic.obo + + >>> reader = OBOReader() + >>> for rec in reader: + print rec + """ + + def __init__(self, obo_file="go-basic.obo", optional_attrs=None): + """Read obo file. Load dictionary.""" + self._init_optional_attrs(optional_attrs) + self.format_version = None + self.data_version = None + self.typedefs = {} + + # True if obo file exists or if a link to an obo file exists. + if os.path.isfile(obo_file): + self.obo_file = obo_file + # GOTerm attributes that are necessary for any operations: + else: + raise Exception("download obo file first\n " + "[http://geneontology.org/ontology/" + "go-basic.obo]") + + def __iter__(self): + """Return one GO Term record at a time from an obo file.""" + # Written by DV Klopfenstein + # Wait to open file until needed. Automatically close file when done. + with open(self.obo_file) as fstream: + rec_curr = None # Stores current GO Term + typedef_curr = None # Stores current typedef + for lnum, line in enumerate(fstream): + # obo lines start with any of: [Term], [Typedef], /^\S+:/, or /^\s*/ + if self.data_version is None: + self._init_obo_version(line) + if line[0:6].lower() == "[term]": + rec_curr = self._init_goterm_ref(rec_curr, "Term", lnum) + elif line[0:9].lower() == "[typedef]": + typedef_curr = self._init_typedef(rec_curr, "Typedef", lnum) + elif rec_curr is not None or typedef_curr is not None: + line = line.rstrip() # chomp + if ":" in line: + if rec_curr is not None: + self._add_to_ref(rec_curr, line, lnum) + else: + self._add_to_typedef(typedef_curr, line, lnum) + elif line == "": + if rec_curr is not None: + yield rec_curr + rec_curr = None + elif typedef_curr is not None: + # Save typedef. + self.typedefs[typedef_curr.id] = typedef_curr + typedef_curr = None + else: + self._die("UNEXPECTED LINE CONTENT: {L}".format(L=line), lnum) + # Return last record, if necessary + if rec_curr is not None: + yield rec_curr + + def _init_obo_version(self, line): + """Save obo version and release.""" + if line[0:14] == "format-version": + self.format_version = line[16:-1] + if line[0:12] == "data-version": + self.data_version = line[14:-1] + + def _init_goterm_ref(self, rec_curr, name, lnum): + """Initialize new reference and perform checks.""" + if rec_curr is None: + return GOTerm() + msg = "PREVIOUS {REC} WAS NOT TERMINATED AS EXPECTED".format(REC=name) + self._die(msg, lnum) + + def _init_typedef(self, typedef_curr, name, lnum): + """Initialize new typedef and perform checks.""" + if typedef_curr is None: + return TypeDef() + msg = "PREVIOUS {REC} WAS NOT TERMINATED AS EXPECTED".format(REC=name) + self._die(msg, lnum) + + def _add_to_ref(self, rec_curr, line, lnum): + """Add new fields to the current reference.""" + # Written by DV Klopfenstein + # Examples of record lines containing ':' include: + # id: GO:0000002 + # name: mitochondrial genome maintenance + # namespace: biological_process + # def: "The maintenance of ... + # is_a: GO:0007005 ! mitochondrion organization + mtch = re.match(r'^(\S+):\s*(\S.*)$', line) + if mtch: + field_name = mtch.group(1) + field_value = mtch.group(2) + if field_name == "id": + self._chk_none(rec_curr.id, lnum) + rec_curr.id = field_value + elif field_name == "alt_id": + rec_curr.alt_ids.append(field_value) + elif field_name == "name": + self._chk_none(rec_curr.name, lnum) + rec_curr.name = field_value + elif field_name == "namespace": + self._chk_none(rec_curr.namespace, lnum) + rec_curr.namespace = field_value + elif field_name == "is_a": + rec_curr._parents.append(field_value.split()[0]) + elif field_name == "is_obsolete" and field_value == "true": + rec_curr.is_obsolete = True + elif field_name in self.optional_attrs: + self.update_rec(rec_curr, field_name, field_value) + else: + self._die("UNEXPECTED FIELD CONTENT: {L}\n".format(L=line), lnum) + + def update_rec(self, rec, name, value): + """Update current GOTerm with optional record.""" + # 'def' is a reserved word in python, do not use it as a Class attr. + if name == "def": + name = "defn" + + # If we have a relationship, then we will split this into a further + # dictionary. + + if hasattr(rec, name): + if name not in self.attrs_scalar: + if name not in self.attrs_nested: + getattr(rec, name).add(value) + else: + self._add_nested(rec, name, value) + else: + raise Exception("ATTR({NAME}) ALREADY SET({VAL})".format( + NAME=name, VAL=getattr(rec, name))) + else: # Initialize new GOTerm attr + if name in self.attrs_scalar: + setattr(rec, name, value) + elif name not in self.attrs_nested: + setattr(rec, name, set([value])) + else: + name = '_{:s}'.format(name) + setattr(rec, name, defaultdict(list)) + self._add_nested(rec, name, value) + + def _add_to_typedef(self, typedef_curr, line, lnum): + """Add new fields to the current typedef.""" + mtch = re.match(r'^(\S+):\s*(\S.*)$', line) + if mtch: + field_name = mtch.group(1) + field_value = mtch.group(2).split('!')[0].rstrip() + + if field_name == "id": + self._chk_none(typedef_curr.id, lnum) + typedef_curr.id = field_value + elif field_name == "name": + self._chk_none(typedef_curr.name, lnum) + typedef_curr.name = field_value + elif field_name == "transitive_over": + typedef_curr.transitive_over.append(field_value) + elif field_name == "inverse_of": + self._chk_none(typedef_curr.inverse_of, lnum) + typedef_curr.inverse_of = field_value + # Note: there are other tags that aren't imported here. + else: + self._die("UNEXPECTED FIELD CONTENT: {L}\n".format(L=line), lnum) + + def _add_nested(self, rec, name, value): + """Adds a term's nested attributes.""" + # Remove comments and split term into typedef / target term. + (typedef, target_term) = value.split('!')[0].rstrip().split(' ') + + # Save the nested term. + getattr(rec, name)[typedef].append(target_term) + + def _init_optional_attrs(self, optional_attrs): + """Prepare to store data from user-desired optional fields. + + Not loading these optional fields by default saves in space and speed. + But allow the possibility for saving these fields, if the user desires, + Including: + comment consider def is_class_level is_metadata_tag is_transitive + relationship replaced_by subset synonym transitive_over xref + """ + # Written by DV Klopfenstein + # Required attributes are always loaded. All others are optionally loaded. + self.attrs_req = ['id', 'alt_id', 'name', 'namespace', 'is_a', 'is_obsolete'] + self.attrs_scalar = ['comment', 'defn', + 'is_class_level', 'is_metadata_tag', + 'is_transitive', 'transitive_over'] + self.attrs_nested = frozenset(['relationship']) + # Allow user to specify either: 'def' or 'defn' + # 'def' is an obo field name, but 'defn' is legal Python attribute name + fnc = lambda aopt: aopt if aopt != "defn" else "def" + if optional_attrs is None: + optional_attrs = [] + elif isinstance(optional_attrs, str): + optional_attrs = [fnc(optional_attrs)] if optional_attrs not in self.attrs_req else [] + elif isinstance(optional_attrs, list) or isinstance(optional_attrs, set): + optional_attrs = set([fnc(f) for f in optional_attrs if f not in self.attrs_req]) + else: + raise Exception("optional_attrs arg MUST BE A str, list, or set.") + self.optional_attrs = optional_attrs + + + def _die(self, msg, lnum): + """Raise an Exception if file read is unexpected.""" + raise Exception("**FATAL {FILE}({LNUM}): {MSG}\n".format( + FILE=self.obo_file, LNUM=lnum, MSG=msg)) + + def _chk_none(self, init_val, lnum): + """Expect these lines to be uninitialized.""" + if init_val is None or init_val is "": + return + self._die("FIELD IS ALREADY INITIALIZED", lnum) + + + + +class GOTerm: + """ + GO term, actually contain a lot more properties than interfaced here + """ + + def __init__(self): + self.id = "" # GO:NNNNNNN + self.name = "" # description + self.namespace = "" # BP, CC, MF + self._parents = [] # is_a basestring of parents + self.parents = [] # parent records + self.children = [] # children records + self.level = None # shortest distance from root node + self.depth = None # longest distance from root node + self.is_obsolete = False # is_obsolete + self.alt_ids = [] # alternative identifiers + + def __str__(self): + obsolete = "obsolete" if self.is_obsolete else "" + return "{GO}\tlevel-{L:>02}\tdepth-{D:>02}\t{NAME} [{NS}] {OLD}".format( + GO=self.id, L=self.level, D=self.depth, + NAME=self.name, NS=self.namespace, OLD=obsolete) + + def __repr__(self): + """Print GO id and all attributes in GOTerm class.""" + ret = ["GOTerm('{ID}'):".format(ID=self.id)] + for key, val in self.__dict__.items(): + if isinstance(val, int) or isinstance(val, str): + ret.append("{K}:{V}".format(K=key, V=val)) + else: + ret.append("{K}: {V} items".format(K=key, V=len(val))) + if len(val) < 10: + if not isinstance(val, dict): + for elem in val: + ret.append(" {ELEM}".format(ELEM=elem)) + else: + for (typedef, terms) in val.items(): + ret.append(" {TYPEDEF}: {NTERMS} items" + .format(TYPEDEF=typedef, + NTERMS=len(terms))) + for t in terms: + ret.append(" {TERM}".format(TERM=t)) + return "\n ".join(ret) + + def has_parent(self, term): + for p in self.parents: + if p.id == term or p.has_parent(term): + return True + return False + + def has_child(self, term): + for p in self.children: + if p.id == term or p.has_child(term): + return True + return False + + def get_all_parents(self): + all_parents = set() + for p in self.parents: + all_parents.add(p.id) + all_parents |= p.get_all_parents() + return all_parents + + def get_all_children(self): + all_children = set() + for p in self.children: + all_children.add(p.id) + all_children |= p.get_all_children() + return all_children + + def get_all_parent_edges(self): + all_parent_edges = set() + for p in self.parents: + all_parent_edges.add((self.id, p.id)) + all_parent_edges |= p.get_all_parent_edges() + return all_parent_edges + + def get_all_child_edges(self): + all_child_edges = set() + for p in self.children: + all_child_edges.add((p.id, self.id)) + all_child_edges |= p.get_all_child_edges() + return all_child_edges + + def write_hier_rec(self, gos_printed, out=sys.stdout, + len_dash=1, max_depth=None, num_child=None, short_prt=False, + include_only=None, go_marks=None, + depth=1, dp="-"): + """Write hierarchy for a GO Term record.""" + # Added by DV Klopfenstein + GO_id = self.id + # Shortens hierarchy report by only printing the hierarchy + # for the sub-set of user-specified GO terms which are connected. + if include_only is not None and GO_id not in include_only: + return + nrp = short_prt and GO_id in gos_printed + if go_marks is not None: + out.write('{} '.format('>' if GO_id in go_marks else ' ')) + if len_dash is not None: + # Default character indicating hierarchy level is '-'. + # '=' is used to indicate a hierarchical path printed in detail previously. + letter = '-' if not nrp or not self.children else '=' + dp = ''.join([letter]*depth) + out.write('{DASHES:{N}} '.format(DASHES=dp, N=len_dash)) + if num_child is not None: + out.write('{N:>5} '.format(N=len(self.get_all_children()))) + out.write('{GO}\tL-{L:>02}\tD-{D:>02}\t{desc}\n'.format( + GO=self.id, L=self.level, D=self.depth, desc=self.name)) + # Track GOs previously printed only if needed + if short_prt: + gos_printed.add(GO_id) + # Do not print hierarchy below this turn if it has already been printed + if nrp: + return + depth += 1 + if max_depth is not None and depth > max_depth: + return + for p in self.children: + p.write_hier_rec(gos_printed, out, len_dash, max_depth, num_child, short_prt, + include_only, go_marks, + depth, dp) + + +class TypeDef(object): + """ + TypeDef term. These contain more tags than included here, but these + are the most important. + """ + + def __init__(self): + self.id = "" # GO:NNNNNNN + self.name = "" # description + self.transitive_over = [] # List of other typedefs + self.inverse_of = "" # Name of inverse typedef. + + def __str__(self): + ret = [] + ret.append("Typedef - {} ({}):".format(self.id, self.name)) + ret.append(" Inverse of: {}".format(self.inverse_of + if self.inverse_of else "None")) + if self.transitive_over: + ret.append(" Transitive over:") + for t in self.transitive_over: + ret.append(" - {}".format(t)) + return "\n".join(ret) + + +class GODag(dict): + + def __init__(self, obo_file="go-basic.obo", optional_attrs=None): + self.load_obo_file(obo_file, optional_attrs) + + def load_obo_file(self, obo_file, optional_attrs): + + print("load obo file %s" % obo_file, file=sys.stderr) + reader = OBOReader(obo_file, optional_attrs) + for rec in reader: + self[rec.id] = rec + for alt in rec.alt_ids: + self[alt] = rec + + print("{OBO}: format-version({FMT}) data-version({REL})".format( + OBO=obo_file, FMT=reader.format_version, REL=reader.data_version)) + + # Save the typedefs and parsed optional_attrs + self.typedefs = reader.typedefs + self.optional_attrs = reader.optional_attrs + + self.populate_terms() + print(len(self), "nodes imported", file=sys.stderr) + + def populate_terms(self): + + def _init_level(rec): + if rec.level is None: + if not rec.parents: + rec.level = 0 + else: + rec.level = min(_init_level(rec) for rec in rec.parents) + 1 + return rec.level + + def _init_depth(rec): + if rec.depth is None: + if not rec.parents: + rec.depth = 0 + else: + rec.depth = max(_init_depth(rec) for rec in rec.parents) + 1 + return rec.depth + + # Make parents and relationships references to the actual GO terms. + for rec in self.values(): + rec.parents = [self[x] for x in rec._parents] + + if hasattr(rec, '_relationship'): + rec.relationship = defaultdict(set) + for (typedef, terms) in rec._relationship.items(): + rec.relationship[typedef].update(set([self[x] for x in terms])) + delattr(rec, '_relationship') + + # populate children, levels and add inverted relationships + for rec in self.values(): + for p in rec.parents: + if rec not in p.children: + p.children.append(rec) + + # Add invert relationships + if hasattr(rec, 'relationship'): + for (typedef, terms) in rec.relationship.items(): + invert_typedef = self.typedefs[typedef].inverse_of + if invert_typedef: + # Add inverted relationship + for t in terms: + if not hasattr(t, 'relationship'): + t.relationship = defaultdict(set) + t.relationship[invert_typedef].add(rec) + + if rec.level is None: + _init_level(rec) + + if rec.depth is None: + _init_depth(rec) + + def write_dag(self, out=sys.stdout): + """Write info for all GO Terms in obo file, sorted numerically.""" + for rec_id, rec in sorted(self.items()): + print(rec, file=out) + + def write_hier_all(self, out=sys.stdout, + len_dash=1, max_depth=None, num_child=None, short_prt=False): + """Write hierarchy for all GO Terms in obo file.""" + # Print: [biological_process, molecular_function, and cellular_component] + for go_id in ['GO:0008150', 'GO:0003674', 'GO:0005575']: + self.write_hier(go_id, out, len_dash, max_depth, num_child, short_prt, None) + + def write_hier(self, GO_id, out=sys.stdout, + len_dash=1, max_depth=None, num_child=None, short_prt=False, + include_only=None, go_marks=None): + """Write hierarchy for a GO Term.""" + gos_printed = set() + self[GO_id].write_hier_rec(gos_printed, out, len_dash, max_depth, num_child, + short_prt, include_only, go_marks) + + @staticmethod + def id2int(GO_id): return int(GO_id.replace("GO:", "", 1)) + + def query_term(self, term, verbose=False): + if term not in self: + print("Term %s not found!" % term, file=sys.stderr) + return + + rec = self[term] + if verbose: + print(rec) + print("all parents:", rec.get_all_parents(), file=sys.stderr) + print("all children:", rec.get_all_children(), file=sys.stderr) + return rec + + def paths_to_top(self, term): + """ Returns all possible paths to the root node + + Each path includes the term given. The order of the path is + top -> bottom, i.e. it starts with the root and ends with the + given term (inclusively). + + Parameters: + ----------- + - term: + the id of the GO term, where the paths begin (i.e. the + accession 'GO:0003682') + + Returns: + -------- + - a list of lists of GO Terms + """ + # error handling consistent with original authors + if term not in self: + print("Term %s not found!" % term, file=sys.stderr) + return + + def _paths_to_top_recursive(rec): + if rec.level == 0: + return [[rec]] + paths = [] + for parent in rec.parents: + top_paths = _paths_to_top_recursive(parent) + for top_path in top_paths: + top_path.append(rec) + paths.append(top_path) + return paths + + go_term = self[term] + return _paths_to_top_recursive(go_term) + + def _label_wrap(self, label): + wrapped_label = r"%s\n%s" % (label, + self[label].name.replace(",", r"\n")) + return wrapped_label + + def make_graph_pydot(self, recs, nodecolor, + edgecolor, dpi, + draw_parents=True, draw_children=True): + """draw AMIGO style network, lineage containing one query record.""" + import pydot + G = pydot.Dot(graph_type='digraph', dpi="{}".format(dpi)) # Directed Graph + edgeset = set() + usr_ids = [rec.id for rec in recs] + for rec in recs: + if draw_parents: + edgeset.update(rec.get_all_parent_edges()) + if draw_children: + edgeset.update(rec.get_all_child_edges()) + + lw = self._label_wrap + rec_id_set = set([rec_id for endpts in edgeset for rec_id in endpts]) + nodes = {str(ID):pydot.Node( + lw(ID).replace("GO:",""), # Node name + shape="box", + style="rounded, filled", + # Highlight query terms in plum: + fillcolor="beige" if ID not in usr_ids else "plum", + color=nodecolor) + for ID in rec_id_set} + + # add nodes explicitly via add_node + for rec_id, node in nodes.items(): + G.add_node(node) + + for src, target in edgeset: + # default layout in graphviz is top->bottom, so we invert + # the direction and plot using dir="back" + G.add_edge(pydot.Edge(nodes[target], nodes[src], + shape="normal", + color=edgecolor, + label="is_a", + dir="back")) + + return G + + def make_graph_pygraphviz(self, recs, nodecolor, + edgecolor, dpi, + draw_parents=True, draw_children=True): + # draw AMIGO style network, lineage containing one query record + import pygraphviz as pgv + + G = pgv.AGraph(name="GO tree") + edgeset = set() + for rec in recs: + if draw_parents: + edgeset.update(rec.get_all_parent_edges()) + if draw_children: + edgeset.update(rec.get_all_child_edges()) + + edgeset = [(self._label_wrap(a), self._label_wrap(b)) + for (a, b) in edgeset] + + # add nodes explicitly via add_node + # adding nodes implicitly via add_edge misses nodes + # without at least one edge + for rec in recs: + G.add_node(self._label_wrap(rec.id)) + + for src, target in edgeset: + # default layout in graphviz is top->bottom, so we invert + # the direction and plot using dir="back" + G.add_edge(target, src) + + G.graph_attr.update(dpi="%d" % dpi) + G.node_attr.update(shape="box", style="rounded,filled", + fillcolor="beige", color=nodecolor) + G.edge_attr.update(shape="normal", color=edgecolor, + dir="back", label="is_a") + # highlight the query terms + for rec in recs: + try: + q = G.get_node(self._label_wrap(rec.id)) + q.attr.update(fillcolor="plum") + except: + continue + + return G + + def draw_lineage(self, recs, nodecolor="mediumseagreen", + edgecolor="lightslateblue", dpi=96, + lineage_img="GO_lineage.png", engine="pygraphviz", + gml=False, draw_parents=True, draw_children=True): + assert engine in GraphEngines + if engine == "pygraphviz": + G = self.make_graph_pygraphviz(recs, nodecolor, edgecolor, dpi, + draw_parents=draw_parents, draw_children=draw_children) + else: + G = self.make_graph_pydot(recs, nodecolor, edgecolor, dpi, + draw_parents=draw_parents, draw_children=draw_children) + + if gml: + import networkx as nx # use networkx to do the conversion + pf = lineage_img.rsplit(".", 1)[0] + NG = nx.from_agraph(G) if engine == "pygraphviz" else nx.from_pydot(G) + + del NG.graph['node'] + del NG.graph['edge'] + gmlfile = pf + ".gml" + nx.write_gml(NG, gmlfile) + print("GML graph written to {0}".format(gmlfile), file=sys.stderr) + + print(("lineage info for terms %s written to %s" % + ([rec.id for rec in recs], lineage_img)), file=sys.stderr) + + if engine == "pygraphviz": + G.draw(lineage_img, prog="dot") + else: + G.write_png(lineage_img) + + def update_association(self, association): + bad_terms = set() + for key, terms in list(association.items()): + parents = set() + for term in terms: + try: + parents.update(self[term].get_all_parents()) + except: + bad_terms.add(term.strip()) + terms.update(parents) + if bad_terms: + print("terms not found: %s" % (bad_terms,), file=sys.stderr) + +# Copyright (C) 2010-2016, H Tang et al., All rights reserved. diff --git a/ga4gh/datamodel/ontologies.py b/ga4gh/datamodel/ontologies.py index 38494859a..f4bd5db5f 100644 --- a/ga4gh/datamodel/ontologies.py +++ b/ga4gh/datamodel/ontologies.py @@ -11,7 +11,7 @@ import ga4gh.protocol as protocol import ga4gh.exceptions as exceptions -import goatools.obo_parser as obo_parser +import ga4gh.datamodel.obo_parser as obo_parser SEQUENCE_ONTOLOGY_PREFIX = "SO" diff --git a/requirements.txt b/requirements.txt index ac979ea55..92dc0d32c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,7 +16,6 @@ pycrypto==2.6.1 Mako==1.0.4 Beaker==1.8.0 funcsigs==0.4 -goatools==0.6.4 alabaster==0.7.7 cryptography==1.3.1 idna==2.1 diff --git a/tests/datadriven/test_ontologies.py b/tests/datadriven/test_ontologies.py index eb5c33680..7f2eed64e 100644 --- a/tests/datadriven/test_ontologies.py +++ b/tests/datadriven/test_ontologies.py @@ -10,7 +10,7 @@ # TODO it may be a bit circular to use obo_parser as our method of # accessing ontology information, since this is the method we use # in the main code. However, other libraries have very heavy dependencies. -import goatools.obo_parser as obo_parser +import ga4gh.datamodel.obo_parser as obo_parser import ga4gh.protocol as protocol import ga4gh.datamodel.ontologies as ontologies diff --git a/tests/unit/test_imports.py b/tests/unit/test_imports.py index bea42cf43..3fa4d4401 100644 --- a/tests/unit/test_imports.py +++ b/tests/unit/test_imports.py @@ -161,6 +161,7 @@ class ImportGraphLayerChecker(object): 'ga4gh/datamodel/variants.py', 'ga4gh/datamodel/datasets.py', 'ga4gh/datamodel/ontologies.py', + 'ga4gh/datamodel/obo_parser.py', 'ga4gh/datamodel/sequenceAnnotations.py', 'ga4gh/gff3Parser.py', 'ga4gh/sqliteBackend.py'], From 354855132cdc2c0c238fb41a3fff2c394a288608 Mon Sep 17 00:00:00 2001 From: David Steinberg Date: Wed, 18 May 2016 14:35:30 -0700 Subject: [PATCH 11/13] Update prepare compliance data to use OBO file. Conflicts: requirements.txt --- scripts/prepare_compliance_data.py | 29 +++++++++++++++++++---------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/scripts/prepare_compliance_data.py b/scripts/prepare_compliance_data.py index 13b44b22a..4a26fe2aa 100644 --- a/scripts/prepare_compliance_data.py +++ b/scripts/prepare_compliance_data.py @@ -136,22 +136,26 @@ def run(self): readGroupSet.setReferenceSet(referenceSet) self.repo.insertReadGroupSet(readGroupSet) - ontologyMapFileName = "sequence_ontology.txt" + ontologyMapFileName = "so-xp-simple.obo" inputOntologyMap = os.path.join( self.inputDirectory, ontologyMapFileName) outputOntologyMap = os.path.join( self.outputDirectory, ontologyMapFileName) shutil.copy(inputOntologyMap, outputOntologyMap) - sequenceOntology = ontologies.OntologyTermMap("sequence_ontology") + sequenceOntology = ontologies.Ontology("so-xp-simple") sequenceOntology.populateFromFile(outputOntologyMap) - self.repo.insertOntologyTermMap(sequenceOntology) - self.repo.addOntologyTermMap(sequenceOntology) - - map(lambda x: self.addVariantSet(x, dataset, referenceSet), - ["brca1_1kgPhase3_variants.vcf", - "brca1_WASH7P_annotation.vcf", - "brca1_OR4F_annotation.vcf"]) + sequenceOntology._id = "so-xp-simple" + self.repo.insertOntology(sequenceOntology) + self.repo.addOntology(sequenceOntology) + + vcfFiles = [ + "brca1_1kgPhase3_variants.vcf", + "brca1_WASH7P_annotation.vcf", + "brca1_OR4F_annotation.vcf"] + for vcfFile in vcfFiles: + self.addVariantSet( + vcfFile, dataset, referenceSet, sequenceOntology) seqAnnFile = "brca1_gencodev19.gff3" seqAnnSrc = os.path.join(self.inputDirectory, seqAnnFile) @@ -159,15 +163,17 @@ def run(self): dbgen = generate_gff3_db.Gff32Db(seqAnnSrc, seqAnnDest) dbgen.run() gencode = sequenceAnnotations.Gff3DbFeatureSet(dataset, "gencodev19") + gencode.setOntology(sequenceOntology) gencode.populateFromFile(seqAnnDest) gencode.setReferenceSet(referenceSet) + self.repo.insertFeatureSet(gencode) self.repo.commit() print("Done converting compliance data.", file=sys.stderr) - def addVariantSet(self, variantFileName, dataset, referenceSet): + def addVariantSet(self, variantFileName, dataset, referenceSet, ontology): inputVcf = os.path.join( self.inputDirectory, variantFileName) outputVcf = os.path.join( @@ -181,6 +187,9 @@ def addVariantSet(self, variantFileName, dataset, referenceSet): [outputVcf + ".gz"], [outputVcf + ".gz.tbi"]) variantSet.checkConsistency() self.repo.insertVariantSet(variantSet) + for annotationSet in variantSet.getVariantAnnotationSets(): + annotationSet.setOntology(ontology) + self.repo.insertVariantAnnotationSet(annotationSet) def cleanup(self): if self.tempdir is not None: From ff79ff3ac5d753b2bc5764ceaa490c69478fd74c Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Fri, 20 May 2016 11:50:27 +0100 Subject: [PATCH 12/13] Bumped example data version number. --- docs/demo.rst | 22 +++++++++++----------- docs/installation.rst | 6 +++--- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/docs/demo.rst b/docs/demo.rst index 72fa73456..f25673db2 100644 --- a/docs/demo.rst +++ b/docs/demo.rst @@ -59,8 +59,8 @@ Now we can download some example data, which we'll use for our demo: .. code-block:: bash - (ga4gh-env) $ wget https://github.com/ga4gh/server/releases/download/data/ga4gh-example-data-v4.0.tar - (ga4gh-env) $ tar -xvf ga4gh-example-data-v4.0.tar + (ga4gh-env) $ wget https://github.com/ga4gh/server/releases/download/data/ga4gh-example-data-v4.1.tar + (ga4gh-env) $ tar -xvf ga4gh-example-data-v4.1.tar After extracting the data, we can then run the ``ga4gh_server`` application: @@ -231,8 +231,8 @@ Repo administrator CLI The CLI has methods for adding and removing Feature Sets, Read Group Sets, Variant Sets, etc. Before we can begin adding files we must first -initialize an empty registry database. The directory that this database -is in should be readable and writable by the current user, as well as the +initialize an empty registry database. The directory that this database +is in should be readable and writable by the current user, as well as the user running the server. .. code-block:: bash @@ -299,17 +299,17 @@ Add sequence annotations ------------------------ The GENCODE Genes dataset provides annotations for features on the -reference assembly. The server uses a custom storage format for sequence -annotations, you can download a prepared set +reference assembly. The server uses a custom storage format for sequence +annotations, you can download a prepared set `here `__. -It can be added to the registry using the following command. Notice -we have told the registry to associate the reference set added above +It can be added to the registry using the following command. Notice +we have told the registry to associate the reference set added above with these annotations. .. code-block:: bash ga4gh_repo add-featureset registry.db 1kgenomes /full/path/to/gencode.v24lift37.annotation.db --referenceSetName NCBI37 - + .. todo:: Demonstrate how to generate your own sequence annotations database. Add the 1000 Genomes VCFs @@ -325,8 +325,8 @@ release. rm release/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz These files are already compressed and indexed. For the server to make use -of the files in this directory we must move the `wgs` file, since it covers -chromosomes that are represented elsewhere and overlapping VCF are not +of the files in this directory we must move the `wgs` file, since it covers +chromosomes that are represented elsewhere and overlapping VCF are not currently supported. This file could be added as a separate variant set. We can now add the directory to the registry using the following command. diff --git a/docs/installation.rst b/docs/installation.rst index 6a1b5064c..a44c2fa8f 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -62,8 +62,8 @@ Download and unpack the example data: .. code-block:: bash - $ wget https://github.com/ga4gh/server/releases/download/data/ga4gh-example-data-v4.0.tar - $ tar -xf ga4gh-example-data-v4.0.tar + $ wget https://github.com/ga4gh/server/releases/download/data/ga4gh-example-data-v4.1.tar + $ tar -xf ga4gh-example-data-v4.1.tar Create the WSGI file at ``/srv/ga4gh/application.wsgi`` and write the following contents: @@ -172,7 +172,7 @@ Troubleshooting Server errors will be output to the web server's error log by default (in Apache on Debian/Ubuntu, for example, this is ``/var/log/apache2/error.log``). Each client request will be logged to the web server's access log (in Apache on Debian/Ubuntu -this is ``/var/log/apache2/access.log``). +this is ``/var/log/apache2/access.log``). For more server configuration options see :ref:`Configuration` From e5553f28d6f37654337777e746eeec6aa6cd36b1 Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Fri, 20 May 2016 15:09:00 +0100 Subject: [PATCH 13/13] Updated documentation for ontologies. --- docs/configuration.rst | 49 ++++++++++++++++++++++++++---------------- docs/demo.rst | 43 ++++++++++++++++++++++-------------- ga4gh/cli.py | 14 ++++++------ 3 files changed, 63 insertions(+), 43 deletions(-) diff --git a/docs/configuration.rst b/docs/configuration.rst index 7302908c5..b9f654d32 100644 --- a/docs/configuration.rst +++ b/docs/configuration.rst @@ -57,18 +57,14 @@ when creating a new GA4GH repository. $ ga4gh_repo init registry.db +++++++ -verify +list +++++++ -The ``verify`` command is used to check that the integrity of the -data in a repository. The command checks each container object in turn -and ensures that it can read data from it. Read errors can occur for -any number of reasons (for example, a VCF file may have been moved -to another location since it was added to the registry), and the -``verify`` command allows an administrator to check that all is -well in their repository. +The ``list`` command is used to print the contents of a repository +to the screen. It is an essential tool for administrators to +understand the structure of the repository that they are managing. -.. note:: The ``verify`` command is under development and will +.. note:: The ``list`` command is under development and will be much more sophisticated in the future. In particular, the output of this command should improve considerably in the near future. @@ -76,24 +72,29 @@ well in their repository. :module: ga4gh.cli :func: getRepoManagerParser :prog: ga4gh_repo - :path: verify + :path: list :nodefault: **Examples:** .. code-block:: bash - $ ga4gh_repo verify registry.db + $ ga4gh_repo list registry.db + +++++++ -list +verify +++++++ -The ``list`` command is used to print the contents of a repository -to the screen. It is an essential tool for administrators to -understand the structure of the repository that they are managing. +The ``verify`` command is used to check that the integrity of the +data in a repository. The command checks each container object in turn +and ensures that it can read data from it. Read errors can occur for +any number of reasons (for example, a VCF file may have been moved +to another location since it was added to the registry), and the +``verify`` command allows an administrator to check that all is +well in their repository. -.. note:: The ``list`` command is under development and will +.. note:: The ``verify`` command is under development and will be much more sophisticated in the future. In particular, the output of this command should improve considerably in the near future. @@ -101,14 +102,15 @@ understand the structure of the repository that they are managing. :module: ga4gh.cli :func: getRepoManagerParser :prog: ga4gh_repo - :path: list + :path: verify :nodefault: **Examples:** .. code-block:: bash - $ ga4gh_repo list registry.db + $ ga4gh_repo verify registry.db + +++++++++++ add-dataset @@ -169,7 +171,13 @@ Adds a reference set used in the 1000 Genomes project using the name add-ontology ++++++++++++++++ -.. todo:: add docs for adding ontologies. +Adds a new ontology to the repository. The ontology supplied must be a text +file in `OBO format +`_. If you wish to +serve sequence or variant annotations from a repository, a sequence ontology +(SO) instance is required to translate ontology term names held in annotations +to ontology IDs. Sequence ontology definitions can be downloaded from +the `Sequence Ontology site `_. .. argparse:: :module: ga4gh.cli @@ -184,6 +192,9 @@ add-ontology $ ga4gh_repo add-ontology registry.db path/to/so-xp.obo +Adds the sequence ontology ``so-xp.obo`` to the repository using the +default naming rules. + +++++++++++++++ add-variantset +++++++++++++++ diff --git a/docs/demo.rst b/docs/demo.rst index f25673db2..13d55b45a 100644 --- a/docs/demo.rst +++ b/docs/demo.rst @@ -237,7 +237,7 @@ user running the server. .. code-block:: bash - ga4gh_repo init registry.db + $ ga4gh_repo init registry.db This command will create a file ``registry.db`` in the current working directory. This file should stay relatively small (a few MB for @@ -249,7 +249,8 @@ description using the ``--description`` flag. .. code-block:: bash - ga4gh_repo add-dataset registry.db 1kgenomes --description "Variants from the 1000 Genomes project and GENCODE genes annotations" + $ ga4gh_repo add-dataset registry.db 1kgenomes \ + --description "Variants from the 1000 Genomes project and GENCODE genes annotations" Add a Reference Set ------------------- @@ -260,7 +261,7 @@ used for the 1000 Genomes VCF. .. code-block:: bash - wget ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz + $ wget ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz This file is provided in ``.gz`` format, which we will decompress, and then with samtools installed on the system, recompress it using @@ -268,15 +269,15 @@ then with samtools installed on the system, recompress it using .. code-block:: bash - gunzip hs37d5.fa.gz - bgzip hs37d5.fa + $ gunzip hs37d5.fa.gz + $ bgzip hs37d5.fa This may take a few minutes depending on your system as this file is around 3GB. Next, we will add the reference set. .. code-block:: bash - ga4gh_repo add-referenceset registry.db /full/path/to/hs37d5.fa.gz \ + $ ga4gh_repo add-referenceset registry.db /full/path/to/hs37d5.fa.gz \ -d “NCBI37 assembly of the human genome” --ncbiTaxonId 9606 --name NCBI37 \ --sourceUri "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz" @@ -284,16 +285,20 @@ A number of optional command line flags have been added. We will be referring to the name of this reference set ``NCBI37`` when we later add the variant set. -Add an ontology TODO --------------------- +Add an ontology +--------------- Ontologies provide a source for parsing variant annotations, as well as -organizing feature types into ontology terms. This is a custom format -created for this server. +organizing feature types into ontology terms. A `sequence ontology +`_ instance must be added to the repository +to translate ontology term names in sequence and variant annotations to IDs. +Sequence ontology definitions can be downloaded from the `Sequence Ontology +site `_. .. code-block:: bash - ga4gh_repo add-ontology registry.db /full/path/to/sequence_ontology.txt + $ wget https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/so-xp.obo + $ ga4gh_repo add-ontology registry.db /full/path/to/so-xp.obo -n so-xp Add sequence annotations ------------------------ @@ -308,7 +313,9 @@ with these annotations. .. code-block:: bash - ga4gh_repo add-featureset registry.db 1kgenomes /full/path/to/gencode.v24lift37.annotation.db --referenceSetName NCBI37 + $ ga4gh_repo add-featureset registry.db 1kgenomes /full/path/to/gencode.v24lift37.annotation.db \ + --referenceSetName NCBI37 --ontologyName so-xp + .. todo:: Demonstrate how to generate your own sequence annotations database. @@ -321,7 +328,7 @@ release. .. code-block:: bash - wget -m ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ -nd -P release -l 1 + $ wget -m ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ -nd -P release -l 1 rm release/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz These files are already compressed and indexed. For the server to make use @@ -334,7 +341,8 @@ Again, notice we have referred to the reference set by name. .. code-block:: bash - ga4gh_repo add-variantset registry.db 1kgenomes /full/path/to/release/ --name phase3-release --referenceSetName NCBI37 + $ ga4gh_repo add-variantset registry.db 1kgenomes /full/path/to/release/ \ + --name phase3-release --referenceSetName NCBI37 Add a BAM as a Read Group Set ----------------------------- @@ -345,8 +353,11 @@ We will first download the index and then add it to the registry. .. code-block:: bash - wget http://s3.amazonaws.com/1000genomes/phase3/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.bai - ga4gh_repo add-readgroupset registry.db 1kgenomes "http://s3.amazonaws.com/1000genomes/phase3/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam" -I "HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.bai" --referenceSetName NCBI37 + $ wget http://s3.amazonaws.com/1000genomes/phase3/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.bai + $ ga4gh_repo add-readgroupset registry.db 1kgenomes \ + -I HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.bai \ + --referenceSetName NCBI37 \ + http://s3.amazonaws.com/1000genomes/phase3/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam \ This might take a moment as some metadata about the file will be retrieved from S3. diff --git a/ga4gh/cli.py b/ga4gh/cli.py index 39f0b47ae..dff8d8e1e 100644 --- a/ga4gh/cli.py +++ b/ga4gh/cli.py @@ -2051,18 +2051,16 @@ def getParser(cls): addOntologyParser = addSubparser( subparsers, "add-ontology", - "Adds an ontology to the repo. Currently ontology support " - "consists of a map between ontology term IDs and names " - "stored in a tab-delimited text file. For example, in " - "Sequence Ontology, we map from the term ID 'SO:0000024' " - "to the name 'sarcin_like_RNA_motif'. ") + "Adds an ontology in OBO format to the repo. Currently, " + "a sequence ontology (SO) instance is required to translate " + "ontology term names held in annotations to ontology IDs. " + "Sequence ontology files can be found at " + "https://github.com/The-Sequence-Ontology/SO-Ontologies") addOntologyParser.set_defaults(runner="addOntology") cls.addRepoArgument(addOntologyParser) cls.addFilePathArgument( addOntologyParser, - "The path to the text file used to define the ontology term " - "map to use. This must be a tab-delimited text file consisting " - "of ontology term IDs and names.") + "The path of the OBO file defining this ontology.") cls.addNameOption(addOntologyParser, "ontology") removeOntologyParser = addSubparser(