Codebase list genometools / 67a45f3
update sequence ontology files To current GitHub HEAD. Also see #910 Gordon Gremme 5 years ago
4 changed file(s) with 2646 addition(s) and 210 deletion(s). Raw diff Collapse all Expand all
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gtdata/obo_files/README less more
00 Source of the files:
11
2 so.obo: https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp-simple.obo
3 so-xp.obo: https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp.obo
4 sofa.obo: https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/subsets/SOFA.obo
2 so.obo: https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/releases/so-xp.owl/so-xp-simple.obo
3 so-xp.obo: https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/releases/so-xp.owl/so-xp.obo
4 sofa.obo: https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/releases/so-xp.owl/subsets/SOFA.obo
55
6 Current HEAD is 3a1b6bd850cff63ffac60ff3452dc01d319c793c
6 Current HEAD is 6f8dfd4aebd4427baad07535b6250f4622b1b075
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gtdata/obo_files/so-xp.obo less more
00 format-version: 1.2
1 date: 04:09:2015 13:56
2 saved-by: kareneilbeck
1 data-version: so-xp/releases/2015-11-24/so-xp.owl
2 date: 28:10:2016 11:25
3 saved-by: nicole
34 auto-generated-by: OBO-Edit 2.3.1
45 subsetdef: biosapiens "biosapiens protein feature ontology"
56 subsetdef: DBVAR "database of genomic structural variation"
1415 synonymtypedef: RNAMOD "RNA modification" EXACT
1516 synonymtypedef: VAR "variant annotation term"
1617 default-namespace: sequence
17 remark: autogenerated-by: DAG-Edit version 1.417\nsaved-by: eilbeck\ndate: Tue May 11 15:18:44 PDT 2004\nversion: $Revision: 1.45 $
1818 ontology: so-xp.obo
1919
2020 [Term]
3030 subset: SOFA
3131 synonym: "sequence" EXACT []
3232 is_a: SO:0000110 ! sequence_feature
33 disjoint_from: SO:0000699 ! junction
3433
3534 [Term]
3635 id: SO:0000002
388387 [Term]
389388 id: SO:0000043
390389 name: processed_pseudogene
391 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]
390 def: "A pseudogene created via retrotranposition of the mRNA of a functional protein-coding parent gene followed by accumulation of deleterious mutations lacking introns and promoters, often including a polyA tail." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
392391 comment: Please not the synonym R psi M uses the spelled out form of the greek letter.
393392 synonym: "processed pseudogene" EXACT []
394393 synonym: "pseudogene by reverse transcription" RELATED []
17871786 [Term]
17881787 id: SO:0000207
17891788 name: simple_sequence_length_variation
1789 def: "SSLP are a kind of sequence alteration where the number of repeated sequences in intergenic regions may differ." [SO:ke]
17901790 synonym: "simple sequence length polymorphism" RELATED []
17911791 synonym: "simple sequence length variation" EXACT []
17921792 synonym: "SSLP" RELATED []
1793 xref: http://en.wikipedia.org/wiki/Simple_sequence_length_polymorphism "WIKI"
17931794 is_a: SO:0000248 ! sequence_length_variation
17941795
17951796 [Term]
20382039 name: chromosome_variation
20392040 synonym: "chromosome variation" EXACT []
20402041 is_a: SO:0001507 ! variant_collection
2041 disjoint_from: SO:0000400 ! sequence_attribute
20422042 relationship: part_of SO:0001524 ! chromosomally_aberrant_genome
20432043
20442044 [Term]
20932093 [Term]
20942094 id: SO:0000248
20952095 name: sequence_length_variation
2096 def: "A kind of kind of sequence alteration where the copies of a region present varies across a population." [SO:ke]
20962097 synonym: "sequence length variation" EXACT []
2097 is_a: SO:1000002 ! substitution
2098 is_a: SO:0001059 ! sequence_alteration
20982099
20992100 [Term]
21002101 id: SO:0000249
23712372 xref: http://en.wikipedia.org/wiki/MiRNA "wiki"
23722373 xref: http://en.wikipedia.org/wiki/StRNA "wiki"
23732374 is_a: SO:0000370 ! small_regulatory_ncRNA
2374 is_a: SO:0000655 ! ncRNA
23752375 relationship: part_of SO:0001244 ! pre_miRNA
23762376
23772377 [Term]
25082508 subset: SOFA
25092509 synonym: "microsatellite locus" EXACT []
25102510 synonym: "microsatellite marker" EXACT []
2511 synonym: "VNTR" EXACT []
2511 synonym: "STR" EXACT [http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9651/]
25122512 xref: http://en.wikipedia.org/wiki/Microsatellite "wiki"
25132513 is_a: SO:0000005 ! satellite_DNA
25142514
30753075 [Term]
30763076 id: SO:0000360
30773077 name: codon
3078 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]
3078 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." [SO:ke]
30793079 subset: SOFA
30803080 xref: http://en.wikipedia.org/wiki/Codon "wiki"
30813081 is_a: SO:0000851 ! CDS_region
39763976 id: SO:0000464
39773977 name: decayed_exon
39783978 def: "A non-functional descendant of an exon." [SO:ke]
3979 comment: Does not have to be part of a pseudogene.
39793980 subset: SOFA
39803981 synonym: "decayed exon" EXACT []
39813982 is_a: SO:0000462 ! pseudogenic_region
55365537 name: minisatellite
55375538 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]
55385539 subset: SOFA
5540 synonym: "VNTR" EXACT [http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9655/]
55395541 xref: http://en.wikipedia.org/wiki/Minisatellite "wiki"
55405542 is_a: SO:0000005 ! satellite_DNA
55415543
66316633 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.
66326634 subset: SOFA
66336635 synonym: "pseudogenic rRNA" EXACT []
6634 is_a: SO:0000462 ! pseudogenic_region
6636 is_a: SO:0000516 ! pseudogenic_transcript
66356637
66366638 [Term]
66376639 id: SO:0000778
66406642 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.
66416643 subset: SOFA
66426644 synonym: "pseudogenic tRNA" EXACT []
6643 is_a: SO:0000462 ! pseudogenic_region
6645 is_a: SO:0000516 ! pseudogenic_transcript
66446646
66456647 [Term]
66466648 id: SO:0000779
86338635 synonym: "copy number polymorphism" EXACT []
86348636 synonym: "copy number variation" EXACT []
86358637 xref: http://en.wikipedia.org/wiki/Copy_number_variation "wiki"
8636 is_a: SO:0001059 ! sequence_alteration
8638 is_a: SO:0000248 ! sequence_length_variation
86378639
86388640 [Term]
86398641 id: SO:0001020
89638965 synonym: "sequence alteration" EXACT []
89648966 synonym: "sequence variation" RELATED []
89658967 synonym: "uncharacterised_change_in_nucleotide_sequence" NARROW []
8966 is_a: SO:0000110 ! sequence_feature
8968 is_a: SO:0002072 ! sequence_comparison
89678969
89688970 [Term]
89698971 id: SO:0001060
89708972 name: sequence_variant
89718973 def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]
89728974 synonym: "ANNOVAR:unknown" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
8975 synonym: "Jannovar:sequence_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
89738976 synonym: "sequence variant" EXACT []
89748977 synonym: "VAAST:sequence_variant" EXACT VAR []
89758978
1313813141 is_a: SO:0001260 ! sequence_collection
1313913142 intersection_of: SO:0001260 ! sequence_collection
1314013143 intersection_of: has_part SO:0001059 ! sequence_alteration
13144 relationship: has_part SO:0001059 ! sequence_alteration
1314113145 created_by: kareneilbeck
1314213146 creation_date: 2010-03-03T02:13:28Z
1314313147
1339113395 id: SO:0001537
1339213396 name: structural_variant
1339313397 def: "A sequence variant that changes one or more sequence features." [SO:ke]
13398 synonym: "Jannovar:structural_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1339413399 synonym: "structural variant" RELATED []
13400 synonym: "VAT:svOverlap" EXACT VAR []
13401 xref: http://vat.gersteinlab.org/formats.php "VAT"
1339513402 is_a: SO:0001060 ! sequence_variant
1339613403 created_by: kareneilbeck
1339713404 creation_date: 2010-03-22T11:31:01Z
1363513642 name: gene_variant
1363613643 def: "A sequence variant where the structure of the gene is changed." [SO:ke]
1363713644 synonym: "gene structure variant" EXACT []
13645 synonym: "Jannovar:gene_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1363813646 synonym: "snpEff:GENE" EXACT VAR []
1363913647 synonym: "VAAST:gene_variant" EXACT VAR []
13648 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1364013649 is_a: SO:0001878 ! feature_variant
1364113650 created_by: kareneilbeck
1364213651 creation_date: 2010-03-22T02:28:01Z
1364713656 def: "A sequence variant whereby a two genes have become joined." [SO:ke]
1364813657 synonym: "gene fusion" EXACT []
1364913658 is_a: SO:0001564 ! gene_variant
13659 is_a: SO:0001882 ! feature_fusion
1365013660 created_by: kareneilbeck
1365113661 creation_date: 2010-03-22T02:28:28Z
1365213662
1365513665 name: regulatory_region_variant
1365613666 def: "A sequence variant located within a regulatory region." [SO:ke]
1365713667 comment: EBI term: Regulatory region variations - In regulatory region annotated by Ensembl.
13668 synonym: "Jannovar:regulatory_region_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1365813669 synonym: "regulatory region variant" EXACT []
1365913670 synonym: "regulatory_region_" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13671 synonym: "snpEff:REGULATION" EXACT VAR []
13672 synonym: "VEP:regulatory_region_variant" EXACT VAR []
13673 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13674 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1366013675 is_a: SO:0001878 ! feature_variant
1366113676 created_by: kareneilbeck
1366213677 creation_date: 2010-03-22T02:28:48Z
1366513680 id: SO:0001567
1366613681 name: stop_retained_variant
1366713682 def: "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]
13683 synonym: "Jannovar:stop_retained_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
13684 synonym: "snpEff:NON_SYNONYMOUS_STOP" EXACT VAR []
1366813685 synonym: "snpEff:SYNONYMOUS_STOP" EXACT VAR []
1366913686 synonym: "stop retained variant" EXACT []
1367013687 synonym: "VAAST:stop_retained" EXACT VAR []
13688 synonym: "VAAST:stop_retained_variant" EXACT VAR []
13689 synonym: "VEP:stop_retained_variant" EXACT VAR []
13690 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13691 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1367113692 is_a: SO:0001590 ! terminator_codon_variant
1367213693 is_a: SO:0001819 ! synonymous_variant
1367313694 created_by: kareneilbeck
1367713698 id: SO:0001568
1367813699 name: splicing_variant
1367913700 def: "A sequence variant that changes the process of splicing." [SO:ke]
13701 synonym: "Jannovar:splicing_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1368013702 synonym: "splicing variant" EXACT []
1368113703 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
1368213704 is_a: SO:0001576 ! transcript_variant
1371613738 name: exon_loss_variant
1371713739 def: "A sequence variant whereby an exon is lost from the transcript." [SO:ke]
1371813740 synonym: "exon loss" EXACT []
13741 synonym: "Jannovar:exon_loss_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1371913742 synonym: "snpEff:EXON_DELETED" EXACT VAR []
13743 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1372013744 is_a: SO:0001568 ! splicing_variant
1372113745 created_by: kareneilbeck
1372213746 creation_date: 2010-03-22T02:31:09Z
1373613760 id: SO:0001574
1373713761 name: splice_acceptor_variant
1373813762 def: "A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke]
13763 synonym: "Jannovar:splice_acceptor_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
13764 synonym: "Seattleseq:splice-acceptor" EXACT VAR []
1373913765 synonym: "snpEff:SPLICE_SITE_ACCEPTOR" EXACT VAR []
1374013766 synonym: "splice acceptor variant" EXACT []
1374113767 synonym: "VAAST:splice_acceptor_variant" EXACT VAR []
13768 synonym: "VEP:splice_acceptor_variant" EXACT VAR []
13769 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
13770 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13771 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1374213772 is_a: SO:0001629 ! splice_site_variant
1374313773 created_by: kareneilbeck
1374413774 creation_date: 2010-03-22T02:31:52Z
1374713777 id: SO:0001575
1374813778 name: splice_donor_variant
1374913779 def: "A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke]
13780 synonym: "Jannovar:splice_donor_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
13781 synonym: "Seattleseq:splice-donor" EXACT VAR []
1375013782 synonym: "snpEff:SPLICE_SITE_DONOR" EXACT VAR []
1375113783 synonym: "splice donor variant" EXACT []
1375213784 synonym: "VAAST:splice_donor_variant" EXACT VAR []
13785 synonym: "VEP:splice_donor_variant" EXACT VAR []
13786 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
13787 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13788 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1375313789 is_a: SO:0001629 ! splice_site_variant
1375413790 created_by: kareneilbeck
1375513791 creation_date: 2010-03-22T02:32:10Z
1375813794 id: SO:0001576
1375913795 name: transcript_variant
1376013796 def: "A sequence variant that changes the structure of the transcript." [SO:ke]
13797 synonym: "Jannovar:transcript_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1376113798 synonym: "snpEff:TRANSCRIPT" EXACT VAR []
1376213799 synonym: "transcript variant" EXACT []
1376313800 synonym: "VAAST:transcript_variant" EXACT VAR []
1376413801 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13802 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1376513803 is_a: SO:0001564 ! gene_variant
1376613804 created_by: kareneilbeck
1376713805 creation_date: 2010-03-22T02:32:41Z
1377113809 name: complex_transcript_variant
1377213810 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]
1377313811 comment: EBI term: Complex InDel - Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.
13812 synonym: "complex change in transcript" EXACT []
1377413813 synonym: "complex transcript variant" EXACT []
1377513814 synonym: "complex_indel" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13776 synonym: "complext change in transcript" EXACT []
13815 synonym: "Seattleseq:codingComplex" RELATED VAR []
13816 synonym: "Seattleseq:codingComplex-near-splice" RELATED VAR []
13817 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
1377713818 is_a: SO:0001576 ! transcript_variant
1377813819 created_by: kareneilbeck
1377913820 creation_date: 2010-03-22T02:33:03Z
1378413825 def: "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]
1378513826 comment: EBI term: Stop lost - In coding sequence, resulting in the loss of a stop codon.
1378613827 synonym: "ANNOVAR:stoploss" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13828 synonym: "Jannovar:stop_lost" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
13829 synonym: "Seattleseq:stop-lost" EXACT VAR []
13830 synonym: "Seattleseq:stop-lost-near-splice" RELATED VAR []
1378713831 synonym: "snpEff:STOP_LOST" EXACT VAR []
1378813832 synonym: "stop codon lost" EXACT []
1378913833 synonym: "stop lost" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
1379013834 synonym: "VAAST:stop_lost" EXACT VAR []
13835 synonym: "VAT:removedStop" EXACT VAR []
13836 synonym: "VEP:stop_lost" EXACT VAR []
13837 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
13838 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13839 xref: http://vat.gersteinlab.org/formats.php "VAT"
13840 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1379113841 is_a: SO:0001590 ! terminator_codon_variant
1379213842 is_a: SO:0001907 ! feature_elongation
1379313843 is_a: SO:0001992 ! nonsynonymous_variant
1380913859 synonym: "coding variant" EXACT []
1381013860 synonym: "codon variant" EXACT []
1381113861 synonym: "codon_variant" EXACT []
13862 synonym: "Jannovar:coding_sequence_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
13863 synonym: "Seattleseq:coding" EXACT VAR []
1381213864 synonym: "snpEff:CDS" EXACT VAR []
1381313865 synonym: "snpEff:CODON_CHANGE" RELATED VAR []
1381413866 synonym: "VAAST:coding_sequence_variant" EXACT VAR []
13867 synonym: "VEP:coding_sequence_variant" EXACT VAR []
1381513868 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13869 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
13870 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13871 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1381613872 is_a: SO:0001791 ! exon_variant
1381713873 is_a: SO:0001968 ! coding_transcript_variant
1381813874 created_by: kareneilbeck
1382513881 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.
1382613882 synonym: "initiatior codon variant" EXACT []
1382713883 synonym: "initiator codon change" EXACT []
13884 synonym: "Jannovar:initiator_codon_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
13885 synonym: "snpEff:NON_SYNONYMOUS_START" RELATED VAR []
13886 synonym: "VAT:startOverlap" EXACT VAR []
1382813887 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13888 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13889 xref: http://vat.gersteinlab.org/formats.php "VAT"
1382913890 xref: loinc:LA6695-6 "Initiating Methionine"
1383013891 is_a: SO:0001580 ! coding_sequence_variant
1383113892 created_by: kareneilbeck
1383913900 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]
1384013901 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.
1384113902 synonym: "ANNOVAR:nonsynonymous SNV" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13903 synonym: "Jannovar:missense_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1384213904 synonym: "missense" EXACT [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
1384313905 synonym: "missense codon" EXACT []
13844 synonym: "snpEff:NON_SYSNONYMOUS_CODING" EXACT VAR []
13906 synonym: "Seattleseq:missense" EXACT VAR []
13907 synonym: "Seattleseq:missense-near-splice" RELATED VAR []
13908 synonym: "snpEff:NON_SYNONYMOUS_CODING" EXACT VAR []
13909 synonym: "VAAST:missense_variant" EXACT VAR []
1384513910 synonym: "VAAST:non_synonymous_codon" RELATED VAR []
13911 synonym: "VAT:nonsynonymous" EXACT VAR []
13912 synonym: "VEP:missense_variant" EXACT VAR []
1384613913 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
1384713914 xref: http://en.wikipedia.org/wiki/Missense_mutation
13915 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
13916 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13917 xref: http://vat.gersteinlab.org/formats.php "VAT"
13918 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1384813919 xref: loinc:LA6698-0 "Missense"
1384913920 is_a: SO:0001992 ! nonsynonymous_variant
1385013921 created_by: kareneilbeck
1387713948 [Term]
1387813949 id: SO:0001587
1387913950 name: stop_gained
13880 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]
13951 def: "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened polypeptide." [SO:ke]
1388113952 comment: EBI term: Stop gained - In coding sequence, resulting in the gain of a stop codon (i.e. leading to a shortened peptide sequence).
1388213953 synonym: "ANNOVAR:stopgain" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13954 synonym: "Jannovar:stop_gained" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1388313955 synonym: "nonsense" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
1388413956 synonym: "nonsense codon" EXACT []
13885 synonym: "snpEFF:STOP_GAINED" EXACT VAR []
13957 synonym: "Seattleseq:stop-gained" EXACT VAR []
13958 synonym: "Seattleseq:stop-gained-near-splice" RELATED VAR []
13959 synonym: "snpEff:STOP_GAINED" EXACT VAR []
1388613960 synonym: "stop codon gained" RELATED []
1388713961 synonym: "stop gained" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
1388813962 synonym: "VAAST:stop_gained" EXACT VAR []
13963 synonym: "VAT:prematureStop" EXACT VAR []
13964 synonym: "VEP:stop_gained" EXACT VAR []
13965 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
13966 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13967 xref: http://vat.gersteinlab.org/formats.php "VAT"
13968 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1388913969 xref: loinc:LA6699-8 "Nonsense"
1389013970 is_a: SO:0001906 ! feature_truncation
1389113971 is_a: SO:0001992 ! nonsynonymous_variant
1389813978 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]
1389913979 comment: EBI term:Frameshift variations - In coding sequence, resulting in a frameshift.
1390013980 synonym: "ANNOVAR:frameshift block substitution" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13981 synonym: "ANNOVAR:frameshift substitution" RELATED []
1390113982 synonym: "frameshift variant" EXACT []
1390213983 synonym: "frameshift_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
1390313984 synonym: "frameshift_coding" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13985 synonym: "Jannovar:frameshift_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
13986 synonym: "Seattleseq:frameshift" EXACT VAR []
13987 synonym: "Seattleseq:frameshift-near-splice" RELATED VAR []
1390413988 synonym: "snpEff:FRAME_SHIFT" EXACT VAR []
1390513989 synonym: "VAAST:frameshift_variant" EXACT VAR []
13990 synonym: "VAT:deletionFS" NARROW VAR []
13991 synonym: "VAT:insertionFS" NARROW VAR []
13992 synonym: "VEP:frameshift_variant" EXACT VAR []
13993 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
13994 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13995 xref: http://vat.gersteinlab.org/formats.php "VAT"
13996 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1390613997 xref: loinc:LA6694-9 "Frameshift"
1390713998 is_a: SO:0001818 ! protein_altering_variant
1390813999 created_by: kareneilbeck
1391714008 synonym: "terminal codon variant" EXACT []
1391814009 synonym: "terminal_codon_variant" EXACT []
1391914010 synonym: "terminator codon variant" EXACT []
14011 synonym: "VAT:endOverlap" EXACT VAR []
14012 xref: http://vat.gersteinlab.org/formats.php "VAT"
1392014013 xref: loinc:LA6700-2 "Stop Codon Mutation"
1392114014 is_a: SO:0001580 ! coding_sequence_variant
1392214015 created_by: kareneilbeck
1418714280 name: non_coding_transcript_variant
1418814281 def: "A transcript variant of a non coding RNA gene." [SO:ke]
1418914282 comment: Within non-coding gene - Located within a gene that does not code for a protein.
14190 synonym: "ANNOVAR:ncRNA" RELATED VAR [http:http\://www.openbioinformatics.org/annovar/annovar_download.html]
14283 synonym: "ANNOVAR:ncRNA" NARROW VAR [http://annovar.openbioinformatics.org/en/latest/user-guide/gene/]
14284 synonym: "Jannovar:non_coding_transcript_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1419114285 synonym: "nc transcript variant" EXACT []
1419214286 synonym: "non coding transcript variant" EXACT []
14287 synonym: "VEP:non_coding_transcript_variant" EXACT VAR []
1419314288 synonym: "within_non_coding_gene" EXACT dbsnp [http://ensembl.org/info/docs/variation/index.html]
14289 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1419414290 is_a: SO:0001576 ! transcript_variant
1419514291 created_by: kareneilbeck
1419614292 creation_date: 2010-03-23T11:16:23Z
1420114297 def: "A transcript variant located with the sequence of the mature miRNA." [SO:ke]
1420214298 comment: EBI term: Within mature miRNA - Located within a microRNA.
1420314299 synonym: "mature miRNA variant" EXACT []
14300 synonym: "snpEff:MICRO_RNA" EXACT VAR []
14301 synonym: "VEP:mature_miRNA_variant" EXACT VAR []
1420414302 synonym: "within_mature_miRNA" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
14303 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
14304 xref: XX:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1420514305 is_a: SO:0001619 ! non_coding_transcript_variant
1420614306 created_by: kareneilbeck
1420714307 creation_date: 2010-03-23T11:16:58Z
1421214312 def: "A variant in a transcript that is the target of NMD." [SO:ke]
1421314313 synonym: "NMD transcript variant" EXACT []
1421414314 synonym: "NMD_transcript" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
14315 synonym: "VEP:NMD_transcript_variant" EXACT VAR []
14316 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1421514317 is_a: SO:0001576 ! transcript_variant
1421614318 created_by: kareneilbeck
1421714319 creation_date: 2010-03-23T11:20:40Z
1423614338 synonym: "5PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
1423714339 synonym: "ANNOVAR:UTR5" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
1423814340 synonym: "five prime UTR variant" EXACT []
14341 synonym: "Jannovar:5_prime_utr_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
14342 synonym: "Seattleseq:5-prime-UTR" EXACT VAR []
1423914343 synonym: "snpEff:UTR_5_PRIME" EXACT VAR []
1424014344 synonym: "untranslated-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
14345 synonym: "VAAST:5_prime_UTR_variant" EXACT VAR []
1424114346 synonym: "VAAST:five_prime_UTR_variant" EXACT VAR []
14347 synonym: "VEP:5_prime_UTR_variant" EXACT VAR []
14348 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
14349 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
14350 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1424214351 is_a: SO:0001622 ! UTR_variant
1424314352 created_by: kareneilbeck
1424414353 creation_date: 2010-03-23T11:23:29Z
1425114360 synonym: "3'UTR variant" EXACT []
1425214361 synonym: "3PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
1425314362 synonym: "ANNOVAR:UTR3" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
14363 synonym: "Jannovar:3_prime_utr_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
14364 synonym: "Seattleseq:3-prime-UTR" EXACT VAR []
1425414365 synonym: "snpEff:UTR_3_PRIME" EXACT VAR []
1425514366 synonym: "three prime UTR variant" EXACT []
1425614367 synonym: "untranslated-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
14368 synonym: "VAAST:3_prime_UTR_variant" EXACT VAR []
1425714369 synonym: "VAAST:three_prime_UTR_variant" EXACT VAR []
14370 synonym: "VEP:3_prime_UTR_variant" EXACT VAR []
14371 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
14372 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
14373 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1425814374 is_a: SO:0001622 ! UTR_variant
1425914375 created_by: kareneilbeck
1426014376 creation_date: 2010-03-23T11:23:54Z
1426614382 comment: EBI term: Partial codon - Located within the final, incomplete codon of a transcript with a shortened coding sequence where the end is unknown.
1426714383 synonym: "incomplete terminal codon variant" EXACT []
1426814384 synonym: "partial_codon" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
14385 synonym: "VEP:incomplete_terminal_codon_variant" EXACT VAR []
14386 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1426914387 is_a: SO:0001590 ! terminator_codon_variant
1427014388 is_a: SO:0001650 ! inframe_variant
1427114389 created_by: kareneilbeck
1428014398 synonym: "intron variant" EXACT []
1428114399 synonym: "intron_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
1428214400 synonym: "intronic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
14401 synonym: "Jannovar:intron_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
14402 synonym: "Seattleseq:intron" EXACT VAR []
14403 synonym: "Seattleseq:intron-near-splice" RELATED VAR []
1428314404 synonym: "snpEff:INTRON" EXACT VAR []
1428414405 synonym: "VAAST:intron_variant" EXACT VAR []
14406 synonym: "VEP:intron_variant" EXACT VAR []
14407 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
14408 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
14409 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1428514410 is_a: SO:0001576 ! transcript_variant
1428614411 created_by: kareneilbeck
1428714412 creation_date: 2010-03-23T03:52:38Z
1429414419 synonym: "ANNOVAR:intergenic" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
1429514420 synonym: "intergenic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
1429614421 synonym: "intergenic variant" EXACT []
14422 synonym: "Jannovar:intergenic_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
14423 synonym: "Seattleseq:intergenic" EXACT VAR []
1429714424 synonym: "snpEff:INTERGENIC" EXACT VAR []
14425 synonym: "VEP:intergenic_variant" EXACT VAR []
14426 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
14427 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
14428 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1429814429 is_a: SO:0001878 ! feature_variant
1429914430 created_by: kareneilbeck
1430014431 creation_date: 2010-03-23T05:07:37Z
1430614437 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.
1430714438 synonym: "essential_splice_site" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
1430814439 synonym: "splice site variant" EXACT []
14440 synonym: "VAT:spliceOverlap" EXACT VAR []
14441 xref: http://vat.gersteinlab.org/formats.php "VAT"
1430914442 is_a: SO:0001568 ! splicing_variant
1431014443 is_a: SO:0001627 ! intron_variant
1431114444 created_by: kareneilbeck
1431714450 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]
1431814451 comment: EBI term: splice site - 1-3 bps into an exon or 3-8 bps into an intron.
1431914452 synonym: "ANNOVAR:splicing" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
14453 synonym: "Jannovar:splice_region_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
14454 synonym: "snpEff:SPLICE_SITE_BRANCH" RELATED VAR []
14455 synonym: "snpEff:SPLICE_SITE_BRANCH_U12" RELATED VAR []
14456 synonym: "snpEff:SPLICE_SITE_REGION" EXACT VAR []
1432014457 synonym: "splice region variant" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
1432114458 synonym: "VAAST:splice_region_variant" EXACT VAR []
14459 synonym: "VEP:splice_region_variant" EXACT VAR []
14460 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
14461 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1432214462 is_a: SO:0001568 ! splicing_variant
1432314463 created_by: kareneilbeck
1432414464 creation_date: 2010-03-24T09:46:02Z
1432914469 def: "A sequence variant located 5' of a gene." [SO:ke]
1433014470 comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
1433114471 synonym: "ANNOVAR:upstream" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
14472 synonym: "Jannovar:upstream_gene_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1433214473 synonym: "snpEff:UPSTREAM" EXACT VAR []
1433314474 synonym: "upstream gene variant" EXACT []
14475 synonym: "VEP:upstream_gene_variant" EXACT VAR []
14476 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
14477 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1433414478 is_a: SO:0001628 ! intergenic_variant
1433514479 created_by: kareneilbeck
1433614480 creation_date: 2010-03-24T09:49:13Z
1434214486 comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
1434314487 synonym: "ANNOVAR:downstream" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
1434414488 synonym: "downstream gene variant" EXACT []
14489 synonym: "Jannovar:downstream_gene_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1434514490 synonym: "snpEff:DOWNSTREAM" EXACT VAR []
14491 synonym: "VEP:downstream_gene_variant" EXACT VAR []
14492 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
14493 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1434614494 is_a: SO:0001628 ! intergenic_variant
1434714495 created_by: kareneilbeck
1434814496 creation_date: 2010-03-24T09:49:38Z
1435414502 comment: EBI term Downstream variations - Within 5 kb downstream of the 3prime end of a transcript.
1435514503 synonym: "5KB downstream variant" EXACT []
1435614504 synonym: "downstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
14505 synonym: "Seattleseq:downstream-gene" EXACT VAR []
1435714506 synonym: "within 5KB downstream" RELATED []
14507 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
1435814508 is_a: SO:0001632 ! downstream_gene_variant
1435914509 created_by: kareneilbeck
1436014510 creation_date: 2010-03-24T09:50:16Z
1436514515 def: "A sequence variant located within a half KB of the end of a gene." [SO:ke]
1436614516 synonym: "500B downstream variant" EXACT []
1436714517 synonym: "near-gene-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
14368 is_a: SO:0001633 ! 5KB_downstream_variant
14518 is_a: SO:0001632 ! downstream_gene_variant
1436914519 created_by: kareneilbeck
1437014520 creation_date: 2010-03-24T09:50:42Z
1437114521
1437514525 def: "A sequence variant located within 5KB 5' of a gene." [SO:ke]
1437614526 comment: EBI term Upstream variations - Within 5 kb upstream of the 5prime end of a transcript.
1437714527 synonym: "5kb upstream variant" EXACT []
14528 synonym: "Seattleseq:upstream-gene" EXACT VAR []
1437814529 synonym: "upstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
14530 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
1437914531 is_a: SO:0001631 ! upstream_gene_variant
1438014532 created_by: kareneilbeck
1438114533 creation_date: 2010-03-24T09:51:06Z
1438614538 def: "A sequence variant located within 2KB 5' of a gene." [SO:ke]
1438714539 synonym: "2KB upstream variant" EXACT []
1438814540 synonym: "near-gene-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
14389 is_a: SO:0001635 ! 5KB_upstream_variant
14541 is_a: SO:0001631 ! upstream_gene_variant
1439014542 created_by: kareneilbeck
1439114543 creation_date: 2010-03-24T09:51:22Z
1439214544
1452714679 name: inframe_variant
1452814680 def: "A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]
1452914681 synonym: "ANNOVAR:nonframeshift block substitution" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
14682 synonym: "ANNOVAR:nonframeshift substitution" RELATED VAR []
1453014683 synonym: "cds-indel" EXACT dbsnp []
1453114684 synonym: "inframe variant" EXACT []
1453214685 synonym: "VAAST:inframe_variant" EXACT VAR []
1490515058 [Term]
1490615059 id: SO:0001691
1490715060 name: blunt_end_restriction_enzyme_cleavage_site
15061 def: "A restriction enzyme recognition site that, when cleaved, results in no overhangs." [SBOL:jgquinn, SO:ke]
1490815062 synonym: "blunt end restriction enzyme cleavage site" EXACT []
1490915063 is_a: SO:0001687 ! restriction_enzyme_recognition_site
1491015064 created_by: kareneilbeck
1502415178 [Term]
1502515179 id: SO:0001703
1502615180 name: H3K9_acetylation_site
15027 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]
15181 def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acetylated." [http://en.wikipedia.org/wiki/Histone]
1502815182 synonym: "H3K9 acetylation site" EXACT []
15029 synonym: "H3K9Ac" RELATED []
15183 synonym: "H3K9ac" EXACT []
1503015184 is_a: SO:0001973 ! histone_3_acetylation_site
1503115185 created_by: kareneilbeck
1503215186 creation_date: 2010-03-31T10:25:05Z
1503415188 [Term]
1503515189 id: SO:0001704
1503615190 name: H3K14_acetylation_site
15037 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]
15191 def: "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acetylated." [http://en.wikipedia.org/wiki/Histone]
1503815192 synonym: "H3K14 acetylation site" EXACT []
15039 synonym: "H3K14Ac" RELATED []
15193 synonym: "H3K14ac" EXACT []
1504015194 is_a: SO:0001973 ! histone_3_acetylation_site
1504115195 created_by: kareneilbeck
1504215196 creation_date: 2010-03-31T10:25:53Z
1517115325 [Term]
1517215326 id: SO:0001718
1517315327 name: H3K18_acetylation_site
15174 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]
15328 def: "A kind of histone modification site, whereby the 18th residue (a lysine), from the start of the H3 histone protein is acetylated." [SO:ke]
1517515329 synonym: "H3K18 acetylation site" EXACT []
15176 synonym: "H3K18Ac" RELATED []
15330 synonym: "H3K18ac" EXACT []
1517715331 is_a: SO:0001973 ! histone_3_acetylation_site
1517815332 created_by: kareneilbeck
1517915333 creation_date: 2010-04-13T10:39:35Z
1518015334
1518115335 [Term]
1518215336 id: SO:0001719
15183 name: H3K23_acylation_site
15184 def: "A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]
15185 synonym: "H3K23 acylation site" RELATED []
15186 synonym: "H3K23Ac" RELATED []
15337 name: H3K23_acetylation_site
15338 def: "A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acetylated." [SO:ke]
15339 synonym: "H3K23 acetylation site" EXACT []
15340 synonym: "H3K23ac" EXACT []
1518715341 is_a: SO:0001973 ! histone_3_acetylation_site
1518815342 created_by: kareneilbeck
1518915343 creation_date: 2010-04-13T10:42:45Z
1520715361 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]
1520815362 synonym: "H3K27 acylation site" EXACT []
1520915363 synonym: "H3K27Ac" RELATED []
15210 is_a: SO:0001973 ! histone_3_acetylation_site
15364 is_obsolete: true
1521115365 created_by: kareneilbeck
1521215366 creation_date: 2010-04-13T10:44:09Z
1521315367
1528315437
1528415438 [Term]
1528515439 id: SO:0001729
15286 name: H4K16_acylation_site
15287 def: "A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]
15288 synonym: "H4K16 acylation_site" RELATED []
15289 synonym: "H4K16Ac" RELATED []
15290 is_a: SO:0001972 ! histone_4_acylation_site
15440 name: H4K16_acetylation_site
15441 def: "A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acetylated." [SO:ke]
15442 synonym: "H4K16 acetylation site" EXACT []
15443 synonym: "H4K16ac" EXACT []
15444 is_a: SO:0001972 ! histone_4_acetylation_site
1529115445 created_by: kareneilbeck
1529215446 creation_date: 2010-04-13T11:09:41Z
1529315447
1529415448 [Term]
1529515449 id: SO:0001730
15296 name: H4K5_acylation_site
15297 def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]
15298 synonym: "H4K5 acylation site" RELATED []
15299 synonym: "H4K5Ac" RELATED []
15300 is_a: SO:0001972 ! histone_4_acylation_site
15450 name: H4K5_acetylation_site
15451 def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acetylated." [SO:ke]
15452 synonym: "H4K5 acetylation site" EXACT []
15453 synonym: "H4K5ac" EXACT []
15454 is_a: SO:0001972 ! histone_4_acetylation_site
1530115455 created_by: kareneilbeck
1530215456 creation_date: 2010-04-13T11:13:00Z
1530315457
1530415458 [Term]
1530515459 id: SO:0001731
15306 name: H4K8_acylation_site
15307 def: "A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]
15308 synonym: "H4K8 acylation site" RELATED []
15309 synonym: "H4K8Ac" RELATED []
15310 is_a: SO:0001972 ! histone_4_acylation_site
15460 name: H4K8_acetylation_site
15461 def: "A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acetylated." [SO:KE]
15462 synonym: "H4K8 acetylation site" EXACT []
15463 synonym: "H4K8ac" EXACT []
15464 is_a: SO:0001972 ! histone_4_acetylation_site
1531115465 created_by: kareneilbeck
1531215466 creation_date: 2010-04-13T11:14:24Z
1531315467
1557115725 [Term]
1557215726 id: SO:0001759
1557315727 name: unitary_pseudogene
15574 def: "A pseudogene, deactivated from original state by mutation, fixed in a population." [http://en.wikipedia.org/wiki/Pseudogene, SO:ke]
15728 def: "A pseudogene, deactivated from original state by mutation, fixed in a population,where the ortholog in a reference species such as mouse remains functional." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, http://en.wikipedia.org/wiki/Pseudogene, SO:ke]
1557515729 comment: This is different from a non processed pseudogene because the gene was not duplicated. An example is the L-gulono-lactone oxidase pseudogene in primates.
1557615730 synonym: "disabled gene" RELATED []
1557715731 synonym: "unitary pseudogene" RELATED []
1558215736 [Term]
1558315737 id: SO:0001760
1558415738 name: non_processed_pseudogene
15585 def: "A pseudogene that arose from a means other than retrotransposition." [SO:ke]
15739 def: "A pseudogene that arose from a means other than retrotransposition. A pseudogene created via genomic duplication of a functional protein-coding parent gene followed by accumulation of deleterious mutations." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, SO:ke]
1558615740 synonym: "non processed pseudogene" RELATED []
15741 synonym: "unprocessed pseudogene" EXACT []
15742 synonym: "unprocessed_pseudogene" EXACT []
1558715743 is_a: SO:0000336 ! pseudogene
1558815744 created_by: kareneilbeck
1558915745 creation_date: 2011-03-09T10:54:47Z
1576515921 id: SO:0001782
1576615922 name: TF_binding_site_variant
1576715923 def: "A sequence variant located within a transcription factor binding site." [EBI:fc]
15924 synonym: "Jannovar:tf_binding_site_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1576815925 synonym: "TF binding site variant" EXACT []
15926 synonym: "VEP:TF_binding_site_variant" EXACT VAR []
15927 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1576915928 is_a: SO:0001566 ! regulatory_region_variant
1577015929 created_by: kareneilbeck
1577115930 creation_date: 2011-03-17T10:59:20Z
1584916008 def: "A sequence variant that changes exon sequence." [SO:ke]
1585016009 synonym: "ANNOVAR:exonic" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
1585116010 synonym: "exon variant" EXACT []
16011 synonym: "Jannovar:exon_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1585216012 synonym: "snpEff:EXON" EXACT VAR []
1585316013 synonym: "VAAST:exon_variant" EXACT VAR []
16014 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1585416015 is_a: SO:0001576 ! transcript_variant
1585516016 created_by: kareneilbeck
1585616017 creation_date: 2011-05-06T01:51:17Z
1585916020 id: SO:0001792
1586016021 name: non_coding_transcript_exon_variant
1586116022 def: "A sequence variant that changes non-coding exon sequence in a non-coding transcript." [EBI:fc, SO:ke]
16023 synonym: "ANNOVAR:ncRNA_exonic" NARROW VAR []
16024 synonym: "Jannovar:non_coding_transcript_exon_variant" NARROW VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1586216025 synonym: "non coding transcript exon variant" EXACT []
16026 synonym: "non_coding_transcript_exon_variant" EXACT VAR []
16027 synonym: "Seattleseq:non-coding-exon" EXACT VAR []
16028 synonym: "Seattleseq:non-coding-exon-near-splice" RELATED VAR []
16029 synonym: "VEP:non_coding_transcript_exon_variant" EXACT VAR []
16030 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
1586316031 is_a: SO:0001619 ! non_coding_transcript_variant
1586416032 is_a: SO:0001791 ! exon_variant
1586516033 created_by: kareneilbeck
1592116089 synonym: "lmr1R" EXACT []
1592216090 synonym: "regional centromere inner repeat region" EXACT []
1592316091 is_a: SO:0001797 ! centromeric_repeat
16092 relationship: part_of SO:0001795 ! regional_centromere
1592416093 relationship: part_of SO:0001796 ! regional_centromere_central_core
1592516094 created_by: kareneilbeck
1592616095 creation_date: 2011-05-31T01:01:08Z
1610816277 name: protein_altering_variant
1610916278 def: "A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]
1611016279 synonym: "protein altering variant" EXACT []
16280 synonym: "VEP:protein_altering_variant" EXACT VAR []
16281 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1611116282 is_a: SO:0001580 ! coding_sequence_variant
1611216283 created_by: kareneilbeck
1611316284 creation_date: 2011-06-24T03:38:02Z
1612016291 comment: EBI term: Synonymous SNPs - In coding sequence, not resulting in an amino acid change (i.e. silent mutation).\nThis term is sometimes used synonomously with the more general term 'silent mutation', although a silent mutation may occur in non coding sequence. The best practice is to annotate to the most specific term.
1612116292 synonym: "ANNOVAR:synonymous SNV" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
1612216293 synonym: "coding-synon" EXACT [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
16294 synonym: "Jannovar:synonymous_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
16295 synonym: "Seattleseq:synonymous" EXACT VAR []
16296 synonym: "Seattleseq:synonymous-near-splice" RELATED VAR []
1612316297 synonym: "silent mutation" RELATED []
1612416298 synonym: "silent substitution" RELATED []
1612516299 synonym: "silent_mutation" RELATED []
1612816302 synonym: "synonymous_coding" EXACT []
1612916303 synonym: "synonymous_codon" EXACT []
1613016304 synonym: "VAAST:synonymous_codon" EXACT VAR []
16305 synonym: "VAAST:synonymous_variant" EXACT VAR []
16306 synonym: "VAT:synonymous" EXACT VAR []
16307 synonym: "VEP:synonymous_variant" EXACT VAR []
1613116308 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
1613216309 xref: http://en.wikipedia.org/wiki/Silent_mutation "wiki"
1613316310 xref: http://en.wikipedia.org/wiki/Synonymous_mutation
16311 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
16312 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
16313 xref: http://vat.gersteinlab.org/formats.php "VAT"
16314 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1613416315 is_a: SO:0001580 ! coding_sequence_variant
1613516316 created_by: kareneilbeck
1613616317 creation_date: 2011-06-24T03:38:30Z
1615516336 synonym: "inframe increase in CDS length" EXACT []
1615616337 synonym: "inframe insertion" EXACT []
1615716338 synonym: "inframe_codon_gain" EXACT []
16339 synonym: "Jannovar:inframe_insertion" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1615816340 synonym: "snpEFF:CODON_INSERTION" EXACT VAR []
16341 synonym: "VAT:insertionNFS" EXACT VAR []
16342 synonym: "VEP:inframe_insertion" EXACT VAR []
16343 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
16344 xref: http://vat.gersteinlab.org/formats.php "VAT"
16345 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1615916346 is_a: SO:0001820 ! inframe_indel
1616016347 is_a: SO:0001908 ! internal_feature_elongation
1616116348 created_by: kareneilbeck
1617116358 synonym: "inframe decrease in CDS length" EXACT []
1617216359 synonym: "inframe deletion" RELATED []
1617316360 synonym: "inframe_codon_loss" EXACT []
16361 synonym: "Jannovar:inframe_deletion" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1617416362 synonym: "snpEff:CODON_DELETION" RELATED VAR []
16363 synonym: "VAT:deletionNFS" EXACT VAR []
16364 synonym: "VEP:inframe_deletion" EXACT VAR []
16365 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
16366 xref: http://vat.gersteinlab.org/formats.php "VAT"
16367 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1617516368 is_a: SO:0001820 ! inframe_indel
1617616369 is_a: SO:0001906 ! feature_truncation
1617716370 created_by: kareneilbeck
1619316386 def: "An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]
1619416387 synonym: "disruptive increase in CDS length" EXACT []
1619516388 synonym: "disruptive inframe insertion" EXACT []
16389 synonym: "Jannovar:disruptive_inframe_insertion" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1619616390 synonym: "snpEff:CODON_CHANGE_PLUS_CODON_INSERTION" EXACT VAR []
16391 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1619716392 is_a: SO:0001821 ! inframe_insertion
1619816393 created_by: kareneilbeck
1619916394 creation_date: 2011-06-27T11:28:37Z
1621416409 def: "An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]
1621516410 synonym: "disruptive decrease in CDS length" EXACT []
1621616411 synonym: "disruptive inframe deletion" EXACT []
16412 synonym: "Jannovar:disruptive_inframe_deletion" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1621716413 synonym: "snpEff:CODON_CHANGE_PLUS_CODON_DELETION" EXACT VAR []
16414 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1621816415 is_a: SO:0001822 ! inframe_deletion
1621916416 created_by: kareneilbeck
1622016417 creation_date: 2011-06-27T11:31:31Z
1636216559 [Term]
1636316560 id: SO:0001841
1636416561 name: polymorphic_pseudogene
16365 def: "Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated." [JAX:hd]
16366 comment: This terms is used by Ensembl and Vega.
16562 def: "A pseudogene in the reference genome, though known to be intact in the genomes of other individuals of the same species. The annotation process has confirmed that the pseudogenisation event is not a genomic sequencing error." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, JAX:hd]
16563 comment: This terms is used by Ensembl and Vega. Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated.
1636716564 synonym: "polymorphic psuedogene" EXACT []
1636816565 is_a: SO:0000336 ! pseudogene
1636916566 created_by: kareneilbeck
1642716624 [Term]
1642816625 id: SO:0001848
1642916626 name: homol_D_box
16430 def: "A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." [PMID:7501449, PMID:8458332]
16627 def: "A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." [PMID:21673110, PMID:7501449, PMID:8458332]
16628 synonym: "homoID" EXACT []
1643116629 synonym: "homol D box" EXACT []
1643216630 is_a: SO:0001660 ! core_promoter_element
1643316631 created_by: kareneilbeck
1684017038 def: "A feature amplification of a region containing a transcript." [SO:ke]
1684117039 comment: Created in conjunction with the EBI.
1684217040 synonym: "transcript amplification" EXACT []
17041 synonym: "VEP:transcript_amplification" EXACT VAR []
17042 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1684317043 is_a: SO:0001880 ! feature_amplification
1684417044 created_by: kareneilbeck
1684517045 creation_date: 2012-04-03T12:39:23Z
1686017060 def: "A feature amplification of a region containing a regulatory region." [SO:ke]
1686117061 comment: Created in conjunction with the EBI.
1686217062 synonym: "regulatory region amplification" EXACT []
17063 synonym: "VEP:regulatory_region_amplification" EXACT VAR []
17064 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1686317065 is_a: SO:0001880 ! feature_amplification
1686417066 created_by: kareneilbeck
1686517067 creation_date: 2012-04-03T12:41:28Z
1687117073 comment: Created in conjunction with the EBI.
1687217074 synonym: "TFBS amplification " EXACT []
1687317075 synonym: "transcription factor binding site amplification" EXACT []
17076 synonym: "VEP:TFBS_amplification" EXACT VAR []
17077 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1687417078 is_a: SO:0001891 ! regulatory_region_amplification
1687517079 created_by: kareneilbeck
1687617080 creation_date: 2012-04-03T12:42:48Z
1688017084 name: transcript_ablation
1688117085 def: "A feature ablation whereby the deleted region includes a transcript feature." [SO:ke]
1688217086 comment: Created in conjunction with the EBI.
17087 synonym: "Jannovar:transcript_ablation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1688317088 synonym: "transcript ablation" EXACT []
17089 synonym: "VEP:transcript_ablation" EXACT VAR []
17090 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1688417091 is_a: SO:0001879 ! feature_ablation
1688517092 created_by: kareneilbeck
1688617093 creation_date: 2012-04-03T12:44:19Z
1689117098 def: "A feature ablation whereby the deleted region includes a regulatory region." [SO:ke]
1689217099 comment: Created in conjunction with the EBI.
1689317100 synonym: "regulatory region ablation" EXACT []
17101 synonym: "VEP:regulatory_region_ablation" EXACT VAR []
17102 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1689417103 is_a: SO:0001879 ! feature_ablation
1689517104 created_by: kareneilbeck
1689617105 creation_date: 2012-04-03T12:45:13Z
1690217111 comment: Created in conjunction with the EBI.
1690317112 synonym: "TFBS ablation" EXACT []
1690417113 synonym: "transcription factor binding site ablation" EXACT []
17114 synonym: "VEP:TFBS_ablation" EXACT VAR []
17115 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1690517116 is_a: SO:0001894 ! regulatory_region_ablation
1690617117 created_by: kareneilbeck
1690717118 creation_date: 2012-04-03T12:45:56Z
1701817229 name: feature_truncation
1701917230 def: "A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." [SO:ke]
1702017231 synonym: "feature truncation" EXACT []
17232 synonym: "Jannovar:feature_truncation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
17233 synonym: "VEP:feature_truncation" EXACT VAR []
17234 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1702117235 is_a: SO:0001878 ! feature_variant
1702217236 created_by: kareneilbeck
1702317237 creation_date: 2012-04-12T05:05:28Z
1702717241 name: feature_elongation
1702817242 def: "A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." [SO:ke]
1702917243 synonym: "feature elongation" EXACT []
17244 synonym: "VEP:feature_elongation" EXACT VAR []
17245 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1703017246 is_a: SO:0001878 ! feature_variant
1703117247 created_by: kareneilbeck
1703217248 creation_date: 2012-04-12T05:05:56Z
1703617252 name: internal_feature_elongation
1703717253 def: "A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence." [SO:ke]
1703817254 synonym: "internal feature elongation" EXACT []
17255 synonym: "Jannovar:internal_feature_elongation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1703917256 is_a: SO:0001907 ! feature_elongation
1704017257 created_by: kareneilbeck
1704117258 creation_date: 2012-04-12T05:06:20Z
1704617263 def: "A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]
1704717264 synonym: "ANNOVAR:frameshift insertion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
1704817265 synonym: "frameshift elongation" EXACT []
17266 synonym: "Jannovar:frameshift_elongation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1704917267 is_a: SO:0001589 ! frameshift_variant
1705017268 is_a: SO:0001908 ! internal_feature_elongation
1705117269 created_by: kareneilbeck
1705517273 id: SO:0001910
1705617274 name: frameshift_truncation
1705717275 def: "A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]
17058 synonym: "ANNOVAR:frameshit deletion" EXACT ebi_variants [http://www.openbioinformatics.org/annovar/annovar_download.html]
17059 synonym: "frameshft truncation" EXACT []
17276 synonym: "ANNOVAR:frameshift deletion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
17277 synonym: "frameshift truncation" EXACT []
17278 synonym: "Jannovar:frameshift_truncation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1706017279 is_a: SO:0001589 ! frameshift_variant
1706117280 is_a: SO:0001906 ! feature_truncation
1706217281 created_by: kareneilbeck
1733817557 [Term]
1733917558 id: SO:0001936
1734017559 name: H3K36_acetylation_site
17341 def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]
17560 def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]
1734217561 synonym: "H3K36 acetylation site" EXACT []
1734317562 synonym: "H3K36ac" EXACT []
1734417563 is_a: SO:0001973 ! histone_3_acetylation_site
1734817567 [Term]
1734917568 id: SO:0001937
1735017569 name: H2BK12_acetylation_site
17351 def: "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]
17570 def: "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is acetylated." [EBI:nj]
1735217571 synonym: "H2BK12 acetylation site" EXACT []
17353 synonym: "H2BK12ac" RELATED []
17354 is_a: SO:0001702 ! histone_acetylation_site
17572 synonym: "H2BK12ac" EXACT []
17573 is_a: SO:0002143 ! histone_2B_acetylation_site
1735517574 created_by: kareneilbeck
1735617575 creation_date: 2013-03-06T10:19:13Z
1735717576
1736117580 def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]
1736217581 synonym: "H2AK5 acetylation site" EXACT []
1736317582 synonym: "H2AK5ac" EXACT []
17364 is_a: SO:0001702 ! histone_acetylation_site
17583 is_a: SO:0002142 ! histone_2A_acetylation_site
1736517584 created_by: kareneilbeck
1736617585 creation_date: 2013-03-06T10:20:57Z
1736717586
1737117590 def: "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]
1737217591 synonym: "H4K12 acetylation site" EXACT []
1737317592 synonym: "H4K12ac" EXACT []
17374 is_a: SO:0001972 ! histone_4_acylation_site
17593 is_a: SO:0001972 ! histone_4_acetylation_site
1737517594 created_by: kareneilbeck
1737617595 creation_date: 2013-03-06T10:26:15Z
1737717596
1737817597 [Term]
1737917598 id: SO:0001940
1738017599 name: H2BK120_acetylation_site
17381 def: "A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]
17600 def: "A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj, http://dx.doi.org/10.4161/epi.6.5.15623]
1738217601 synonym: "H2BK120 acetylation site" EXACT []
1738317602 synonym: "H2BK120ac" EXACT []
17384 is_a: SO:0001702 ! histone_acetylation_site
17603 is_a: SO:0002143 ! histone_2B_acetylation_site
1738517604 created_by: kareneilbeck
1738617605 creation_date: 2013-03-06T10:28:38Z
1738717606
1739017609 name: H4K91_acetylation_site
1739117610 def: "A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]
1739217611 synonym: "H4K91 acetylation site" EXACT []
17393 is_a: SO:0001972 ! histone_4_acylation_site
17612 synonym: "H4K91ac" EXACT []
17613 is_a: SO:0001972 ! histone_4_acetylation_site
1739417614 created_by: kareneilbeck
1739517615 creation_date: 2013-03-06T10:41:04Z
1739617616
1739817618 id: SO:0001942
1739917619 name: H2BK20_acetylation_site
1740017620 def: "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]
17401 synonym: "H2BK20 acetylation site" RELATED []
17621 synonym: "H2BK20 acetylation site" EXACT []
1740217622 synonym: "H2BK20ac" EXACT []
17403 is_a: SO:0001702 ! histone_acetylation_site
17623 is_a: SO:0002143 ! histone_2B_acetylation_site
1740417624 created_by: kareneilbeck
1740517625 creation_date: 2013-03-06T10:44:31Z
1740617626
1740717627 [Term]
1740817628 id: SO:0001943
17409 name: H3K4ac_acetylation_site
17629 name: H3K4_acetylation_site
1741017630 def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]
17631 synonym: "H3K4 acetylation site" EXACT []
1741117632 synonym: "H3K4ac" EXACT []
17412 synonym: "H3K4ac acetylation site" EXACT []
1741317633 is_a: SO:0001973 ! histone_3_acetylation_site
1741417634 created_by: kareneilbeck
1741517635 creation_date: 2013-03-06T10:46:32Z
1742017640 def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]
1742117641 synonym: "H2AK9 acetylation site" EXACT []
1742217642 synonym: "H2AK9ac" EXACT []
17423 is_a: SO:0001702 ! histone_acetylation_site
17643 is_a: SO:0002142 ! histone_2A_acetylation_site
1742417644 created_by: kareneilbeck
1742517645 creation_date: 2013-03-06T10:48:11Z
1742617646
1744017660 def: "A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]
1744117661 synonym: "H2BK15 acetylation site" EXACT []
1744217662 synonym: "H2BK15ac" EXACT []
17443 is_a: SO:0001702 ! histone_acetylation_site
17663 is_a: SO:0002143 ! histone_2B_acetylation_site
1744417664 created_by: kareneilbeck
1744517665 creation_date: 2013-03-06T10:53:23Z
1744617666
1765217872 name: coding_transcript_variant
1765317873 def: "A transcript variant of a protein coding gene." [SO:ke]
1765417874 synonym: "coding transcript variant" EXACT []
17875 synonym: "Jannovar:coding_transcript_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1765517876 is_a: SO:0001576 ! transcript_variant
1765617877 created_by: kareneilbeck
1765717878 creation_date: 2013-05-22T04:34:49Z
1766117882 name: coding_transcript_intron_variant
1766217883 def: "A transcript variant occurring within an intron of a coding transcript." [SO:ke]
1766317884 synonym: "coding sequence intron variant" EXACT []
17885 synonym: "Jannovar:coding_transcript_intron_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1766417886 is_a: SO:0001627 ! intron_variant
1766517887 is_a: SO:0001968 ! coding_transcript_variant
1766617888 created_by: kareneilbeck
1767017892 id: SO:0001970
1767117893 name: non_coding_transcript_intron_variant
1767217894 def: "A transcript variant occurring within an intron of a non coding transcript." [SO:ke]
17895 synonym: "ANNOVAR:ncRNA_intronic" NARROW VAR []
17896 synonym: "Jannovar:non_coding_transcript_intron_variant" NARROW VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1767317897 synonym: "non coding transcript intron variant" EXACT []
1767417898 is_a: SO:0001619 ! non_coding_transcript_variant
1767517899 is_a: SO:0001627 ! intron_variant
1768717911
1768817912 [Term]
1768917913 id: SO:0001972
17690 name: histone_4_acylation_site
17691 def: "A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]
17914 name: histone_4_acetylation_site
17915 def: "A histone 4 modification where the modification is the acetylation of the residue." [EBI:nj, ISBN:0815341059, SO:ke]
1769217916 synonym: "H4ac" EXACT []
17917 synonym: "histone 4 acetylation site" EXACT []
1769317918 is_a: SO:0001702 ! histone_acetylation_site
1769417919 created_by: kareneilbeck
1769517920 creation_date: 2013-07-30T10:43:04Z
1769717922 [Term]
1769817923 id: SO:0001973
1769917924 name: histone_3_acetylation_site
17700 def: "A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]
17925 def: "A histone 3 modification where the modification is the acetylation of the residue." [EBI:nj, ISBN:0815341059, SO:ke]
1770117926 synonym: "H3ac" EXACT []
17927 synonym: "histone 3 acetylation site" EXACT []
1770217928 is_a: SO:0001702 ! histone_acetylation_site
1770317929 created_by: kareneilbeck
1770417930 creation_date: 2013-07-30T10:46:42Z
1779718023 def: "A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]
1779818024 comment: Requested by Andy Menzies at the Sanger. This isn't necessarily a protein coding change. A premature start codon can effect the production of a mature protein product by providing a competing translation start point. Some genes balance their expression this way, eg THPO requires the presence of a premature start to limit expression, its loss leads to Familial thrombocythemia.
1779918025 synonym: "5' UTR premature start codon variant" EXACT []
17800 synonym: "snpEff:START_GAINED" EXACT VAR []
1780118026 is_a: SO:0001623 ! 5_prime_UTR_variant
1780218027 created_by: kareneilbeck
1780318028 creation_date: 2013-07-30T04:36:25Z
1784518070 name: 5_prime_UTR_premature_start_codon_gain_variant
1784618071 def: "A 5' UTR variant where a premature start codon is gained." [Sanger:am]
1784718072 synonym: "5 prime UTR premature start codon gain variant" EXACT []
18073 synonym: "Jannovar:5_prime_UTR_premature_start_codon_gain_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
18074 synonym: "snpEff:START_GAINED" EXACT VAR []
18075 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1784818076 is_a: SO:0001983 ! 5_prime_UTR_premature_start_codon_variant
1784918077 created_by: kareneilbeck
1785018078 creation_date: 2013-07-31T03:53:06Z
1803018258 name: rare_amino_acid_variant
1803118259 def: "A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]
1803218260 comment: Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
18261 synonym: "Jannovar:rare_amino_acid_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1803318262 synonym: "rare amino acid variant" EXACT []
18263 synonym: "snpEff:RARE_AMINO_ACID" EXACT VAR []
18264 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1803418265 is_a: SO:0001586 ! non_conservative_missense_variant
1803518266 created_by: kareneilbeck
1803618267 creation_date: 2014-03-24T02:24:01Z
1806118292 def: "A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence." [SO:ke]
1806218293 comment: Requested by Pablo Cingolani, for use in SnpEff.
1806318294 synonym: "intragenic variant" EXACT []
18295 synonym: "Jannovar:intragenic_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1806418296 synonym: "snpEff:INTRAGENIC" EXACT VAR []
18297 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1806518298 is_a: SO:0001576 ! transcript_variant
1806618299 created_by: kareneilbeck
1806718300 creation_date: 2014-03-24T02:33:13Z
1807118304 name: start_lost
1807218305 def: "A codon variant that changes at least one base of the canonical start codon." [SO:ke]
1807318306 comment: Request from Uma Devi Paila, UVA. This term should not be applied to incomplete transcripts.
18307 synonym: "Jannovar:start_lost" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1807418308 synonym: "snpEff:START_LOST" EXACT VAR []
18309 synonym: "VEP:start_lost" EXACT VAR []
18310 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
18311 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1807518312 is_a: SO:0001582 ! initiator_codon_variant
1807618313 is_a: SO:0001992 ! nonsynonymous_variant
1807718314 created_by: kareneilbeck
1808218319 name: 5_prime_UTR_truncation
1808318320 def: "A sequence variant that causes the reduction of a the 5'UTR with regard to the reference sequence." [SO:ke]
1808418321 synonym: "5 prime UTR truncation" EXACT []
18322 synonym: "Jannovar:5_prime_utr_truncation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1808518323 synonym: "snpEff:UTR_5_DELETED" EXACT VAR []
18324 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1808618325 is_a: SO:0001623 ! 5_prime_UTR_variant
1808718326 created_by: kareneilbeck
1808818327 creation_date: 2014-03-25T10:46:42Z
1810118340 name: 3_prime_UTR_truncation
1810218341 def: "A sequence variant that causes the reduction of a the 3' UTR with regard to the reference sequence." [SO:ke]
1810318342 synonym: "3 prime UTR truncation" EXACT []
18343 synonym: "Jannovar:3_prime_utr_truncation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1810418344 synonym: "snpEff:UTR_3_DELETED" EXACT VAR []
18345 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1810518346 is_a: SO:0001624 ! 3_prime_UTR_variant
1810618347 created_by: kareneilbeck
1810718348 creation_date: 2014-03-25T10:54:50Z
1812118362 def: "A sequence variant located in a conserved intergenic region, between genes." [SO:ke]
1812218363 comment: Requested by Uma Paila (UVA) for snpEff.
1812318364 synonym: "conserved intergenic variant" EXACT []
18365 synonym: "Jannovar:conserved_intergenic_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1812418366 synonym: "snpEff:INTERGENIC_CONSERVED" EXACT VAR []
18367 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1812518368 is_a: SO:0001628 ! intergenic_variant
1812618369 created_by: kareneilbeck
1812718370 creation_date: 2014-03-25T02:54:39Z
1813218375 def: "A transcript variant occurring within a conserved region of an intron." [SO:ke]
1813318376 comment: Requested by Uma Paila (UVA) for snpEff.
1813418377 synonym: "conserved intron variant" EXACT []
18378 synonym: "Jannovar:conserved_intron_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1813518379 synonym: "snpEff:INTRON_CONSERVED" EXACT VAR []
18380 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1813618381 is_a: SO:0001627 ! intron_variant
1813718382 created_by: kareneilbeck
1813818383 creation_date: 2014-03-25T02:58:41Z
1814218387 name: start_retained_variant
1814318388 def: "A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]
1814418389 comment: Requested by Uma Paila as this term is annotated by snpEff. This would be used for non_AUG start codon annotation.
18390 synonym: "snpEff:SYNONYMOUS_START" EXACT VAR []
1814518391 is_a: SO:0001582 ! initiator_codon_variant
1814618392 is_a: SO:0001819 ! synonymous_variant
1814718393 created_by: kareneilbeck
1821918465 id: SO:0002027
1822018466 name: uORF
1822118467 def: "A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation." [PMID:12890013, PMID:16153175, POMBASE:mah]
18468 synonym: "regulatory uORF" EXACT []
1822218469 synonym: "upstream ORF" EXACT []
18470 xref: PMID:26684391
1822318471 is_a: SO:0000236 ! ORF
1822418472 created_by: kareneilbeck
1822518473 creation_date: 2014-07-14T11:59:23Z
1844018688 def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acetylated." [SO:rs]
1844118689 comment: Requested by: Sagar Jain, Richard Scheuermann.
1844218690 synonym: "H3K27 acetylation site" EXACT []
18691 synonym: "H3K27ac" EXACT []
1844318692 is_a: SO:0001973 ! histone_3_acetylation_site
1844418693 created_by: kareneilbeck
1844518694 creation_date: 2015-05-14T10:17:11Z
1863518884 is_a: SO:0002066 ! mobile_element_deletion
1863618885 created_by: kareneilbeck
1863718886 creation_date: 2015-09-04T13:47:16Z
18887
18888 [Term]
18889 id: SO:0002071
18890 name: CDS_supported_by_peptide_spectrum_match
18891 def: "A CDS that is supported by proteomics data." [SO:ke]
18892 is_a: SO:1001251 ! CDS_supported_by_sequence_similarity_data
18893 created_by: kareneilbeck
18894 creation_date: 2015-10-12T13:25:02Z
18895
18896 [Term]
18897 id: SO:0002072
18898 name: sequence_comparison
18899 is_a: SO:0000110 ! sequence_feature
18900 created_by: kareneilbeck
18901 creation_date: 2015-11-23T14:14:32Z
18902
18903 [Term]
18904 id: SO:0002073
18905 name: no_sequence_alteration
18906 def: "A position or feature within a sequence that is identical to the comparable position or feature of a specified reference sequence." [SO:ke]
18907 comment: This term is requested by the ClinVar data model group for use in the allele registry and such. A sequence at a defined location that is defined to match the reference assembly.
18908 is_a: SO:0002072 ! sequence_comparison
18909 created_by: kareneilbeck
18910 creation_date: 2015-11-23T14:15:08Z
18911
18912 [Term]
18913 id: SO:0002074
18914 name: intergenic_1kb_variant
18915 def: "A variant that falls in an intergenic region that is 1 kb or less between 2 genes." [SO:ke]
18916 comment: This term is added to map to the Annovar annotation 'upstream,downstream' .
18917 synonym: "ANNOVAR:upstream;downstream" EXACT VAR []
18918 is_a: SO:0001628 ! intergenic_variant
18919 created_by: kareneilbeck
18920 creation_date: 2015-11-23T14:24:16Z
18921
18922 [Term]
18923 id: SO:0002075
18924 name: incomplete_transcript_variant
18925 def: "A sequence variant that intersects an incompletely annotated transcript." [SO:ke]
18926 comment: This term is to map to the ANNOVAR term 'ncRNA' http://annovar.openbioinformatics.org/en/latest/user-guide/gene/ . The description in the documentation (11/23/15) 'variant overlaps a transcript without coding annotation in the gene definition'. and this is further clarified in the document: ncRNA above refers to RNA without coding annotation. It does not mean that this is a RNA that will never be translated; it merely means that the user-selected gene annotation system was not able to give a coding sequence annotation. It could still code protein products and may have such annotations in future versions of gene annotation or in another gene annotation system. For example, BC039000 is regarded as ncRNA by ANNOVAR when using UCSC Known Gene annotation, but it is regarded as a protein-coding gene by ANNOVAR when using ENSEMBL annotation. \n\nIt is further clarified in the comments section as: ncRNA does NOT mean conventional non-coding RNA. It means a RNA without complete coding sequence, and it can be a coding RNA that is annotated incorrectly by RefSeq or other gene definition systems.
18927 synonym: "incomplete transcript variant" EXACT []
18928 xref: http://annovar.openbioinformatics.org/en/latest/user-guide/gene/
18929 is_a: SO:0001576 ! transcript_variant
18930 created_by: kareneilbeck
18931 creation_date: 2015-11-23T14:43:51Z
18932
18933 [Term]
18934 id: SO:0002076
18935 name: incomplete_transcript_3UTR_variant
18936 def: "A sequence variant that intersects the 3' UTR of an incompletely annotated transcript." [SO:ke]
18937 synonym: "ANNOVAR:ncRNA_UTR3" EXACT VAR [http://annovar.openbioinformatics.org/en/latest/user-guide/gene/]
18938 synonym: "incomplete transcript 3UTR variant" RELATED []
18939 xref: http://annovar.openbioinformatics.org/en/latest/user-guide/gene/
18940 is_a: SO:0002075 ! incomplete_transcript_variant
18941 created_by: kareneilbeck
18942 creation_date: 2015-11-23T14:45:52Z
18943
18944 [Term]
18945 id: SO:0002077
18946 name: incomplete_transcript_5UTR_variant
18947 def: "A sequence variant that intersects the 5' UTR of an incompletely annotated transcript." [SO:ke]
18948 synonym: "ANNOVAR:ncRNA_UTR5" EXACT VAR [http://annovar.openbioinformatics.org/en/latest/user-guide/gene/]
18949 synonym: "incomplete transcript 5UTR variant" EXACT []
18950 xref: http://annovar.openbioinformatics.org/en/latest/user-guide/gene/
18951 is_a: SO:0002075 ! incomplete_transcript_variant
18952 created_by: kareneilbeck
18953 creation_date: 2015-11-24T12:39:17Z
18954
18955 [Term]
18956 id: SO:0002078
18957 name: incomplete_transcript_intronic_variant
18958 def: "A sequence variant that intersects the intron of an incompletely annotated transcript." [SO:ke]
18959 synonym: "incomplete transcript intronic variant" EXACT []
18960 is_a: SO:0002075 ! incomplete_transcript_variant
18961 created_by: kareneilbeck
18962 creation_date: 2015-11-24T12:51:45Z
18963
18964 [Term]
18965 id: SO:0002079
18966 name: incomplete_transcript_splice_region_variant
18967 def: "A sequence variant that intersects the splice region of an incompletely annotated transcript." [SO:ke]
18968 synonym: "incomplete transcript splice region variant" EXACT []
18969 is_a: SO:0002075 ! incomplete_transcript_variant
18970 created_by: kareneilbeck
18971 creation_date: 2015-11-24T12:52:06Z
18972
18973 [Term]
18974 id: SO:0002080
18975 name: incomplete_transcript_exonic_variant
18976 def: "A sequence variant that intersects the exon of an incompletely annotated transcript." [SO:ke]
18977 synonym: "incomplete transcript exonic variant" EXACT []
18978 is_a: SO:0002075 ! incomplete_transcript_variant
18979 created_by: kareneilbeck
18980 creation_date: 2015-11-24T12:52:10Z
18981
18982 [Term]
18983 id: SO:0002081
18984 name: incomplete_transcript_CDS
18985 def: "A sequence variant that intersects the coding regions of an incompletely annotated transcript." [SO:ke]
18986 synonym: "Seattleseq:coding-notMod3" EXACT VAR []
18987 synonym: "Seattleseq:coding-unknown" EXACT VAR []
18988 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
18989 is_a: SO:0002075 ! incomplete_transcript_variant
18990 created_by: kareneilbeck
18991 creation_date: 2015-11-24T15:32:27Z
18992
18993 [Term]
18994 id: SO:0002082
18995 name: incomplete_transcript_coding_splice_variant
18996 def: "A sequence variant that intersects the coding sequence near a splice region of an incompletely annotated transcript." [SO:ke]
18997 synonym: "incomplete transcript coding splice variant" EXACT []
18998 synonym: "Seattleseq:coding-notMod3-near-splice" EXACT VAR []
18999 synonym: "Seattleseq:coding-unknown-near-splice" EXACT VAR []
19000 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
19001 is_a: SO:0002079 ! incomplete_transcript_splice_region_variant
19002 created_by: kareneilbeck
19003 creation_date: 2015-11-24T15:51:06Z
19004
19005 [Term]
19006 id: SO:0002083
19007 name: 2KB_downstream_variant
19008 def: "A sequence variant located within 2KB 3' of a gene." [SO:ke]
19009 synonym: "Seattleseq:near-gene-3" EXACT VAR []
19010 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
19011 is_a: SO:0001632 ! downstream_gene_variant
19012 created_by: kareneilbeck
19013 creation_date: 2015-11-24T15:55:49Z
19014
19015 [Term]
19016 id: SO:0002084
19017 name: exonic_splice_region_variant
19018 def: "A sequence variant in which a change has occurred within the exonic region of the splice site, 1-2 bases from boundary." [SO:ke]
19019 synonym: "ANNOVAR:exonic;splicing" EXACT VAR []
19020 synonym: "exonic splice region variant" EXACT []
19021 synonym: "Seattleseq:coding-near-splice" RELATED VAR []
19022 is_a: SO:0001630 ! splice_region_variant
19023 created_by: kareneilbeck
19024 creation_date: 2015-12-01T14:38:47Z
19025
19026 [Term]
19027 id: SO:0002085
19028 name: unidirectional_gene_fusion
19029 def: "A sequence variant whereby two genes, on the same strand have become joined." [SO:ke]
19030 comment: Requested by SNPEFF team. Feb 2016.
19031 synonym: "unidirectional gene fusion" EXACT []
19032 is_a: SO:0001565 ! gene_fusion
19033 created_by: kareneilbeck
19034 creation_date: 2016-02-23T12:16:48Z
19035
19036 [Term]
19037 id: SO:0002086
19038 name: bidirectional_gene_fusion
19039 def: "A sequence variant whereby two genes, on alternate strands have become joined." [SO:ke]
19040 comment: Requested by SNPEFF team. Feb 2016.
19041 synonym: "bidirectional gene fusion" EXACT []
19042 is_a: SO:0001565 ! gene_fusion
19043 created_by: kareneilbeck
19044 creation_date: 2016-02-23T12:17:18Z
19045
19046 [Term]
19047 id: SO:0002087
19048 name: pseudogenic_CDS
19049 def: "A non functional descendant of the coding portion of a coding transcript, part of a pseudogene." [SO:ke]
19050 synonym: "pseudogenic CDS" EXACT []
19051 is_a: SO:0000462 ! pseudogenic_region
19052 relationship: part_of SO:0000516 ! pseudogenic_transcript
19053 created_by: kareneilbeck
19054 creation_date: 2016-02-29T12:58:52Z
19055
19056 [Term]
19057 id: SO:0002088
19058 name: non_coding_transcript_splice_region_variant
19059 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]
19060 synonym: "ANNOVAR:ncRNA_splicing" NARROW []
19061 is_a: SO:0001619 ! non_coding_transcript_variant
19062 is_a: SO:0001630 ! splice_region_variant
19063 created_by: kareneilbeck
19064 creation_date: 2016-03-07T09:40:46Z
19065
19066 [Term]
19067 id: SO:0002089
19068 name: 3_prime_UTR_exon_variant
19069 def: "A UTR variant of exonic sequence of the 3' UTR." [SO:ke]
19070 comment: Requested by visze github tracker ID 346.
19071 synonym: "3 prime UTR exon variant" EXACT []
19072 is_a: SO:0001624 ! 3_prime_UTR_variant
19073 created_by: kareneilbeck
19074 creation_date: 2016-03-07T10:37:04Z
19075
19076 [Term]
19077 id: SO:0002090
19078 name: 3_prime_UTR_intron_variant
19079 def: "A UTR variant of intronic sequence of the 3' UTR." [SO:ke]
19080 comment: Requested by visze github tracker ID 346.
19081 synonym: "3 prime UTR intron variant" EXACT []
19082 is_a: SO:0001624 ! 3_prime_UTR_variant
19083 is_a: SO:0001969 ! coding_transcript_intron_variant
19084 created_by: kareneilbeck
19085 creation_date: 2016-03-07T10:37:41Z
19086
19087 [Term]
19088 id: SO:0002091
19089 name: 5_prime_UTR_intron_variant
19090 def: "A UTR variant of intronic sequence of the 5' UTR." [SO:ke]
19091 comment: Requested by visze github tracker ID 346.
19092 synonym: "5 prime UTR intron variant" EXACT []
19093 is_a: SO:0001623 ! 5_prime_UTR_variant
19094 is_a: SO:0001969 ! coding_transcript_intron_variant
19095 created_by: kareneilbeck
19096 creation_date: 2016-03-07T10:38:04Z
19097
19098 [Term]
19099 id: SO:0002092
19100 name: 5_prime_UTR_exon_variant
19101 def: "A UTR variant of exonic sequence of the 5' UTR." [SO:ke]
19102 comment: Requested by visze github tracker ID 346.
19103 synonym: "5 prime UTR exon variant" EXACT []
19104 is_a: SO:0001623 ! 5_prime_UTR_variant
19105 created_by: kareneilbeck
19106 creation_date: 2016-03-07T10:38:26Z
19107
19108 [Term]
19109 id: SO:0002093
19110 name: structural_interaction_variant
19111 def: "A variant that impacts the internal interactions of the resulting polypeptide structure." [SO:ke]
19112 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.
19113 synonym: "structural interaction variant" EXACT []
19114 is_a: SO:0001599 ! 3D_polypeptide_structure_variant
19115 created_by: kareneilbeck
19116 creation_date: 2016-03-07T11:43:55Z
19117
19118 [Term]
19119 id: SO:0002094
19120 name: non_allelic_homologous_recombination_region
19121 def: "A genomic region at a non-allelic position where exchange of genetic material happens as a result of homologous recombination." []
19122 synonym: "NAHRR" EXACT []
19123 synonym: "non allelic homologous recombination region" EXACT []
19124 is_a: SO:0000339 ! recombination_hotspot
19125 created_by: nicole
19126 creation_date: 2016-05-17T13:34:12Z
19127
19128 [Term]
19129 id: SO:0002095
19130 name: scaRNA
19131 def: "A ncRNA, specific to the Cajal body, that has been demonstrated to function as a guide RNA in the site-specific synthesis of 2'-O-ribose-methylated nucleotides and pseudouridines in the RNA polymerase II-transcribed U1, U2, U4 and U5 spliceosomal small nuclear RNAs (snRNAs)." [PMC:126017, SO:nrs]
19132 synonym: "small Cajal body specific RNA" EXACT []
19133 synonym: "small Cajal body-specific RNA" EXACT []
19134 xref: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC126017/
19135 is_a: SO:0000655 ! ncRNA
19136 created_by: nicole
19137 creation_date: 2016-05-19T13:42:45Z
19138
19139 [Term]
19140 id: SO:0002096
19141 name: short_tandem_repeat_variation
19142 def: "A kind of sequence variant whereby a tandem repeat is expanded or contracted with regard to a reference." [SO:ke]
19143 synonym: "str variation" RELATED []
19144 is_a: SO:0000248 ! sequence_length_variation
19145 created_by: kareneilbeck
19146 creation_date: 2016-07-14T16:04:40Z
19147
19148 [Term]
19149 id: SO:0002097
19150 name: vertebrate_immune_system_pseudogene
19151 def: "A pseudogene derived from a vertebrate immune system gene." [SO:ke]
19152 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19153 synonym: "vertebrate immune system pseudogene" EXACT []
19154 is_a: SO:0000336 ! pseudogene
19155 created_by: kareneilbeck
19156 creation_date: 2016-07-15T16:00:22Z
19157
19158 [Term]
19159 id: SO:0002098
19160 name: immunoglobulin_pseudogene
19161 def: "A pseudogene derived from an immunoglobulin gene." [SO:ke]
19162 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19163 synonym: "immunoglobulin pseudogene" EXACT []
19164 is_a: SO:0002097 ! vertebrate_immune_system_pseudogene
19165 created_by: kareneilbeck
19166 creation_date: 2016-07-15T16:01:47Z
19167
19168 [Term]
19169 id: SO:0002099
19170 name: T_cell_receptor_pseudogene
19171 def: "A pseudogene derived from a T-cell receptor gene." [SO:ke]
19172 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19173 is_a: SO:0002097 ! vertebrate_immune_system_pseudogene
19174 created_by: kareneilbeck
19175 creation_date: 2016-07-15T16:02:18Z
19176
19177 [Term]
19178 id: SO:0002100
19179 name: IG_C_pseudogene
19180 def: "A pseudogenic constant region of an immunoglobulin gene which closely resembles a known functional Imunoglobulin constant gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19181 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19182 synonym: "IG C pseudogene" EXACT []
19183 is_a: SO:0002098 ! immunoglobulin_pseudogene
19184 created_by: kareneilbeck
19185 creation_date: 2016-07-15T16:05:08Z
19186
19187 [Term]
19188 id: SO:0002101
19189 name: IG_J_pseudogene
19190 def: "A pseudogenic joining region which closely resembles a known functional imunoglobulin joining gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19191 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19192 synonym: "IG J pseudogene" EXACT []
19193 is_a: SO:0002098 ! immunoglobulin_pseudogene
19194 created_by: kareneilbeck
19195 creation_date: 2016-07-15T16:05:34Z
19196
19197 [Term]
19198 id: SO:0002102
19199 name: IG_V_pseudogene
19200 def: "A pseudogenic variable region which closely resembles a known functional imunoglobulin variable gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the variable region of an immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19201 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19202 synonym: "IG V pseudogene" EXACT []
19203 is_a: SO:0002098 ! immunoglobulin_pseudogene
19204 created_by: kareneilbeck
19205 creation_date: 2016-07-15T16:05:56Z
19206
19207 [Term]
19208 id: SO:0002103
19209 name: TR_V_pseudogene
19210 def: "A pseudogenic variable region which closely resembles a known functional T receptor variable gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the variable region of an immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19211 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19212 synonym: "TR V pseudogene" EXACT []
19213 is_a: SO:0002099 ! T_cell_receptor_pseudogene
19214 created_by: kareneilbeck
19215 creation_date: 2016-07-15T16:06:29Z
19216
19217 [Term]
19218 id: SO:0002104
19219 name: TR_J_pseudogene
19220 def: "A pseudogenic joining region which closely resembles a known functional T receptor (TR) joining gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19221 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19222 synonym: "TR J pseudogene" EXACT []
19223 is_a: SO:0002099 ! T_cell_receptor_pseudogene
19224 created_by: kareneilbeck
19225 creation_date: 2016-07-15T16:06:51Z
19226
19227 [Term]
19228 id: SO:0002105
19229 name: translated_processed_pseudogene
19230 def: "A processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19231 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
19232 synonym: "translated processed pseudogene" EXACT []
19233 is_a: SO:0000043 ! processed_pseudogene
19234 created_by: kareneilbeck
19235 creation_date: 2016-07-18T12:31:53Z
19236
19237 [Term]
19238 id: SO:0002106
19239 name: translated_unprocessed_pseudogene
19240 def: "A non-processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19241 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
19242 synonym: "translated unprocessed pseudogene" EXACT []
19243 is_a: SO:0001760 ! non_processed_pseudogene
19244 created_by: kareneilbeck
19245 creation_date: 2016-07-18T12:34:42Z
19246
19247 [Term]
19248 id: SO:0002107
19249 name: transcribed_unprocessed_pseudogene
19250 def: "A unprocessed pseudogene supported by locus-specific evidence of transcription." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19251 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
19252 synonym: "transcribed unprocessed pseudogene" EXACT []
19253 is_a: SO:0001760 ! non_processed_pseudogene
19254 created_by: kareneilbeck
19255 creation_date: 2016-07-18T12:41:53Z
19256
19257 [Term]
19258 id: SO:0002108
19259 name: transcribed_unitary_pseudogene
19260 def: "A species specific unprocessed pseudogene without a parent gene, as it has an active orthologue in another species." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19261 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
19262 synonym: "transcribed unitary pseudogene" EXACT []
19263 is_a: SO:0001759 ! unitary_pseudogene
19264 created_by: kareneilbeck
19265 creation_date: 2016-07-18T12:44:26Z
19266
19267 [Term]
19268 id: SO:0002109
19269 name: transcribed_processed_pseudogene
19270 def: "A processed_pseudogene overlapped by locus-specific evidence of transcription." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19271 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
19272 synonym: "transcribed processed pseudogene" EXACT []
19273 is_a: SO:0000043 ! processed_pseudogene
19274 created_by: kareneilbeck
19275 creation_date: 2016-07-18T12:45:48Z
19276
19277 [Term]
19278 id: SO:0002110
19279 name: polymorphic_pseudogene_with_retained_intron
19280 def: "A polymorphic pseudogene in the reference genome, containing a retained intron, known to be intact in the genomes of other individuals of the same species. The annotation process has confirmed that the pseudogenisation event is not a genomic sequencing error." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19281 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
19282 synonym: "polymorphic pseudogene with retained intron" EXACT []
19283 is_a: SO:0001841 ! polymorphic_pseudogene
19284 created_by: kareneilbeck
19285 creation_date: 2016-07-18T12:47:33Z
19286
19287 [Term]
19288 id: SO:0002111
19289 name: pseudogene_processed_transcript
19290 def: "A processed_transcript supported by EST and/or mRNA evidence that aligns unambiguously to a pseudogene locus (i.e. alignment to the pseudogene locus clearly better than alignment to parent locus)." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19291 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
19292 synonym: "pseudogene processed transcript" EXACT []
19293 is_a: SO:0001503 ! processed_transcript
19294 created_by: kareneilbeck
19295 creation_date: 2016-07-18T14:07:00Z
19296
19297 [Term]
19298 id: SO:0002112
19299 name: coding_transcript_with_retained_intron
19300 def: "A protein coding transcript containing a retained intron." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19301 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
19302 synonym: "mRNA with retained intron" RELATED []
19303 is_a: SO:0000120 ! protein_coding_primary_transcript
19304 created_by: kareneilbeck
19305 creation_date: 2016-07-18T14:09:49Z
19306
19307 [Term]
19308 id: SO:0002113
19309 name: lncRNA_with_retained_intron
19310 def: "A lncRNA transcript containing a retained intron." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19311 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
19312 synonym: "lncRNA with retained intron" EXACT []
19313 synonym: "lncRNA_retained_intron" EXACT []
19314 is_a: SO:0002035 ! lncRNA_primary_transcript
19315 created_by: kareneilbeck
19316 creation_date: 2016-07-18T14:13:07Z
19317
19318 [Term]
19319 id: SO:0002114
19320 name: NMD_transcript
19321 def: "A protein coding transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon, making it susceptible to nonsense mediated decay." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19322 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
19323 synonym: "NMD transcript" EXACT []
19324 synonym: "nonsense mediated decay transcript" EXACT []
19325 is_a: SO:0000120 ! protein_coding_primary_transcript
19326 created_by: kareneilbeck
19327 creation_date: 2016-07-18T14:16:13Z
19328
19329 [Term]
19330 id: SO:0002115
19331 name: pseudogenic_transcript_with_retained_intron
19332 def: "A transcript supported by EST and/or mRNA evidence that aligns unambiguously to the pseudogene locus; has retained intronic sequence compared to a reference transcript sequence." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19333 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes.
19334 synonym: "pseudogene retained intron" EXACT []
19335 is_a: SO:0000185 ! primary_transcript
19336 created_by: kareneilbeck
19337 creation_date: 2016-07-18T14:19:04Z
19338
19339 [Term]
19340 id: SO:0002116
19341 name: polymorphic_pseudogene_processed_transcript
19342 def: "A processed transcript that does not contain a CDS that fullfills annotation criteria and not necessarily functionally non-coding." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19343 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
19344 synonym: "polymorphic pseudogene processed transcript" EXACT []
19345 is_a: SO:0002111 ! pseudogene_processed_transcript
19346 created_by: kareneilbeck
19347 creation_date: 2016-07-18T14:23:59Z
19348
19349 [Term]
19350 id: SO:0002117
19351 name: <new term>
19352 is_obsolete: true
19353 created_by: kareneilbeck
19354 creation_date: 2016-07-18T14:27:21Z
19355
19356 [Term]
19357 id: SO:0002118
19358 name: NMD_polymorphic_pseudogene_transcript
19359 def: "A polymorphic pseudogene transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon. Premature stop codon is not introduced, directly or indirectly, as a result of the variation i.e. must be present in both protein_coding and pseudogenic alleles." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19360 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
19361 synonym: "NMD polymorphic pseudogene transcript" EXACT []
19362 synonym: "nonsense_mediated_decay_polymorphic_pseudogene" EXACT []
19363 is_a: SO:0002114 ! NMD_transcript
19364 created_by: kareneilbeck
19365 creation_date: 2016-07-18T14:28:02Z
19366
19367 [Term]
19368 id: SO:0002119
19369 name: allelic_frequency
19370 def: "A physical quality which inheres to the allele by virtue of the number instances of the allele within a population. This is the relative frequency of the allele at a given locus in a population." [SO:ke]
19371 comment: Requested by HL7 clinical genomics group.
19372 xref: WIKI:https\://en.wikipedia.org/wiki/Allele_frequency
19373 is_a: SO:0001763 ! variant_frequency
19374 created_by: kareneilbeck
19375 creation_date: 2016-07-21T11:58:55Z
19376
19377 [Term]
19378 id: SO:0002120
19379 name: 3_prime_overlapping_ncrna
19380 def: "Transcript where ditag (digital gene expression profiling)and/or published experimental data strongly supports the existence of short non-coding transcripts transcribed from the 3'UTR." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19381 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes.
19382 synonym: "3'_overlapping_ncrna" EXACT []
19383 synonym: "3prime_overlapping_ncRNA" EXACT []
19384 synonym: "three prime overlapping noncoding rna" EXACT []
19385 is_a: SO:0000655 ! ncRNA
19386 created_by: nicole
19387 creation_date: 2016-08-23T15:48:21Z
19388
19389 [Term]
19390 id: SO:0002121
19391 name: vertebrate_immune_system_gene
19392 def: "The configuration of the IG and TR variable (V), diversity (D) and joining (J) germline genes before DNA rearrangements (with or without constant (C) genes in undefined configuration. (germline, non rearranged regions of the IG DNA loci)." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19393 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19394 synonym: "immune_gene" EXACT []
19395 is_a: SO:0000704 ! gene
19396 created_by: nicole
19397 creation_date: 2016-08-23T15:54:51Z
19398
19399 [Term]
19400 id: SO:0002122
19401 name: immunoglobulin_gene
19402 def: "A germline immunoglobulin gene." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19403 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19404 synonym: "All_IG_genes" EXACT []
19405 synonym: "IG_genes" EXACT []
19406 is_a: SO:0002121 ! vertebrate_immune_system_gene
19407 created_by: nicole
19408 creation_date: 2016-08-23T15:56:09Z
19409
19410 [Term]
19411 id: SO:0002123
19412 name: IG_C_gene
19413 def: "A constant (C) gene, a gene that codes the constant region of an immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19414 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19415 synonym: "IGC_gene" EXACT []
19416 synonym: "immunoglobulin_C_gene" EXACT []
19417 synonym: "Immunoglobulin_Constant_germline_Gene" EXACT []
19418 is_a: SO:0002122 ! immunoglobulin_gene
19419 created_by: nicole
19420 creation_date: 2016-08-23T15:57:29Z
19421
19422 [Term]
19423 id: SO:0002124
19424 name: IG_D_gene
19425 def: "A gene that rearranges at the DNA level and codes the diversity region of the variable domain of an immunoglobuin (IG) gene." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19426 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19427 synonym: "IGD_gene" EXACT []
19428 synonym: "immunoglobulin_D_gene" EXACT []
19429 synonym: "Immunoglobulin_Diversity_ gene" EXACT []
19430 is_a: SO:0002122 ! immunoglobulin_gene
19431 created_by: nicole
19432 creation_date: 2016-08-23T15:59:10Z
19433
19434 [Term]
19435 id: SO:0002125
19436 name: IG_J_gene
19437 def: "A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19438 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19439 synonym: "IG_joining_gene" EXACT []
19440 synonym: "immunoglobulin_J_gene" EXACT []
19441 synonym: "Immunoglobulin_Joining_Gene" EXACT []
19442 is_a: SO:0002122 ! immunoglobulin_gene
19443 created_by: nicole
19444 creation_date: 2016-08-23T16:00:36Z
19445
19446 [Term]
19447 id: SO:0002126
19448 name: IG_V_gene
19449 def: "A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of an Immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19450 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19451 synonym: "IG_variable_gene" EXACT []
19452 synonym: "IGV_gene" EXACT []
19453 synonym: "Immunoglobulin_variable_gene" EXACT []
19454 is_a: SO:0002122 ! immunoglobulin_gene
19455 created_by: nicole
19456 creation_date: 2016-08-23T16:02:09Z
19457
19458 [Term]
19459 id: SO:0002127
19460 name: lncRNA_gene
19461 def: "A gene that encodes a long non-coding RNA." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19462 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes.
19463 synonym: "lnc RNA gene" EXACT []
19464 synonym: "lnc_RNA_gene" EXACT []
19465 synonym: "long_non_coding_RNA_gene" EXACT []
19466 is_a: SO:0001263 ! ncRNA_gene
19467 created_by: nicole
19468 creation_date: 2016-08-23T16:03:33Z
19469
19470 [Term]
19471 id: SO:0002128
19472 name: mt_rRNA
19473 def: "Mitochondrial ribosomal RNA." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19474 synonym: "mitochondrial_rRNA" EXACT []
19475 synonym: "Mt_rRNA" EXACT []
19476 is_a: SO:0000252 ! rRNA
19477 created_by: nicole
19478 creation_date: 2016-08-23T16:08:59Z
19479
19480 [Term]
19481 id: SO:0002129
19482 name: mt_tRNA
19483 def: "Mitochondrial transfer RNA." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19484 synonym: "mitochondrial_tRNA" EXACT []
19485 synonym: "Mt_tRNA" EXACT []
19486 is_a: SO:0000253 ! tRNA
19487 created_by: nicole
19488 creation_date: 2016-08-23T16:10:17Z
19489
19490 [Term]
19491 id: SO:0002130
19492 name: NSD_transcript
19493 def: "A transcript that contains a CDS but has no stop codon before the polyA site is reached." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19494 synonym: "non_stop_decay_transcript" EXACT []
19495 is_a: SO:0000234 ! mRNA
19496 created_by: nicole
19497 creation_date: 2016-08-23T16:11:34Z
19498
19499 [Term]
19500 id: SO:0002131
19501 name: sense_intronic_ncRNA
19502 def: "A non-coding transcript found within an intron of a coding or non-coding gene, with no overlap of exonic sequence." [GENECODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19503 synonym: "sense_intronic" EXACT []
19504 synonym: "sense_intronic_non-coding_RNA" EXACT []
19505 is_a: SO:0000655 ! ncRNA
19506 created_by: nicole
19507 creation_date: 2016-08-23T16:15:02Z
19508
19509 [Term]
19510 id: SO:0002132
19511 name: sense_overlap_ncRNA
19512 def: "A non-coding transcript that contains a protein coding gene within its intronic sequence on the same strand, with no overlap of exonic sequence." [GENECODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19513 synonym: "sense_overlapping" EXACT []
19514 is_a: SO:0000655 ! ncRNA
19515 created_by: nicole
19516 creation_date: 2016-08-23T16:16:13Z
19517
19518 [Term]
19519 id: SO:0002133
19520 name: T_cell_receptor_gene
19521 def: "A T-cell receptor germline gene." []
19522 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19523 synonym: "TR_gene" EXACT []
19524 is_a: SO:0002121 ! vertebrate_immune_system_gene
19525 created_by: nicole
19526 creation_date: 2016-08-23T16:17:12Z
19527
19528 [Term]
19529 id: SO:0002134
19530 name: TR_C_Gene
19531 def: "A constant (C) gene, a gene that codes the constant region of a T-cell receptor chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19532 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19533 synonym: "T_cell_receptor_C_gene" EXACT []
19534 is_a: SO:0002133 ! T_cell_receptor_gene
19535 created_by: nicole
19536 creation_date: 2016-08-23T16:19:20Z
19537
19538 [Term]
19539 id: SO:0002135
19540 name: TR_D_Gene
19541 def: "A gene that rearranges at the DNA level and codes the diversity region of the variable domain of aT-cell receptor gene." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19542 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19543 synonym: "T_cell_receptor_D_gene" EXACT []
19544 is_a: SO:0002133 ! T_cell_receptor_gene
19545 created_by: nicole
19546 creation_date: 2016-08-23T16:20:06Z
19547
19548 [Term]
19549 id: SO:0002136
19550 name: TR_J_Gene
19551 def: "A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of aT-cell receptor chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19552 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19553 synonym: "T_cell_receptor_J_gene" EXACT []
19554 is_a: SO:0002133 ! T_cell_receptor_gene
19555 created_by: nicole
19556 creation_date: 2016-08-23T16:20:36Z
19557
19558 [Term]
19559 id: SO:0002137
19560 name: TR_V_Gene
19561 def: "A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of aT-cell receptor chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19562 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19563 synonym: "T_cell_receptor_V_gene" EXACT []
19564 is_a: SO:0002133 ! T_cell_receptor_gene
19565 created_by: nicole
19566 creation_date: 2016-08-23T16:21:04Z
19567
19568 [Term]
19569 id: SO:0002138
19570 name: predicted_transcript
19571 def: "A transcript feature that has been predicted but is not yet validated." [SO:ke]
19572 synonym: "predicted transcript" EXACT []
19573 is_a: SO:0000673 ! transcript
19574 created_by: nicole
19575 creation_date: 2016-08-23T16:27:38Z
19576
19577 [Term]
19578 id: SO:0002139
19579 name: unconfirmed_transcript
19580 def: "This is used for non-spliced EST clusters that have polyA features. This category has been specifically created for the ENCODE project to highlight regions that could indicate the presence of protein coding genes that require experimental validation, either by 5' RACE or RT-PCR to extend the transcripts, or by confirming expression of the putatively-encoded peptide with specific antibodies." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19581 synonym: "TEC" EXACT []
19582 synonym: "to_be_experimentally_confirmed_transcript" EXACT []
19583 is_a: SO:0002138 ! predicted_transcript
19584 created_by: nicole
19585 creation_date: 2016-08-23T16:28:07Z
19586
19587 [Term]
19588 id: SO:0002140
19589 name: early_origin_of_replication
19590 def: "An origin of replication that initiates early in S phase." [PMID:23348837, PMID:9115207]
19591 synonym: "early origin" EXACT []
19592 synonym: "early origin of replication" EXACT []
19593 synonym: "early replication origin" EXACT []
19594 is_a: SO:0000296 ! origin_of_replication
19595 created_by: nicole
19596 creation_date: 2016-09-15T15:53:36Z
19597
19598 [Term]
19599 id: SO:0002141
19600 name: late_origin_of_replication
19601 def: "An origin of replication that initiates late in S phase." [PMID:23348837, PMID:9115207]
19602 synonym: "late origin" EXACT []
19603 synonym: "late origin of replication" EXACT []
19604 synonym: "late replication origin" EXACT []
19605 is_a: SO:0000296 ! origin_of_replication
19606 created_by: nicole
19607 creation_date: 2016-09-15T15:56:07Z
19608
19609 [Term]
19610 id: SO:0002142
19611 name: histone_2A_acetylation_site
19612 def: "A histone 2A modification where the modification is the acetylation of the residue." [ISBN:0815341059]
19613 synonym: "H2Aac" EXACT []
19614 synonym: "histone 2A acetylation site" EXACT []
19615 is_a: SO:0001702 ! histone_acetylation_site
19616 created_by: nicole
19617 creation_date: 2016-10-25T12:03:46Z
19618
19619 [Term]
19620 id: SO:0002143
19621 name: histone_2B_acetylation_site
19622 def: "A histone 2B modification where the modification is the acetylation of the residue." [ISBN:0815341059]
19623 synonym: "H2Bac" EXACT []
19624 synonym: "histone 2B acetylation site" EXACT []
19625 is_a: SO:0001702 ! histone_acetylation_site
19626 created_by: nicole
19627 creation_date: 2016-10-25T12:04:04Z
19628
19629 [Term]
19630 id: SO:0002144
19631 name: histone_2AZ_acetylation_site
19632 def: "A histone 2AZ modification where the modification is the acetylation of the residue." [PMID:19385636, PMID:24316985, PMID:27087541]
19633 synonym: "H2A.Zac" EXACT []
19634 synonym: "H2AZac" EXACT []
19635 synonym: "histone 2AZ acetylation site" EXACT []
19636 is_a: SO:0002142 ! histone_2A_acetylation_site
19637 created_by: nicole
19638 creation_date: 2016-10-25T14:11:49Z
19639
19640 [Term]
19641 id: SO:0002145
19642 name: H2AZK4_acetylation_site
19643 def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H2AZ histone protein is acetylated." [PMID:19385636, PMID:24316985, PMID:27087541]
19644 synonym: "H2A.ZK4ac" EXACT []
19645 synonym: "H2AZK4 acetylation site" EXACT []
19646 synonym: "H2AZK4ac" EXACT []
19647 is_a: SO:0002144 ! histone_2AZ_acetylation_site
19648 created_by: nicole
19649 creation_date: 2016-10-25T14:19:43Z
19650
19651 [Term]
19652 id: SO:0002146
19653 name: H2AZK7_acetylation_site
19654 def: "A kind of histone modification site, whereby the 7th residue (a lysine), from the start of the H2AZ histone protein is acetylated." [PMID:19385636, PMID:24316985, PMID:27087541]
19655 synonym: "H2A.ZK7ac" EXACT []
19656 synonym: "H2AZK7 acetylation site" EXACT []
19657 synonym: "H2AZK7ac" EXACT []
19658 is_a: SO:0002144 ! histone_2AZ_acetylation_site
19659 created_by: nicole
19660 creation_date: 2016-10-25T14:23:11Z
19661
19662 [Term]
19663 id: SO:0002147
19664 name: H2AZK11_acetylation_site
19665 def: "A kind of histone modification site, whereby the 11th residue (a lysine), from the start of the H2AZ histone protein is acetylated." [PMID:19385636, PMID:24316985, PMID:27087541]
19666 synonym: "H2A.ZK11ac" EXACT []
19667 synonym: "H2AZK11 acetylation site" EXACT []
19668 synonym: "H2AZK11ac" EXACT []
19669 is_a: SO:0002144 ! histone_2AZ_acetylation_site
19670 created_by: nicole
19671 creation_date: 2016-10-25T14:23:31Z
19672
19673 [Term]
19674 id: SO:0002148
19675 name: H2AZK13_acetylation_site
19676 def: "A kind of histone modification site, whereby the 13th residue (a lysine), from the start of the H2AZ histone protein is acetylated." [PMID:19385636, PMID:24316985, PMID:27087541]
19677 synonym: "H2A.ZK13ac" EXACT []
19678 synonym: "H2AZK13 acetylation site" EXACT []
19679 synonym: "H2AZK13ac" EXACT []
19680 is_a: SO:0002144 ! histone_2AZ_acetylation_site
19681 created_by: nicole
19682 creation_date: 2016-10-25T14:23:50Z
19683
19684 [Term]
19685 id: SO:0002149
19686 name: H2AZK15_acetylation_site
19687 def: "A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2AZ histone protein is acetylated." [PMID:19385636, PMID:24316985, PMID:27087541]
19688 synonym: "H2A.ZK15ac" EXACT []
19689 synonym: "H2AZK15 acetylation site" EXACT []
19690 synonym: "H2AZK15ac" EXACT []
19691 is_a: SO:0002144 ! histone_2AZ_acetylation_site
19692 created_by: nicole
19693 creation_date: 2016-10-25T14:24:08Z
19694
19695 [Term]
19696 id: SO:0002150
19697 name: AUG_initiated_uORF
19698 def: "A uORF beginning with the canonical start codon AUG." [PMID:26684391, PMID:27313038]
19699 synonym: "AUG initiated uORF" EXACT []
19700 is_a: SO:0002027 ! uORF
19701 created_by: nicole
19702 creation_date: 2016-10-26T09:37:11Z
19703
19704 [Term]
19705 id: SO:0002151
19706 name: non_AUG_initiated_uORF
19707 def: "A uORF beginning with a codon other than AUG." [PMID:26684391, PMID:27313038]
19708 synonym: "non AUG initiated uORF" EXACT []
19709 is_a: SO:0002027 ! uORF
19710 created_by: nicole
19711 creation_date: 2016-10-26T09:37:45Z
19712
19713 [Term]
19714 id: SO:0002152
19715 name: genic_downstream_transcript_variant
19716 def: "A variant that falls downstream of a transcript, but within the genic region of the gene due to alternately transcribed isoforms." [NCBI:dm, SO:ke]
19717 synonym: "genic 3 prime transcript variant" EXACT []
19718 synonym: "genic 3' transcript variant" EXACT []
19719 synonym: "genic downstream transcript variant" EXACT []
19720 is_a: SO:0001564 ! gene_variant
19721 created_by: nicole
19722 creation_date: 2016-10-28T10:20:55Z
19723
19724 [Term]
19725 id: SO:0002153
19726 name: genic_upstream_transcript_variant
19727 def: "A variant that falls upstream of a transcript, but within the genic region of the gene due to alternately transcribed isoforms." [NCBI:dm, SO:ke]
19728 synonym: "genic 5 prime transcript variant" EXACT []
19729 synonym: "genic 5' transcript variant" EXACT []
19730 synonym: "genic upstream transcript variant" EXACT []
19731 is_a: SO:0001564 ! gene_variant
19732 created_by: nicole
19733 creation_date: 2016-10-28T10:23:17Z
19734
19735 [Term]
19736 id: SO:0002154
19737 name: mitotic_recombination_region
19738 def: "A genomic region where there is an exchange of genetic material with another genomic region, occurring in somatic cells." [NCBI:cf, SO:ke]
19739 synonym: "mitotic recombination region" EXACT []
19740 is_a: SO:0000298 ! recombination_feature
19741 created_by: nicole
19742 creation_date: 2016-10-28T10:33:54Z
19743
19744 [Term]
19745 id: SO:0002155
19746 name: meiotic_recombination_region
19747 def: "A genomic region in which there is an exchange of genetic material as a result of the repair of meiosis-specific double strand breaks that occur during meiotic prophase." [NCBI:cf, SO:ke]
19748 synonym: "meiotic recombination region" EXACT []
19749 is_a: SO:0000298 ! recombination_feature
19750 created_by: nicole
19751 creation_date: 2016-10-28T10:34:55Z
19752
19753 [Term]
19754 id: SO:0002156
19755 name: CArG_box
19756 def: "A promoter element bound by the MADS family of transcription factors with consensus 5'-(C/T)TA(T/A)4TA(G/A)-3'." [PMID:1748287, PMID:7623803]
19757 comment: Requested by Antonia Lock
19758 synonym: "CArG box" EXACT []
19759 is_a: SO:0001659 ! promoter_element
19760 created_by: nicole
19761 creation_date: 2016-10-28T10:42:06Z
1863819762
1863919763 [Term]
1864019764 id: SO:0005836
1924820372 intersection_of: SO:1000028 ! intrachromosomal_mutation
1924920373 intersection_of: has_part SO:0000199 ! translocation
1925020374 intersection_of: has_part SO:1000035 ! duplication
20375 relationship: has_part SO:0000199 ! translocation
1925120376 relationship: has_part SO:1000035 ! duplication
1925220377
1925320378 [Term]
2029921424 name: chromosome_number_variation
2030021425 def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]
2030121426 synonym: "chromosome number variation" EXACT []
21427 synonym: "Jannovar:chromosome_number_variation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
2030221428 is_a: SO:0000240 ! chromosome_variation
2030321429
2030421430 [Term]
2030521431 id: SO:1000183
2030621432 name: chromosome_structure_variation
2030721433 synonym: "chromosome structure variation" EXACT []
21434 synonym: "snpEff:CHROMOSOME_LARGE_DELETION" EXACT VAR []
21435 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
2030821436 is_a: SO:0000240 ! chromosome_variation
2030921437
2031021438 [Term]
+1285
-114
gtdata/obo_files/so.obo less more
00 format-version: 1.2
1 date: 22:06:2015 10:18
2 saved-by: kareneilbeck
1 data-version: so-xp/releases/2015-11-24/so-xp.owl
2 date: 28:10:2016 11:25
3 saved-by: nicole
34 auto-generated-by: OBO-Edit 2.3.1
45 subsetdef: biosapiens "biosapiens protein feature ontology"
56 subsetdef: DBVAR "database of genomic structural variation"
67 subsetdef: SOFA "SO feature annotation"
7 synonymtypedef: aa1 "amino acid 1 letter code"
8 synonymtypedef: aa3 "amino acid 3 letter code"
9 synonymtypedef: AAMOD "amino acid modification"
10 synonymtypedef: BS "biosapiens"
11 synonymtypedef: dbsnp "dbsnp variant terms"
12 synonymtypedef: dbvar "DBVAR"
13 synonymtypedef: ebi_variants "ensembl variant terms"
8 synonymtypedef: aa1 "amino acid 1 letter code"
9 synonymtypedef: aa3 "amino acid 3 letter code"
10 synonymtypedef: AAMOD "amino acid modification"
11 synonymtypedef: BS "biosapiens"
12 synonymtypedef: dbsnp "dbsnp variant terms"
13 synonymtypedef: dbvar "DBVAR"
14 synonymtypedef: ebi_variants "ensembl variant terms"
1415 synonymtypedef: RNAMOD "RNA modification" EXACT
15 synonymtypedef: VAR "variant annotation term"
16 synonymtypedef: VAR "variant annotation term"
1617 default-namespace: sequence
17 remark: autogenerated-by: DAG-Edit version 1.417\nsaved-by: eilbeck\ndate: Tue May 11 15:18:44 PDT 2004\nversion: $Revision: 1.45 $
1818 ontology: so-xp.obo
1919
2020 [Term]
3030 subset: SOFA
3131 synonym: "sequence" EXACT []
3232 is_a: SO:0000110 ! sequence_feature
33 disjoint_from: SO:0000699 ! junction
3433
3534 [Term]
3635 id: SO:0000002
148147 [Term]
149148 id: SO:0000015
150149 name: DPE_motif
151 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]
150 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]
152151 comment: Binds TAF6, TAF9.
153152 synonym: "CRWMGCGWKCGCTTS" NARROW []
154153 synonym: "downstream core promoter element" EXACT []
384383 [Term]
385384 id: SO:0000043
386385 name: processed_pseudogene
387 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]
386 def: "A pseudogene created via retrotranposition of the mRNA of a functional protein-coding parent gene followed by accumulation of deleterious mutations lacking introns and promoters, often including a polyA tail." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
388387 comment: Please not the synonym R psi M uses the spelled out form of the greek letter.
389388 synonym: "processed pseudogene" EXACT []
390389 synonym: "pseudogene by reverse transcription" RELATED []
10821081 def: "Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke]
10831082 synonym: "genomically imprinted" EXACT []
10841083 synonym: "imprinted" BROAD []
1085 xref: http:http://en.wikipedia.org/wiki/Genomic_imprinting "wiki"
1084 xref: http:http\://en.wikipedia.org/wiki/Genomic_imprinting "wiki"
10861085 is_a: SO:0000119 ! regulated
10871086 is_a: SO:0000133 ! epigenetically_modified
10881087
12191218 name: clone
12201219 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]
12211220 subset: SOFA
1222 xref: http:http://en.wikipedia.org/wiki/Clone_(genetics) "wiki"
1221 xref: http:http\://en.wikipedia.org/wiki/Clone_(genetics) "wiki"
12231222 is_a: SO:0000695 ! reagent
12241223
12251224 [Term]
17311730 [Term]
17321731 id: SO:0000207
17331732 name: simple_sequence_length_variation
1733 def: "SSLP are a kind of sequence alteration where the number of repeated sequences in intergenic regions may differ." [SO:ke]
17341734 synonym: "simple sequence length polymorphism" RELATED []
17351735 synonym: "simple sequence length variation" EXACT []
17361736 synonym: "SSLP" RELATED []
1737 xref: http://en.wikipedia.org/wiki/Simple_sequence_length_polymorphism "WIKI"
17371738 is_a: SO:0000248 ! sequence_length_variation
17381739
17391740 [Term]
19821983 name: chromosome_variation
19831984 synonym: "chromosome variation" EXACT []
19841985 is_a: SO:0001507 ! variant_collection
1985 disjoint_from: SO:0000400 ! sequence_attribute
19861986 relationship: part_of SO:0001524 ! chromosomally_aberrant_genome
19871987
19881988 [Term]
20372037 [Term]
20382038 id: SO:0000248
20392039 name: sequence_length_variation
2040 def: "A kind of kind of sequence alteration where the copies of a region present varies across a population." [SO:ke]
20402041 synonym: "sequence length variation" EXACT []
2041 is_a: SO:1000002 ! substitution
2042 is_a: SO:0001059 ! sequence_alteration
20422043
20432044 [Term]
20442045 id: SO:0000249
24312432 subset: SOFA
24322433 synonym: "microsatellite locus" EXACT []
24332434 synonym: "microsatellite marker" EXACT []
2434 synonym: "VNTR" EXACT []
2435 synonym: "STR" EXACT [http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9651/]
24352436 xref: http://en.wikipedia.org/wiki/Microsatellite "wiki"
24362437 is_a: SO:0000005 ! satellite_DNA
24372438
29872988 [Term]
29882989 id: SO:0000360
29892990 name: codon
2990 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]
2991 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." [SO:ke]
29912992 subset: SOFA
29922993 xref: http://en.wikipedia.org/wiki/Codon "wiki"
29932994 is_a: SO:0000851 ! CDS_region
38663867 id: SO:0000464
38673868 name: decayed_exon
38683869 def: "A non-functional descendant of an exon." [SO:ke]
3870 comment: Does not have to be part of a pseudogene.
38693871 subset: SOFA
38703872 synonym: "decayed exon" EXACT []
38713873 is_a: SO:0000462 ! pseudogenic_region
50065008 [Term]
50075009 id: SO:0000592
50085010 name: H_pseudoknot
5009 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]
5011 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]
50105012 synonym: "classical pseudoknot" EXACT []
50115013 synonym: "H pseudoknot" EXACT []
50125014 synonym: "H-pseudoknot" EXACT []
54105412 name: minisatellite
54115413 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]
54125414 subset: SOFA
5415 synonym: "VNTR" EXACT [http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9655/]
54135416 xref: http://en.wikipedia.org/wiki/Minisatellite "wiki"
54145417 is_a: SO:0000005 ! satellite_DNA
54155418
57315734 [Term]
57325735 id: SO:0000683
57335736 name: exonic_splice_enhancer
5734 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]
5737 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]
57355738 synonym: "exonic splice enhancer" EXACT []
57365739 is_a: SO:0000344 ! splice_enhancer
57375740
64666469 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.
64676470 subset: SOFA
64686471 synonym: "pseudogenic rRNA" EXACT []
6469 is_a: SO:0000462 ! pseudogenic_region
6472 is_a: SO:0000516 ! pseudogenic_transcript
64706473
64716474 [Term]
64726475 id: SO:0000778
64756478 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.
64766479 subset: SOFA
64776480 synonym: "pseudogenic tRNA" EXACT []
6478 is_a: SO:0000462 ! pseudogenic_region
6481 is_a: SO:0000516 ! pseudogenic_transcript
64796482
64806483 [Term]
64816484 id: SO:0000779
82098212 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]
82108213 comment: This is not cryptic in the same sense as a cryptic gene or cryptic splice site.
82118214 synonym: "cryptic prophage" EXACT []
8212 xref: http://ecoliwiki.net/colipedia/index.php/Category:Cryptic_Prophage.w
8215 xref: http://ecoliwiki.net/colipedia/index.php/Category\:Cryptic_Prophage.w
82138216 is_a: SO:0000772 ! genomic_island
82148217
82158218 [Term]
83178320 synonym: "copy number polymorphism" EXACT []
83188321 synonym: "copy number variation" EXACT []
83198322 xref: http://en.wikipedia.org/wiki/Copy_number_variation "wiki"
8320 is_a: SO:0001059 ! sequence_alteration
8323 is_a: SO:0000248 ! sequence_length_variation
83218324
83228325 [Term]
83238326 id: SO:0001020
86378640 synonym: "sequence alteration" EXACT []
86388641 synonym: "sequence variation" RELATED []
86398642 synonym: "uncharacterised_change_in_nucleotide_sequence" NARROW []
8640 is_a: SO:0000110 ! sequence_feature
8643 is_a: SO:0002072 ! sequence_comparison
86418644
86428645 [Term]
86438646 id: SO:0001060
86448647 name: sequence_variant
86458648 def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]
86468649 synonym: "ANNOVAR:unknown" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
8650 synonym: "Jannovar:sequence_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
86478651 synonym: "sequence variant" EXACT []
86488652 synonym: "VAAST:sequence_variant" EXACT VAR []
86498653
96649668 [Term]
96659669 id: SO:0001157
96669670 name: DMv4_motif
9667 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]
9671 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]
96689672 synonym: "directional motif v4" EXACT []
96699673 synonym: "DMv4" EXACT []
96709674 synonym: "DMv4 motif" EXACT []
96769680 [Term]
96779681 id: SO:0001158
96789682 name: E_box_motif
9679 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]
9683 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]
96809684 synonym: "AWCAGCTGWT" NARROW []
96819685 synonym: "E box motif" EXACT []
96829686 synonym: "generic E box motif" EXACT []
96879691 [Term]
96889692 id: SO:0001159
96899693 name: DMv5_motif
9690 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]
9694 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]
96919695 synonym: "directional motif v5" EXACT []
96929696 synonym: "DMv5" EXACT []
96939697 synonym: "DMv5 motif" EXACT []
96999703 [Term]
97009704 id: SO:0001160
97019705 name: DMv3_motif
9702 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]
9706 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]
97039707 synonym: "directional motif v3" EXACT []
97049708 synonym: "DMv3" EXACT []
97059709 synonym: "DMv3 motif" EXACT []
97119715 [Term]
97129716 id: SO:0001161
97139717 name: DMv2_motif
9714 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]
9718 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]
97159719 synonym: "directional motif v2" EXACT []
97169720 synonym: "DMv2" EXACT []
97179721 synonym: "DMv2 motif" EXACT []
97239727 [Term]
97249728 id: SO:0001162
97259729 name: MTE
9726 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]
9730 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]
97279731 synonym: "CSARCSSAACGS" NARROW []
97289732 synonym: "motif ten element" EXACT []
97299733 synonym: "motif_ten_element" EXACT []
1253012534 [Term]
1253112535 id: SO:0001485
1253212536 name: Y_prime_element
12533 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]
12537 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]
1253412538 comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.
1253512539 synonym: "Y' element" EXACT []
1253612540 is_a: SO:0000657 ! repeat_region
1301113015 id: SO:0001537
1301213016 name: structural_variant
1301313017 def: "A sequence variant that changes one or more sequence features." [SO:ke]
13018 synonym: "Jannovar:structural_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1301413019 synonym: "structural variant" RELATED []
13020 synonym: "VAT:svOverlap" EXACT VAR []
13021 xref: http://vat.gersteinlab.org/formats.php "VAT"
1301513022 is_a: SO:0001060 ! sequence_variant
1301613023 created_by: kareneilbeck
1301713024 creation_date: 2010-03-22T11:31:01Z
1325513262 name: gene_variant
1325613263 def: "A sequence variant where the structure of the gene is changed." [SO:ke]
1325713264 synonym: "gene structure variant" EXACT []
13265 synonym: "Jannovar:gene_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1325813266 synonym: "snpEff:GENE" EXACT VAR []
1325913267 synonym: "VAAST:gene_variant" EXACT VAR []
13268 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1326013269 is_a: SO:0001878 ! feature_variant
1326113270 created_by: kareneilbeck
1326213271 creation_date: 2010-03-22T02:28:01Z
1326713276 def: "A sequence variant whereby a two genes have become joined." [SO:ke]
1326813277 synonym: "gene fusion" EXACT []
1326913278 is_a: SO:0001564 ! gene_variant
13279 is_a: SO:0001882 ! feature_fusion
1327013280 created_by: kareneilbeck
1327113281 creation_date: 2010-03-22T02:28:28Z
1327213282
1327513285 name: regulatory_region_variant
1327613286 def: "A sequence variant located within a regulatory region." [SO:ke]
1327713287 comment: EBI term: Regulatory region variations - In regulatory region annotated by Ensembl.
13288 synonym: "Jannovar:regulatory_region_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1327813289 synonym: "regulatory region variant" EXACT []
1327913290 synonym: "regulatory_region_" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13291 synonym: "snpEff:REGULATION" EXACT VAR []
13292 synonym: "VEP:regulatory_region_variant" EXACT VAR []
13293 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13294 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1328013295 is_a: SO:0001878 ! feature_variant
1328113296 created_by: kareneilbeck
1328213297 creation_date: 2010-03-22T02:28:48Z
1328513300 id: SO:0001567
1328613301 name: stop_retained_variant
1328713302 def: "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]
13303 synonym: "Jannovar:stop_retained_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
13304 synonym: "snpEff:NON_SYNONYMOUS_STOP" EXACT VAR []
1328813305 synonym: "snpEff:SYNONYMOUS_STOP" EXACT VAR []
1328913306 synonym: "stop retained variant" EXACT []
1329013307 synonym: "VAAST:stop_retained" EXACT VAR []
13308 synonym: "VAAST:stop_retained_variant" EXACT VAR []
13309 synonym: "VEP:stop_retained_variant" EXACT VAR []
13310 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13311 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1329113312 is_a: SO:0001590 ! terminator_codon_variant
1329213313 is_a: SO:0001819 ! synonymous_variant
1329313314 created_by: kareneilbeck
1329713318 id: SO:0001568
1329813319 name: splicing_variant
1329913320 def: "A sequence variant that changes the process of splicing." [SO:ke]
13321 synonym: "Jannovar:splicing_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1330013322 synonym: "splicing variant" EXACT []
1330113323 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
1330213324 is_a: SO:0001576 ! transcript_variant
1333613358 name: exon_loss_variant
1333713359 def: "A sequence variant whereby an exon is lost from the transcript." [SO:ke]
1333813360 synonym: "exon loss" EXACT []
13361 synonym: "Jannovar:exon_loss_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1333913362 synonym: "snpEff:EXON_DELETED" EXACT VAR []
13363 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1334013364 is_a: SO:0001568 ! splicing_variant
1334113365 created_by: kareneilbeck
1334213366 creation_date: 2010-03-22T02:31:09Z
1335613380 id: SO:0001574
1335713381 name: splice_acceptor_variant
1335813382 def: "A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke]
13383 synonym: "Jannovar:splice_acceptor_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
13384 synonym: "Seattleseq:splice-acceptor" EXACT VAR []
1335913385 synonym: "snpEff:SPLICE_SITE_ACCEPTOR" EXACT VAR []
1336013386 synonym: "splice acceptor variant" EXACT []
1336113387 synonym: "VAAST:splice_acceptor_variant" EXACT VAR []
13388 synonym: "VEP:splice_acceptor_variant" EXACT VAR []
13389 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
13390 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13391 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1336213392 is_a: SO:0001629 ! splice_site_variant
1336313393 created_by: kareneilbeck
1336413394 creation_date: 2010-03-22T02:31:52Z
1336713397 id: SO:0001575
1336813398 name: splice_donor_variant
1336913399 def: "A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke]
13400 synonym: "Jannovar:splice_donor_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
13401 synonym: "Seattleseq:splice-donor" EXACT VAR []
1337013402 synonym: "snpEff:SPLICE_SITE_DONOR" EXACT VAR []
1337113403 synonym: "splice donor variant" EXACT []
1337213404 synonym: "VAAST:splice_donor_variant" EXACT VAR []
13405 synonym: "VEP:splice_donor_variant" EXACT VAR []
13406 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
13407 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13408 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1337313409 is_a: SO:0001629 ! splice_site_variant
1337413410 created_by: kareneilbeck
1337513411 creation_date: 2010-03-22T02:32:10Z
1337813414 id: SO:0001576
1337913415 name: transcript_variant
1338013416 def: "A sequence variant that changes the structure of the transcript." [SO:ke]
13417 synonym: "Jannovar:transcript_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1338113418 synonym: "snpEff:TRANSCRIPT" EXACT VAR []
1338213419 synonym: "transcript variant" EXACT []
1338313420 synonym: "VAAST:transcript_variant" EXACT VAR []
1338413421 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13422 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1338513423 is_a: SO:0001564 ! gene_variant
1338613424 created_by: kareneilbeck
1338713425 creation_date: 2010-03-22T02:32:41Z
1339113429 name: complex_transcript_variant
1339213430 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]
1339313431 comment: EBI term: Complex InDel - Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.
13432 synonym: "complex change in transcript" EXACT []
1339413433 synonym: "complex transcript variant" EXACT []
1339513434 synonym: "complex_indel" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13396 synonym: "complext change in transcript" EXACT []
13435 synonym: "Seattleseq:codingComplex" RELATED VAR []
13436 synonym: "Seattleseq:codingComplex-near-splice" RELATED VAR []
13437 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
1339713438 is_a: SO:0001576 ! transcript_variant
1339813439 created_by: kareneilbeck
1339913440 creation_date: 2010-03-22T02:33:03Z
1340413445 def: "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]
1340513446 comment: EBI term: Stop lost - In coding sequence, resulting in the loss of a stop codon.
1340613447 synonym: "ANNOVAR:stoploss" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13448 synonym: "Jannovar:stop_lost" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
13449 synonym: "Seattleseq:stop-lost" EXACT VAR []
13450 synonym: "Seattleseq:stop-lost-near-splice" RELATED VAR []
1340713451 synonym: "snpEff:STOP_LOST" EXACT VAR []
1340813452 synonym: "stop codon lost" EXACT []
1340913453 synonym: "stop lost" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
1341013454 synonym: "VAAST:stop_lost" EXACT VAR []
13455 synonym: "VAT:removedStop" EXACT VAR []
13456 synonym: "VEP:stop_lost" EXACT VAR []
13457 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
13458 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13459 xref: http://vat.gersteinlab.org/formats.php "VAT"
13460 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1341113461 is_a: SO:0001590 ! terminator_codon_variant
1341213462 is_a: SO:0001907 ! feature_elongation
1341313463 is_a: SO:0001992 ! nonsynonymous_variant
1342913479 synonym: "coding variant" EXACT []
1343013480 synonym: "codon variant" EXACT []
1343113481 synonym: "codon_variant" EXACT []
13482 synonym: "Jannovar:coding_sequence_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
13483 synonym: "Seattleseq:coding" EXACT VAR []
1343213484 synonym: "snpEff:CDS" EXACT VAR []
1343313485 synonym: "snpEff:CODON_CHANGE" RELATED VAR []
1343413486 synonym: "VAAST:coding_sequence_variant" EXACT VAR []
13487 synonym: "VEP:coding_sequence_variant" EXACT VAR []
1343513488 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13489 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
13490 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13491 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1343613492 is_a: SO:0001791 ! exon_variant
1343713493 is_a: SO:0001968 ! coding_transcript_variant
1343813494 created_by: kareneilbeck
1344513501 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.
1344613502 synonym: "initiatior codon variant" EXACT []
1344713503 synonym: "initiator codon change" EXACT []
13504 synonym: "Jannovar:initiator_codon_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
13505 synonym: "snpEff:NON_SYNONYMOUS_START" RELATED VAR []
13506 synonym: "VAT:startOverlap" EXACT VAR []
1344813507 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13508 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13509 xref: http://vat.gersteinlab.org/formats.php "VAT"
1344913510 xref: loinc:LA6695-6 "Initiating Methionine"
1345013511 is_a: SO:0001580 ! coding_sequence_variant
1345113512 created_by: kareneilbeck
1345913520 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]
1346013521 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.
1346113522 synonym: "ANNOVAR:nonsynonymous SNV" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13523 synonym: "Jannovar:missense_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1346213524 synonym: "missense" EXACT [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
1346313525 synonym: "missense codon" EXACT []
13464 synonym: "snpEff:NON_SYSNONYMOUS_CODING" EXACT VAR []
13526 synonym: "Seattleseq:missense" EXACT VAR []
13527 synonym: "Seattleseq:missense-near-splice" RELATED VAR []
13528 synonym: "snpEff:NON_SYNONYMOUS_CODING" EXACT VAR []
13529 synonym: "VAAST:missense_variant" EXACT VAR []
1346513530 synonym: "VAAST:non_synonymous_codon" RELATED VAR []
13531 synonym: "VAT:nonsynonymous" EXACT VAR []
13532 synonym: "VEP:missense_variant" EXACT VAR []
1346613533 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
1346713534 xref: http://en.wikipedia.org/wiki/Missense_mutation
13535 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
13536 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13537 xref: http://vat.gersteinlab.org/formats.php "VAT"
13538 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1346813539 xref: loinc:LA6698-0 "Missense"
1346913540 is_a: SO:0001992 ! nonsynonymous_variant
1347013541 created_by: kareneilbeck
1349713568 [Term]
1349813569 id: SO:0001587
1349913570 name: stop_gained
13500 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]
13571 def: "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened polypeptide." [SO:ke]
1350113572 comment: EBI term: Stop gained - In coding sequence, resulting in the gain of a stop codon (i.e. leading to a shortened peptide sequence).
1350213573 synonym: "ANNOVAR:stopgain" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13574 synonym: "Jannovar:stop_gained" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1350313575 synonym: "nonsense" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
1350413576 synonym: "nonsense codon" EXACT []
13505 synonym: "snpEFF:STOP_GAINED" EXACT VAR []
13577 synonym: "Seattleseq:stop-gained" EXACT VAR []
13578 synonym: "Seattleseq:stop-gained-near-splice" RELATED VAR []
13579 synonym: "snpEff:STOP_GAINED" EXACT VAR []
1350613580 synonym: "stop codon gained" RELATED []
1350713581 synonym: "stop gained" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
1350813582 synonym: "VAAST:stop_gained" EXACT VAR []
13583 synonym: "VAT:prematureStop" EXACT VAR []
13584 synonym: "VEP:stop_gained" EXACT VAR []
13585 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
13586 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13587 xref: http://vat.gersteinlab.org/formats.php "VAT"
13588 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1350913589 xref: loinc:LA6699-8 "Nonsense"
1351013590 is_a: SO:0001906 ! feature_truncation
1351113591 is_a: SO:0001992 ! nonsynonymous_variant
1351813598 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]
1351913599 comment: EBI term:Frameshift variations - In coding sequence, resulting in a frameshift.
1352013600 synonym: "ANNOVAR:frameshift block substitution" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13601 synonym: "ANNOVAR:frameshift substitution" RELATED []
1352113602 synonym: "frameshift variant" EXACT []
1352213603 synonym: "frameshift_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
1352313604 synonym: "frameshift_coding" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13605 synonym: "Jannovar:frameshift_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
13606 synonym: "Seattleseq:frameshift" EXACT VAR []
13607 synonym: "Seattleseq:frameshift-near-splice" RELATED VAR []
1352413608 synonym: "snpEff:FRAME_SHIFT" EXACT VAR []
1352513609 synonym: "VAAST:frameshift_variant" EXACT VAR []
13610 synonym: "VAT:deletionFS" NARROW VAR []
13611 synonym: "VAT:insertionFS" NARROW VAR []
13612 synonym: "VEP:frameshift_variant" EXACT VAR []
13613 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
13614 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13615 xref: http://vat.gersteinlab.org/formats.php "VAT"
13616 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1352613617 xref: loinc:LA6694-9 "Frameshift"
1352713618 is_a: SO:0001818 ! protein_altering_variant
1352813619 created_by: kareneilbeck
1353713628 synonym: "terminal codon variant" EXACT []
1353813629 synonym: "terminal_codon_variant" EXACT []
1353913630 synonym: "terminator codon variant" EXACT []
13631 synonym: "VAT:endOverlap" EXACT VAR []
13632 xref: http://vat.gersteinlab.org/formats.php "VAT"
1354013633 xref: loinc:LA6700-2 "Stop Codon Mutation"
1354113634 is_a: SO:0001580 ! coding_sequence_variant
1354213635 created_by: kareneilbeck
1380713900 name: non_coding_transcript_variant
1380813901 def: "A transcript variant of a non coding RNA gene." [SO:ke]
1380913902 comment: Within non-coding gene - Located within a gene that does not code for a protein.
13810 synonym: "ANNOVAR:ncRNA" RELATED VAR [http:http://www.openbioinformatics.org/annovar/annovar_download.html]
13903 synonym: "ANNOVAR:ncRNA" NARROW VAR [http://annovar.openbioinformatics.org/en/latest/user-guide/gene/]
13904 synonym: "Jannovar:non_coding_transcript_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1381113905 synonym: "nc transcript variant" EXACT []
1381213906 synonym: "non coding transcript variant" EXACT []
13907 synonym: "VEP:non_coding_transcript_variant" EXACT VAR []
1381313908 synonym: "within_non_coding_gene" EXACT dbsnp [http://ensembl.org/info/docs/variation/index.html]
13909 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1381413910 is_a: SO:0001576 ! transcript_variant
1381513911 created_by: kareneilbeck
1381613912 creation_date: 2010-03-23T11:16:23Z
1382113917 def: "A transcript variant located with the sequence of the mature miRNA." [SO:ke]
1382213918 comment: EBI term: Within mature miRNA - Located within a microRNA.
1382313919 synonym: "mature miRNA variant" EXACT []
13920 synonym: "snpEff:MICRO_RNA" EXACT VAR []
13921 synonym: "VEP:mature_miRNA_variant" EXACT VAR []
1382413922 synonym: "within_mature_miRNA" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13923 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13924 xref: XX:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1382513925 is_a: SO:0001619 ! non_coding_transcript_variant
1382613926 created_by: kareneilbeck
1382713927 creation_date: 2010-03-23T11:16:58Z
1383213932 def: "A variant in a transcript that is the target of NMD." [SO:ke]
1383313933 synonym: "NMD transcript variant" EXACT []
1383413934 synonym: "NMD_transcript" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13935 synonym: "VEP:NMD_transcript_variant" EXACT VAR []
13936 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1383513937 is_a: SO:0001576 ! transcript_variant
1383613938 created_by: kareneilbeck
1383713939 creation_date: 2010-03-23T11:20:40Z
1385613958 synonym: "5PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
1385713959 synonym: "ANNOVAR:UTR5" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
1385813960 synonym: "five prime UTR variant" EXACT []
13961 synonym: "Jannovar:5_prime_utr_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
13962 synonym: "Seattleseq:5-prime-UTR" EXACT VAR []
1385913963 synonym: "snpEff:UTR_5_PRIME" EXACT VAR []
1386013964 synonym: "untranslated-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
13965 synonym: "VAAST:5_prime_UTR_variant" EXACT VAR []
1386113966 synonym: "VAAST:five_prime_UTR_variant" EXACT VAR []
13967 synonym: "VEP:5_prime_UTR_variant" EXACT VAR []
13968 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
13969 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13970 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1386213971 is_a: SO:0001622 ! UTR_variant
1386313972 created_by: kareneilbeck
1386413973 creation_date: 2010-03-23T11:23:29Z
1387113980 synonym: "3'UTR variant" EXACT []
1387213981 synonym: "3PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
1387313982 synonym: "ANNOVAR:UTR3" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13983 synonym: "Jannovar:3_prime_utr_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
13984 synonym: "Seattleseq:3-prime-UTR" EXACT VAR []
1387413985 synonym: "snpEff:UTR_3_PRIME" EXACT VAR []
1387513986 synonym: "three prime UTR variant" EXACT []
1387613987 synonym: "untranslated-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
13988 synonym: "VAAST:3_prime_UTR_variant" EXACT VAR []
1387713989 synonym: "VAAST:three_prime_UTR_variant" EXACT VAR []
13990 synonym: "VEP:3_prime_UTR_variant" EXACT VAR []
13991 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
13992 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
13993 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1387813994 is_a: SO:0001622 ! UTR_variant
1387913995 created_by: kareneilbeck
1388013996 creation_date: 2010-03-23T11:23:54Z
1388614002 comment: EBI term: Partial codon - Located within the final, incomplete codon of a transcript with a shortened coding sequence where the end is unknown.
1388714003 synonym: "incomplete terminal codon variant" EXACT []
1388814004 synonym: "partial_codon" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
14005 synonym: "VEP:incomplete_terminal_codon_variant" EXACT VAR []
14006 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1388914007 is_a: SO:0001590 ! terminator_codon_variant
1389014008 is_a: SO:0001650 ! inframe_variant
1389114009 created_by: kareneilbeck
1390014018 synonym: "intron variant" EXACT []
1390114019 synonym: "intron_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
1390214020 synonym: "intronic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
14021 synonym: "Jannovar:intron_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
14022 synonym: "Seattleseq:intron" EXACT VAR []
14023 synonym: "Seattleseq:intron-near-splice" RELATED VAR []
1390314024 synonym: "snpEff:INTRON" EXACT VAR []
1390414025 synonym: "VAAST:intron_variant" EXACT VAR []
14026 synonym: "VEP:intron_variant" EXACT VAR []
14027 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
14028 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
14029 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1390514030 is_a: SO:0001576 ! transcript_variant
1390614031 created_by: kareneilbeck
1390714032 creation_date: 2010-03-23T03:52:38Z
1391414039 synonym: "ANNOVAR:intergenic" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
1391514040 synonym: "intergenic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
1391614041 synonym: "intergenic variant" EXACT []
14042 synonym: "Jannovar:intergenic_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
14043 synonym: "Seattleseq:intergenic" EXACT VAR []
1391714044 synonym: "snpEff:INTERGENIC" EXACT VAR []
14045 synonym: "VEP:intergenic_variant" EXACT VAR []
14046 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
14047 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
14048 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1391814049 is_a: SO:0001878 ! feature_variant
1391914050 created_by: kareneilbeck
1392014051 creation_date: 2010-03-23T05:07:37Z
1392614057 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.
1392714058 synonym: "essential_splice_site" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
1392814059 synonym: "splice site variant" EXACT []
14060 synonym: "VAT:spliceOverlap" EXACT VAR []
14061 xref: http://vat.gersteinlab.org/formats.php "VAT"
1392914062 is_a: SO:0001568 ! splicing_variant
1393014063 is_a: SO:0001627 ! intron_variant
1393114064 created_by: kareneilbeck
1393714070 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]
1393814071 comment: EBI term: splice site - 1-3 bps into an exon or 3-8 bps into an intron.
1393914072 synonym: "ANNOVAR:splicing" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
14073 synonym: "Jannovar:splice_region_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
14074 synonym: "snpEff:SPLICE_SITE_BRANCH" RELATED VAR []
14075 synonym: "snpEff:SPLICE_SITE_BRANCH_U12" RELATED VAR []
14076 synonym: "snpEff:SPLICE_SITE_REGION" EXACT VAR []
1394014077 synonym: "splice region variant" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
1394114078 synonym: "VAAST:splice_region_variant" EXACT VAR []
14079 synonym: "VEP:splice_region_variant" EXACT VAR []
14080 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
14081 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1394214082 is_a: SO:0001568 ! splicing_variant
1394314083 created_by: kareneilbeck
1394414084 creation_date: 2010-03-24T09:46:02Z
1394914089 def: "A sequence variant located 5' of a gene." [SO:ke]
1395014090 comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
1395114091 synonym: "ANNOVAR:upstream" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
14092 synonym: "Jannovar:upstream_gene_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1395214093 synonym: "snpEff:UPSTREAM" EXACT VAR []
1395314094 synonym: "upstream gene variant" EXACT []
14095 synonym: "VEP:upstream_gene_variant" EXACT VAR []
14096 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
14097 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1395414098 is_a: SO:0001628 ! intergenic_variant
1395514099 created_by: kareneilbeck
1395614100 creation_date: 2010-03-24T09:49:13Z
1396214106 comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
1396314107 synonym: "ANNOVAR:downstream" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
1396414108 synonym: "downstream gene variant" EXACT []
14109 synonym: "Jannovar:downstream_gene_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1396514110 synonym: "snpEff:DOWNSTREAM" EXACT VAR []
14111 synonym: "VEP:downstream_gene_variant" EXACT VAR []
14112 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
14113 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1396614114 is_a: SO:0001628 ! intergenic_variant
1396714115 created_by: kareneilbeck
1396814116 creation_date: 2010-03-24T09:49:38Z
1397414122 comment: EBI term Downstream variations - Within 5 kb downstream of the 3prime end of a transcript.
1397514123 synonym: "5KB downstream variant" EXACT []
1397614124 synonym: "downstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
14125 synonym: "Seattleseq:downstream-gene" EXACT VAR []
1397714126 synonym: "within 5KB downstream" RELATED []
14127 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
1397814128 is_a: SO:0001632 ! downstream_gene_variant
1397914129 created_by: kareneilbeck
1398014130 creation_date: 2010-03-24T09:50:16Z
1398514135 def: "A sequence variant located within a half KB of the end of a gene." [SO:ke]
1398614136 synonym: "500B downstream variant" EXACT []
1398714137 synonym: "near-gene-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
13988 is_a: SO:0001633 ! 5KB_downstream_variant
14138 is_a: SO:0001632 ! downstream_gene_variant
1398914139 created_by: kareneilbeck
1399014140 creation_date: 2010-03-24T09:50:42Z
1399114141
1399514145 def: "A sequence variant located within 5KB 5' of a gene." [SO:ke]
1399614146 comment: EBI term Upstream variations - Within 5 kb upstream of the 5prime end of a transcript.
1399714147 synonym: "5kb upstream variant" EXACT []
14148 synonym: "Seattleseq:upstream-gene" EXACT VAR []
1399814149 synonym: "upstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
14150 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
1399914151 is_a: SO:0001631 ! upstream_gene_variant
1400014152 created_by: kareneilbeck
1400114153 creation_date: 2010-03-24T09:51:06Z
1400614158 def: "A sequence variant located within 2KB 5' of a gene." [SO:ke]
1400714159 synonym: "2KB upstream variant" EXACT []
1400814160 synonym: "near-gene-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
14009 is_a: SO:0001635 ! 5KB_upstream_variant
14161 is_a: SO:0001631 ! upstream_gene_variant
1401014162 created_by: kareneilbeck
1401114163 creation_date: 2010-03-24T09:51:22Z
1401214164
1407314225 synonym: "Telomerase RNA component" EXACT []
1407414226 synonym: "telomerase RNA gene" EXACT []
1407514227 synonym: "TERC" EXACT []
14076 xref: http:http://en.wikipedia.org/wiki/Telomerase_RNA_component "wikipedia"
14228 xref: http:http\://en.wikipedia.org/wiki/Telomerase_RNA_component "wikipedia"
1407714229 is_a: SO:0001263 ! ncRNA_gene
1407814230 created_by: kareneilbeck
1407914231 creation_date: 2010-05-18T05:26:38Z
1414414296 name: inframe_variant
1414514297 def: "A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]
1414614298 synonym: "ANNOVAR:nonframeshift block substitution" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
14299 synonym: "ANNOVAR:nonframeshift substitution" RELATED VAR []
1414714300 synonym: "cds-indel" EXACT dbsnp []
1414814301 synonym: "inframe variant" EXACT []
1414914302 synonym: "VAAST:inframe_variant" EXACT VAR []
1452214675 [Term]
1452314676 id: SO:0001691
1452414677 name: blunt_end_restriction_enzyme_cleavage_site
14678 def: "A restriction enzyme recognition site that, when cleaved, results in no overhangs." [SBOL:jgquinn, SO:ke]
1452514679 synonym: "blunt end restriction enzyme cleavage site" EXACT []
1452614680 is_a: SO:0001687 ! restriction_enzyme_recognition_site
1452714681 created_by: kareneilbeck
1463914793 [Term]
1464014794 id: SO:0001703
1464114795 name: H3K9_acetylation_site
14642 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]
14796 def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acetylated." [http://en.wikipedia.org/wiki/Histone]
1464314797 synonym: "H3K9 acetylation site" EXACT []
14644 synonym: "H3K9Ac" RELATED []
14798 synonym: "H3K9ac" EXACT []
1464514799 is_a: SO:0001973 ! histone_3_acetylation_site
1464614800 created_by: kareneilbeck
1464714801 creation_date: 2010-03-31T10:25:05Z
1464914803 [Term]
1465014804 id: SO:0001704
1465114805 name: H3K14_acetylation_site
14652 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]
14806 def: "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acetylated." [http://en.wikipedia.org/wiki/Histone]
1465314807 synonym: "H3K14 acetylation site" EXACT []
14654 synonym: "H3K14Ac" RELATED []
14808 synonym: "H3K14ac" EXACT []
1465514809 is_a: SO:0001973 ! histone_3_acetylation_site
1465614810 created_by: kareneilbeck
1465714811 creation_date: 2010-03-31T10:25:53Z
1478614940 [Term]
1478714941 id: SO:0001718
1478814942 name: H3K18_acetylation_site
14789 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]
14943 def: "A kind of histone modification site, whereby the 18th residue (a lysine), from the start of the H3 histone protein is acetylated." [SO:ke]
1479014944 synonym: "H3K18 acetylation site" EXACT []
14791 synonym: "H3K18Ac" RELATED []
14945 synonym: "H3K18ac" EXACT []
1479214946 is_a: SO:0001973 ! histone_3_acetylation_site
1479314947 created_by: kareneilbeck
1479414948 creation_date: 2010-04-13T10:39:35Z
1479514949
1479614950 [Term]
1479714951 id: SO:0001719
14798 name: H3K23_acylation_site
14799 def: "A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]
14800 synonym: "H3K23 acylation site" RELATED []
14801 synonym: "H3K23Ac" RELATED []
14952 name: H3K23_acetylation_site
14953 def: "A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acetylated." [SO:ke]
14954 synonym: "H3K23 acetylation site" EXACT []
14955 synonym: "H3K23ac" EXACT []
1480214956 is_a: SO:0001973 ! histone_3_acetylation_site
1480314957 created_by: kareneilbeck
1480414958 creation_date: 2010-04-13T10:42:45Z
1482014974 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]
1482114975 synonym: "H3K27 acylation site" EXACT []
1482214976 synonym: "H3K27Ac" RELATED []
14823 is_a: SO:0001973 ! histone_3_acetylation_site
14977 is_obsolete: true
1482414978 created_by: kareneilbeck
1482514979 creation_date: 2010-04-13T10:44:09Z
1482614980
1489615050
1489715051 [Term]
1489815052 id: SO:0001729
14899 name: H4K16_acylation_site
14900 def: "A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]
14901 synonym: "H4K16 acylation_site" RELATED []
14902 synonym: "H4K16Ac" RELATED []
14903 is_a: SO:0001972 ! histone_4_acylation_site
15053 name: H4K16_acetylation_site
15054 def: "A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acetylated." [SO:ke]
15055 synonym: "H4K16 acetylation site" EXACT []
15056 synonym: "H4K16ac" EXACT []
15057 is_a: SO:0001972 ! histone_4_acetylation_site
1490415058 created_by: kareneilbeck
1490515059 creation_date: 2010-04-13T11:09:41Z
1490615060
1490715061 [Term]
1490815062 id: SO:0001730
14909 name: H4K5_acylation_site
14910 def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]
14911 synonym: "H4K5 acylation site" RELATED []
14912 synonym: "H4K5Ac" RELATED []
14913 is_a: SO:0001972 ! histone_4_acylation_site
15063 name: H4K5_acetylation_site
15064 def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acetylated." [SO:ke]
15065 synonym: "H4K5 acetylation site" EXACT []
15066 synonym: "H4K5ac" EXACT []
15067 is_a: SO:0001972 ! histone_4_acetylation_site
1491415068 created_by: kareneilbeck
1491515069 creation_date: 2010-04-13T11:13:00Z
1491615070
1491715071 [Term]
1491815072 id: SO:0001731
14919 name: H4K8_acylation_site
14920 def: "A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]
14921 synonym: "H4K8 acylation site" RELATED []
14922 synonym: "H4K8Ac" RELATED []
14923 is_a: SO:0001972 ! histone_4_acylation_site
15073 name: H4K8_acetylation_site
15074 def: "A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acetylated." [SO:KE]
15075 synonym: "H4K8 acetylation site" EXACT []
15076 synonym: "H4K8ac" EXACT []
15077 is_a: SO:0001972 ! histone_4_acetylation_site
1492415078 created_by: kareneilbeck
1492515079 creation_date: 2010-04-13T11:14:24Z
1492615080
1504715201 subset: DBVAR
1504815202 synonym: "uniparental disomy" EXACT []
1504915203 synonym: "UPD" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
15050 xref: http:http://en.wikipedia.org/wiki/Uniparental_disomy "wikipedia"
15204 xref: http:http\://en.wikipedia.org/wiki/Uniparental_disomy "wikipedia"
1505115205 is_a: SO:0001059 ! sequence_alteration
1505215206 created_by: kareneilbeck
1505315207 creation_date: 2011-02-28T02:01:05Z
1518215336 [Term]
1518315337 id: SO:0001759
1518415338 name: unitary_pseudogene
15185 def: "A pseudogene, deactivated from original state by mutation, fixed in a population." [http://en.wikipedia.org/wiki/Pseudogene, SO:ke]
15339 def: "A pseudogene, deactivated from original state by mutation, fixed in a population,where the ortholog in a reference species such as mouse remains functional." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, http://en.wikipedia.org/wiki/Pseudogene, SO:ke]
1518615340 comment: This is different from a non processed pseudogene because the gene was not duplicated. An example is the L-gulono-lactone oxidase pseudogene in primates.
1518715341 synonym: "disabled gene" RELATED []
1518815342 synonym: "unitary pseudogene" RELATED []
1519315347 [Term]
1519415348 id: SO:0001760
1519515349 name: non_processed_pseudogene
15196 def: "A pseudogene that arose from a means other than retrotransposition." [SO:ke]
15350 def: "A pseudogene that arose from a means other than retrotransposition. A pseudogene created via genomic duplication of a functional protein-coding parent gene followed by accumulation of deleterious mutations." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, SO:ke]
1519715351 synonym: "non processed pseudogene" RELATED []
15352 synonym: "unprocessed pseudogene" EXACT []
15353 synonym: "unprocessed_pseudogene" EXACT []
1519815354 is_a: SO:0000336 ! pseudogene
1519915355 created_by: kareneilbeck
1520015356 creation_date: 2011-03-09T10:54:47Z
1537615532 id: SO:0001782
1537715533 name: TF_binding_site_variant
1537815534 def: "A sequence variant located within a transcription factor binding site." [EBI:fc]
15535 synonym: "Jannovar:tf_binding_site_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1537915536 synonym: "TF binding site variant" EXACT []
15537 synonym: "VEP:TF_binding_site_variant" EXACT VAR []
15538 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1538015539 is_a: SO:0001566 ! regulatory_region_variant
1538115540 created_by: kareneilbeck
1538215541 creation_date: 2011-03-17T10:59:20Z
1546015619 def: "A sequence variant that changes exon sequence." [SO:ke]
1546115620 synonym: "ANNOVAR:exonic" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
1546215621 synonym: "exon variant" EXACT []
15622 synonym: "Jannovar:exon_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1546315623 synonym: "snpEff:EXON" EXACT VAR []
1546415624 synonym: "VAAST:exon_variant" EXACT VAR []
15625 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1546515626 is_a: SO:0001576 ! transcript_variant
1546615627 created_by: kareneilbeck
1546715628 creation_date: 2011-05-06T01:51:17Z
1547015631 id: SO:0001792
1547115632 name: non_coding_transcript_exon_variant
1547215633 def: "A sequence variant that changes non-coding exon sequence in a non-coding transcript." [EBI:fc, SO:ke]
15634 synonym: "ANNOVAR:ncRNA_exonic" NARROW VAR []
15635 synonym: "Jannovar:non_coding_transcript_exon_variant" NARROW VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1547315636 synonym: "non coding transcript exon variant" EXACT []
15637 synonym: "non_coding_transcript_exon_variant" EXACT VAR []
15638 synonym: "Seattleseq:non-coding-exon" EXACT VAR []
15639 synonym: "Seattleseq:non-coding-exon-near-splice" RELATED VAR []
15640 synonym: "VEP:non_coding_transcript_exon_variant" EXACT VAR []
15641 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
1547415642 is_a: SO:0001619 ! non_coding_transcript_variant
1547515643 is_a: SO:0001791 ! exon_variant
1547615644 created_by: kareneilbeck
1553215700 synonym: "lmr1R" EXACT []
1553315701 synonym: "regional centromere inner repeat region" EXACT []
1553415702 is_a: SO:0001797 ! centromeric_repeat
15703 relationship: part_of SO:0001795 ! regional_centromere
1553515704 relationship: part_of SO:0001796 ! regional_centromere_central_core
1553615705 created_by: kareneilbeck
1553715706 creation_date: 2011-05-31T01:01:08Z
1571915888 name: protein_altering_variant
1572015889 def: "A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]
1572115890 synonym: "protein altering variant" EXACT []
15891 synonym: "VEP:protein_altering_variant" EXACT VAR []
15892 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1572215893 is_a: SO:0001580 ! coding_sequence_variant
1572315894 created_by: kareneilbeck
1572415895 creation_date: 2011-06-24T03:38:02Z
1573115902 comment: EBI term: Synonymous SNPs - In coding sequence, not resulting in an amino acid change (i.e. silent mutation).\nThis term is sometimes used synonomously with the more general term 'silent mutation', although a silent mutation may occur in non coding sequence. The best practice is to annotate to the most specific term.
1573215903 synonym: "ANNOVAR:synonymous SNV" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
1573315904 synonym: "coding-synon" EXACT [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
15905 synonym: "Jannovar:synonymous_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
15906 synonym: "Seattleseq:synonymous" EXACT VAR []
15907 synonym: "Seattleseq:synonymous-near-splice" RELATED VAR []
1573415908 synonym: "silent mutation" RELATED []
1573515909 synonym: "silent substitution" RELATED []
1573615910 synonym: "silent_mutation" RELATED []
1573915913 synonym: "synonymous_coding" EXACT []
1574015914 synonym: "synonymous_codon" EXACT []
1574115915 synonym: "VAAST:synonymous_codon" EXACT VAR []
15916 synonym: "VAAST:synonymous_variant" EXACT VAR []
15917 synonym: "VAT:synonymous" EXACT VAR []
15918 synonym: "VEP:synonymous_variant" EXACT VAR []
1574215919 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
1574315920 xref: http://en.wikipedia.org/wiki/Silent_mutation "wiki"
1574415921 xref: http://en.wikipedia.org/wiki/Synonymous_mutation
15922 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
15923 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
15924 xref: http://vat.gersteinlab.org/formats.php "VAT"
15925 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1574515926 is_a: SO:0001580 ! coding_sequence_variant
1574615927 created_by: kareneilbeck
1574715928 creation_date: 2011-06-24T03:38:30Z
1576615947 synonym: "inframe increase in CDS length" EXACT []
1576715948 synonym: "inframe insertion" EXACT []
1576815949 synonym: "inframe_codon_gain" EXACT []
15950 synonym: "Jannovar:inframe_insertion" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1576915951 synonym: "snpEFF:CODON_INSERTION" EXACT VAR []
15952 synonym: "VAT:insertionNFS" EXACT VAR []
15953 synonym: "VEP:inframe_insertion" EXACT VAR []
15954 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
15955 xref: http://vat.gersteinlab.org/formats.php "VAT"
15956 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1577015957 is_a: SO:0001820 ! inframe_indel
1577115958 is_a: SO:0001908 ! internal_feature_elongation
1577215959 created_by: kareneilbeck
1578215969 synonym: "inframe decrease in CDS length" EXACT []
1578315970 synonym: "inframe deletion" RELATED []
1578415971 synonym: "inframe_codon_loss" EXACT []
15972 synonym: "Jannovar:inframe_deletion" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1578515973 synonym: "snpEff:CODON_DELETION" RELATED VAR []
15974 synonym: "VAT:deletionNFS" EXACT VAR []
15975 synonym: "VEP:inframe_deletion" EXACT VAR []
15976 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
15977 xref: http://vat.gersteinlab.org/formats.php "VAT"
15978 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1578615979 is_a: SO:0001820 ! inframe_indel
1578715980 is_a: SO:0001906 ! feature_truncation
1578815981 created_by: kareneilbeck
1580415997 def: "An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]
1580515998 synonym: "disruptive increase in CDS length" EXACT []
1580615999 synonym: "disruptive inframe insertion" EXACT []
16000 synonym: "Jannovar:disruptive_inframe_insertion" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1580716001 synonym: "snpEff:CODON_CHANGE_PLUS_CODON_INSERTION" EXACT VAR []
16002 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1580816003 is_a: SO:0001821 ! inframe_insertion
1580916004 created_by: kareneilbeck
1581016005 creation_date: 2011-06-27T11:28:37Z
1582516020 def: "An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]
1582616021 synonym: "disruptive decrease in CDS length" EXACT []
1582716022 synonym: "disruptive inframe deletion" EXACT []
16023 synonym: "Jannovar:disruptive_inframe_deletion" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1582816024 synonym: "snpEff:CODON_CHANGE_PLUS_CODON_DELETION" EXACT VAR []
16025 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1582916026 is_a: SO:0001822 ! inframe_deletion
1583016027 created_by: kareneilbeck
1583116028 creation_date: 2011-06-27T11:31:31Z
1597116168 [Term]
1597216169 id: SO:0001841
1597316170 name: polymorphic_pseudogene
15974 def: "Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated." [JAX:hd]
15975 comment: This terms is used by Ensembl and Vega.
16171 def: "A pseudogene in the reference genome, though known to be intact in the genomes of other individuals of the same species. The annotation process has confirmed that the pseudogenisation event is not a genomic sequencing error." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, JAX:hd]
16172 comment: This terms is used by Ensembl and Vega. Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated.
1597616173 synonym: "polymorphic psuedogene" EXACT []
1597716174 is_a: SO:0000336 ! pseudogene
1597816175 created_by: kareneilbeck
1603616233 [Term]
1603716234 id: SO:0001848
1603816235 name: homol_D_box
16039 def: "A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." [PMID:7501449, PMID:8458332]
16236 def: "A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." [PMID:21673110, PMID:7501449, PMID:8458332]
16237 synonym: "homoID" EXACT []
1604016238 synonym: "homol D box" EXACT []
1604116239 is_a: SO:0001660 ! core_promoter_element
1604216240 created_by: kareneilbeck
1644516643 def: "A feature amplification of a region containing a transcript." [SO:ke]
1644616644 comment: Created in conjunction with the EBI.
1644716645 synonym: "transcript amplification" EXACT []
16646 synonym: "VEP:transcript_amplification" EXACT VAR []
16647 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1644816648 is_a: SO:0001880 ! feature_amplification
1644916649 created_by: kareneilbeck
1645016650 creation_date: 2012-04-03T12:39:23Z
1646516665 def: "A feature amplification of a region containing a regulatory region." [SO:ke]
1646616666 comment: Created in conjunction with the EBI.
1646716667 synonym: "regulatory region amplification" EXACT []
16668 synonym: "VEP:regulatory_region_amplification" EXACT VAR []
16669 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1646816670 is_a: SO:0001880 ! feature_amplification
1646916671 created_by: kareneilbeck
1647016672 creation_date: 2012-04-03T12:41:28Z
1647616678 comment: Created in conjunction with the EBI.
1647716679 synonym: "TFBS amplification " EXACT []
1647816680 synonym: "transcription factor binding site amplification" EXACT []
16681 synonym: "VEP:TFBS_amplification" EXACT VAR []
16682 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1647916683 is_a: SO:0001891 ! regulatory_region_amplification
1648016684 created_by: kareneilbeck
1648116685 creation_date: 2012-04-03T12:42:48Z
1648516689 name: transcript_ablation
1648616690 def: "A feature ablation whereby the deleted region includes a transcript feature." [SO:ke]
1648716691 comment: Created in conjunction with the EBI.
16692 synonym: "Jannovar:transcript_ablation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1648816693 synonym: "transcript ablation" EXACT []
16694 synonym: "VEP:transcript_ablation" EXACT VAR []
16695 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1648916696 is_a: SO:0001879 ! feature_ablation
1649016697 created_by: kareneilbeck
1649116698 creation_date: 2012-04-03T12:44:19Z
1649616703 def: "A feature ablation whereby the deleted region includes a regulatory region." [SO:ke]
1649716704 comment: Created in conjunction with the EBI.
1649816705 synonym: "regulatory region ablation" EXACT []
16706 synonym: "VEP:regulatory_region_ablation" EXACT VAR []
16707 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1649916708 is_a: SO:0001879 ! feature_ablation
1650016709 created_by: kareneilbeck
1650116710 creation_date: 2012-04-03T12:45:13Z
1650716716 comment: Created in conjunction with the EBI.
1650816717 synonym: "TFBS ablation" EXACT []
1650916718 synonym: "transcription factor binding site ablation" EXACT []
16719 synonym: "VEP:TFBS_ablation" EXACT VAR []
16720 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1651016721 is_a: SO:0001894 ! regulatory_region_ablation
1651116722 created_by: kareneilbeck
1651216723 creation_date: 2012-04-03T12:45:56Z
1661716828 name: feature_truncation
1661816829 def: "A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." [SO:ke]
1661916830 synonym: "feature truncation" EXACT []
16831 synonym: "Jannovar:feature_truncation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
16832 synonym: "VEP:feature_truncation" EXACT VAR []
16833 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1662016834 is_a: SO:0001878 ! feature_variant
1662116835 created_by: kareneilbeck
1662216836 creation_date: 2012-04-12T05:05:28Z
1662616840 name: feature_elongation
1662716841 def: "A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." [SO:ke]
1662816842 synonym: "feature elongation" EXACT []
16843 synonym: "VEP:feature_elongation" EXACT VAR []
16844 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1662916845 is_a: SO:0001878 ! feature_variant
1663016846 created_by: kareneilbeck
1663116847 creation_date: 2012-04-12T05:05:56Z
1663516851 name: internal_feature_elongation
1663616852 def: "A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence." [SO:ke]
1663716853 synonym: "internal feature elongation" EXACT []
16854 synonym: "Jannovar:internal_feature_elongation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1663816855 is_a: SO:0001907 ! feature_elongation
1663916856 created_by: kareneilbeck
1664016857 creation_date: 2012-04-12T05:06:20Z
1664516862 def: "A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]
1664616863 synonym: "ANNOVAR:frameshift insertion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
1664716864 synonym: "frameshift elongation" EXACT []
16865 synonym: "Jannovar:frameshift_elongation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1664816866 is_a: SO:0001589 ! frameshift_variant
1664916867 is_a: SO:0001908 ! internal_feature_elongation
1665016868 created_by: kareneilbeck
1665416872 id: SO:0001910
1665516873 name: frameshift_truncation
1665616874 def: "A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]
16657 synonym: "ANNOVAR:frameshit deletion" EXACT ebi_variants [http://www.openbioinformatics.org/annovar/annovar_download.html]
16658 synonym: "frameshft truncation" EXACT []
16875 synonym: "ANNOVAR:frameshift deletion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
16876 synonym: "frameshift truncation" EXACT []
16877 synonym: "Jannovar:frameshift_truncation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1665916878 is_a: SO:0001589 ! frameshift_variant
1666016879 is_a: SO:0001906 ! feature_truncation
1666116880 created_by: kareneilbeck
1674316962 synonym: "m-5C" EXACT []
1674416963 synonym: "m5c" EXACT []
1674516964 xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#7.4.2
16746 xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
16965 xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
1674716966 is_a: SO:0000114 ! methylated_cytosine
1674816967 created_by: kareneilbeck
1674916968 creation_date: 2012-10-17T12:46:10Z
1676016979 synonym: "N4-methylcytosine" EXACT []
1676116980 synonym: "N4_methylcytosine" EXACT []
1676216981 xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#7.4.2
16763 xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
16982 xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
1676416983 is_a: SO:0000114 ! methylated_cytosine
1676516984 created_by: kareneilbeck
1676616985 creation_date: 2012-10-17T12:50:40Z
1677516994 synonym: "m-6A" EXACT []
1677616995 synonym: "m6a" EXACT []
1677716996 synonym: "N6-methyladenine" EXACT []
16778 xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
16997 xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
1677916998 is_a: SO:0000161 ! methylated_adenine
1678016999 created_by: kareneilbeck
1678117000 creation_date: 2012-10-17T12:54:23Z
1693117150 [Term]
1693217151 id: SO:0001936
1693317152 name: H3K36_acetylation_site
16934 def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]
17153 def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]
1693517154 synonym: "H3K36 acetylation site" EXACT []
1693617155 synonym: "H3K36ac" EXACT []
1693717156 is_a: SO:0001973 ! histone_3_acetylation_site
1694117160 [Term]
1694217161 id: SO:0001937
1694317162 name: H2BK12_acetylation_site
16944 def: "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]
17163 def: "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is acetylated." [EBI:nj]
1694517164 synonym: "H2BK12 acetylation site" EXACT []
16946 synonym: "H2BK12ac" RELATED []
16947 is_a: SO:0001702 ! histone_acetylation_site
17165 synonym: "H2BK12ac" EXACT []
17166 is_a: SO:0002143 ! histone_2B_acetylation_site
1694817167 created_by: kareneilbeck
1694917168 creation_date: 2013-03-06T10:19:13Z
1695017169
1695417173 def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]
1695517174 synonym: "H2AK5 acetylation site" EXACT []
1695617175 synonym: "H2AK5ac" EXACT []
16957 is_a: SO:0001702 ! histone_acetylation_site
17176 is_a: SO:0002142 ! histone_2A_acetylation_site
1695817177 created_by: kareneilbeck
1695917178 creation_date: 2013-03-06T10:20:57Z
1696017179
1696417183 def: "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]
1696517184 synonym: "H4K12 acetylation site" EXACT []
1696617185 synonym: "H4K12ac" EXACT []
16967 is_a: SO:0001972 ! histone_4_acylation_site
17186 is_a: SO:0001972 ! histone_4_acetylation_site
1696817187 created_by: kareneilbeck
1696917188 creation_date: 2013-03-06T10:26:15Z
1697017189
1697117190 [Term]
1697217191 id: SO:0001940
1697317192 name: H2BK120_acetylation_site
16974 def: "A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]
17193 def: "A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj, http://dx.doi.org/10.4161/epi.6.5.15623]
1697517194 synonym: "H2BK120 acetylation site" EXACT []
1697617195 synonym: "H2BK120ac" EXACT []
16977 is_a: SO:0001702 ! histone_acetylation_site
17196 is_a: SO:0002143 ! histone_2B_acetylation_site
1697817197 created_by: kareneilbeck
1697917198 creation_date: 2013-03-06T10:28:38Z
1698017199
1698317202 name: H4K91_acetylation_site
1698417203 def: "A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]
1698517204 synonym: "H4K91 acetylation site" EXACT []
16986 is_a: SO:0001972 ! histone_4_acylation_site
17205 synonym: "H4K91ac" EXACT []
17206 is_a: SO:0001972 ! histone_4_acetylation_site
1698717207 created_by: kareneilbeck
1698817208 creation_date: 2013-03-06T10:41:04Z
1698917209
1699117211 id: SO:0001942
1699217212 name: H2BK20_acetylation_site
1699317213 def: "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]
16994 synonym: "H2BK20 acetylation site" RELATED []
17214 synonym: "H2BK20 acetylation site" EXACT []
1699517215 synonym: "H2BK20ac" EXACT []
16996 is_a: SO:0001702 ! histone_acetylation_site
17216 is_a: SO:0002143 ! histone_2B_acetylation_site
1699717217 created_by: kareneilbeck
1699817218 creation_date: 2013-03-06T10:44:31Z
1699917219
1700017220 [Term]
1700117221 id: SO:0001943
17002 name: H3K4ac_acetylation_site
17222 name: H3K4_acetylation_site
1700317223 def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]
17224 synonym: "H3K4 acetylation site" EXACT []
1700417225 synonym: "H3K4ac" EXACT []
17005 synonym: "H3K4ac acetylation site" EXACT []
1700617226 is_a: SO:0001973 ! histone_3_acetylation_site
1700717227 created_by: kareneilbeck
1700817228 creation_date: 2013-03-06T10:46:32Z
1701317233 def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]
1701417234 synonym: "H2AK9 acetylation site" EXACT []
1701517235 synonym: "H2AK9ac" EXACT []
17016 is_a: SO:0001702 ! histone_acetylation_site
17236 is_a: SO:0002142 ! histone_2A_acetylation_site
1701717237 created_by: kareneilbeck
1701817238 creation_date: 2013-03-06T10:48:11Z
1701917239
1703317253 def: "A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]
1703417254 synonym: "H2BK15 acetylation site" EXACT []
1703517255 synonym: "H2BK15ac" EXACT []
17036 is_a: SO:0001702 ! histone_acetylation_site
17256 is_a: SO:0002143 ! histone_2B_acetylation_site
1703717257 created_by: kareneilbeck
1703817258 creation_date: 2013-03-06T10:53:23Z
1703917259
1713717357 name: RNA_stability_element
1713817358 def: "RNA secondary structure that affects the stability of an RNA molecule." [SO:ke]
1713917359 synonym: "rna stability element" RELATED []
17360 is_obsolete: true
1714017361 created_by: kareneilbeck
1714117362 creation_date: 2013-03-06T03:38:35Z
17142 is_obsolete: true
1714317363
1714417364 [Term]
1714517365 id: SO:0001958
1716717387 def: "A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke]
1716817388 synonym: "5-hmC" EXACT []
1716917389 synonym: "5-hydroxymethylcytosine" EXACT []
17170 xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
17390 xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
1717117391 is_a: SO:0000114 ! methylated_cytosine
1717217392 created_by: kareneilbeck
1717317393 creation_date: 2013-05-17T05:05:31Z
1717817398 def: "A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon." [SO:ke]
1717917399 synonym: "5-fC" EXACT []
1718017400 synonym: "5-formylcytosine" EXACT []
17181 xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
17401 xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
1718217402 is_a: SO:0001963 ! modified_cytosine
1718317403 created_by: kareneilbeck
1718417404 creation_date: 2013-05-17T05:06:13Z
1721317433 def: "A modified DNA guanine base,at the 8 carbon, often the product of DNA damage." [SO:ke]
1721417434 synonym: "8-oxoG" EXACT []
1721517435 synonym: "8-oxoguanine" EXACT []
17216 xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
17436 xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
1721717437 is_a: SO:0001964 ! modified_guanine
1721817438 created_by: kareneilbeck
1721917439 creation_date: 2013-05-20T01:27:51Z
1722417444 def: "A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon." [SO:ke]
1722517445 synonym: "5-caC" EXACT []
1722617446 synonym: "5-carboxycytosine" EXACT []
17227 xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
17447 xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
1722817448 is_a: SO:0001963 ! modified_cytosine
1722917449 created_by: kareneilbeck
1723017450 creation_date: 2013-05-20T01:30:01Z
1723517455 def: "A modified DNA adenine base,at the 8 carbon, often the product of DNA damage." [SO:ke]
1723617456 synonym: "8-oxoA" EXACT []
1723717457 synonym: "8-oxoadenine" EXACT []
17238 xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
17458 xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
1723917459 is_a: SO:0001962 ! modified_adenine
1724017460 created_by: kareneilbeck
1724117461 creation_date: 2013-05-20T01:31:05Z
1724517465 name: coding_transcript_variant
1724617466 def: "A transcript variant of a protein coding gene." [SO:ke]
1724717467 synonym: "coding transcript variant" EXACT []
17468 synonym: "Jannovar:coding_transcript_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1724817469 is_a: SO:0001576 ! transcript_variant
1724917470 created_by: kareneilbeck
1725017471 creation_date: 2013-05-22T04:34:49Z
1725417475 name: coding_transcript_intron_variant
1725517476 def: "A transcript variant occurring within an intron of a coding transcript." [SO:ke]
1725617477 synonym: "coding sequence intron variant" EXACT []
17478 synonym: "Jannovar:coding_transcript_intron_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1725717479 is_a: SO:0001627 ! intron_variant
1725817480 is_a: SO:0001968 ! coding_transcript_variant
1725917481 created_by: kareneilbeck
1726317485 id: SO:0001970
1726417486 name: non_coding_transcript_intron_variant
1726517487 def: "A transcript variant occurring within an intron of a non coding transcript." [SO:ke]
17488 synonym: "ANNOVAR:ncRNA_intronic" NARROW VAR []
17489 synonym: "Jannovar:non_coding_transcript_intron_variant" NARROW VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1726617490 synonym: "non coding transcript intron variant" EXACT []
1726717491 is_a: SO:0001619 ! non_coding_transcript_variant
1726817492 is_a: SO:0001627 ! intron_variant
1728017504
1728117505 [Term]
1728217506 id: SO:0001972
17283 name: histone_4_acylation_site
17284 def: "A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]
17507 name: histone_4_acetylation_site
17508 def: "A histone 4 modification where the modification is the acetylation of the residue." [EBI:nj, ISBN:0815341059, SO:ke]
1728517509 synonym: "H4ac" EXACT []
17510 synonym: "histone 4 acetylation site" EXACT []
1728617511 is_a: SO:0001702 ! histone_acetylation_site
1728717512 created_by: kareneilbeck
1728817513 creation_date: 2013-07-30T10:43:04Z
1729017515 [Term]
1729117516 id: SO:0001973
1729217517 name: histone_3_acetylation_site
17293 def: "A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]
17518 def: "A histone 3 modification where the modification is the acetylation of the residue." [EBI:nj, ISBN:0815341059, SO:ke]
1729417519 synonym: "H3ac" EXACT []
17520 synonym: "histone 3 acetylation site" EXACT []
1729517521 is_a: SO:0001702 ! histone_acetylation_site
1729617522 created_by: kareneilbeck
1729717523 creation_date: 2013-07-30T10:46:42Z
1739017616 def: "A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]
1739117617 comment: Requested by Andy Menzies at the Sanger. This isn't necessarily a protein coding change. A premature start codon can effect the production of a mature protein product by providing a competing translation start point. Some genes balance their expression this way, eg THPO requires the presence of a premature start to limit expression, its loss leads to Familial thrombocythemia.
1739217618 synonym: "5' UTR premature start codon variant" EXACT []
17393 synonym: "snpEff:START_GAINED" EXACT VAR []
1739417619 is_a: SO:0001623 ! 5_prime_UTR_variant
1739517620 created_by: kareneilbeck
1739617621 creation_date: 2013-07-30T04:36:25Z
1743817663 name: 5_prime_UTR_premature_start_codon_gain_variant
1743917664 def: "A 5' UTR variant where a premature start codon is gained." [Sanger:am]
1744017665 synonym: "5 prime UTR premature start codon gain variant" EXACT []
17666 synonym: "Jannovar:5_prime_UTR_premature_start_codon_gain_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
17667 synonym: "snpEff:START_GAINED" EXACT VAR []
17668 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1744117669 is_a: SO:0001983 ! 5_prime_UTR_premature_start_codon_variant
1744217670 created_by: kareneilbeck
1744317671 creation_date: 2013-07-31T03:53:06Z
1762317851 name: rare_amino_acid_variant
1762417852 def: "A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]
1762517853 comment: Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
17854 synonym: "Jannovar:rare_amino_acid_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1762617855 synonym: "rare amino acid variant" EXACT []
17856 synonym: "snpEff:RARE_AMINO_ACID" EXACT VAR []
17857 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1762717858 is_a: SO:0001586 ! non_conservative_missense_variant
1762817859 created_by: kareneilbeck
1762917860 creation_date: 2014-03-24T02:24:01Z
1765417885 def: "A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence." [SO:ke]
1765517886 comment: Requested by Pablo Cingolani, for use in SnpEff.
1765617887 synonym: "intragenic variant" EXACT []
17888 synonym: "Jannovar:intragenic_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1765717889 synonym: "snpEff:INTRAGENIC" EXACT VAR []
17890 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1765817891 is_a: SO:0001576 ! transcript_variant
1765917892 created_by: kareneilbeck
1766017893 creation_date: 2014-03-24T02:33:13Z
1766417897 name: start_lost
1766517898 def: "A codon variant that changes at least one base of the canonical start codon." [SO:ke]
1766617899 comment: Request from Uma Devi Paila, UVA. This term should not be applied to incomplete transcripts.
17900 synonym: "Jannovar:start_lost" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1766717901 synonym: "snpEff:START_LOST" EXACT VAR []
17902 synonym: "VEP:start_lost" EXACT VAR []
17903 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
17904 xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences
1766817905 is_a: SO:0001582 ! initiator_codon_variant
1766917906 is_a: SO:0001992 ! nonsynonymous_variant
1767017907 created_by: kareneilbeck
1767517912 name: 5_prime_UTR_truncation
1767617913 def: "A sequence variant that causes the reduction of a the 5'UTR with regard to the reference sequence." [SO:ke]
1767717914 synonym: "5 prime UTR truncation" EXACT []
17915 synonym: "Jannovar:5_prime_utr_truncation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1767817916 synonym: "snpEff:UTR_5_DELETED" EXACT VAR []
17917 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1767917918 is_a: SO:0001623 ! 5_prime_UTR_variant
1768017919 created_by: kareneilbeck
1768117920 creation_date: 2014-03-25T10:46:42Z
1769417933 name: 3_prime_UTR_truncation
1769517934 def: "A sequence variant that causes the reduction of a the 3' UTR with regard to the reference sequence." [SO:ke]
1769617935 synonym: "3 prime UTR truncation" EXACT []
17936 synonym: "Jannovar:3_prime_utr_truncation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1769717937 synonym: "snpEff:UTR_3_DELETED" EXACT VAR []
17938 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1769817939 is_a: SO:0001624 ! 3_prime_UTR_variant
1769917940 created_by: kareneilbeck
1770017941 creation_date: 2014-03-25T10:54:50Z
1771417955 def: "A sequence variant located in a conserved intergenic region, between genes." [SO:ke]
1771517956 comment: Requested by Uma Paila (UVA) for snpEff.
1771617957 synonym: "conserved intergenic variant" EXACT []
17958 synonym: "Jannovar:conserved_intergenic_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1771717959 synonym: "snpEff:INTERGENIC_CONSERVED" EXACT VAR []
17960 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1771817961 is_a: SO:0001628 ! intergenic_variant
1771917962 created_by: kareneilbeck
1772017963 creation_date: 2014-03-25T02:54:39Z
1772517968 def: "A transcript variant occurring within a conserved region of an intron." [SO:ke]
1772617969 comment: Requested by Uma Paila (UVA) for snpEff.
1772717970 synonym: "conserved intron variant" EXACT []
17971 synonym: "Jannovar:conserved_intron_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1772817972 synonym: "snpEff:INTRON_CONSERVED" EXACT VAR []
17973 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1772917974 is_a: SO:0001627 ! intron_variant
1773017975 created_by: kareneilbeck
1773117976 creation_date: 2014-03-25T02:58:41Z
1773517980 name: start_retained_variant
1773617981 def: "A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]
1773717982 comment: Requested by Uma Paila as this term is annotated by snpEff. This would be used for non_AUG start codon annotation.
17983 synonym: "snpEff:SYNONYMOUS_START" EXACT VAR []
1773817984 is_a: SO:0001582 ! initiator_codon_variant
1773917985 is_a: SO:0001819 ! synonymous_variant
1774017986 created_by: kareneilbeck
1781218058 id: SO:0002027
1781318059 name: uORF
1781418060 def: "A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation." [PMID:12890013, PMID:16153175, POMBASE:mah]
18061 synonym: "regulatory uORF" EXACT []
1781518062 synonym: "upstream ORF" EXACT []
18063 xref: PMID:26684391
1781618064 is_a: SO:0000236 ! ORF
1781718065 created_by: kareneilbeck
1781818066 creation_date: 2014-07-14T11:59:23Z
1785118099 def: "A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference." [PMID:6699500, SO:ke]
1785218100 synonym: "short hairpin RNA" EXACT []
1785318101 synonym: "small hairpin RNA" EXACT []
17854 xref: http:http:en.wikipedia.org/wiki/Small_hairpin_RNA "wikipedia"
18102 xref: http:http\:en.wikipedia.org/wiki/Small_hairpin_RNA "wikipedia"
1785518103 is_a: SO:0000655 ! ncRNA
1785618104 created_by: kareneilbeck
1785718105 creation_date: 2014-10-23T09:16:29Z
1803318281 def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acetylated." [SO:rs]
1803418282 comment: Requested by: Sagar Jain, Richard Scheuermann.
1803518283 synonym: "H3K27 acetylation site" EXACT []
18284 synonym: "H3K27ac" EXACT []
1803618285 is_a: SO:0001973 ! histone_3_acetylation_site
1803718286 created_by: kareneilbeck
1803818287 creation_date: 2015-05-14T10:17:11Z
1810918358 id: SO:0002057
1811018359 name: intronic_splicing_enhancer
1811118360 synonym: "ISE" EXACT []
18361 is_obsolete: true
1811218362 created_by: kareneilbeck
1811318363 creation_date: 2015-05-14T12:28:31Z
18114 is_obsolete: true
1811518364
1811618365 [Term]
1811718366 id: SO:0002058
1813618385
1813718386 [Term]
1813818387 id: SO:0002060
18139 name: interchomosomal_translocation
18388 name: interchromosomal_translocation
1814018389 def: "A translocation where the regions involved are from different chromosomes." [NCBI:th]
1814118390 is_a: SO:1000044 ! chromosomal_translocation
1814218391 created_by: kareneilbeck
1814418393
1814518394 [Term]
1814618395 id: SO:0002061
18147 name: intrachomosomal_translocation
18396 name: intrachromosomal_translocation
1814818397 def: "A translocation where the regions involved are from the same chromosome." [NCBI:th]
1814918398 is_a: SO:1000044 ! chromosomal_translocation
1815018399 created_by: kareneilbeck
1816118410
1816218411 [Term]
1816318412 id: SO:0002063
18164 name: alu_insertion
18413 name: Alu_insertion
1816518414 def: "An insertion of sequence from the Alu family of mobile elements." [NCBI:th]
18166 synonym: "alu insertion" EXACT []
18415 synonym: "Alu insertion" EXACT []
1816718416 is_a: SO:0001837 ! mobile_element_insertion
1816818417 created_by: kareneilbeck
1816918418 creation_date: 2015-06-18T11:30:36Z
1818418433 is_a: SO:0001837 ! mobile_element_insertion
1818518434 created_by: kareneilbeck
1818618435 creation_date: 2015-06-18T11:36:12Z
18436
18437 [Term]
18438 id: SO:0002066
18439 name: mobile_element_deletion
18440 def: "A deletion of a mobile element when comparing a reference sequence (has mobile element) to a individual sequence (does not have mobile element)." [NCBI:th]
18441 synonym: "mobile element deletion" EXACT []
18442 is_a: SO:0000159 ! deletion
18443 created_by: kareneilbeck
18444 creation_date: 2015-09-04T13:40:43Z
18445
18446 [Term]
18447 id: SO:0002067
18448 name: HERV_deletion
18449 def: "A deletion of the HERV mobile element with respect to a reference." [NCBI:th]
18450 synonym: "HERV deletion" EXACT []
18451 is_a: SO:0002066 ! mobile_element_deletion
18452 created_by: kareneilbeck
18453 creation_date: 2015-09-04T13:42:52Z
18454
18455 [Term]
18456 id: SO:0002068
18457 name: SVA_deletion
18458 def: "A deletion of an SVA mobile element." [NCBI:th]
18459 synonym: "SVA deletion" EXACT []
18460 is_a: SO:0002066 ! mobile_element_deletion
18461 created_by: kareneilbeck
18462 creation_date: 2015-09-04T13:45:22Z
18463
18464 [Term]
18465 id: SO:0002069
18466 name: LINE1_deletion
18467 def: "A deletion of a LINE1 mobile element with respect to a reference." [NCBI:th]
18468 synonym: "LINE1 deletion" RELATED []
18469 is_a: SO:0002066 ! mobile_element_deletion
18470 created_by: kareneilbeck
18471 creation_date: 2015-09-04T13:46:26Z
18472
18473 [Term]
18474 id: SO:0002070
18475 name: Alu_deletion
18476 def: "A deletion of an Alu mobile element with respect to a reference." [NCBI:th]
18477 is_a: SO:0002066 ! mobile_element_deletion
18478 created_by: kareneilbeck
18479 creation_date: 2015-09-04T13:47:16Z
18480
18481 [Term]
18482 id: SO:0002071
18483 name: CDS_supported_by_peptide_spectrum_match
18484 def: "A CDS that is supported by proteomics data." [SO:ke]
18485 is_a: SO:1001251 ! CDS_supported_by_sequence_similarity_data
18486 created_by: kareneilbeck
18487 creation_date: 2015-10-12T13:25:02Z
18488
18489 [Term]
18490 id: SO:0002072
18491 name: sequence_comparison
18492 is_a: SO:0000110 ! sequence_feature
18493 created_by: kareneilbeck
18494 creation_date: 2015-11-23T14:14:32Z
18495
18496 [Term]
18497 id: SO:0002073
18498 name: no_sequence_alteration
18499 def: "A position or feature within a sequence that is identical to the comparable position or feature of a specified reference sequence." [SO:ke]
18500 comment: This term is requested by the ClinVar data model group for use in the allele registry and such. A sequence at a defined location that is defined to match the reference assembly.
18501 is_a: SO:0002072 ! sequence_comparison
18502 created_by: kareneilbeck
18503 creation_date: 2015-11-23T14:15:08Z
18504
18505 [Term]
18506 id: SO:0002074
18507 name: intergenic_1kb_variant
18508 def: "A variant that falls in an intergenic region that is 1 kb or less between 2 genes." [SO:ke]
18509 comment: This term is added to map to the Annovar annotation 'upstream,downstream' .
18510 synonym: "ANNOVAR:upstream;downstream" EXACT VAR []
18511 is_a: SO:0001628 ! intergenic_variant
18512 created_by: kareneilbeck
18513 creation_date: 2015-11-23T14:24:16Z
18514
18515 [Term]
18516 id: SO:0002075
18517 name: incomplete_transcript_variant
18518 def: "A sequence variant that intersects an incompletely annotated transcript." [SO:ke]
18519 comment: This term is to map to the ANNOVAR term 'ncRNA' http://annovar.openbioinformatics.org/en/latest/user-guide/gene/ . The description in the documentation (11/23/15) 'variant overlaps a transcript without coding annotation in the gene definition'. and this is further clarified in the document: ncRNA above refers to RNA without coding annotation. It does not mean that this is a RNA that will never be translated; it merely means that the user-selected gene annotation system was not able to give a coding sequence annotation. It could still code protein products and may have such annotations in future versions of gene annotation or in another gene annotation system. For example, BC039000 is regarded as ncRNA by ANNOVAR when using UCSC Known Gene annotation, but it is regarded as a protein-coding gene by ANNOVAR when using ENSEMBL annotation. \n\nIt is further clarified in the comments section as: ncRNA does NOT mean conventional non-coding RNA. It means a RNA without complete coding sequence, and it can be a coding RNA that is annotated incorrectly by RefSeq or other gene definition systems.
18520 synonym: "incomplete transcript variant" EXACT []
18521 xref: http://annovar.openbioinformatics.org/en/latest/user-guide/gene/
18522 is_a: SO:0001576 ! transcript_variant
18523 created_by: kareneilbeck
18524 creation_date: 2015-11-23T14:43:51Z
18525
18526 [Term]
18527 id: SO:0002076
18528 name: incomplete_transcript_3UTR_variant
18529 def: "A sequence variant that intersects the 3' UTR of an incompletely annotated transcript." [SO:ke]
18530 synonym: "ANNOVAR:ncRNA_UTR3" EXACT VAR [http://annovar.openbioinformatics.org/en/latest/user-guide/gene/]
18531 synonym: "incomplete transcript 3UTR variant" RELATED []
18532 xref: http://annovar.openbioinformatics.org/en/latest/user-guide/gene/
18533 is_a: SO:0002075 ! incomplete_transcript_variant
18534 created_by: kareneilbeck
18535 creation_date: 2015-11-23T14:45:52Z
18536
18537 [Term]
18538 id: SO:0002077
18539 name: incomplete_transcript_5UTR_variant
18540 def: "A sequence variant that intersects the 5' UTR of an incompletely annotated transcript." [SO:ke]
18541 synonym: "ANNOVAR:ncRNA_UTR5" EXACT VAR [http://annovar.openbioinformatics.org/en/latest/user-guide/gene/]
18542 synonym: "incomplete transcript 5UTR variant" EXACT []
18543 xref: http://annovar.openbioinformatics.org/en/latest/user-guide/gene/
18544 is_a: SO:0002075 ! incomplete_transcript_variant
18545 created_by: kareneilbeck
18546 creation_date: 2015-11-24T12:39:17Z
18547
18548 [Term]
18549 id: SO:0002078
18550 name: incomplete_transcript_intronic_variant
18551 def: "A sequence variant that intersects the intron of an incompletely annotated transcript." [SO:ke]
18552 synonym: "incomplete transcript intronic variant" EXACT []
18553 is_a: SO:0002075 ! incomplete_transcript_variant
18554 created_by: kareneilbeck
18555 creation_date: 2015-11-24T12:51:45Z
18556
18557 [Term]
18558 id: SO:0002079
18559 name: incomplete_transcript_splice_region_variant
18560 def: "A sequence variant that intersects the splice region of an incompletely annotated transcript." [SO:ke]
18561 synonym: "incomplete transcript splice region variant" EXACT []
18562 is_a: SO:0002075 ! incomplete_transcript_variant
18563 created_by: kareneilbeck
18564 creation_date: 2015-11-24T12:52:06Z
18565
18566 [Term]
18567 id: SO:0002080
18568 name: incomplete_transcript_exonic_variant
18569 def: "A sequence variant that intersects the exon of an incompletely annotated transcript." [SO:ke]
18570 synonym: "incomplete transcript exonic variant" EXACT []
18571 is_a: SO:0002075 ! incomplete_transcript_variant
18572 created_by: kareneilbeck
18573 creation_date: 2015-11-24T12:52:10Z
18574
18575 [Term]
18576 id: SO:0002081
18577 name: incomplete_transcript_CDS
18578 def: "A sequence variant that intersects the coding regions of an incompletely annotated transcript." [SO:ke]
18579 synonym: "Seattleseq:coding-notMod3" EXACT VAR []
18580 synonym: "Seattleseq:coding-unknown" EXACT VAR []
18581 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
18582 is_a: SO:0002075 ! incomplete_transcript_variant
18583 created_by: kareneilbeck
18584 creation_date: 2015-11-24T15:32:27Z
18585
18586 [Term]
18587 id: SO:0002082
18588 name: incomplete_transcript_coding_splice_variant
18589 def: "A sequence variant that intersects the coding sequence near a splice region of an incompletely annotated transcript." [SO:ke]
18590 synonym: "incomplete transcript coding splice variant" EXACT []
18591 synonym: "Seattleseq:coding-notMod3-near-splice" EXACT VAR []
18592 synonym: "Seattleseq:coding-unknown-near-splice" EXACT VAR []
18593 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
18594 is_a: SO:0002079 ! incomplete_transcript_splice_region_variant
18595 created_by: kareneilbeck
18596 creation_date: 2015-11-24T15:51:06Z
18597
18598 [Term]
18599 id: SO:0002083
18600 name: 2KB_downstream_variant
18601 def: "A sequence variant located within 2KB 3' of a gene." [SO:ke]
18602 synonym: "Seattleseq:near-gene-3" EXACT VAR []
18603 xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq"
18604 is_a: SO:0001632 ! downstream_gene_variant
18605 created_by: kareneilbeck
18606 creation_date: 2015-11-24T15:55:49Z
18607
18608 [Term]
18609 id: SO:0002084
18610 name: exonic_splice_region_variant
18611 def: "A sequence variant in which a change has occurred within the exonic region of the splice site, 1-2 bases from boundary." [SO:ke]
18612 synonym: "ANNOVAR:exonic;splicing" EXACT VAR []
18613 synonym: "exonic splice region variant" EXACT []
18614 synonym: "Seattleseq:coding-near-splice" RELATED VAR []
18615 is_a: SO:0001630 ! splice_region_variant
18616 created_by: kareneilbeck
18617 creation_date: 2015-12-01T14:38:47Z
18618
18619 [Term]
18620 id: SO:0002085
18621 name: unidirectional_gene_fusion
18622 def: "A sequence variant whereby two genes, on the same strand have become joined." [SO:ke]
18623 comment: Requested by SNPEFF team. Feb 2016.
18624 synonym: "unidirectional gene fusion" EXACT []
18625 is_a: SO:0001565 ! gene_fusion
18626 created_by: kareneilbeck
18627 creation_date: 2016-02-23T12:16:48Z
18628
18629 [Term]
18630 id: SO:0002086
18631 name: bidirectional_gene_fusion
18632 def: "A sequence variant whereby two genes, on alternate strands have become joined." [SO:ke]
18633 comment: Requested by SNPEFF team. Feb 2016.
18634 synonym: "bidirectional gene fusion" EXACT []
18635 is_a: SO:0001565 ! gene_fusion
18636 created_by: kareneilbeck
18637 creation_date: 2016-02-23T12:17:18Z
18638
18639 [Term]
18640 id: SO:0002087
18641 name: pseudogenic_CDS
18642 def: "A non functional descendant of the coding portion of a coding transcript, part of a pseudogene." [SO:ke]
18643 synonym: "pseudogenic CDS" EXACT []
18644 is_a: SO:0000462 ! pseudogenic_region
18645 relationship: part_of SO:0000516 ! pseudogenic_transcript
18646 created_by: kareneilbeck
18647 creation_date: 2016-02-29T12:58:52Z
18648
18649 [Term]
18650 id: SO:0002088
18651 name: non_coding_transcript_splice_region_variant
18652 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]
18653 synonym: "ANNOVAR:ncRNA_splicing" NARROW []
18654 is_a: SO:0001619 ! non_coding_transcript_variant
18655 is_a: SO:0001630 ! splice_region_variant
18656 created_by: kareneilbeck
18657 creation_date: 2016-03-07T09:40:46Z
18658
18659 [Term]
18660 id: SO:0002089
18661 name: 3_prime_UTR_exon_variant
18662 def: "A UTR variant of exonic sequence of the 3' UTR." [SO:ke]
18663 comment: Requested by visze github tracker ID 346.
18664 synonym: "3 prime UTR exon variant" EXACT []
18665 is_a: SO:0001624 ! 3_prime_UTR_variant
18666 created_by: kareneilbeck
18667 creation_date: 2016-03-07T10:37:04Z
18668
18669 [Term]
18670 id: SO:0002090
18671 name: 3_prime_UTR_intron_variant
18672 def: "A UTR variant of intronic sequence of the 3' UTR." [SO:ke]
18673 comment: Requested by visze github tracker ID 346.
18674 synonym: "3 prime UTR intron variant" EXACT []
18675 is_a: SO:0001624 ! 3_prime_UTR_variant
18676 is_a: SO:0001969 ! coding_transcript_intron_variant
18677 created_by: kareneilbeck
18678 creation_date: 2016-03-07T10:37:41Z
18679
18680 [Term]
18681 id: SO:0002091
18682 name: 5_prime_UTR_intron_variant
18683 def: "A UTR variant of intronic sequence of the 5' UTR." [SO:ke]
18684 comment: Requested by visze github tracker ID 346.
18685 synonym: "5 prime UTR intron variant" EXACT []
18686 is_a: SO:0001623 ! 5_prime_UTR_variant
18687 is_a: SO:0001969 ! coding_transcript_intron_variant
18688 created_by: kareneilbeck
18689 creation_date: 2016-03-07T10:38:04Z
18690
18691 [Term]
18692 id: SO:0002092
18693 name: 5_prime_UTR_exon_variant
18694 def: "A UTR variant of exonic sequence of the 5' UTR." [SO:ke]
18695 comment: Requested by visze github tracker ID 346.
18696 synonym: "5 prime UTR exon variant" EXACT []
18697 is_a: SO:0001623 ! 5_prime_UTR_variant
18698 created_by: kareneilbeck
18699 creation_date: 2016-03-07T10:38:26Z
18700
18701 [Term]
18702 id: SO:0002093
18703 name: structural_interaction_variant
18704 def: "A variant that impacts the internal interactions of the resulting polypeptide structure." [SO:ke]
18705 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.
18706 synonym: "structural interaction variant" EXACT []
18707 is_a: SO:0001599 ! 3D_polypeptide_structure_variant
18708 created_by: kareneilbeck
18709 creation_date: 2016-03-07T11:43:55Z
18710
18711 [Term]
18712 id: SO:0002094
18713 name: non_allelic_homologous_recombination_region
18714 def: "A genomic region at a non-allelic position where exchange of genetic material happens as a result of homologous recombination." []
18715 synonym: "NAHRR" EXACT []
18716 synonym: "non allelic homologous recombination region" EXACT []
18717 is_a: SO:0000339 ! recombination_hotspot
18718 created_by: nicole
18719 creation_date: 2016-05-17T13:34:12Z
18720
18721 [Term]
18722 id: SO:0002095
18723 name: scaRNA
18724 def: "A ncRNA, specific to the Cajal body, that has been demonstrated to function as a guide RNA in the site-specific synthesis of 2'-O-ribose-methylated nucleotides and pseudouridines in the RNA polymerase II-transcribed U1, U2, U4 and U5 spliceosomal small nuclear RNAs (snRNAs)." [PMC:126017, SO:nrs]
18725 synonym: "small Cajal body specific RNA" EXACT []
18726 synonym: "small Cajal body-specific RNA" EXACT []
18727 xref: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC126017/
18728 is_a: SO:0000655 ! ncRNA
18729 created_by: nicole
18730 creation_date: 2016-05-19T13:42:45Z
18731
18732 [Term]
18733 id: SO:0002096
18734 name: short_tandem_repeat_variation
18735 def: "A kind of sequence variant whereby a tandem repeat is expanded or contracted with regard to a reference." [SO:ke]
18736 synonym: "str variation" RELATED []
18737 is_a: SO:0000248 ! sequence_length_variation
18738 created_by: kareneilbeck
18739 creation_date: 2016-07-14T16:04:40Z
18740
18741 [Term]
18742 id: SO:0002097
18743 name: vertebrate_immune_system_pseudogene
18744 def: "A pseudogene derived from a vertebrate immune system gene." [SO:ke]
18745 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
18746 synonym: "vertebrate immune system pseudogene" EXACT []
18747 is_a: SO:0000336 ! pseudogene
18748 created_by: kareneilbeck
18749 creation_date: 2016-07-15T16:00:22Z
18750
18751 [Term]
18752 id: SO:0002098
18753 name: immunoglobulin_pseudogene
18754 def: "A pseudogene derived from an immunoglobulin gene." [SO:ke]
18755 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
18756 synonym: "immunoglobulin pseudogene" EXACT []
18757 is_a: SO:0002097 ! vertebrate_immune_system_pseudogene
18758 created_by: kareneilbeck
18759 creation_date: 2016-07-15T16:01:47Z
18760
18761 [Term]
18762 id: SO:0002099
18763 name: T_cell_receptor_pseudogene
18764 def: "A pseudogene derived from a T-cell receptor gene." [SO:ke]
18765 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
18766 is_a: SO:0002097 ! vertebrate_immune_system_pseudogene
18767 created_by: kareneilbeck
18768 creation_date: 2016-07-15T16:02:18Z
18769
18770 [Term]
18771 id: SO:0002100
18772 name: IG_C_pseudogene
18773 def: "A pseudogenic constant region of an immunoglobulin gene which closely resembles a known functional Imunoglobulin constant gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
18774 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
18775 synonym: "IG C pseudogene" EXACT []
18776 is_a: SO:0002098 ! immunoglobulin_pseudogene
18777 created_by: kareneilbeck
18778 creation_date: 2016-07-15T16:05:08Z
18779
18780 [Term]
18781 id: SO:0002101
18782 name: IG_J_pseudogene
18783 def: "A pseudogenic joining region which closely resembles a known functional imunoglobulin joining gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
18784 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
18785 synonym: "IG J pseudogene" EXACT []
18786 is_a: SO:0002098 ! immunoglobulin_pseudogene
18787 created_by: kareneilbeck
18788 creation_date: 2016-07-15T16:05:34Z
18789
18790 [Term]
18791 id: SO:0002102
18792 name: IG_V_pseudogene
18793 def: "A pseudogenic variable region which closely resembles a known functional imunoglobulin variable gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the variable region of an immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
18794 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
18795 synonym: "IG V pseudogene" EXACT []
18796 is_a: SO:0002098 ! immunoglobulin_pseudogene
18797 created_by: kareneilbeck
18798 creation_date: 2016-07-15T16:05:56Z
18799
18800 [Term]
18801 id: SO:0002103
18802 name: TR_V_pseudogene
18803 def: "A pseudogenic variable region which closely resembles a known functional T receptor variable gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the variable region of an immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
18804 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
18805 synonym: "TR V pseudogene" EXACT []
18806 is_a: SO:0002099 ! T_cell_receptor_pseudogene
18807 created_by: kareneilbeck
18808 creation_date: 2016-07-15T16:06:29Z
18809
18810 [Term]
18811 id: SO:0002104
18812 name: TR_J_pseudogene
18813 def: "A pseudogenic joining region which closely resembles a known functional T receptor (TR) joining gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
18814 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
18815 synonym: "TR J pseudogene" EXACT []
18816 is_a: SO:0002099 ! T_cell_receptor_pseudogene
18817 created_by: kareneilbeck
18818 creation_date: 2016-07-15T16:06:51Z
18819
18820 [Term]
18821 id: SO:0002105
18822 name: translated_processed_pseudogene
18823 def: "A processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
18824 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
18825 synonym: "translated processed pseudogene" EXACT []
18826 is_a: SO:0000043 ! processed_pseudogene
18827 created_by: kareneilbeck
18828 creation_date: 2016-07-18T12:31:53Z
18829
18830 [Term]
18831 id: SO:0002106
18832 name: translated_unprocessed_pseudogene
18833 def: "A non-processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
18834 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
18835 synonym: "translated unprocessed pseudogene" EXACT []
18836 is_a: SO:0001760 ! non_processed_pseudogene
18837 created_by: kareneilbeck
18838 creation_date: 2016-07-18T12:34:42Z
18839
18840 [Term]
18841 id: SO:0002107
18842 name: transcribed_unprocessed_pseudogene
18843 def: "A unprocessed pseudogene supported by locus-specific evidence of transcription." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
18844 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
18845 synonym: "transcribed unprocessed pseudogene" EXACT []
18846 is_a: SO:0001760 ! non_processed_pseudogene
18847 created_by: kareneilbeck
18848 creation_date: 2016-07-18T12:41:53Z
18849
18850 [Term]
18851 id: SO:0002108
18852 name: transcribed_unitary_pseudogene
18853 def: "A species specific unprocessed pseudogene without a parent gene, as it has an active orthologue in another species." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
18854 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
18855 synonym: "transcribed unitary pseudogene" EXACT []
18856 is_a: SO:0001759 ! unitary_pseudogene
18857 created_by: kareneilbeck
18858 creation_date: 2016-07-18T12:44:26Z
18859
18860 [Term]
18861 id: SO:0002109
18862 name: transcribed_processed_pseudogene
18863 def: "A processed_pseudogene overlapped by locus-specific evidence of transcription." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
18864 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
18865 synonym: "transcribed processed pseudogene" EXACT []
18866 is_a: SO:0000043 ! processed_pseudogene
18867 created_by: kareneilbeck
18868 creation_date: 2016-07-18T12:45:48Z
18869
18870 [Term]
18871 id: SO:0002110
18872 name: polymorphic_pseudogene_with_retained_intron
18873 def: "A polymorphic pseudogene in the reference genome, containing a retained intron, known to be intact in the genomes of other individuals of the same species. The annotation process has confirmed that the pseudogenisation event is not a genomic sequencing error." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
18874 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
18875 synonym: "polymorphic pseudogene with retained intron" EXACT []
18876 is_a: SO:0001841 ! polymorphic_pseudogene
18877 created_by: kareneilbeck
18878 creation_date: 2016-07-18T12:47:33Z
18879
18880 [Term]
18881 id: SO:0002111
18882 name: pseudogene_processed_transcript
18883 def: "A processed_transcript supported by EST and/or mRNA evidence that aligns unambiguously to a pseudogene locus (i.e. alignment to the pseudogene locus clearly better than alignment to parent locus)." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
18884 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
18885 synonym: "pseudogene processed transcript" EXACT []
18886 is_a: SO:0001503 ! processed_transcript
18887 created_by: kareneilbeck
18888 creation_date: 2016-07-18T14:07:00Z
18889
18890 [Term]
18891 id: SO:0002112
18892 name: coding_transcript_with_retained_intron
18893 def: "A protein coding transcript containing a retained intron." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
18894 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
18895 synonym: "mRNA with retained intron" RELATED []
18896 is_a: SO:0000120 ! protein_coding_primary_transcript
18897 created_by: kareneilbeck
18898 creation_date: 2016-07-18T14:09:49Z
18899
18900 [Term]
18901 id: SO:0002113
18902 name: lncRNA_with_retained_intron
18903 def: "A lncRNA transcript containing a retained intron." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
18904 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
18905 synonym: "lncRNA with retained intron" EXACT []
18906 synonym: "lncRNA_retained_intron" EXACT []
18907 is_a: SO:0002035 ! lncRNA_primary_transcript
18908 created_by: kareneilbeck
18909 creation_date: 2016-07-18T14:13:07Z
18910
18911 [Term]
18912 id: SO:0002114
18913 name: NMD_transcript
18914 def: "A protein coding transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon, making it susceptible to nonsense mediated decay." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
18915 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
18916 synonym: "NMD transcript" EXACT []
18917 synonym: "nonsense mediated decay transcript" EXACT []
18918 is_a: SO:0000120 ! protein_coding_primary_transcript
18919 created_by: kareneilbeck
18920 creation_date: 2016-07-18T14:16:13Z
18921
18922 [Term]
18923 id: SO:0002115
18924 name: pseudogenic_transcript_with_retained_intron
18925 def: "A transcript supported by EST and/or mRNA evidence that aligns unambiguously to the pseudogene locus; has retained intronic sequence compared to a reference transcript sequence." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
18926 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes.
18927 synonym: "pseudogene retained intron" EXACT []
18928 is_a: SO:0000185 ! primary_transcript
18929 created_by: kareneilbeck
18930 creation_date: 2016-07-18T14:19:04Z
18931
18932 [Term]
18933 id: SO:0002116
18934 name: polymorphic_pseudogene_processed_transcript
18935 def: "A processed transcript that does not contain a CDS that fullfills annotation criteria and not necessarily functionally non-coding." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
18936 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
18937 synonym: "polymorphic pseudogene processed transcript" EXACT []
18938 is_a: SO:0002111 ! pseudogene_processed_transcript
18939 created_by: kareneilbeck
18940 creation_date: 2016-07-18T14:23:59Z
18941
18942 [Term]
18943 id: SO:0002117
18944 name: <new term>
18945 is_obsolete: true
18946 created_by: kareneilbeck
18947 creation_date: 2016-07-18T14:27:21Z
18948
18949 [Term]
18950 id: SO:0002118
18951 name: NMD_polymorphic_pseudogene_transcript
18952 def: "A polymorphic pseudogene transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon. Premature stop codon is not introduced, directly or indirectly, as a result of the variation i.e. must be present in both protein_coding and pseudogenic alleles." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
18953 comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation.
18954 synonym: "NMD polymorphic pseudogene transcript" EXACT []
18955 synonym: "nonsense_mediated_decay_polymorphic_pseudogene" EXACT []
18956 is_a: SO:0002114 ! NMD_transcript
18957 created_by: kareneilbeck
18958 creation_date: 2016-07-18T14:28:02Z
18959
18960 [Term]
18961 id: SO:0002119
18962 name: allelic_frequency
18963 def: "A physical quality which inheres to the allele by virtue of the number instances of the allele within a population. This is the relative frequency of the allele at a given locus in a population." [SO:ke]
18964 comment: Requested by HL7 clinical genomics group.
18965 xref: WIKI:https\://en.wikipedia.org/wiki/Allele_frequency
18966 is_a: SO:0001763 ! variant_frequency
18967 created_by: kareneilbeck
18968 creation_date: 2016-07-21T11:58:55Z
18969
18970 [Term]
18971 id: SO:0002120
18972 name: 3_prime_overlapping_ncrna
18973 def: "Transcript where ditag (digital gene expression profiling)and/or published experimental data strongly supports the existence of short non-coding transcripts transcribed from the 3'UTR." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
18974 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes.
18975 synonym: "3'_overlapping_ncrna" EXACT []
18976 synonym: "3prime_overlapping_ncRNA" EXACT []
18977 synonym: "three prime overlapping noncoding rna" EXACT []
18978 is_a: SO:0000655 ! ncRNA
18979 created_by: nicole
18980 creation_date: 2016-08-23T15:48:21Z
18981
18982 [Term]
18983 id: SO:0002121
18984 name: vertebrate_immune_system_gene
18985 def: "The configuration of the IG and TR variable (V), diversity (D) and joining (J) germline genes before DNA rearrangements (with or without constant (C) genes in undefined configuration. (germline, non rearranged regions of the IG DNA loci)." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
18986 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
18987 synonym: "immune_gene" EXACT []
18988 is_a: SO:0000704 ! gene
18989 created_by: nicole
18990 creation_date: 2016-08-23T15:54:51Z
18991
18992 [Term]
18993 id: SO:0002122
18994 name: immunoglobulin_gene
18995 def: "A germline immunoglobulin gene." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
18996 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
18997 synonym: "All_IG_genes" EXACT []
18998 synonym: "IG_genes" EXACT []
18999 is_a: SO:0002121 ! vertebrate_immune_system_gene
19000 created_by: nicole
19001 creation_date: 2016-08-23T15:56:09Z
19002
19003 [Term]
19004 id: SO:0002123
19005 name: IG_C_gene
19006 def: "A constant (C) gene, a gene that codes the constant region of an immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19007 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19008 synonym: "IGC_gene" EXACT []
19009 synonym: "immunoglobulin_C_gene" EXACT []
19010 synonym: "Immunoglobulin_Constant_germline_Gene" EXACT []
19011 is_a: SO:0002122 ! immunoglobulin_gene
19012 created_by: nicole
19013 creation_date: 2016-08-23T15:57:29Z
19014
19015 [Term]
19016 id: SO:0002124
19017 name: IG_D_gene
19018 def: "A gene that rearranges at the DNA level and codes the diversity region of the variable domain of an immunoglobuin (IG) gene." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19019 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19020 synonym: "IGD_gene" EXACT []
19021 synonym: "immunoglobulin_D_gene" EXACT []
19022 synonym: "Immunoglobulin_Diversity_ gene" EXACT []
19023 is_a: SO:0002122 ! immunoglobulin_gene
19024 created_by: nicole
19025 creation_date: 2016-08-23T15:59:10Z
19026
19027 [Term]
19028 id: SO:0002125
19029 name: IG_J_gene
19030 def: "A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19031 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19032 synonym: "IG_joining_gene" EXACT []
19033 synonym: "immunoglobulin_J_gene" EXACT []
19034 synonym: "Immunoglobulin_Joining_Gene" EXACT []
19035 is_a: SO:0002122 ! immunoglobulin_gene
19036 created_by: nicole
19037 creation_date: 2016-08-23T16:00:36Z
19038
19039 [Term]
19040 id: SO:0002126
19041 name: IG_V_gene
19042 def: "A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of an Immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19043 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19044 synonym: "IG_variable_gene" EXACT []
19045 synonym: "IGV_gene" EXACT []
19046 synonym: "Immunoglobulin_variable_gene" EXACT []
19047 is_a: SO:0002122 ! immunoglobulin_gene
19048 created_by: nicole
19049 creation_date: 2016-08-23T16:02:09Z
19050
19051 [Term]
19052 id: SO:0002127
19053 name: lncRNA_gene
19054 def: "A gene that encodes a long non-coding RNA." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19055 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes.
19056 synonym: "lnc RNA gene" EXACT []
19057 synonym: "lnc_RNA_gene" EXACT []
19058 synonym: "long_non_coding_RNA_gene" EXACT []
19059 is_a: SO:0001263 ! ncRNA_gene
19060 created_by: nicole
19061 creation_date: 2016-08-23T16:03:33Z
19062
19063 [Term]
19064 id: SO:0002128
19065 name: mt_rRNA
19066 def: "Mitochondrial ribosomal RNA." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19067 synonym: "mitochondrial_rRNA" EXACT []
19068 synonym: "Mt_rRNA" EXACT []
19069 is_a: SO:0000252 ! rRNA
19070 created_by: nicole
19071 creation_date: 2016-08-23T16:08:59Z
19072
19073 [Term]
19074 id: SO:0002129
19075 name: mt_tRNA
19076 def: "Mitochondrial transfer RNA." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19077 synonym: "mitochondrial_tRNA" EXACT []
19078 synonym: "Mt_tRNA" EXACT []
19079 is_a: SO:0000253 ! tRNA
19080 created_by: nicole
19081 creation_date: 2016-08-23T16:10:17Z
19082
19083 [Term]
19084 id: SO:0002130
19085 name: NSD_transcript
19086 def: "A transcript that contains a CDS but has no stop codon before the polyA site is reached." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19087 synonym: "non_stop_decay_transcript" EXACT []
19088 is_a: SO:0000234 ! mRNA
19089 created_by: nicole
19090 creation_date: 2016-08-23T16:11:34Z
19091
19092 [Term]
19093 id: SO:0002131
19094 name: sense_intronic_ncRNA
19095 def: "A non-coding transcript found within an intron of a coding or non-coding gene, with no overlap of exonic sequence." [GENECODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19096 synonym: "sense_intronic" EXACT []
19097 synonym: "sense_intronic_non-coding_RNA" EXACT []
19098 is_a: SO:0000655 ! ncRNA
19099 created_by: nicole
19100 creation_date: 2016-08-23T16:15:02Z
19101
19102 [Term]
19103 id: SO:0002132
19104 name: sense_overlap_ncRNA
19105 def: "A non-coding transcript that contains a protein coding gene within its intronic sequence on the same strand, with no overlap of exonic sequence." [GENECODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19106 synonym: "sense_overlapping" EXACT []
19107 is_a: SO:0000655 ! ncRNA
19108 created_by: nicole
19109 creation_date: 2016-08-23T16:16:13Z
19110
19111 [Term]
19112 id: SO:0002133
19113 name: T_cell_receptor_gene
19114 def: "A T-cell receptor germline gene." []
19115 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19116 synonym: "TR_gene" EXACT []
19117 is_a: SO:0002121 ! vertebrate_immune_system_gene
19118 created_by: nicole
19119 creation_date: 2016-08-23T16:17:12Z
19120
19121 [Term]
19122 id: SO:0002134
19123 name: TR_C_Gene
19124 def: "A constant (C) gene, a gene that codes the constant region of a T-cell receptor chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19125 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19126 synonym: "T_cell_receptor_C_gene" EXACT []
19127 is_a: SO:0002133 ! T_cell_receptor_gene
19128 created_by: nicole
19129 creation_date: 2016-08-23T16:19:20Z
19130
19131 [Term]
19132 id: SO:0002135
19133 name: TR_D_Gene
19134 def: "A gene that rearranges at the DNA level and codes the diversity region of the variable domain of aT-cell receptor gene." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19135 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19136 synonym: "T_cell_receptor_D_gene" EXACT []
19137 is_a: SO:0002133 ! T_cell_receptor_gene
19138 created_by: nicole
19139 creation_date: 2016-08-23T16:20:06Z
19140
19141 [Term]
19142 id: SO:0002136
19143 name: TR_J_Gene
19144 def: "A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of aT-cell receptor chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19145 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19146 synonym: "T_cell_receptor_J_gene" EXACT []
19147 is_a: SO:0002133 ! T_cell_receptor_gene
19148 created_by: nicole
19149 creation_date: 2016-08-23T16:20:36Z
19150
19151 [Term]
19152 id: SO:0002137
19153 name: TR_V_Gene
19154 def: "A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of aT-cell receptor chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]
19155 comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
19156 synonym: "T_cell_receptor_V_gene" EXACT []
19157 is_a: SO:0002133 ! T_cell_receptor_gene
19158 created_by: nicole
19159 creation_date: 2016-08-23T16:21:04Z
19160
19161 [Term]
19162 id: SO:0002138
19163 name: predicted_transcript
19164 def: "A transcript feature that has been predicted but is not yet validated." [SO:ke]
19165 synonym: "predicted transcript" EXACT []
19166 is_a: SO:0000673 ! transcript
19167 created_by: nicole
19168 creation_date: 2016-08-23T16:27:38Z
19169
19170 [Term]
19171 id: SO:0002139
19172 name: unconfirmed_transcript
19173 def: "This is used for non-spliced EST clusters that have polyA features. This category has been specifically created for the ENCODE project to highlight regions that could indicate the presence of protein coding genes that require experimental validation, either by 5' RACE or RT-PCR to extend the transcripts, or by confirming expression of the putatively-encoded peptide with specific antibodies." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html]
19174 synonym: "TEC" EXACT []
19175 synonym: "to_be_experimentally_confirmed_transcript" EXACT []
19176 is_a: SO:0002138 ! predicted_transcript
19177 created_by: nicole
19178 creation_date: 2016-08-23T16:28:07Z
19179
19180 [Term]
19181 id: SO:0002140
19182 name: early_origin_of_replication
19183 def: "An origin of replication that initiates early in S phase." [PMID:23348837, PMID:9115207]
19184 synonym: "early origin" EXACT []
19185 synonym: "early origin of replication" EXACT []
19186 synonym: "early replication origin" EXACT []
19187 is_a: SO:0000296 ! origin_of_replication
19188 created_by: nicole
19189 creation_date: 2016-09-15T15:53:36Z
19190
19191 [Term]
19192 id: SO:0002141
19193 name: late_origin_of_replication
19194 def: "An origin of replication that initiates late in S phase." [PMID:23348837, PMID:9115207]
19195 synonym: "late origin" EXACT []
19196 synonym: "late origin of replication" EXACT []
19197 synonym: "late replication origin" EXACT []
19198 is_a: SO:0000296 ! origin_of_replication
19199 created_by: nicole
19200 creation_date: 2016-09-15T15:56:07Z
19201
19202 [Term]
19203 id: SO:0002142
19204 name: histone_2A_acetylation_site
19205 def: "A histone 2A modification where the modification is the acetylation of the residue." [ISBN:0815341059]
19206 synonym: "H2Aac" EXACT []
19207 synonym: "histone 2A acetylation site" EXACT []
19208 is_a: SO:0001702 ! histone_acetylation_site
19209 created_by: nicole
19210 creation_date: 2016-10-25T12:03:46Z
19211
19212 [Term]
19213 id: SO:0002143
19214 name: histone_2B_acetylation_site
19215 def: "A histone 2B modification where the modification is the acetylation of the residue." [ISBN:0815341059]
19216 synonym: "H2Bac" EXACT []
19217 synonym: "histone 2B acetylation site" EXACT []
19218 is_a: SO:0001702 ! histone_acetylation_site
19219 created_by: nicole
19220 creation_date: 2016-10-25T12:04:04Z
19221
19222 [Term]
19223 id: SO:0002144
19224 name: histone_2AZ_acetylation_site
19225 def: "A histone 2AZ modification where the modification is the acetylation of the residue." [PMID:19385636, PMID:24316985, PMID:27087541]
19226 synonym: "H2A.Zac" EXACT []
19227 synonym: "H2AZac" EXACT []
19228 synonym: "histone 2AZ acetylation site" EXACT []
19229 is_a: SO:0002142 ! histone_2A_acetylation_site
19230 created_by: nicole
19231 creation_date: 2016-10-25T14:11:49Z
19232
19233 [Term]
19234 id: SO:0002145
19235 name: H2AZK4_acetylation_site
19236 def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H2AZ histone protein is acetylated." [PMID:19385636, PMID:24316985, PMID:27087541]
19237 synonym: "H2A.ZK4ac" EXACT []
19238 synonym: "H2AZK4 acetylation site" EXACT []
19239 synonym: "H2AZK4ac" EXACT []
19240 is_a: SO:0002144 ! histone_2AZ_acetylation_site
19241 created_by: nicole
19242 creation_date: 2016-10-25T14:19:43Z
19243
19244 [Term]
19245 id: SO:0002146
19246 name: H2AZK7_acetylation_site
19247 def: "A kind of histone modification site, whereby the 7th residue (a lysine), from the start of the H2AZ histone protein is acetylated." [PMID:19385636, PMID:24316985, PMID:27087541]
19248 synonym: "H2A.ZK7ac" EXACT []
19249 synonym: "H2AZK7 acetylation site" EXACT []
19250 synonym: "H2AZK7ac" EXACT []
19251 is_a: SO:0002144 ! histone_2AZ_acetylation_site
19252 created_by: nicole
19253 creation_date: 2016-10-25T14:23:11Z
19254
19255 [Term]
19256 id: SO:0002147
19257 name: H2AZK11_acetylation_site
19258 def: "A kind of histone modification site, whereby the 11th residue (a lysine), from the start of the H2AZ histone protein is acetylated." [PMID:19385636, PMID:24316985, PMID:27087541]
19259 synonym: "H2A.ZK11ac" EXACT []
19260 synonym: "H2AZK11 acetylation site" EXACT []
19261 synonym: "H2AZK11ac" EXACT []
19262 is_a: SO:0002144 ! histone_2AZ_acetylation_site
19263 created_by: nicole
19264 creation_date: 2016-10-25T14:23:31Z
19265
19266 [Term]
19267 id: SO:0002148
19268 name: H2AZK13_acetylation_site
19269 def: "A kind of histone modification site, whereby the 13th residue (a lysine), from the start of the H2AZ histone protein is acetylated." [PMID:19385636, PMID:24316985, PMID:27087541]
19270 synonym: "H2A.ZK13ac" EXACT []
19271 synonym: "H2AZK13 acetylation site" EXACT []
19272 synonym: "H2AZK13ac" EXACT []
19273 is_a: SO:0002144 ! histone_2AZ_acetylation_site
19274 created_by: nicole
19275 creation_date: 2016-10-25T14:23:50Z
19276
19277 [Term]
19278 id: SO:0002149
19279 name: H2AZK15_acetylation_site
19280 def: "A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2AZ histone protein is acetylated." [PMID:19385636, PMID:24316985, PMID:27087541]
19281 synonym: "H2A.ZK15ac" EXACT []
19282 synonym: "H2AZK15 acetylation site" EXACT []
19283 synonym: "H2AZK15ac" EXACT []
19284 is_a: SO:0002144 ! histone_2AZ_acetylation_site
19285 created_by: nicole
19286 creation_date: 2016-10-25T14:24:08Z
19287
19288 [Term]
19289 id: SO:0002150
19290 name: AUG_initiated_uORF
19291 def: "A uORF beginning with the canonical start codon AUG." [PMID:26684391, PMID:27313038]
19292 synonym: "AUG initiated uORF" EXACT []
19293 is_a: SO:0002027 ! uORF
19294 created_by: nicole
19295 creation_date: 2016-10-26T09:37:11Z
19296
19297 [Term]
19298 id: SO:0002151
19299 name: non_AUG_initiated_uORF
19300 def: "A uORF beginning with a codon other than AUG." [PMID:26684391, PMID:27313038]
19301 synonym: "non AUG initiated uORF" EXACT []
19302 is_a: SO:0002027 ! uORF
19303 created_by: nicole
19304 creation_date: 2016-10-26T09:37:45Z
19305
19306 [Term]
19307 id: SO:0002152
19308 name: genic_downstream_transcript_variant
19309 def: "A variant that falls downstream of a transcript, but within the genic region of the gene due to alternately transcribed isoforms." [NCBI:dm, SO:ke]
19310 synonym: "genic 3 prime transcript variant" EXACT []
19311 synonym: "genic 3' transcript variant" EXACT []
19312 synonym: "genic downstream transcript variant" EXACT []
19313 is_a: SO:0001564 ! gene_variant
19314 created_by: nicole
19315 creation_date: 2016-10-28T10:20:55Z
19316
19317 [Term]
19318 id: SO:0002153
19319 name: genic_upstream_transcript_variant
19320 def: "A variant that falls upstream of a transcript, but within the genic region of the gene due to alternately transcribed isoforms." [NCBI:dm, SO:ke]
19321 synonym: "genic 5 prime transcript variant" EXACT []
19322 synonym: "genic 5' transcript variant" EXACT []
19323 synonym: "genic upstream transcript variant" EXACT []
19324 is_a: SO:0001564 ! gene_variant
19325 created_by: nicole
19326 creation_date: 2016-10-28T10:23:17Z
19327
19328 [Term]
19329 id: SO:0002154
19330 name: mitotic_recombination_region
19331 def: "A genomic region where there is an exchange of genetic material with another genomic region, occurring in somatic cells." [NCBI:cf, SO:ke]
19332 synonym: "mitotic recombination region" EXACT []
19333 is_a: SO:0000298 ! recombination_feature
19334 created_by: nicole
19335 creation_date: 2016-10-28T10:33:54Z
19336
19337 [Term]
19338 id: SO:0002155
19339 name: meiotic_recombination_region
19340 def: "A genomic region in which there is an exchange of genetic material as a result of the repair of meiosis-specific double strand breaks that occur during meiotic prophase." [NCBI:cf, SO:ke]
19341 synonym: "meiotic recombination region" EXACT []
19342 is_a: SO:0000298 ! recombination_feature
19343 created_by: nicole
19344 creation_date: 2016-10-28T10:34:55Z
19345
19346 [Term]
19347 id: SO:0002156
19348 name: CArG_box
19349 def: "A promoter element bound by the MADS family of transcription factors with consensus 5'-(C/T)TA(T/A)4TA(G/A)-3'." [PMID:1748287, PMID:7623803]
19350 comment: Requested by Antonia Lock
19351 synonym: "CArG box" EXACT []
19352 is_a: SO:0001659 ! promoter_element
19353 created_by: nicole
19354 creation_date: 2016-10-28T10:42:06Z
1818719355
1818819356 [Term]
1818919357 id: SO:0005836
1871419882 [Term]
1871519883 id: SO:1000032
1871619884 name: indel
18717 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]
19885 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]
1871819886 comment: Indels can have a different number of bases than the corresponding reference sequence.
1871919887 xref: http://en.wikipedia.org/wiki/Indel "wiki"
1872019888 xref: loinc:LA9659-9 "Insertion and Deletion"
1880519973 [Term]
1880619974 id: SO:1000044
1880719975 name: chromosomal_translocation
18808 def: "An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]
19976 def: "A chromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]
1880919977 synonym: "(Drosophila)T" RELATED []
1881019978 synonym: "(fungi)T" RELATED []
1881119979 synonym: "chromosomal translocation" EXACT []
1966220830 name: cyclic_translocation
1966320831 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]
1966420832 synonym: "cyclic translocation" EXACT []
19665 is_a: SO:0002060 ! interchomosomal_translocation
20833 is_a: SO:0002060 ! interchromosomal_translocation
1966620834
1966720835 [Term]
1966820836 id: SO:1000151
1982420992 name: chromosome_number_variation
1982520993 def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]
1982620994 synonym: "chromosome number variation" EXACT []
20995 synonym: "Jannovar:chromosome_number_variation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html]
1982720996 is_a: SO:0000240 ! chromosome_variation
1982820997
1982920998 [Term]
1983020999 id: SO:1000183
1983121000 name: chromosome_structure_variation
1983221001 synonym: "chromosome structure variation" EXACT []
21002 synonym: "snpEff:CHROMOSOME_LARGE_DELETION" EXACT VAR []
21003 xref: http://snpeff.sourceforge.net/SnpEff_manual.html
1983321004 is_a: SO:0000240 ! chromosome_variation
1983421005
1983521006 [Term]
2019321364 [Term]
2019421365 id: SO:1001287
2019521366 name: distant_three_prime_recoding_signal
20196 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]
21367 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]
2019721368 synonym: "distant three prime recoding signal" EXACT []
2019821369 is_a: SO:1001277 ! three_prime_recoding_site
2019921370
+156
-19
gtdata/obo_files/sofa.obo less more
11 subsetdef: biosapiens "biosapiens protein feature ontology"
22 subsetdef: DBVAR "database of genomic structural variation"
33 subsetdef: SOFA "SO feature annotation"
4 synonymtypedef: aa1 "amino acid 1 letter code"
5 synonymtypedef: aa3 "amino acid 3 letter code"
6 synonymtypedef: AAMOD "amino acid modification"
7 synonymtypedef: BS "biosapiens"
8 synonymtypedef: dbsnp "dbsnp variant terms"
9 synonymtypedef: dbvar "DBVAR"
10 synonymtypedef: ebi_variants "ensembl variant terms"
4 synonymtypedef: aa1 "amino acid 1 letter code"
5 synonymtypedef: aa3 "amino acid 3 letter code"
6 synonymtypedef: AAMOD "amino acid modification"
7 synonymtypedef: BS "biosapiens"
8 synonymtypedef: dbsnp "dbsnp variant terms"
9 synonymtypedef: dbvar "DBVAR"
10 synonymtypedef: ebi_variants "ensembl variant terms"
1111 synonymtypedef: RNAMOD "RNA modification" EXACT
12 synonymtypedef: VAR "variant annotation term"
13 ontology: so-xp/subsets/SOFA
12 synonymtypedef: VAR "variant annotation term"
13 ontology: so/subsets/SOFA
1414
1515 [Term]
1616 id: SO:0000000
2727 subset: SOFA
2828 synonym: "sequence" EXACT []
2929 is_a: SO:0000110 ! sequence_feature
30 disjoint_from: SO:0000699 ! junction
3130
3231 [Term]
3332 id: SO:0000004
4342 namespace: sequence
4443 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]
4544 subset: SOFA
45 synonym: "INSDC_feature:repeat_region" BROAD []
46 synonym: "INSDC_qualifier:satellite" EXACT []
4647 synonym: "satellite DNA" EXACT []
4748 xref: http://en.wikipedia.org/wiki/Satellite_DNA "wiki"
4849 is_a: SO:0000705 ! tandem_repeat
7778 namespace: sequence
7879 def: "A small non coding RNA sequence, present in the cytoplasm." [SO:ke]
7980 subset: SOFA
81 synonym: "INSDC_feature:ncRNA" BROAD []
82 synonym: "INSDC_qualifier:scRNA" EXACT []
8083 synonym: "small cytoplasmic RNA" EXACT []
8184 is_a: SO:0000655 ! ncRNA
8285 relationship: derives_from SO:0000483 ! nc_primary_transcript
184187 namespace: sequence
185188 def: "Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]
186189 subset: SOFA
190 synonym: "INSDC_feature:misc_feature" EXACT []
191 synonym: "INSDC_note:other" EXACT []
192 synonym: "INSDC_note:sequence_feature" EXACT []
187193 synonym: "located sequence feature" RELATED []
188194 synonym: "located_sequence_feature" EXACT []
189195 synonym: "sequence feature" EXACT []
241247 namespace: sequence
242248 def: "Region in mRNA where ribosome assembles." [SO:ke]
243249 subset: SOFA
250 synonym: "INSDC_feature:regulatory" BROAD []
251 synonym: "INSDC_qualifier:ribosome_binding_site" EXACT []
244252 synonym: "ribosome entry site" EXACT []
245253 is_a: SO:0000836 ! mRNA_region
246254 relationship: part_of SO:0000204 ! five_prime_UTR
252260 def: "A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as]
253261 subset: SOFA
254262 synonym: "attenuator sequence" EXACT []
263 synonym: "INSDC_feature:regulatory" BROAD []
264 synonym: "INSDC_qualifier:attenuator" EXACT []
255265 xref: http://en.wikipedia.org/wiki/Attenuator "wiki"
256266 is_a: SO:0005836 ! regulatory_region
257267 relationship: part_of SO:0000234 ! mRNA
262272 namespace: sequence
263273 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]
264274 subset: SOFA
275 synonym: "INSDC_feature:regulatory" BROAD []
276 synonym: "INSDC_qualifier:terminator" EXACT []
265277 synonym: "terminator sequence" EXACT []
266278 xref: http://en.wikipedia.org/wiki/Terminator_(genetics) "wiki"
267279 is_a: SO:0001679 ! transcription_regulatory_region
283295 def: "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]
284296 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
285297 subset: SOFA
298 synonym: "INSDC_feature:exon" EXACT []
286299 xref: http://en.wikipedia.org/wiki/Exon "wiki"
287300 is_a: SO:0000833 ! transcript_region
288301
322335 namespace: sequence
323336 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]
324337 subset: SOFA
325 xref: http:http://en.wikipedia.org/wiki/Clone_(genetics) "wiki"
338 xref: http:http\://en.wikipedia.org/wiki/Clone_(genetics) "wiki"
326339 is_a: SO:0000695 ! reagent
327340
328341 [Term]
397410 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]
398411 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.
399412 subset: SOFA
413 synonym: "INSDC_feature:regulatory" BROAD []
414 synonym: "INSDC_qualifier:enhancer" EXACT []
400415 xref: http://en.wikipedia.org/wiki/Enhancer_(genetics) "wiki"
401416 is_a: SO:0000727 ! CRM
402417
407422 def: "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]
408423 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.
409424 subset: SOFA
425 synonym: "INSDC_feature:regulatory" BROAD []
426 synonym: "INSDC_qualifier:promoter" EXACT []
410427 synonym: "promoter sequence" EXACT []
411428 xref: http://en.wikipedia.org/wiki/Promoter "wiki"
412429 is_a: SO:0001055 ! transcriptional_cis_regulatory_region
427444 def: "A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma]
428445 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
429446 subset: SOFA
447 synonym: "INSDC_feature:operon" EXACT []
430448 xref: http://en.wikipedia.org/wiki/Operon "wiki"
431449 is_a: SO:0005855 ! gene_group
432450
467485 namespace: sequence
468486 def: "A transcript that in its initial state requires modification to be functional." [SO:ma]
469487 subset: SOFA
488 synonym: "INSDC_feature:precursor_RNA" EXACT []
489 synonym: "INSDC_feature:prim_transcript" EXACT []
470490 synonym: "precursor RNA" EXACT []
471491 synonym: "primary transcript" EXACT []
472492 xref: http://en.wikipedia.org/wiki/Primary_transcript "wiki"
487507 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]
488508 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
489509 subset: SOFA
510 synonym: "INSDC_feature:intron" EXACT []
490511 xref: http://en.wikipedia.org/wiki/Intron "wiki"
491512 is_a: SO:0000835 ! primary_transcript_region
492513
568589 synonym: "5' UTR" EXACT []
569590 synonym: "five prime UTR" EXACT []
570591 synonym: "five_prime_untranslated_region" EXACT []
592 synonym: "INSDC_feature:5'UTR" EXACT []
571593 xref: http://en.wikipedia.org/wiki/5'_UTR "wiki"
572594 is_a: SO:0000203 ! UTR
573595
577599 namespace: sequence
578600 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]
579601 subset: SOFA
602 synonym: "INSDC_feature:3'UTR" EXACT []
580603 synonym: "three prime untranslated region" EXACT []
581604 synonym: "three prime UTR" EXACT []
582605 xref: http://en.wikipedia.org/wiki/Three_prime_untranslated_region "wiki"
611634 def: "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]
612635 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.
613636 subset: SOFA
637 synonym: "INSDC_feature:mRNA" EXACT []
614638 synonym: "messenger RNA" EXACT []
639 synonym: "protein_coding_transcript" EXACT []
615640 xref: http://en.wikipedia.org/wiki/MRNA "wiki"
641 xref: http://www.gencodegenes.org/gencode_biotypes.html "GENCODE"
616642 is_a: SO:0000233 ! mature_transcript
617643
618644 [Term]
651677 namespace: sequence
652678 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]
653679 subset: SOFA
680 synonym: "INSDC_feature:rRNA" EXACT []
681 synonym: "INSDC_qualifier:unknown" BROAD []
654682 synonym: "ribosomal ribonucleic acid" EXACT []
655683 synonym: "ribosomal RNA" EXACT []
656684 xref: http://en.wikipedia.org/wiki/RRNA "wiki"
664692 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]
665693 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
666694 subset: SOFA
695 synonym: "INSDC_feature:tRNA" EXACT []
696 synonym: "INSDC_qualifier:unknown" BROAD []
667697 synonym: "transfer ribonucleic acid" RELATED []
668698 synonym: "transfer RNA" RELATED []
669699 xref: http://en.wikipedia.org/wiki/TRNA "wiki"
677707 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]
678708 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
679709 subset: SOFA
710 synonym: "INSDC_feature:ncRNA" BROAD []
711 synonym: "INSDC_qualifier:snRNA" EXACT []
680712 synonym: "small nuclear RNA" EXACT []
681713 xref: http://en.wikipedia.org/wiki/SnRNA "wiki"
682714 is_a: SO:0000655 ! ncRNA
688720 namespace: sequence
689721 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]
690722 subset: SOFA
723 synonym: "INSDC_feature:ncRNA" BROAD []
724 synonym: "INSDC_qualifier:snoRNA" EXACT []
691725 synonym: "small nucleolar RNA" EXACT []
692726 xref: http://en.wikipedia.org/wiki/SnoRNA "wiki"
693727 is_a: SO:0000655 ! ncRNA
700734 alt_id: SO:0000649
701735 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]
702736 subset: SOFA
737 synonym: "INSDC_feature:ncRNA" BROAD []
738 synonym: "INSDC_qualifier:miRNA" EXACT []
703739 synonym: "micro RNA" EXACT []
704740 synonym: "microRNA" EXACT []
705741 synonym: "small temporal RNA" EXACT []
715751 namespace: sequence
716752 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]
717753 subset: SOFA
754 synonym: "INSDC_feature:repeat_region" BROAD []
755 synonym: "INSDC_qualifier:microsatellite" EXACT []
718756 synonym: "microsatellite locus" EXACT []
719757 synonym: "microsatellite marker" EXACT []
720 synonym: "VNTR" EXACT []
758 synonym: "short tandem repeat" EXACT []
759 synonym: "STR" EXACT [http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9651/]
721760 xref: http://en.wikipedia.org/wiki/Microsatellite "wiki"
722761 is_a: SO:0000005 ! satellite_DNA
723762
727766 namespace: sequence
728767 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]
729768 subset: SOFA
769 synonym: "INSDC_feature:repeat_region" BROAD []
770 synonym: "INSDC_qualifier:inverted" EXACT []
730771 synonym: "inverted repeat" EXACT []
731772 synonym: "inverted repeat sequence" EXACT []
732773 xref: http://en.wikipedia.org/wiki/Inverted_repeat "wiki"
736777 id: SO:0000296
737778 name: origin_of_replication
738779 namespace: sequence
739 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]
740 subset: SOFA
780 def: "A region of nucleic acid from which replication initiates; includes sequences that are recognized by replication proteins, the site from which the first separation of complementary strands occurs, and specific replication start sites." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, NCBI:cf]
781 subset: SOFA
782 synonym: "INSDC_feature:rep_origin" EXACT []
741783 synonym: "ori" EXACT []
742784 synonym: "origin of replication" EXACT []
743785 xref: http://en.wikipedia.org/wiki/Origin_of_replication "wiki"
759801 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]
760802 comment: Modified base:<modified_base>.
761803 subset: SOFA
804 synonym: "INSDC_feature:modified_base" EXACT []
762805 synonym: "modified base site" EXACT []
763806 is_a: SO:0001236 ! base
764807 is_a: SO:0001720 ! epigenetically_modified_region
790833 def: "A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA." [SO:ke]
791834 subset: SOFA
792835 synonym: "direct repeat" EXACT []
836 synonym: "INSDC_feature:repeat_region" BROAD []
837 synonym: "INSDC_qualifier:direct" EXACT []
793838 xref: http://en.wikipedia.org/wiki/Direct_repeat "wiki"
794839 is_a: SO:0000657 ! repeat_region
795840
799844 namespace: sequence
800845 def: "The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]
801846 subset: SOFA
847 synonym: "INSDC_feature:misc_feature" BROAD []
848 synonym: "INSDC_note:transcription_start_site" EXACT []
802849 synonym: "transcription start site" EXACT []
803850 synonym: "transcription_start_site" EXACT []
804851 is_a: SO:0000835 ! primary_transcript_region
811858 subset: SOFA
812859 synonym: "coding sequence" EXACT []
813860 synonym: "coding_sequence" EXACT []
861 synonym: "INSDC_feature:CDS" EXACT []
814862 is_a: SO:0000836 ! mRNA_region
815863
816864 [Term]
868916 def: "Region of sequence similarity by descent from a common ancestor." [SO:ke]
869917 subset: SOFA
870918 synonym: "conserved region" EXACT []
919 synonym: "INSDC_feature:misc_feature" BROAD []
920 synonym: "INSDC_note:conserved_region" EXACT []
871921 xref: http://en.wikipedia.org/wiki/Conserved_region "wiki"
872922 is_a: SO:0001410 ! experimental_feature
873923
877927 namespace: sequence
878928 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]
879929 subset: SOFA
930 synonym: "INSDC_feature:STS" EXACT []
880931 synonym: "sequence tag site" EXACT []
881932 is_a: SO:0000324 ! tag
882933
905956 namespace: sequence
906957 def: "Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke]
907958 subset: SOFA
959 synonym: "conserved non-coding element" EXACT []
960 synonym: "conserved non-coding sequence" EXACT []
908961 synonym: "nc conserved region" EXACT []
909962 synonym: "noncoding conserved region" EXACT []
910963 is_a: SO:0000330 ! conserved_region
915968 namespace: sequence
916969 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]
917970 subset: SOFA
971 synonym: "INSDC_feature:gene" BROAD []
972 synonym: "INSDC_qualifier:pseudo" EXACT []
973 synonym: "INSDC_qualifier:unknown" EXACT []
918974 xref: http://en.wikipedia.org/wiki/Pseudogene "wiki"
919975 is_a: SO:0001411 ! biological_region
920976 relationship: non_functional_homolog_of SO:0000704 ! gene
10111067 id: SO:0000360
10121068 name: codon
10131069 namespace: sequence
1014 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]
1070 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." [SO:ke]
10151071 subset: SOFA
10161072 xref: http://en.wikipedia.org/wiki/Codon "wiki"
10171073 is_a: SO:0000851 ! CDS_region
10381094 id: SO:0000370
10391095 name: small_regulatory_ncRNA
10401096 namespace: sequence
1041 def: "A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]
1097 def: "A non-coding RNA less than 200 nucleotides long, usually with a specific secondary structure, that acts to regulate gene expression. These include short ncRNAs such as piRNA, miRNA and siRNAs (among others)." [PMID:28541282, PomBase:al, SO:ma]
10421098 subset: SOFA
10431099 synonym: "small regulatory ncRNA" EXACT []
10441100 is_a: SO:0000655 ! ncRNA
10591115 namespace: sequence
10601116 def: "An RNA with catalytic activity." [SO:ma]
10611117 subset: SOFA
1118 synonym: "INSDC_feature:ncRNA" BROAD []
1119 synonym: "INSDC_qualifier:ribozyme" EXACT []
10621120 xref: http://en.wikipedia.org/wiki/Ribozyme "wiki"
10631121 is_a: SO:0000372 ! enzymatic_RNA
10641122
10821140 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]
10831141 subset: SOFA
10841142 synonym: "hammerhead ribozyme" EXACT []
1143 synonym: "INSDC_feature:ncRNA" BROAD []
1144 synonym: "INSDC_qualifier:hammerhead_ribozyme" EXACT []
10851145 xref: http://en.wikipedia.org/wiki/Hammerhead_ribozyme "wiki"
10861146 is_a: SO:0000715 ! RNA_motif
10871147
10911151 namespace: sequence
10921152 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]
10931153 subset: SOFA
1154 synonym: "INSDC_feature:ncRNA" BROAD []
1155 synonym: "INSDC_qualifier:RNase_MRP_RNA" EXACT []
10941156 synonym: "RNase MRP RNA" EXACT []
10951157 is_a: SO:0000655 ! ncRNA
10961158
11001162 namespace: sequence
11011163 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]
11021164 subset: SOFA
1165 synonym: "INSDC_feature:ncRNA" BROAD []
1166 synonym: "INSDC_qualifier:RNase_P_RNA" EXACT []
11031167 synonym: "RNase P RNA" EXACT []
11041168 is_a: SO:0000655 ! ncRNA
11051169
11091173 namespace: sequence
11101174 def: "The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]
11111175 subset: SOFA
1176 synonym: "INSDC_feature:ncRNA" BROAD []
1177 synonym: "INSDC_qualifier:telomerase_RNA" EXACT []
11121178 synonym: "telomerase RNA" EXACT []
11131179 xref: http://en.wikipedia.org/wiki/Telomerase_RNA "wiki"
11141180 is_a: SO:0000655 ! ncRNA
12471313 namespace: sequence
12481314 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]
12491315 subset: SOFA
1316 synonym: "INSDC_feature:ncRNA" BROAD []
1317 synonym: "INSDC_qualifier:vault_RNA" EXACT []
12501318 synonym: "vault RNA" EXACT []
12511319 xref: http://en.wikipedia.org/wiki/Vault_RNA "wiki"
12521320 is_a: SO:0000655 ! ncRNA
12571325 namespace: sequence
12581326 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]
12591327 subset: SOFA
1328 synonym: "INSDC_feature:ncRNA" BROAD []
1329 synonym: "INSDC_qualifier:Y_RNA" EXACT []
12601330 synonym: "Y RNA" EXACT []
12611331 xref: http://en.wikipedia.org/wiki/Y_RNA "wiki"
12621332 is_a: SO:0000655 ! ncRNA
12821352 comment: See GO:0005488 : binding.
12831353 subset: biosapiens
12841354 subset: SOFA
1355 synonym: "binding site" EXACT []
12851356 synonym: "binding_or_interaction_site" EXACT []
1357 synonym: "INSDC_feature:misc_binding" EXACT []
12861358 synonym: "site" RELATED []
12871359 xref: http://en.wikipedia.org/wiki/Binding_site "wiki"
12881360 is_a: SO:0001411 ! biological_region
12941366 def: "A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]
12951367 comment: See GO:0042277 : peptide binding.
12961368 subset: SOFA
1369 synonym: "INSDC_feature:protein_bind" EXACT []
12971370 synonym: "protein binding site" EXACT []
12981371 is_a: SO:0000409 ! binding_site
12991372
13131386 namespace: sequence
13141387 def: "A region where the sequence differs from that of a specified sequence." [SO:ke]
13151388 subset: SOFA
1389 synonym: "INSDC_feature:misc_difference" EXACT []
13161390 synonym: "sequence difference" EXACT []
13171391 is_a: SO:0000700 ! remark
13181392
13251399 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.
13261400 subset: biosapiens
13271401 subset: SOFA
1402 synonym: "INSDC_feature:sig_peptide" EXACT []
13281403 synonym: "signal" RELATED [uniprot:feature_type]
13291404 synonym: "signal peptide" EXACT []
13301405 synonym: "signal peptide coding sequence" EXACT []
13421417 subset: biosapiens
13431418 subset: SOFA
13441419 synonym: "chain" RELATED [uniprot:feature_type]
1420 synonym: "INSDC_feature:mat_peptide" EXACT []
13451421 synonym: "mature peptide" RELATED []
13461422 synonym: "mature protein region" EXACT []
13471423 is_a: SO:0000839 ! polypeptide_region
13881464 namespace: sequence
13891465 def: "A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284]
13901466 subset: SOFA
1467 synonym: "INSDC_feature:ncRNA" BROAD []
1468 synonym: "INSDC_qualifier:rasiRNA" EXACT []
13911469 synonym: "repeat associated small interfering RNA" EXACT []
13921470 xref: http://en.wikipedia.org/wiki/RasiRNA "wiki"
13931471 is_a: SO:0000655 ! ncRNA
14061484 name: decayed_exon
14071485 namespace: sequence
14081486 def: "A non-functional descendant of an exon." [SO:ke]
1487 comment: Does not have to be part of a pseudogene.
14091488 subset: SOFA
14101489 synonym: "decayed exon" EXACT []
14111490 is_a: SO:0000462 ! pseudogenic_region
14961575 namespace: sequence
14971576 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]
14981577 subset: SOFA
1578 synonym: "INSDC_feature:regulatory" BROAD []
1579 synonym: "INSDC_qualifier:polyA_signal_sequence" EXACT []
14991580 synonym: "poly(A) signal" EXACT []
15001581 synonym: "polyA signal sequence" EXACT []
15011582 synonym: "polyadenylation termination signal" EXACT []
15081589 alt_id: SO:0001430
15091590 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]
15101591 subset: SOFA
1592 synonym: "INSDC_feature:polyA_site" EXACT []
15111593 synonym: "polyA cleavage site" EXACT []
15121594 synonym: "polyA junction" EXACT []
15131595 synonym: "polyA site" EXACT []
15231605 namespace: sequence
15241606 def: "A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]
15251607 subset: SOFA
1608 synonym: "INSDC_feature:centromere" EXACT []
15261609 xref: http://en.wikipedia.org/wiki/Centromere "wiki"
15271610 is_a: SO:0000628 ! chromosomal_structural_element
15281611
15531636 def: "A self spliced intron." [SO:ke]
15541637 subset: SOFA
15551638 synonym: "autocatalytically spliced intron" EXACT []
1639 synonym: "INSDC_feature:ncRNA" BROAD []
1640 synonym: "INSDC_qualifier:autocatalytically_spliced_intron" EXACT []
15561641 is_a: SO:0000188 ! intron
15571642
15581643 [Term]
15621647 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]
15631648 subset: SOFA
15641649 synonym: "7S RNA" RELATED []
1650 synonym: "INSDC_feature:ncRNA" BROAD []
1651 synonym: "INSDC_qualifier:SRP_RNA" EXACT []
15651652 synonym: "signal recognition particle RNA" RELATED []
15661653 synonym: "SRP RNA" EXACT []
15671654 is_a: SO:0000655 ! ncRNA
15861673 subset: SOFA
15871674 synonym: "gRNA" EXACT []
15881675 synonym: "guide RNA" EXACT []
1676 synonym: "INSDC_feature:ncRNA" BROAD []
1677 synonym: "INSDC_qualifier:guide_RNA" EXACT []
15891678 xref: http://en.wikipedia.org/wiki/Guide_RNA "wiki"
15901679 is_a: SO:0000655 ! ncRNA
15911680
16571746 namespace: sequence
16581747 def: "A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]
16591748 subset: SOFA
1749 synonym: "INSDC_feature:telomere" EXACT []
16601750 synonym: "telomeric DNA" EXACT []
16611751 synonym: "telomeric sequence" EXACT []
16621752 xref: http://en.wikipedia.org/wiki/Telomere "wiki"
16681758 namespace: sequence
16691759 def: "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke]
16701760 subset: SOFA
1761 synonym: "INSDC_feature:regulatory" BROAD []
1762 synonym: "INSDC_qualifier:silencer" EXACT []
16711763 xref: http://en.wikipedia.org/wiki/Silencer_(DNA) "wiki"
16721764 is_a: SO:0000727 ! CRM
16731765
16751767 id: SO:0000627
16761768 name: insulator
16771769 namespace: sequence
1678 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]
1679 subset: SOFA
1770 def: "A regulatory region that 1) when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression and 2) acts as a chromatin boundary element or barrier that can block the encroachment of condensed chromatin from an adjacent region." [NCBI:cf, PMID:12154228, SO:regcreative]
1771 subset: SOFA
1772 synonym: "INSDC_feature:regulatory" BROAD []
1773 synonym: "INSDC_qualifier:insulator" EXACT []
16801774 synonym: "insulator element" EXACT []
16811775 xref: http://en.wikipedia.org/wiki/Insulator_(genetics) "wiki"
16821776 is_a: SO:0001055 ! transcriptional_cis_regulatory_region
16951789 namespace: sequence
16961790 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]
16971791 subset: SOFA
1792 synonym: "INSDC_feature:repeat_region" BROAD []
1793 synonym: "INSDC_qualifier:minisatellite" EXACT []
1794 synonym: "VNTR" EXACT [http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9655/]
16981795 xref: http://en.wikipedia.org/wiki/Minisatellite "wiki"
16991796 is_a: SO:0000005 ! satellite_DNA
17001797
17051802 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]
17061803 subset: SOFA
17071804 synonym: "antisense RNA" EXACT []
1805 synonym: "INSDC_feature:ncRNA" BROAD []
1806 synonym: "INSDC_qualifier:antisense_RNA" EXACT []
17081807 xref: http://en.wikipedia.org/wiki/Antisense_RNA "wiki"
17091808 is_a: SO:0000655 ! ncRNA
17101809 relationship: derives_from SO:0000645 ! antisense_primary_transcript
17241823 namespace: sequence
17251824 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]
17261825 subset: SOFA
1826 synonym: "INSDC_feature:ncRNA" BROAD []
1827 synonym: "INSDC_qualifier:siRNA" EXACT []
17271828 synonym: "small interfering RNA" EXACT []
17281829 xref: http://en.wikipedia.org/wiki/SiRNA "wiki"
1729 is_a: SO:0000655 ! ncRNA
1830 is_a: SO:0000370 ! small_regulatory_ncRNA
17301831
17311832 [Term]
17321833 id: SO:0000650
17841885 def: "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]
17851886 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.
17861887 subset: SOFA
1888 synonym: "INSDC_qualifier:other" BROAD []
1889 synonym: "known_ncrna" EXACT []
17871890 synonym: "noncoding RNA" EXACT []
17881891 xref: http://en.wikipedia.org/wiki/NcRNA "wiki"
1892 xref: http://www.gencodegenes.org/gencode_biotypes.html "GENCODE"
17891893 is_a: SO:0000233 ! mature_transcript
17901894
17911895 [Term]
17941898 namespace: sequence
17951899 def: "A region of sequence containing one or more repeat units." [SO:ke]
17961900 subset: SOFA
1901 synonym: "INSDC_feature:repeat_region" BROAD []
1902 synonym: "INSDC_qualifier:other" EXACT []
17971903 synonym: "repeat region" EXACT []
17981904 is_a: SO:0001411 ! biological_region
17991905 relationship: has_part SO:0001411 ! biological_region
18051911 def: "A repeat that is located at dispersed sites in the genome." [SO:ke]
18061912 subset: SOFA
18071913 synonym: "dispersed repeat" EXACT []
1914 synonym: "INSDC_feature:repeat_region" BROAD []
1915 synonym: "INSDC_qualifier:dispersed" EXACT []
18081916 synonym: "interspersed repeat" EXACT []
18091917 xref: http://en.wikipedia.org/wiki/Interspersed_repeat "wiki"
18101918 is_a: SO:0000657 ! repeat_region
18491957 namespace: sequence
18501958 def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]
18511959 subset: SOFA
1960 synonym: "INSDC_feature:misc_RNA" BROAD []
18521961 xref: http://en.wikipedia.org/wiki/RNA "wiki"
18531962 is_a: SO:0000831 ! gene_member_region
18541963
19692078 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]
19702079 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.
19712080 subset: SOFA
2081 synonym: "INSDC_feature:gene" EXACT []
19722082 xref: http://en.wikipedia.org/wiki/Gene "wiki"
19732083 is_a: SO:0001411 ! biological_region
19742084 relationship: member_of SO:0005855 ! gene_group
19792089 namespace: sequence
19802090 def: "Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]
19812091 subset: SOFA
2092 synonym: "INSDC_feature:repeat_region" BROAD []
2093 synonym: "INSDC_qualifier:tandem" EXACT []
19822094 synonym: "tandem repeat" EXACT []
19832095 xref: http://en.wikipedia.org/wiki/Tandem_repeat "wiki"
19842096 xref: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html
20012113 namespace: sequence
20022114 def: "A region of nucleotide sequence corresponding to a known motif." [SO:ke]
20032115 subset: SOFA
2116 synonym: "INSDC_feature:misc_feature" BROAD []
2117 synonym: "INSDC_note:nucleotide_motif" EXACT []
20042118 synonym: "nucleotide motif" EXACT []
20052119 is_a: SO:0001683 ! sequence_motif
20062120
20302144 namespace: sequence
20312145 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]
20322146 subset: SOFA
2147 synonym: "pseudochromosome" EXACT []
20332148 synonym: "superscaffold" RELATED []
20342149 is_a: SO:0000353 ! sequence_assembly
20352150
20392154 namespace: sequence
20402155 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]
20412156 subset: SOFA
2157 synonym: "INSDC_feature:oriT" EXACT []
20422158 synonym: "origin of transfer" EXACT []
20432159 xref: http://en.wikipedia.org/wiki/Origin_of_transfer "wiki"
20442160 is_a: SO:0000296 ! origin_of_replication
20522168 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.
20532169 subset: biosapiens
20542170 subset: SOFA
2171 synonym: "INSDC_feature:transit_peptide" EXACT []
20552172 synonym: "signal" RELATED []
20562173 synonym: "transit" RELATED [uniprot:feature_type]
20572174 synonym: "transit peptide" EXACT []
20782195 namespace: sequence
20792196 def: "A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke]
20802197 subset: SOFA
2198 synonym: "INSDC_feature:assembly_gap" NARROW []
2199 synonym: "INSDC_feature:gap" EXACT []
20812200 is_a: SO:0000143 ! assembly_component
20822201 relationship: part_of SO:0000353 ! sequence_assembly
20832202
21072226 def: "A non functional descendant of an rRNA." [SO:ke]
21082227 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.
21092228 subset: SOFA
2229 synonym: "INSDC_feature:rRNA" BROAD []
2230 synonym: "INSDC_qualifier:pseudo" EXACT []
21102231 synonym: "pseudogenic rRNA" EXACT []
21112232 is_a: SO:0000462 ! pseudogenic_region
2233 relationship: non_functional_homolog_of SO:0000673 ! transcript
2234 relationship: part_of SO:0000336 ! pseudogene
21122235
21132236 [Term]
21142237 id: SO:0000778
21172240 def: "A non functional descendent of a tRNA." [SO:ke]
21182241 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.
21192242 subset: SOFA
2243 synonym: "INSDC_feature:tRNA" BROAD []
2244 synonym: "INSDC_qualifier:pseudo" EXACT []
21202245 synonym: "pseudogenic tRNA" EXACT []
21212246 is_a: SO:0000462 ! pseudogenic_region
2247 relationship: non_functional_homolog_of SO:0000673 ! transcript
2248 relationship: part_of SO:0000336 ! pseudogene
21222249
21232250 [Term]
21242251 id: SO:0000830
23092436 namespace: sequence
23102437 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]
23112438 subset: SOFA
2439 synonym: "INSDC_feature:mobile_element" EXACT []
23122440 synonym: "MGE" EXACT []
23132441 synonym: "mobile genetic element" EXACT []
23142442 xref: http://en.wikipedia.org/wiki/Mobile_genetic_element "wiki"
23292457 namespace: sequence
23302458 def: "A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]
23312459 subset: SOFA
2460 synonym: "INSDC_feature:regulatory" BROAD []
2461 synonym: "INSDC_qualifier:transcriptional_cis_regulatory_region" EXACT []
23322462 synonym: "transcription-control region" EXACT []
23332463 synonym: "transcriptional cis regulatory region" EXACT []
23342464 is_a: SO:0001679 ! transcription_regulatory_region
23512481 def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]
23522482 comment: Merged with partially characterized change in nucleotide sequence.
23532483 subset: SOFA
2484 synonym: "INSDC_feature:misc_feature" BROAD []
2485 synonym: "INSDC_feature:variation" EXACT []
2486 synonym: "INSDC_note:sequence_alteration" EXACT []
23542487 synonym: "partially characterised change in DNA sequence" NARROW []
23552488 synonym: "partially_characterised_change_in_DNA_sequence" NARROW []
23562489 synonym: "sequence alteration" EXACT []
24442577 def: "A region defined by its disposition to be involved in a biological process." [SO:cb]
24452578 subset: SOFA
24462579 synonym: "biological region" EXACT []
2580 synonym: "INSDC_misc_feature" BROAD []
2581 synonym: "INSDC_note:biological_region" EXACT []
24472582 is_a: SO:0000001 ! region
24482583
24492584 [Term]
25722707 namespace: sequence
25732708 def: "A region of sequence that is involved in the control of a biological process." [SO:ke]
25742709 subset: SOFA
2710 synonym: "INSDC_feature:regulatory" BROAD []
2711 synonym: "INSDC_qualifier:other" EXACT []
25752712 synonym: "regulatory region" EXACT []
25762713 xref: http://en.wikipedia.org/wiki/Regulatory_region "wiki"
25772714 is_a: SO:0000831 ! gene_member_region