format-version: 1.2 date: 01:06:2010 10:46 saved-by: kareneilbeck auto-generated-by: OBO-Edit 2.1-beta3 subsetdef: biosapiens "biosapiens protein feature ontology" subsetdef: SOFA "SO feature annotation" synonymtypedef: aa1 "amino acid 1 letter code" synonymtypedef: aa3 "amino acid 3 letter code" synonymtypedef: AAMOD "amino acid modification" synonymtypedef: BS "biosapiens" synonymtypedef: dbsnp "dbsnp variant terms" synonymtypedef: ebi_variants "ensembl variant terms" synonymtypedef: RNAMOD "RNA modification" EXACT default-namespace: sequence remark: autogenerated-by\: DAG-Edit version 1.417\nsaved-by\: eilbeck\ndate\: Tue May 11 15\:18\:44 PDT 2004\nversion\: $Revision\: 1.45 $ [Term] id: SO:0000000 name: Sequence_Ontology subset: SOFA is_obsolete: true [Term] id: SO:0000001 name: region def: "A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke] subset: SOFA synonym: "sequence" EXACT [] is_a: SO:0000110 ! sequence_feature [Term] id: SO:0000004 name: interior_coding_exon subset: SOFA synonym: "interior coding exon" EXACT [] is_a: SO:0000195 ! coding_exon [Term] id: SO:0000005 name: satellite_DNA def: "The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "satellite DNA" EXACT [] xref: http://en.wikipedia.org/wiki/Satellite_DNA "wiki" is_a: SO:0000705 ! tandem_repeat [Term] id: SO:0000006 name: PCR_product def: "A region amplified by a PCR reaction." [SO:ke] comment: This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406. subset: SOFA synonym: "amplicon" RELATED [] synonym: "PCR product" EXACT [] xref: http://en.wikipedia.org/wiki/RAPD "wiki" is_a: SO:0000695 ! reagent [Term] id: SO:0000007 name: read_pair def: "A pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls] subset: SOFA synonym: "read-pair" EXACT [] is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000149 ! contig [Term] id: SO:0000013 name: scRNA def: "Any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html] subset: SOFA synonym: "small cytoplasmic RNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000038 name: match_set def: "A collection of match parts." [SO:ke] subset: SOFA is_obsolete: true [Term] id: SO:0000039 name: match_part def: "A part of a match, for example an hsp from blast is a match_part." [SO:ke] subset: SOFA synonym: "match part" EXACT [] is_a: SO:0001410 ! experimental_feature relationship: part_of SO:0000343 ! match [Term] id: SO:0000050 name: gene_part def: "A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene." [SO:ke] subset: SOFA is_obsolete: true [Term] id: SO:0000057 name: operator def: "A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma] subset: SOFA synonym: "operator segment" EXACT [] xref: http://en.wikipedia.org/wiki/Operator_(biology)#Operator "wiki" is_a: SO:0000752 ! gene_group_regulatory_region [Term] id: SO:0000059 name: nuclease_binding_site def: "A region of a molecule that binds to a nuclease." [SO:cb] subset: SOFA synonym: "nuclease binding site" EXACT [] is_a: SO:0000410 ! protein_binding_site [Term] id: SO:0000101 name: transposable_element def: "A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html] subset: SOFA synonym: "transposable element" EXACT [] synonym: "transposon" EXACT [] xref: http://en.wikipedia.org/wiki/Transposable_element "wiki" is_a: SO:0001039 ! integrated_mobile_genetic_element [Term] id: SO:0000102 name: expressed_sequence_match def: "A match to an EST or cDNA sequence." [SO:ke] subset: SOFA synonym: "expressed sequence match" EXACT [] is_a: SO:0000347 ! nucleotide_match [Term] id: SO:0000103 name: clone_insert_end def: "The end of the clone insert." [SO:ke] subset: SOFA synonym: "clone insert end" EXACT [] is_a: SO:0000699 ! junction relationship: part_of SO:0000753 ! clone_insert [Term] id: SO:0000104 name: polypeptide alt_id: SO:0000358 def: "A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute. subset: SOFA synonym: "protein" EXACT [] xref: http://en.wikipedia.org/wiki/Polypeptide "wiki" is_a: SO:0001411 ! biological_region relationship: derives_from SO:0000316 ! CDS [Term] id: SO:0000109 name: sequence_variant_obs def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke] subset: SOFA synonym: "mutation" RELATED [] is_obsolete: true [Term] id: SO:0000110 name: sequence_feature def: "An extent of biological sequence." [SO:ke] subset: SOFA synonym: "located sequence feature" RELATED [] synonym: "located_sequence_feature" EXACT [] synonym: "sequence feature" EXACT [] [Term] id: SO:0000112 name: primer def: "A short preexisting polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase." [http://www.ornl.gov/TechResources/Human_Genome/publicat/primer2001/glossary.html] subset: SOFA synonym: "DNA primer" EXACT [] synonym: "primer oligonucleotide" EXACT [] synonym: "primer polynucleotide" EXACT [] synonym: "primer sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Primer_(molecular_biology) "wiki" is_a: SO:0000441 ! ss_oligo [Term] id: SO:0000113 name: proviral_region def: "A viral sequence which has integrated into a host genome." [SO:ke] subset: SOFA synonym: "proviral region" EXACT [] synonym: "proviral sequence" RELATED [] is_a: SO:0001039 ! integrated_mobile_genetic_element [Term] id: SO:0000114 name: methylated_C def: "A methylated deoxy-cytosine." [SO:ke] subset: SOFA synonym: "methylated C" EXACT [] synonym: "methylated cytosine" EXACT [] synonym: "methylated cytosine base" EXACT [] synonym: "methylated cytosine residue" EXACT [] is_a: SO:0000306 ! methylated_base_feature [Term] id: SO:0000120 name: protein_coding_primary_transcript def: "A primary transcript that, at least in part, encodes one or more proteins." [SO:ke] comment: May contain introns. subset: SOFA synonym: "pre mRNA" RELATED [] synonym: "protein coding primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000139 name: ribosome_entry_site def: "Region in mRNA where ribosome assembles." [SO:ke] subset: SOFA synonym: "ribosome entry site" EXACT [] is_a: SO:0000837 ! UTR_region relationship: part_of SO:0000203 ! UTR [Term] id: SO:0000140 name: attenuator def: "A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as] subset: SOFA synonym: "attenuator sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Attenuator "wiki" is_a: SO:0005836 ! regulatory_region relationship: part_of SO:0000234 ! mRNA [Term] id: SO:0000141 name: terminator def: "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "terminator sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Terminator_(genetics) "wiki" is_a: SO:0005836 ! regulatory_region relationship: part_of SO:0000673 ! transcript [Term] id: SO:0000143 name: assembly_component def: "A region of known length which may be used to manufacture a longer region." [SO:ke] subset: SOFA synonym: "assembly component" EXACT [] is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000147 name: exon def: "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA xref: http://en.wikipedia.org/wiki/Exon "wiki" is_a: SO:0000833 ! transcript_region [Term] id: SO:0000148 name: supercontig def: "One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls] subset: SOFA synonym: "scaffold" RELATED [] is_a: SO:0000353 ! sequence_assembly relationship: part_of SO:0000719 ! ultracontig [Term] id: SO:0000149 name: contig def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls] subset: SOFA xref: http://en.wikipedia.org/wiki/Contig "wiki" is_a: SO:0000143 ! assembly_component is_a: SO:0000353 ! sequence_assembly relationship: part_of SO:0000148 ! supercontig [Term] id: SO:0000150 name: read def: "A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd] subset: SOFA is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000149 ! contig [Term] id: SO:0000151 name: clone def: "A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke] subset: SOFA xref: http:http\://en.wikipedia.org/wiki/Clone_(genetics) "wiki" is_a: SO:0000695 ! reagent [Term] id: SO:0000159 name: deletion alt_id: SO:1000033 def: "The point at which one or more contiguous nucleotides were excised." [SO:ke] subset: SOFA synonym: "deleted_sequence" EXACT [] synonym: "nucleotide deletion" EXACT [] synonym: "nucleotide_deletion" EXACT [] xref: http://en.wikipedia.org/wiki/Nucleotide_deletion "wiki" is_a: SO:0001059 ! sequence_alteration is_a: SO:0001411 ! biological_region [Term] id: SO:0000161 name: methylated_A def: "A modified RNA base in which adenine has been methylated." [SO:ke] subset: SOFA synonym: "methylated A" EXACT [] synonym: "methylated adenine" EXACT [] synonym: "methylated adenine base" EXACT [] synonym: "methylated adenine residue" EXACT [] is_a: SO:0000306 ! methylated_base_feature [Term] id: SO:0000162 name: splice_site def: "Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke] comment: With spliceosomal introns, the splice sites bind the spliceosomal machinery. subset: SOFA synonym: "splice site" EXACT [] xref: http://en.wikipedia.org/wiki/Splice_site "wiki" is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000163 name: five_prime_cis_splice_site def: "Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke] subset: SOFA synonym: "5' splice site" EXACT [] synonym: "donor" RELATED [] synonym: "donor splice site" EXACT [] synonym: "five prime splice site" EXACT [] synonym: "splice donor site" EXACT [] is_a: SO:0001419 ! cis_splice_site [Term] id: SO:0000164 name: three_prime_cis_splice_site def: "Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke] subset: SOFA synonym: "3' splice site" RELATED [] synonym: "acceptor" RELATED [] synonym: "acceptor splice site" EXACT [] synonym: "splice acceptor site" EXACT [] synonym: "three prime splice site" EXACT [] is_a: SO:0001419 ! cis_splice_site [Term] id: SO:0000165 name: enhancer def: "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO. subset: SOFA xref: http://en.wikipedia.org/wiki/Enhancer_(genetics) "wiki" is_a: SO:0000727 ! CRM [Term] id: SO:0000167 name: promoter def: "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription. subset: SOFA synonym: "promoter sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Promoter "wiki" is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0000177 name: cross_genome_match def: "A nucleotide match against a sequence from another organism." [SO:ma] subset: SOFA synonym: "cross genome match" EXACT [] is_a: SO:0000347 ! nucleotide_match [Term] id: SO:0000178 name: operon def: "A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA xref: http://en.wikipedia.org/wiki/Operon "wiki" is_a: SO:0005855 ! gene_group [Term] id: SO:0000179 name: clone_insert_start def: "The start of the clone insert." [SO:ke] subset: SOFA synonym: "clone insert start" EXACT [] is_a: SO:0000699 ! junction relationship: part_of SO:0000753 ! clone_insert [Term] id: SO:0000181 name: translated_nucleotide_match def: "A match against a translated sequence." [SO:ke] subset: SOFA synonym: "translated nucleotide match" EXACT [] is_a: SO:0000347 ! nucleotide_match [Term] id: SO:0000183 name: non_transcribed_region def: "A region of the gene which is not transcribed." [SO:ke] subset: SOFA synonym: "non transcribed region" EXACT [] synonym: "non-transcribed sequence" EXACT [] synonym: "nontranscribed region" EXACT [] synonym: "nontranscribed sequence" EXACT [] is_a: SO:0000842 ! gene_component_region [Term] id: SO:0000185 name: primary_transcript def: "A transcript that in its initial state requires modification to be functional." [SO:ma] subset: SOFA synonym: "precursor RNA" EXACT [] synonym: "primary transcript" EXACT [] xref: http://en.wikipedia.org/wiki/Primary_transcript "wiki" is_a: SO:0000673 ! transcript [Term] id: SO:0000187 name: repeat_family def: "A group of characterized repeat sequences." [SO:ke] subset: SOFA is_obsolete: true [Term] id: SO:0000188 name: intron def: "A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA xref: http://en.wikipedia.org/wiki/Intron "wiki" is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000193 name: RFLP_fragment def: "A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme." [GOC:pj] subset: SOFA synonym: "restriction fragment length polymorphism" EXACT [] synonym: "RFLP" EXACT [] synonym: "RFLP fragment" EXACT [] xref: http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism "wiki" is_a: SO:0000412 ! restriction_fragment [Term] id: SO:0000195 name: coding_exon def: "An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke] subset: SOFA synonym: "coding exon" EXACT [] is_a: SO:0000147 ! exon [Term] id: SO:0000196 name: five_prime_coding_exon_coding_region def: "The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm] subset: SOFA synonym: "five prime exon coding region" EXACT [] is_a: SO:0001215 ! coding_region_of_exon relationship: part_of SO:0000200 ! five_prime_coding_exon [Term] id: SO:0000197 name: three_prime_coding_exon_coding_region def: "The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm] subset: SOFA synonym: "three prime exon coding region" EXACT [] is_a: SO:0001215 ! coding_region_of_exon [Term] id: SO:0000198 name: noncoding_exon def: "An exon that does not contain any codons." [SO:ke] subset: SOFA synonym: "noncoding exon" EXACT [] is_a: SO:0000147 ! exon [Term] id: SO:0000200 name: five_prime_coding_exon def: "The 5' most coding exon." [SO:ke] subset: SOFA synonym: "5' coding exon" EXACT [] synonym: "five prime coding exon" EXACT [] is_a: SO:0000195 ! coding_exon [Term] id: SO:0000203 name: UTR def: "Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke] subset: SOFA synonym: "untranslated region" EXACT [] is_a: SO:0000836 ! mRNA_region [Term] id: SO:0000204 name: five_prime_UTR def: "A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "5' UTR" EXACT [] synonym: "five prime UTR" EXACT [] synonym: "five_prime_untranslated_region" EXACT [] xref: http://en.wikipedia.org/wiki/5'_UTR "wiki" is_a: SO:0000203 ! UTR [Term] id: SO:0000205 name: three_prime_UTR def: "A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "three prime untranslated region" EXACT [] synonym: "three prime UTR" EXACT [] xref: http://en.wikipedia.org/wiki/Three_prime_untranslated_region "wiki" is_a: SO:0000203 ! UTR [Term] id: SO:0000209 name: rRNA_primary_transcript def: "A primary transcript encoding a ribosomal RNA." [SO:ke] subset: SOFA synonym: "ribosomal RNA primary transcript" EXACT [] synonym: "rRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000233 name: mature_transcript def: "A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke] comment: A processed transcript cannot contain introns. subset: SOFA synonym: "mature transcript" EXACT [] xref: http://en.wikipedia.org/wiki/Mature_transcript "wiki" is_a: SO:0000673 ! transcript relationship: derives_from SO:0000185 ! primary_transcript [Term] id: SO:0000234 name: mRNA def: "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma] comment: An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "messenger RNA" EXACT [] xref: http://en.wikipedia.org/wiki/MRNA "wiki" is_a: SO:0000233 ! mature_transcript [Term] id: SO:0000235 name: TF_binding_site def: "A region of a molecule that binds a TF complex [GO:0005667]." [SO:ke] subset: SOFA synonym: "TF binding site" EXACT [] synonym: "transcription factor binding site" EXACT [] is_a: SO:0000410 ! protein_binding_site is_a: SO:0005836 ! regulatory_region [Term] id: SO:0000236 name: ORF def: "The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma] comment: The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "open reading frame" EXACT [] is_a: SO:0000717 ! reading_frame [Term] id: SO:0000239 name: flanking_region def: "The sequences extending on either side of a specific region." [SO:ke] subset: SOFA synonym: "flanking region" EXACT [] is_a: SO:0001412 ! topologically_defined_region [Term] id: SO:0000252 name: rRNA def: "RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732] subset: SOFA synonym: "ribosomal ribonucleic acid" EXACT [] synonym: "ribosomal RNA" EXACT [] xref: http://en.wikipedia.org/wiki/RRNA "wiki" is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000209 ! rRNA_primary_transcript [Term] id: SO:0000253 name: tRNA def: "Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "transfer ribonucleic acid" RELATED [] synonym: "transfer RNA" RELATED [] xref: http://en.wikipedia.org/wiki/TRNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000274 name: snRNA def: "A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "small nuclear RNA" EXACT [] xref: http://en.wikipedia.org/wiki/SnRNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000275 name: snoRNA def: "A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc] subset: SOFA synonym: "small nucleolar RNA" EXACT [] xref: http://en.wikipedia.org/wiki/SnoRNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000276 name: miRNA def: "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (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:12592000] subset: SOFA synonym: "micro RNA" EXACT [] synonym: "microRNA" EXACT [] xref: http://en.wikipedia.org/wiki/MiRNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000289 name: microsatellite def: "A repeat_region containing repeat_units (2 to 4 bp) that is repeated multiple times in tandem." [http://www.informatics.jax.org/silver/glossary.shtml] subset: SOFA synonym: "microsatellite locus" EXACT [] synonym: "microsatellite marker" EXACT [] synonym: "VNTR" EXACT [] xref: http://en.wikipedia.org/wiki/Microsatellite "wiki" is_a: SO:0000005 ! satellite_DNA [Term] id: SO:0000294 name: inverted_repeat def: "The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:ke] subset: SOFA synonym: "inverted repeat" EXACT [] synonym: "inverted repeat sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Inverted_repeat "wiki" is_a: SO:0000657 ! repeat_region [Term] id: SO:0000296 name: origin_of_replication def: "The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "ori" EXACT [] synonym: "origin of replication" EXACT [] xref: http://en.wikipedia.org/wiki/Origin_of_replication "wiki" is_a: SO:0001411 ! biological_region relationship: part_of SO:0001235 ! replicon [Term] id: SO:0000303 name: clip def: "Part of the primary transcript that is clipped off during processing." [SO:ke] subset: SOFA is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000305 name: modified_base def: "A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: Modified base:. subset: SOFA synonym: "modified base site" EXACT [] is_a: SO:0001720 ! epigenetically_modified_region [Term] id: SO:0000306 name: methylated_base_feature def: "A nucleotide modified by methylation." [SO:ke] subset: SOFA synonym: "methylated base feature" EXACT [] is_a: SO:0000305 ! modified_base [Term] id: SO:0000307 name: CpG_island def: "Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." [SO:rd] subset: SOFA synonym: "CG island" EXACT [] synonym: "CpG island" EXACT [] xref: http://en.wikipedia.org/wiki/CpG_island "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000314 name: direct_repeat def: "A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA." [SO:ke] subset: SOFA synonym: "direct repeat" EXACT [] xref: http://en.wikipedia.org/wiki/Direct_repeat "wiki" is_a: SO:0000657 ! repeat_region [Term] id: SO:0000315 name: TSS def: "The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke] subset: SOFA synonym: "transcription start site" EXACT [] is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000316 name: CDS def: "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma] subset: SOFA synonym: "coding sequence" EXACT [] is_a: SO:0000836 ! mRNA_region [Term] id: SO:0000318 name: start_codon def: "First codon to be translated by a ribosome." [SO:ke] subset: SOFA synonym: "initiation codon" EXACT [] synonym: "start codon" EXACT [] xref: http://en.wikipedia.org/wiki/Start_codon "wiki" is_a: SO:0000360 ! codon [Term] id: SO:0000319 name: stop_codon def: "In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke] subset: SOFA synonym: "stop codon" EXACT [] xref: http://en.wikipedia.org/wiki/Stop_codon "wiki" is_a: SO:0000360 ! codon [Term] id: SO:0000324 name: tag def: "A nucleotide sequence that may be used to identify a larger sequence." [SO:ke] subset: SOFA is_a: SO:0000696 ! oligo [Term] id: SO:0000325 name: rRNA_large_subunit_primary_transcript def: "A primary transcript encoding a large ribosomal subunit RNA." [SO:ke] subset: SOFA synonym: "rRNA large subunit primary transcript" EXACT [] is_a: SO:0000209 ! rRNA_primary_transcript [Term] id: SO:0000326 name: SAGE_tag def: "A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract] subset: SOFA synonym: "SAGE tag" EXACT [] is_a: SO:0000324 ! tag [Term] id: SO:0000330 name: conserved_region def: "Region of sequence similarity by descent from a common ancestor." [SO:ke] subset: SOFA synonym: "conserved region" EXACT [] xref: http://en.wikipedia.org/wiki/Conserved_region "wiki" is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000331 name: STS def: "Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com] subset: SOFA synonym: "sequence tag site" EXACT [] is_a: SO:0000324 ! tag [Term] id: SO:0000332 name: coding_conserved_region def: "Coding region of sequence similarity by descent from a common ancestor." [SO:ke] subset: SOFA synonym: "coding conserved region" EXACT [] is_a: SO:0000330 ! conserved_region [Term] id: SO:0000333 name: exon_junction def: "The boundary between two exons in a processed transcript." [SO:ke] subset: SOFA synonym: "exon junction" EXACT [] is_a: SO:0000699 ! junction relationship: part_of SO:0000233 ! mature_transcript [Term] id: SO:0000334 name: nc_conserved_region def: "Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke] subset: SOFA synonym: "nc conserved region" EXACT [] synonym: "noncoding conserved region" EXACT [] is_a: SO:0000330 ! conserved_region [Term] id: SO:0000336 name: pseudogene def: "A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html] subset: SOFA xref: http://en.wikipedia.org/wiki/Pseudogene "wiki" is_a: SO:0000462 ! pseudogenic_region relationship: non_functional_homolog_of SO:0000704 ! gene [Term] id: SO:0000337 name: RNAi_reagent def: "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd] subset: SOFA synonym: "RNAi reagent" EXACT [] is_a: SO:0000442 ! ds_oligo [Term] id: SO:0000340 name: chromosome def: "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA xref: http://en.wikipedia.org/wiki/Chromosome "wiki" is_a: SO:0001235 ! replicon [Term] id: SO:0000341 name: chromosome_band def: "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma] subset: SOFA synonym: "chromosome band" EXACT [] synonym: "cytoband" EXACT [] synonym: "cytological band" EXACT [] xref: http://en.wikipedia.org/wiki/Cytological_band "wiki" is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000343 name: match def: "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke] subset: SOFA is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000344 name: splice_enhancer def: "Region of a transcript that regulates splicing." [SO:ke] subset: SOFA synonym: "splice enhancer" EXACT [] is_a: SO:0001056 ! splicing_regulatory_region [Term] id: SO:0000345 name: EST def: "A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "expressed sequence tag" EXACT [] is_a: SO:0000324 ! tag relationship: derives_from SO:0000234 ! mRNA [Term] id: SO:0000347 name: nucleotide_match def: "A match against a nucleotide sequence." [SO:ke] subset: SOFA synonym: "nucleotide match" EXACT [] is_a: SO:0000343 ! match [Term] id: SO:0000349 name: protein_match def: "A match against a protein sequence." [SO:ke] subset: SOFA synonym: "protein match" EXACT [] is_a: SO:0000343 ! match [Term] id: SO:0000353 name: sequence_assembly def: "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma] subset: SOFA synonym: "sequence assembly" EXACT [] xref: http://en.wikipedia.org/wiki/Sequence_assembly "wiki" is_a: SO:0001248 ! assembly [Term] id: SO:0000360 name: codon def: "A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Codon "wiki" is_a: SO:0000851 ! CDS_region [Term] id: SO:0000366 name: insertion_site def: "The junction where an insertion occurred." [SO:ke] subset: SOFA synonym: "insertion site" EXACT [] is_a: SO:0000699 ! junction [Term] id: SO:0000368 name: transposable_element_insertion_site def: "The junction in a genome where a transposable_element has inserted." [SO:ke] subset: SOFA synonym: "transposable element insertion site" EXACT [] is_a: SO:0000366 ! insertion_site [Term] id: SO:0000370 name: small_regulatory_ncRNA def: "A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma] subset: SOFA synonym: "small regulatory ncRNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000372 name: enzymatic_RNA def: "An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb] comment: This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts. subset: SOFA synonym: "enzymatic RNA" EXACT [] is_a: SO:0000673 ! implied link automatically realized ! transcript intersection_of: SO:0000673 ! transcript [Term] id: SO:0000374 name: ribozyme def: "An RNA with catalytic activity." [SO:ma] subset: SOFA xref: http://en.wikipedia.org/wiki/Ribozyme "wiki" is_a: SO:0000372 ! implied link automatically realized ! enzymatic_RNA intersection_of: SO:0000372 ! enzymatic_RNA [Term] id: SO:0000375 name: rRNA_5_8S def: "5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002] subset: SOFA synonym: "5.8S LSU rRNA" EXACT [] synonym: "5.8S ribosomal RNA" EXACT [] synonym: "5.8S rRNA" EXACT [] synonym: "rRNA 5 8S" EXACT [] xref: http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA "wiki" is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0000380 name: hammerhead_ribozyme def: "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [http://rnaworld.bio.ku.edu/class/RNA/RNA00/RNA_World_3.html] subset: SOFA synonym: "hammerhead ribozyme" EXACT [] xref: http://en.wikipedia.org/wiki/Hammerhead_ribozyme "wiki" is_a: SO:0000715 ! implied link automatically realized ! RNA_motif intersection_of: SO:0000715 ! RNA_motif [Term] id: SO:0000385 name: RNase_MRP_RNA def: "The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030] subset: SOFA synonym: "RNase MRP RNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000386 name: RNase_P_RNA def: "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010] subset: SOFA synonym: "RNase P RNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000390 name: telomerase_RNA def: "The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025] subset: SOFA synonym: "telomerase RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Telomerase_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000391 name: U1_snRNA def: "U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003] subset: SOFA synonym: "small nuclear RNA U1" EXACT [RSC:cb] synonym: "snRNA U1" EXACT [RSC:cb] synonym: "U1 small nuclear RNA" EXACT [RSC:cb] synonym: "U1 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U1_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000392 name: U2_snRNA def: "U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004] subset: SOFA synonym: "small nuclear RNA U2" EXACT [RSC:CB] synonym: "snRNA U2" EXACT [RSC:CB] synonym: "U2 small nuclear RNA" EXACT [RSC:CB] synonym: "U2 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U2_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000393 name: U4_snRNA def: "U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015] subset: SOFA synonym: "small nuclear RNA U4" EXACT [RSC:cb] synonym: "snRNA U4" EXACT [RSC:cb] synonym: "U4 small nuclear RNA" EXACT [RSC:cb] synonym: "U4 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U4_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000394 name: U4atac_snRNA def: "An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455] subset: SOFA synonym: "small nuclear RNA U4atac" EXACT [RSC:cb] synonym: "snRNA U4atac" EXACT [RSC:cb] synonym: "U4atac small nuclear RNA" EXACT [RSC:cb] synonym: "U4atac snRNA" EXACT [] is_a: SO:0000274 ! snRNA [Term] id: SO:0000395 name: U5_snRNA def: "U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020] subset: SOFA synonym: "small nuclear RNA U5" EXACT [RSC:cb] synonym: "snRNA U5" EXACT [RSC:cb] synonym: "U5 small nuclear RNA" EXACT [RSC:cb] synonym: "U5 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U5_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000396 name: U6_snRNA def: "U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015] subset: SOFA synonym: "small nuclear RNA U6" EXACT [RSC:cb] synonym: "snRNA U6" EXACT [RSC:cb] synonym: "U6 small nuclear RNA" EXACT [RSC:cb] synonym: "U6 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U6_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000397 name: U6atac_snRNA def: "U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract] subset: SOFA synonym: "snRNA U6atac" EXACT [RSC:cb] synonym: "U6atac small nuclear RNA" EXACT [RSC:cb] synonym: "U6atac snRNA" EXACT [RSC:cb] is_a: SO:0000274 ! snRNA [Term] id: SO:0000398 name: U11_snRNA def: "U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129] subset: SOFA synonym: "small nuclear RNA U11" EXACT [RSC:cb] synonym: "snRNA U11" EXACT [RSC:cb] synonym: "U11 small nuclear RNA" EXACT [RSC:cb] synonym: "U11 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U11_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000399 name: U12_snRNA def: "The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007] subset: SOFA synonym: "small nuclear RNA U12" EXACT [RSC:cb] synonym: "snRNA U12" EXACT [RSC:cb] synonym: "U12 small nuclear RNA" EXACT [RSC:cb] synonym: "U12 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U12_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000403 name: U14_snoRNA alt_id: SO:0005839 def: "U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119] comment: An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA. subset: SOFA synonym: "small nucleolar RNA U14" EXACT [] synonym: "snoRNA U14" EXACT [] synonym: "U14 small nucleolar RNA" EXACT [] synonym: "U14 snoRNA" EXACT [] is_a: SO:0000593 ! C_D_box_snoRNA [Term] id: SO:0000404 name: vault_RNA def: "A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006] subset: SOFA synonym: "vault RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Vault_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000405 name: Y_RNA def: "Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019] subset: SOFA synonym: "Y RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Y_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000407 name: rRNA_18S def: "A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke] subset: SOFA synonym: "18S ribosomal RNA" EXACT [] synonym: "18S rRNA" EXACT [] synonym: "rRNA 18S" EXACT [] xref: http://en.wikipedia.org/wiki/18S_ribosomal_RNA "wiki" is_a: SO:0000650 ! small_subunit_rRNA [Term] id: SO:0000409 name: binding_site alt_id: BS:00033 def: "A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke] comment: Discrete. subset: biosapiens subset: SOFA synonym: "binding_or_interaction_site" EXACT [] synonym: "site" RELATED [] xref: http://en.wikipedia.org/wiki/Binding_site "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000410 name: protein_binding_site def: "A region of a molecule that binds to a protein." [SO:ke] subset: SOFA synonym: "protein binding site" EXACT [] is_a: SO:0000409 ! binding_site [Term] id: SO:0000412 name: restriction_fragment def: "A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke] subset: SOFA synonym: "restriction fragment" EXACT [] xref: http://en.wikipedia.org/wiki/Restriction_fragment "wiki" is_a: SO:0000143 ! assembly_component [Term] id: SO:0000413 name: sequence_difference def: "A region where the sequence differs from that of a specified sequence." [SO:ke] subset: SOFA synonym: "sequence difference" EXACT [] is_a: SO:0000700 ! remark [Term] id: SO:0000418 name: signal_peptide alt_id: BS:00159 def: "The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence. subset: biosapiens subset: SOFA synonym: "signal" RELATED [uniprot:feature_type] synonym: "signal peptide" EXACT [] synonym: "signal peptide coding sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Signal_peptide "wiki" is_a: SO:0001527 ! peptide_localization_signal [Term] id: SO:0000419 name: mature_protein_region alt_id: BS:00149 def: "The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb] comment: This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification. subset: biosapiens subset: SOFA synonym: "chain" RELATED [uniprot:feature_type] synonym: "mature peptide" RELATED [] synonym: "mature protein region" EXACT [] is_a: SO:0000839 ! polypeptide_region relationship: part_of SO:0001063 ! immature_peptide_region [Term] id: SO:0000436 name: ARS def: "A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma] subset: SOFA synonym: "autonomously replicating sequence" EXACT [] is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000441 name: ss_oligo def: "A single stranded oligonucleotide." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "single strand oligo" EXACT [] synonym: "single strand oligonucleotide" EXACT [] synonym: "single stranded oligonucleotide" EXACT [] synonym: "ss oligo" EXACT [] synonym: "ss oligonucleotide" EXACT [] is_a: SO:0000696 ! oligo [Term] id: SO:0000442 name: ds_oligo def: "A double stranded oligonucleotide." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "double stranded oligonucleotide" EXACT [] synonym: "ds oligo" EXACT [] synonym: "ds-oligonucleotide" EXACT [] is_a: SO:0000696 ! oligo [Term] id: SO:0000454 name: rasiRNA def: "A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284] subset: SOFA synonym: "repeat associated small interfering RNA" EXACT [] xref: http://en.wikipedia.org/wiki/RasiRNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000462 name: pseudogenic_region def: "A non-functional descendent of a functional entity." [SO:cjm] subset: SOFA synonym: "pseudogenic region" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0000464 name: decayed_exon def: "A non-functional descendant of an exon." [SO:ke] subset: SOFA synonym: "decayed exon" EXACT [] is_a: SO:0000462 ! pseudogenic_region relationship: non_functional_homolog_of SO:0000147 ! exon [Term] id: SO:0000468 name: golden_path_fragment def: "One of the pieces of sequence that make up a golden path." [SO:rd] subset: SOFA synonym: "golden path fragment" EXACT [] is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000688 ! golden_path [Term] id: SO:0000472 name: tiling_path def: "A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm] subset: SOFA synonym: "tiling path" EXACT [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0000474 name: tiling_path_fragment def: "A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke] subset: SOFA synonym: "tiling path fragment" EXACT [] is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000472 ! tiling_path [Term] id: SO:0000483 name: nc_primary_transcript def: "A primary transcript that is never translated into a protein." [SO:ke] subset: SOFA synonym: "nc primary transcript" EXACT [] synonym: "noncoding primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000484 name: three_prime_coding_exon_noncoding_region def: "The sequence of the 3' exon that is not coding." [SO:ke] subset: SOFA synonym: "three prime coding exon noncoding region" EXACT [] synonym: "three_prime_exon_noncoding_region" EXACT [] is_a: SO:0001214 ! noncoding_region_of_exon [Term] id: SO:0000486 name: five_prime_coding_exon_noncoding_region def: "The sequence of the 5' exon preceding the start codon." [SO:ke] subset: SOFA synonym: "five prime coding exon noncoding region" EXACT [] synonym: "five_prime_exon_noncoding_region" EXACT [] is_a: SO:0001214 ! noncoding_region_of_exon relationship: part_of SO:0000200 ! five_prime_coding_exon [Term] id: SO:0000499 name: virtual_sequence def: "A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke] subset: SOFA synonym: "virtual sequence" EXACT [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0000502 name: transcribed_region def: "A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes." [SO:ke] comment: This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being. subset: SOFA is_obsolete: true [Term] id: SO:0000551 name: polyA_signal_sequence def: "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "poly(A) signal" EXACT [] synonym: "polyA signal sequence" EXACT [] synonym: "polyadenylation termination signal" EXACT [] is_a: SO:0005836 ! regulatory_region [Term] id: SO:0000553 name: polyA_site def: "The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "polyA cleavage site" EXACT [] synonym: "polyA site" EXACT [] synonym: "polyadenylation site" RELATED [] is_a: SO:0000837 ! UTR_region relationship: part_of SO:0000205 ! three_prime_UTR relationship: part_of SO:0000233 ! mature_transcript [Term] id: SO:0000577 name: centromere def: "A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Centromere "wiki" is_a: SO:0000628 ! chromosomal_structural_element [Term] id: SO:0000581 name: cap def: "A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html] subset: SOFA xref: http://en.wikipedia.org/wiki/5%27_cap "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000587 name: group_I_intron def: "Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028] comment: GO:0000372. subset: SOFA synonym: "group I intron" EXACT [] xref: http://en.wikipedia.org/wiki/Group_I_intron "wiki" is_a: SO:0000588 ! autocatalytically_spliced_intron [Term] id: SO:0000588 name: autocatalytically_spliced_intron def: "A self spliced intron." [SO:ke] subset: SOFA synonym: "autocatalytically spliced intron" EXACT [] is_a: SO:0000188 ! implied link automatically realized ! intron intersection_of: SO:0000188 ! intron [Term] id: SO:0000590 name: SRP_RNA def: "The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017] subset: SOFA synonym: "7S RNA" RELATED [] synonym: "signal recognition particle RNA" RELATED [] synonym: "SRP RNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000593 name: C_D_box_snoRNA def: "Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html] subset: SOFA synonym: "box C/D snoRNA" EXACT [] synonym: "C D box snoRNA" EXACT [] synonym: "C/D box snoRNA" EXACT [] is_a: SO:0000275 ! snoRNA [Term] id: SO:0000602 name: guide_RNA def: "A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html] subset: SOFA synonym: "gRNA" EXACT [] synonym: "guide RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Guide_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000603 name: group_II_intron def: "Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml] comment: GO:0000373. subset: SOFA synonym: "group II intron" EXACT [] xref: http://en.wikipedia.org/wiki/Group_II_intron "wiki" is_a: SO:0000588 ! autocatalytically_spliced_intron [Term] id: SO:0000605 name: intergenic_region def: "A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome." [SO:cjm] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "intergenic region" EXACT [] xref: http://en.wikipedia.org/wiki/Intergenic_region "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000610 name: polyA_sequence def: "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke] subset: SOFA synonym: "polyA sequence" EXACT [] is_a: SO:0001411 ! biological_region relationship: adjacent_to SO:0000234 ! mRNA [Term] id: SO:0000611 name: branch_site def: "A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke] subset: SOFA synonym: "branch point" EXACT [] synonym: "branch site" EXACT [] synonym: "branch_point" EXACT [] is_a: SO:0000841 ! spliceosomal_intron_region [Term] id: SO:0000612 name: polypyrimidine_tract def: "The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888] subset: SOFA synonym: "polypyrimidine tract" EXACT [] xref: http://en.wikipedia.org/wiki/Polypyrimidine_tract "wiki" is_a: SO:0000841 ! spliceosomal_intron_region [Term] id: SO:0000616 name: transcription_end_site def: "The base where transcription ends." [SO:ke] subset: SOFA synonym: "transcription end site" EXACT [] is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000624 name: telomere def: "A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma] subset: SOFA synonym: "telomeric DNA" EXACT [] synonym: "telomeric sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Telomere "wiki" is_a: SO:0000628 ! chromosomal_structural_element [Term] id: SO:0000625 name: silencer def: "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Silencer_(DNA) "wiki" is_a: SO:0000727 ! CRM [Term] id: SO:0000627 name: insulator def: "A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative] subset: SOFA synonym: "insulator element" EXACT [] xref: http://en.wikipedia.org/wiki/Insulator_(genetics) "wiki" is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0000628 name: chromosomal_structural_element subset: SOFA synonym: "chromosomal structural element" EXACT [] is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000643 name: minisatellite def: "A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml] subset: SOFA xref: http://en.wikipedia.org/wiki/Minisatellite "wiki" is_a: SO:0000005 ! satellite_DNA [Term] id: SO:0000644 name: antisense_RNA def: "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke] subset: SOFA synonym: "antisense RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Antisense_RNA "wiki" is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000645 ! antisense_primary_transcript [Term] id: SO:0000645 name: antisense_primary_transcript def: "The reverse complement of the primary transcript." [SO:ke] subset: SOFA synonym: "antisense primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000646 name: siRNA def: "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000] subset: SOFA synonym: "small interfering RNA" EXACT [] xref: http://en.wikipedia.org/wiki/SiRNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000649 name: stRNA def: "Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans." [PMID:11081512] subset: SOFA synonym: "small temporal RNA" EXACT [] xref: http://en.wikipedia.org/wiki/StRNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000650 name: small_subunit_rRNA def: "Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke] subset: SOFA synonym: "small subunit rRNA" EXACT [] synonym: "SSU RNA" EXACT [RSC:cb] synonym: "SSU rRNA" EXACT [RSC:cb] is_a: SO:0000252 ! rRNA [Term] id: SO:0000651 name: large_subunit_rRNA def: "Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke] subset: SOFA synonym: "large subunit rRNA" EXACT [] synonym: "LSU RNA" EXACT [RSC:cb] synonym: "LSU rRNA" EXACT [RSC:cb] is_a: SO:0000252 ! rRNA relationship: derives_from SO:0000325 ! rRNA_large_subunit_primary_transcript [Term] id: SO:0000652 name: rRNA_5S def: "5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001] subset: SOFA synonym: "5S LSU rRNA" EXACT [] synonym: "5S ribosomal RNA" EXACT [] synonym: "5S rRNA" EXACT [] synonym: "rRNA 5S" EXACT [] xref: http://en.wikipedia.org/wiki/5S_ribosomal_RNA "wiki" is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0000653 name: rRNA_28S def: "A component of the large ribosomal subunit." [SO:ke] subset: SOFA synonym: "28S LSU rRNA" EXACT [] synonym: "28S ribosomal RNA" EXACT [] synonym: "28S rRNA" EXACT [] synonym: "rRNA 28S" EXACT [] xref: http://en.wikipedia.org/wiki/28S_ribosomal_RNA "wiki" is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0000655 name: ncRNA def: "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke] comment: A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript. subset: SOFA synonym: "noncoding RNA" EXACT [] xref: http://en.wikipedia.org/wiki/NcRNA "wiki" is_a: SO:0000233 ! mature_transcript [Term] id: SO:0000657 name: repeat_region def: "A region of sequence containing one or more repeat units." [SO:ke] subset: SOFA synonym: "repeat region" EXACT [] is_a: SO:0001412 ! topologically_defined_region [Term] id: SO:0000658 name: dispersed_repeat def: "A repeat that is located at dispersed sites in the genome." [SO:ke] subset: SOFA synonym: "dispersed repeat" EXACT [] synonym: "interspersed repeat" EXACT [] xref: http://en.wikipedia.org/wiki/Interspersed_repeat "wiki" is_a: SO:0000657 ! repeat_region [Term] id: SO:0000662 name: spliceosomal_intron def: "An intron which is spliced by the spliceosome." [SO:ke] comment: GO:0000398. subset: SOFA synonym: "spliceosomal intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000667 name: insertion alt_id: SO:1000034 def: "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke] subset: SOFA synonym: "nucleotide insertion" EXACT [] synonym: "nucleotide_insertion" EXACT [] is_a: SO:0001059 ! sequence_alteration is_a: SO:0001411 ! biological_region [Term] id: SO:0000668 name: EST_match def: "A match against an EST sequence." [SO:ke] subset: SOFA synonym: "EST match" EXACT [] is_a: SO:0000102 ! expressed_sequence_match [Term] id: SO:0000673 name: transcript def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma] subset: SOFA xref: http://en.wikipedia.org/wiki/RNA "wiki" is_a: SO:0000831 ! gene_member_region [Term] id: SO:0000684 name: nuclease_sensitive_site def: "A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma] subset: SOFA synonym: "nuclease sensitive site" EXACT [] is_a: SO:0000059 ! nuclease_binding_site [Term] id: SO:0000687 name: deletion_junction def: "The space between two bases in a sequence which marks the position where a deletion has occurred." [SO:ke] subset: SOFA synonym: "deletion junction" EXACT [] is_a: SO:0000699 ! junction [Term] id: SO:0000688 name: golden_path def: "A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls] subset: SOFA synonym: "golden path" EXACT [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0000689 name: cDNA_match def: "A match against cDNA sequence." [SO:ke] subset: SOFA synonym: "cDNA match" EXACT [] is_a: SO:0000102 ! expressed_sequence_match [Term] id: SO:0000694 name: SNP def: "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb] subset: SOFA synonym: "single nucleotide polymorphism" EXACT [] is_a: SO:0001483 ! SNV [Term] id: SO:0000695 name: reagent def: "A sequence used in experiment." [SO:ke] comment: Requested by Lynn Crosby, jan 2006. subset: SOFA is_a: SO:0001409 ! biomaterial_region [Term] id: SO:0000696 name: oligo def: "A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma] subset: SOFA synonym: "oligonucleotide" EXACT [] xref: http://en.wikipedia.org/wiki/Oligonucleotide "wiki" is_a: SO:0000695 ! reagent [Term] id: SO:0000699 name: junction def: "A sequence_feature with an extent of zero." [SO:ke] comment: A junction is a boundary between regions. A boundary has an extent of zero. subset: SOFA synonym: "boundary" EXACT [] synonym: "breakpoint" EXACT [] is_a: SO:0000110 ! sequence_feature disjoint_from: SO:0000001 ! region [Term] id: SO:0000700 name: remark def: "A comment about the sequence." [SO:ke] subset: SOFA is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000701 name: possible_base_call_error def: "A region of sequence where the validity of the base calling is questionable." [SO:ke] subset: SOFA synonym: "possible base call error" EXACT [] is_a: SO:0000413 ! sequence_difference [Term] id: SO:0000702 name: possible_assembly_error def: "A region of sequence where there may have been an error in the assembly." [SO:ke] subset: SOFA synonym: "possible assembly error" EXACT [] is_a: SO:0000413 ! sequence_difference [Term] id: SO:0000703 name: experimental_result_region def: "A region of sequence implicated in an experimental result." [SO:ke] subset: SOFA synonym: "experimental result region" EXACT [] is_a: SO:0000700 ! remark [Term] id: SO:0000704 name: gene def: "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance. subset: SOFA xref: http://en.wikipedia.org/wiki/Gene "wiki" is_a: SO:0001411 ! biological_region relationship: member_of SO:0005855 ! gene_group [Term] id: SO:0000705 name: tandem_repeat def: "Two or more adjcent copies of a region (of length greater than 1)." [SO:ke] subset: SOFA synonym: "tandem repeat" EXACT [] xref: http://en.wikipedia.org/wiki/Tandem_repeat "wiki" xref: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html is_a: SO:0000657 ! repeat_region [Term] id: SO:0000706 name: trans_splice_acceptor_site def: "The 3' splice site of the acceptor primary transcript." [SO:ke] comment: This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans. subset: SOFA synonym: "3' trans splice site" RELATED [] synonym: "trans splice acceptor site" EXACT [] is_a: SO:0001420 ! trans_splice_site [Term] id: SO:0000714 name: nucleotide_motif def: "A region of nucleotide sequence corresponding to a known motif." [SO:ke] subset: SOFA synonym: "nucleotide motif" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0000715 name: RNA_motif def: "A motif that is active in RNA sequence." [SO:ke] subset: SOFA synonym: "RNA motif" EXACT [] is_a: SO:0000714 ! nucleotide_motif [Term] id: SO:0000717 name: reading_frame def: "A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb] comment: This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop. subset: SOFA synonym: "reading frame" EXACT [] xref: http://en.wikipedia.org/wiki/Reading_frame "wiki" is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000719 name: ultracontig def: "An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG] subset: SOFA is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0000724 name: oriT def: "A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "origin of transfer" EXACT [] xref: http://en.wikipedia.org/wiki/Origin_of_transfer "wiki" is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000725 name: transit_peptide alt_id: BS:00055 def: "The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: Added to bring SO inline with the embl ddbj genbank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle. subset: biosapiens subset: SOFA synonym: "signal" RELATED [] synonym: "transit" RELATED [uniprot:feature_type] synonym: "transit peptide" EXACT [] is_a: SO:0001527 ! peptide_localization_signal [Term] id: SO:0000727 name: CRM def: "A regulatory_region where more than 1 TF_binding_site together are regulatorily active." [SO:SG] comment: Requested by Stepen Grossmann Dec 2004. subset: SOFA synonym: "cis regulatory module" EXACT [] synonym: "TF module" EXACT [] is_a: SO:0001055 ! implied link automatically realized ! transcriptional_cis_regulatory_region intersection_of: SO:0001055 ! transcriptional_cis_regulatory_region intersection_of: has_part SO:0000235 ! TF_binding_site [Term] id: SO:0000730 name: gap def: "A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke] subset: SOFA is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000353 ! sequence_assembly [Term] id: SO:0000752 name: gene_group_regulatory_region subset: SOFA synonym: "gene group regulatory region" EXACT [] is_a: SO:0005836 ! regulatory_region relationship: member_of SO:0005855 ! gene_group [Term] id: SO:0000753 name: clone_insert def: "The region of sequence that has been inserted and is being propogated by the clone." [SO:ke] subset: SOFA synonym: "clone insert" EXACT [] is_a: SO:0000695 ! reagent relationship: part_of SO:0000151 ! clone [Term] id: SO:0000777 name: pseudogenic_rRNA def: "A non functional descendent of an rRNA." [SO:ke] comment: Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations. subset: SOFA synonym: "pseudogenic rRNA" EXACT [] is_a: SO:0000462 ! pseudogenic_region [Term] id: SO:0000778 name: pseudogenic_tRNA def: "A non functional descendent of a tRNA." [SO:ke] comment: Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations. subset: SOFA synonym: "pseudogenic tRNA" EXACT [] is_a: SO:0000462 ! pseudogenic_region [Term] id: SO:0000830 name: chromosome_part def: "A region of a chromosome." [SO:ke] comment: This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root. subset: SOFA synonym: "chromosome part" EXACT [] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000340 ! chromosome [Term] id: SO:0000831 name: gene_member_region def: "A region of a gene." [SO:ke] comment: A manufactured term used to allow the parts of a gene to have an is_a path to the root. subset: SOFA synonym: "gene member region" EXACT [] is_a: SO:0001411 ! biological_region relationship: member_of SO:0000704 ! gene [Term] id: SO:0000833 name: transcript_region def: "A region of a transcript." [SO:ke] comment: This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root. subset: SOFA synonym: "transcript region" EXACT [] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000673 ! transcript [Term] id: SO:0000834 name: mature_transcript_region def: "A region of a mature transcript." [SO:ke] comment: A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root. subset: SOFA synonym: "mature transcript region" EXACT [] is_a: SO:0000833 ! transcript_region [Term] id: SO:0000835 name: primary_transcript_region def: "A part of a primary transcript." [SO:ke] comment: This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root. subset: SOFA synonym: "primary transcript region" EXACT [] is_a: SO:0000833 ! transcript_region relationship: part_of SO:0000185 ! primary_transcript [Term] id: SO:0000836 name: mRNA_region def: "A region of an mRNA." [SO:cb] comment: This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root. subset: SOFA synonym: "mRNA region" EXACT [] is_a: SO:0000834 ! mature_transcript_region relationship: part_of SO:0000234 ! mRNA [Term] id: SO:0000837 name: UTR_region def: "A region of UTR." [SO:ke] comment: A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root. subset: SOFA synonym: "UTR region" EXACT [] is_a: SO:0000836 ! mRNA_region [Term] id: SO:0000839 name: polypeptide_region alt_id: BS:00124 alt_id: BS:00331 def: "Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke] comment: Added to allow the polypeptide regions to have is_a paths back to the root. subset: biosapiens subset: SOFA synonym: "positional" RELATED [] synonym: "positional polypeptide feature" RELATED [] synonym: "region" NARROW [uniprot:feature_type] synonym: "region or site annotation" RELATED [] synonym: "site" NARROW [uniprot:feature_type] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000104 ! polypeptide [Term] id: SO:0000841 name: spliceosomal_intron_region def: "A region within an intron." [SO:ke] comment: A terms added to allow the parts of introns to have is_a paths to the root. subset: SOFA synonym: "spliceosomal intron region" EXACT [] is_a: SO:0000835 ! primary_transcript_region relationship: part_of SO:0000662 ! spliceosomal_intron [Term] id: SO:0000842 name: gene_component_region subset: SOFA synonym: "gene component region" EXACT [] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000704 ! gene [Term] id: SO:0000851 name: CDS_region def: "A region of a CDS." [SO:cb] subset: SOFA synonym: "CDS region" EXACT [] is_a: SO:0000836 ! mRNA_region relationship: part_of SO:0000316 ! CDS [Term] id: SO:0000852 name: exon_region def: "A region of an exon." [RSC:cb] subset: SOFA synonym: "exon region" EXACT [] is_a: SO:0000833 ! transcript_region relationship: part_of SO:0000147 ! exon [Term] id: SO:0001000 name: rRNA_16S def: "A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke] subset: SOFA synonym: "16S ribosomal RNA" EXACT [] synonym: "16S rRNA" RELATED [] synonym: "16S SSU RNA" EXACT [] synonym: "rRNA 16S" EXACT [] xref: http://en.wikipedia.org/wiki/16S_ribosomal_RNA "wiki" is_a: SO:0000650 ! small_subunit_rRNA [Term] id: SO:0001001 name: rRNA_23S def: "A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke] subset: SOFA synonym: "23S LSU rRNA" EXACT [] synonym: "23S ribosomal RNA" RELATED [] synonym: "23S rRNA" EXACT [] synonym: "rRNA 23S" EXACT [] is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0001002 name: rRNA_25S def: "A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb] subset: SOFA synonym: "25S LSU rRNA" EXACT [] synonym: "25S ribosomal RNA" EXACT [] synonym: "25S rRNA" EXACT [] synonym: "rRNA 25S" EXACT [] is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0001019 name: copy_number_variation def: "A variation that increases or decreases the copy number of a given region." [SO:ke] subset: SOFA synonym: "CNP" EXACT [] synonym: "CNV" EXACT [] synonym: "copy number polymorphism" EXACT [] synonym: "copy number variation" EXACT [] xref: http://en.wikipedia.org/wiki/Copy_number_variation "wiki" is_a: SO:0001059 ! sequence_alteration [Term] id: SO:0001037 name: mobile_genetic_element def: "A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355] subset: SOFA synonym: "MGE" EXACT [] synonym: "mobile genetic element" EXACT [] xref: http://en.wikipedia.org/wiki/Mobile_genetic_element "wiki" is_a: SO:0001411 ! biological_region intersection_of: SO:0000001 ! region [Term] id: SO:0001039 name: integrated_mobile_genetic_element def: "An MGE that is integrated into the host chromosome." [SO:ke] subset: SOFA synonym: "integrated mobile genetic element" EXACT [] is_a: SO:0001037 ! mobile_genetic_element [Term] id: SO:0001055 name: transcriptional_cis_regulatory_region def: "A regulatory_region that modulates the transcription of a gene or genes." [SO:regcreative] subset: SOFA synonym: "transcriptional cis regulatory region" EXACT [] is_a: SO:0005836 ! regulatory_region [Term] id: SO:0001056 name: splicing_regulatory_region def: "A regulatory_region that modulates splicing." [SO:ke] subset: SOFA synonym: "splicing regulatory region" EXACT [] is_a: SO:0005836 ! regulatory_region [Term] id: SO:0001059 name: sequence_alteration alt_id: SO:1000004 alt_id: SO:1000007 def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke] comment: Merged with partially characterized change in nucleotide sequence. subset: SOFA synonym: "partially characterised change in DNA sequence" EXACT [] synonym: "partially_characterised_change_in_DNA_sequence" EXACT [] synonym: "sequence alteration" EXACT [] is_a: SO:0000110 ! sequence_feature [Term] id: SO:0001063 name: immature_peptide_region alt_id: BS:00129 def: "An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR] comment: Range. subset: biosapiens subset: SOFA synonym: "immature_peptide_region" EXACT [] is_a: SO:0000839 ! polypeptide_region [Term] id: SO:0001214 name: noncoding_region_of_exon def: "The maximal intersection of exon and UTR." [SO:ke] comment: An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding. subset: SOFA synonym: "noncoding region of exon" EXACT [] is_a: SO:0000852 ! exon_region [Term] id: SO:0001215 name: coding_region_of_exon def: "The region of an exon that encodes for protein sequence." [SO:ke] comment: An exon containing either a start or stop codon will be partially coding and partially non coding. subset: SOFA synonym: "coding region of exon" EXACT [] is_a: SO:0000852 ! exon_region [Term] id: SO:0001235 name: replicon def: "A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207] subset: SOFA xref: http://en.wikipedia.org/wiki/Replicon_(genetics) "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0001236 name: base def: "A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Nucleobase "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0001248 name: assembly def: "A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly "wiki" is_a: SO:0001410 ! experimental_feature [Term] id: SO:0001409 name: biomaterial_region def: "A region which is intended for use in an experiment." [SO:cb] subset: SOFA synonym: "biomaterial region" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001410 name: experimental_feature def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb] subset: SOFA synonym: "analysis feature" RELATED [] synonym: "experimental output artefact" EXACT [] synonym: "experimental_output_artefact" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001411 name: biological_region def: "A region defined by its disposition to be involved in a biological process." [SO:cb] subset: SOFA synonym: "biological region" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001412 name: topologically_defined_region def: "A region that is defined according to its relations with other regions within the same sequence." [SO:cb] subset: SOFA synonym: "topologically defined region" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001419 name: cis_splice_site def: "Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke] subset: SOFA synonym: "cis splice site" EXACT [] is_a: SO:0000162 ! splice_site [Term] id: SO:0001420 name: trans_splice_site def: "Primary transcript region bordering trans-splice junction." [SO:ke] subset: SOFA synonym: "trans splice site" EXACT [] is_a: SO:0000162 ! splice_site [Term] id: SO:0001483 name: SNV def: "SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist." [SO:bm] subset: SOFA synonym: "single nucleotide variant" EXACT [] is_a: SO:1000002 ! substitution created_by: kareneilbeck creation_date: 2009-10-08T11:37:49Z [Term] id: SO:0001527 name: peptide_localization_signal def: "A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke] subset: SOFA synonym: "localization signal" RELATED [] synonym: "peptide localization signal" EXACT [] is_a: SO:0000839 ! polypeptide_region created_by: kareneilbeck creation_date: 2010-03-11T02:15:05Z [Term] id: SO:0001720 name: epigenetically_modified_region def: "A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke] subset: SOFA synonym: "epigenetically modified region" RELATED [] is_a: SO:0001411 ! biological_region intersection_of: SO:0001411 ! biological_region created_by: kareneilbeck creation_date: 2010-03-27T12:02:29Z [Term] id: SO:0005836 name: regulatory_region def: "A DNA sequence that controls the expression of a gene." [SO:ke] subset: SOFA synonym: "regulatory region" EXACT [] xref: http://en.wikipedia.org/wiki/Regulatory_region "wiki" is_a: SO:0000831 ! gene_member_region [Term] id: SO:0005855 name: gene_group def: "A collection of related genes." [SO:ma] subset: SOFA synonym: "gene group" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0100011 name: cleaved_peptide_region def: "The cleaved_peptide_regon is the a region of peptide sequence that is cleaved during maturation." [EBIBS:GAR] comment: Range. subset: biosapiens subset: SOFA synonym: "cleaved peptide region" EXACT [] is_a: SO:0000839 ! polypeptide_region relationship: part_of SO:0001063 ! immature_peptide_region [Term] id: SO:1000002 name: substitution def: "Any change in genomic DNA caused by a single event." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] subset: SOFA is_a: SO:0001059 ! sequence_alteration is_a: SO:0001411 ! biological_region [Term] id: SO:1000005 name: complex_substitution def: "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] subset: SOFA synonym: "complex substitution" EXACT [] is_a: SO:1000002 ! substitution [Term] id: SO:1000008 name: point_mutation def: "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop] subset: SOFA synonym: "point mutation" EXACT [] xref: http://en.wikipedia.org/wiki/Point_mutation "wiki" is_a: SO:0001483 ! SNV [Term] id: SO:1000036 name: inversion def: "A continuous nucleotide sequence is inverted in the same position." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] subset: SOFA is_a: SO:0001059 ! sequence_alteration is_a: SO:0001411 ! biological_region [Term] id: SO:1001284 name: regulon def: "A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732] subset: SOFA xref: http://en.wikipedia.org/wiki/Regulon "wiki" is_a: SO:0005855 ! gene_group [Term] id: SO:2000061 name: databank_entry def: "The sequence referred to by an entry in a databank such as Genbank or SwissProt." [SO:ke] subset: SOFA synonym: "accession" RELATED [] synonym: "databank entry" EXACT [] is_a: SO:0000695 ! reagent [Typedef] id: adjacent_to name: adjacent_to def: "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence." [SO:ke] subset: SOFA [Typedef] id: associated_with name: associated_with comment: This relationship is vague and up for discussion. [Typedef] id: complete_evidence_for_feature name: complete_evidence_for_feature def: "B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A." [SO:ke] comment: If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222. is_transitive: true is_a: evidence_for_feature ! evidence_for_feature [Typedef] id: derives_from name: derives_from subset: SOFA is_transitive: true [Typedef] id: edited_from name: edited_from created_by: kareneilbeck creation_date: 2009-08-19T02:19:45Z [Typedef] id: edited_to name: edited_to created_by: kareneilbeck creation_date: 2009-08-19T02:19:11Z [Typedef] id: evidence_for_feature name: evidence_for_feature def: "B is evidence_for_feature A, if an instance of B supports the existence of A." [SO:ke] comment: This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222. is_transitive: true [Typedef] id: exemplar_of name: exemplar_of def: "X is exemplar of Y if X is the best evidence for Y." [SO:ke] comment: Tracker id: 2594157. [Typedef] id: genome_of name: genome_of [Typedef] id: guided_by name: guided_by created_by: kareneilbeck creation_date: 2009-08-19T02:27:04Z [Typedef] id: guides name: guides created_by: kareneilbeck creation_date: 2009-08-19T02:27:24Z [Typedef] id: has_genome_location name: has_genome_location is_obsolete: true [Typedef] id: has_intergral_part name: has_integral_part def: "X has_integral_part Y if and only if: X has_part Y and Y part_of X." [http://precedings.nature.com/documents/3495/version/1] comment: Example: mRNA has_integral_part CDS. created_by: kareneilbeck creation_date: 2009-08-19T12:01:46Z [Typedef] id: has_origin name: has_origin [Typedef] id: has_part name: has_part def: "Inverse of part_of." [http://precedings.nature.com/documents/3495/version/1] comment: Example: operon has_part gene. [Typedef] id: has_quality name: has_quality comment: The relationship between a feature and an attribute. [Typedef] id: homologous_to name: homologous_to subset: SOFA is_symmetric: true is_a: similar_to ! similar_to [Typedef] id: integral_part_of name: integral_part_of def: "X integral_part_of Y if and only if: X part_of Y and Y has_part X." [http://precedings.nature.com/documents/3495/version/1] comment: Example: exon integral_part_of transcript. created_by: kareneilbeck creation_date: 2009-08-19T12:03:28Z [Typedef] id: member_of name: member_of comment: A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444. subset: SOFA is_transitive: true [Typedef] id: non_functional_homolog_of name: non_functional_homolog_of def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke] subset: SOFA is_a: homologous_to ! homologous_to [Typedef] id: orthologous_to name: orthologous_to subset: SOFA is_symmetric: true is_a: homologous_to ! homologous_to [Typedef] id: paralogous_to name: paralogous_to subset: SOFA is_symmetric: true is_a: homologous_to ! homologous_to [Typedef] id: part_of name: part_of def: "X part_of Y if X is a subregion of Y." [http://precedings.nature.com/documents/3495/version/1] comment: Example: amino_acid part_of polypeptide. subset: SOFA is_transitive: true [Typedef] id: partial_evidence_for_feature name: partial_evidence_for_feature def: "B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A." [SO:ke] is_a: evidence_for_feature ! evidence_for_feature [Typedef] id: position_of name: position_of [Typedef] id: processed_from name: processed_from def: "Inverse of processed_into." [http://precedings.nature.com/documents/3495/version/1] comment: Example: miRNA processed_from miRNA_primary_transcript. created_by: kareneilbeck creation_date: 2009-08-19T12:14:00Z [Typedef] id: processed_into name: processed_into def: "X is processed_into Y if a region X is modified to create Y." [http://precedings.nature.com/documents/3495/version/1] comment: Example: miRNA_primary_transcript processed into miRNA. created_by: kareneilbeck creation_date: 2009-08-19T12:15:02Z [Typedef] id: recombined_from name: recombined_from created_by: kareneilbeck creation_date: 2009-08-19T02:21:03Z [Typedef] id: recombined_to name: recombined_to created_by: kareneilbeck creation_date: 2009-08-19T02:20:07Z [Typedef] id: regulated_by name: regulated_by is_obsolete: true [Typedef] id: sequence_of name: sequence_of [Typedef] id: similar_to name: similar_to subset: SOFA is_symmetric: true [Typedef] id: trans_spliced_from name: trans_spliced_from created_by: kareneilbeck creation_date: 2009-08-19T02:22:14Z [Typedef] id: trans_spliced_to name: trans_spliced_to created_by: kareneilbeck creation_date: 2009-08-19T02:22:00Z [Typedef] id: transcribed_from name: transcribed_from def: "X is transcribed_from Y if X is synthesized from template Y." [http://precedings.nature.com/documents/3495/version/1] comment: Example: primary_transcript transcribed_from gene. created_by: kareneilbeck creation_date: 2009-08-19T12:05:39Z [Typedef] id: transcribed_to name: transcribed_to def: "Inverse of transcribed_from." [http://precedings.nature.com/documents/3495/version/1] comment: Example: gene transcribed_to primary_transcript. created_by: kareneilbeck creation_date: 2009-08-19T12:08:24Z [Typedef] id: translates_to name: translates_to def: "Inverse of translation _of." [http://precedings.nature.com/documents/3495/version/1] comment: Example: codon translates_to amino_acid. created_by: kareneilbeck creation_date: 2009-08-19T12:11:53Z [Typedef] id: translation_of name: translation_of def: "X is translation of Y if X is translated by ribosome to create Y." [http://precedings.nature.com/documents/3495/version/1] comment: Example: Polypeptide translation_of CDS. created_by: kareneilbeck creation_date: 2009-08-19T12:09:59Z [Typedef] id: variant_of name: variant_of def: "A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A." [SO:immuno_workshop] comment: Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.