1format-version: 1.2 2date: 01:06:2010 10:46 3saved-by: kareneilbeck 4auto-generated-by: OBO-Edit 2.1-beta3 5subsetdef: biosapiens "biosapiens protein feature ontology" 6subsetdef: SOFA "SO feature annotation" 7synonymtypedef: aa1 "amino acid 1 letter code" 8synonymtypedef: aa3 "amino acid 3 letter code" 9synonymtypedef: AAMOD "amino acid modification" 10synonymtypedef: BS "biosapiens" 11synonymtypedef: dbsnp "dbsnp variant terms" 12synonymtypedef: ebi_variants "ensembl variant terms" 13synonymtypedef: RNAMOD "RNA modification" EXACT 14default-namespace: sequence 15remark: autogenerated-by\: DAG-Edit version 1.417\nsaved-by\: eilbeck\ndate\: Tue May 11 15\:18\:44 PDT 2004\nversion\: $Revision\: 1.45 $ 16 17[Term] 18id: SO:0000000 19name: Sequence_Ontology 20subset: SOFA 21is_obsolete: true 22 23[Term] 24id: SO:0000001 25name: region 26def: "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] 27subset: SOFA 28synonym: "sequence" EXACT [] 29is_a: SO:0000110 ! sequence_feature 30 31[Term] 32id: SO:0000004 33name: interior_coding_exon 34subset: SOFA 35synonym: "interior coding exon" EXACT [] 36is_a: SO:0000195 ! coding_exon 37 38[Term] 39id: SO:0000005 40name: satellite_DNA 41def: "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] 42subset: SOFA 43synonym: "satellite DNA" EXACT [] 44xref: http://en.wikipedia.org/wiki/Satellite_DNA "wiki" 45is_a: SO:0000705 ! tandem_repeat 46 47[Term] 48id: SO:0000006 49name: PCR_product 50def: "A region amplified by a PCR reaction." [SO:ke] 51comment: This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406. 52subset: SOFA 53synonym: "amplicon" RELATED [] 54synonym: "PCR product" EXACT [] 55xref: http://en.wikipedia.org/wiki/RAPD "wiki" 56is_a: SO:0000695 ! reagent 57 58[Term] 59id: SO:0000007 60name: read_pair 61def: "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] 62subset: SOFA 63synonym: "read-pair" EXACT [] 64is_a: SO:0000143 ! assembly_component 65relationship: part_of SO:0000149 ! contig 66 67[Term] 68id: SO:0000013 69name: scRNA 70def: "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] 71subset: SOFA 72synonym: "small cytoplasmic RNA" EXACT [] 73is_a: SO:0000655 ! ncRNA 74 75[Term] 76id: SO:0000038 77name: match_set 78def: "A collection of match parts." [SO:ke] 79subset: SOFA 80is_obsolete: true 81 82[Term] 83id: SO:0000039 84name: match_part 85def: "A part of a match, for example an hsp from blast is a match_part." [SO:ke] 86subset: SOFA 87synonym: "match part" EXACT [] 88is_a: SO:0001410 ! experimental_feature 89relationship: part_of SO:0000343 ! match 90 91[Term] 92id: SO:0000050 93name: gene_part 94def: "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] 95subset: SOFA 96is_obsolete: true 97 98[Term] 99id: SO:0000057 100name: operator 101def: "A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma] 102subset: SOFA 103synonym: "operator segment" EXACT [] 104xref: http://en.wikipedia.org/wiki/Operator_(biology)#Operator "wiki" 105is_a: SO:0000752 ! gene_group_regulatory_region 106 107[Term] 108id: SO:0000059 109name: nuclease_binding_site 110def: "A region of a molecule that binds to a nuclease." [SO:cb] 111subset: SOFA 112synonym: "nuclease binding site" EXACT [] 113is_a: SO:0000410 ! protein_binding_site 114 115[Term] 116id: SO:0000101 117name: transposable_element 118def: "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] 119subset: SOFA 120synonym: "transposable element" EXACT [] 121synonym: "transposon" EXACT [] 122xref: http://en.wikipedia.org/wiki/Transposable_element "wiki" 123is_a: SO:0001039 ! integrated_mobile_genetic_element 124 125[Term] 126id: SO:0000102 127name: expressed_sequence_match 128def: "A match to an EST or cDNA sequence." [SO:ke] 129subset: SOFA 130synonym: "expressed sequence match" EXACT [] 131is_a: SO:0000347 ! nucleotide_match 132 133[Term] 134id: SO:0000103 135name: clone_insert_end 136def: "The end of the clone insert." [SO:ke] 137subset: SOFA 138synonym: "clone insert end" EXACT [] 139is_a: SO:0000699 ! junction 140relationship: part_of SO:0000753 ! clone_insert 141 142[Term] 143id: SO:0000104 144name: polypeptide 145alt_id: SO:0000358 146def: "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] 147comment: 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. 148subset: SOFA 149synonym: "protein" EXACT [] 150xref: http://en.wikipedia.org/wiki/Polypeptide "wiki" 151is_a: SO:0001411 ! biological_region 152relationship: derives_from SO:0000316 ! CDS 153 154[Term] 155id: SO:0000109 156name: sequence_variant_obs 157def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke] 158subset: SOFA 159synonym: "mutation" RELATED [] 160is_obsolete: true 161 162[Term] 163id: SO:0000110 164name: sequence_feature 165def: "An extent of biological sequence." [SO:ke] 166subset: SOFA 167synonym: "located sequence feature" RELATED [] 168synonym: "located_sequence_feature" EXACT [] 169synonym: "sequence feature" EXACT [] 170 171[Term] 172id: SO:0000112 173name: primer 174def: "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] 175subset: SOFA 176synonym: "DNA primer" EXACT [] 177synonym: "primer oligonucleotide" EXACT [] 178synonym: "primer polynucleotide" EXACT [] 179synonym: "primer sequence" EXACT [] 180xref: http://en.wikipedia.org/wiki/Primer_(molecular_biology) "wiki" 181is_a: SO:0000441 ! ss_oligo 182 183[Term] 184id: SO:0000113 185name: proviral_region 186def: "A viral sequence which has integrated into a host genome." [SO:ke] 187subset: SOFA 188synonym: "proviral region" EXACT [] 189synonym: "proviral sequence" RELATED [] 190is_a: SO:0001039 ! integrated_mobile_genetic_element 191 192[Term] 193id: SO:0000114 194name: methylated_C 195def: "A methylated deoxy-cytosine." [SO:ke] 196subset: SOFA 197synonym: "methylated C" EXACT [] 198synonym: "methylated cytosine" EXACT [] 199synonym: "methylated cytosine base" EXACT [] 200synonym: "methylated cytosine residue" EXACT [] 201is_a: SO:0000306 ! methylated_base_feature 202 203[Term] 204id: SO:0000120 205name: protein_coding_primary_transcript 206def: "A primary transcript that, at least in part, encodes one or more proteins." [SO:ke] 207comment: May contain introns. 208subset: SOFA 209synonym: "pre mRNA" RELATED [] 210synonym: "protein coding primary transcript" EXACT [] 211is_a: SO:0000185 ! primary_transcript 212 213[Term] 214id: SO:0000139 215name: ribosome_entry_site 216def: "Region in mRNA where ribosome assembles." [SO:ke] 217subset: SOFA 218synonym: "ribosome entry site" EXACT [] 219is_a: SO:0000837 ! UTR_region 220relationship: part_of SO:0000203 ! UTR 221 222[Term] 223id: SO:0000140 224name: attenuator 225def: "A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as] 226subset: SOFA 227synonym: "attenuator sequence" EXACT [] 228xref: http://en.wikipedia.org/wiki/Attenuator "wiki" 229is_a: SO:0005836 ! regulatory_region 230relationship: part_of SO:0000234 ! mRNA 231 232[Term] 233id: SO:0000141 234name: terminator 235def: "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] 236subset: SOFA 237synonym: "terminator sequence" EXACT [] 238xref: http://en.wikipedia.org/wiki/Terminator_(genetics) "wiki" 239is_a: SO:0005836 ! regulatory_region 240relationship: part_of SO:0000673 ! transcript 241 242[Term] 243id: SO:0000143 244name: assembly_component 245def: "A region of known length which may be used to manufacture a longer region." [SO:ke] 246subset: SOFA 247synonym: "assembly component" EXACT [] 248is_a: SO:0001410 ! experimental_feature 249 250[Term] 251id: SO:0000147 252name: exon 253def: "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke] 254comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. 255subset: SOFA 256xref: http://en.wikipedia.org/wiki/Exon "wiki" 257is_a: SO:0000833 ! transcript_region 258 259[Term] 260id: SO:0000148 261name: supercontig 262def: "One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls] 263subset: SOFA 264synonym: "scaffold" RELATED [] 265is_a: SO:0000353 ! sequence_assembly 266relationship: part_of SO:0000719 ! ultracontig 267 268[Term] 269id: SO:0000149 270name: contig 271def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls] 272subset: SOFA 273xref: http://en.wikipedia.org/wiki/Contig "wiki" 274is_a: SO:0000143 ! assembly_component 275is_a: SO:0000353 ! sequence_assembly 276relationship: part_of SO:0000148 ! supercontig 277 278[Term] 279id: SO:0000150 280name: read 281def: "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] 282subset: SOFA 283is_a: SO:0000143 ! assembly_component 284relationship: part_of SO:0000149 ! contig 285 286[Term] 287id: SO:0000151 288name: clone 289def: "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] 290subset: SOFA 291xref: http:http\://en.wikipedia.org/wiki/Clone_(genetics) "wiki" 292is_a: SO:0000695 ! reagent 293 294[Term] 295id: SO:0000159 296name: deletion 297alt_id: SO:1000033 298def: "The point at which one or more contiguous nucleotides were excised." [SO:ke] 299subset: SOFA 300synonym: "deleted_sequence" EXACT [] 301synonym: "nucleotide deletion" EXACT [] 302synonym: "nucleotide_deletion" EXACT [] 303xref: http://en.wikipedia.org/wiki/Nucleotide_deletion "wiki" 304is_a: SO:0001059 ! sequence_alteration 305is_a: SO:0001411 ! biological_region 306 307[Term] 308id: SO:0000161 309name: methylated_A 310def: "A modified RNA base in which adenine has been methylated." [SO:ke] 311subset: SOFA 312synonym: "methylated A" EXACT [] 313synonym: "methylated adenine" EXACT [] 314synonym: "methylated adenine base" EXACT [] 315synonym: "methylated adenine residue" EXACT [] 316is_a: SO:0000306 ! methylated_base_feature 317 318[Term] 319id: SO:0000162 320name: splice_site 321def: "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] 322comment: With spliceosomal introns, the splice sites bind the spliceosomal machinery. 323subset: SOFA 324synonym: "splice site" EXACT [] 325xref: http://en.wikipedia.org/wiki/Splice_site "wiki" 326is_a: SO:0000835 ! primary_transcript_region 327 328[Term] 329id: SO:0000163 330name: five_prime_cis_splice_site 331def: "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] 332subset: SOFA 333synonym: "5' splice site" EXACT [] 334synonym: "donor" RELATED [] 335synonym: "donor splice site" EXACT [] 336synonym: "five prime splice site" EXACT [] 337synonym: "splice donor site" EXACT [] 338is_a: SO:0001419 ! cis_splice_site 339 340[Term] 341id: SO:0000164 342name: three_prime_cis_splice_site 343def: "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] 344subset: SOFA 345synonym: "3' splice site" RELATED [] 346synonym: "acceptor" RELATED [] 347synonym: "acceptor splice site" EXACT [] 348synonym: "splice acceptor site" EXACT [] 349synonym: "three prime splice site" EXACT [] 350is_a: SO:0001419 ! cis_splice_site 351 352[Term] 353id: SO:0000165 354name: enhancer 355def: "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] 356comment: 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. 357subset: SOFA 358xref: http://en.wikipedia.org/wiki/Enhancer_(genetics) "wiki" 359is_a: SO:0000727 ! CRM 360 361[Term] 362id: SO:0000167 363name: promoter 364def: "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative] 365comment: 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. 366subset: SOFA 367synonym: "promoter sequence" EXACT [] 368xref: http://en.wikipedia.org/wiki/Promoter "wiki" 369is_a: SO:0001055 ! transcriptional_cis_regulatory_region 370 371[Term] 372id: SO:0000177 373name: cross_genome_match 374def: "A nucleotide match against a sequence from another organism." [SO:ma] 375subset: SOFA 376synonym: "cross genome match" EXACT [] 377is_a: SO:0000347 ! nucleotide_match 378 379[Term] 380id: SO:0000178 381name: operon 382def: "A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma] 383comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. 384subset: SOFA 385xref: http://en.wikipedia.org/wiki/Operon "wiki" 386is_a: SO:0005855 ! gene_group 387 388[Term] 389id: SO:0000179 390name: clone_insert_start 391def: "The start of the clone insert." [SO:ke] 392subset: SOFA 393synonym: "clone insert start" EXACT [] 394is_a: SO:0000699 ! junction 395relationship: part_of SO:0000753 ! clone_insert 396 397[Term] 398id: SO:0000181 399name: translated_nucleotide_match 400def: "A match against a translated sequence." [SO:ke] 401subset: SOFA 402synonym: "translated nucleotide match" EXACT [] 403is_a: SO:0000347 ! nucleotide_match 404 405[Term] 406id: SO:0000183 407name: non_transcribed_region 408def: "A region of the gene which is not transcribed." [SO:ke] 409subset: SOFA 410synonym: "non transcribed region" EXACT [] 411synonym: "non-transcribed sequence" EXACT [] 412synonym: "nontranscribed region" EXACT [] 413synonym: "nontranscribed sequence" EXACT [] 414is_a: SO:0000842 ! gene_component_region 415 416[Term] 417id: SO:0000185 418name: primary_transcript 419def: "A transcript that in its initial state requires modification to be functional." [SO:ma] 420subset: SOFA 421synonym: "precursor RNA" EXACT [] 422synonym: "primary transcript" EXACT [] 423xref: http://en.wikipedia.org/wiki/Primary_transcript "wiki" 424is_a: SO:0000673 ! transcript 425 426[Term] 427id: SO:0000187 428name: repeat_family 429def: "A group of characterized repeat sequences." [SO:ke] 430subset: SOFA 431is_obsolete: true 432 433[Term] 434id: SO:0000188 435name: intron 436def: "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] 437comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. 438subset: SOFA 439xref: http://en.wikipedia.org/wiki/Intron "wiki" 440is_a: SO:0000835 ! primary_transcript_region 441 442[Term] 443id: SO:0000193 444name: RFLP_fragment 445def: "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] 446subset: SOFA 447synonym: "restriction fragment length polymorphism" EXACT [] 448synonym: "RFLP" EXACT [] 449synonym: "RFLP fragment" EXACT [] 450xref: http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism "wiki" 451is_a: SO:0000412 ! restriction_fragment 452 453[Term] 454id: SO:0000195 455name: coding_exon 456def: "An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke] 457subset: SOFA 458synonym: "coding exon" EXACT [] 459is_a: SO:0000147 ! exon 460 461[Term] 462id: SO:0000196 463name: five_prime_coding_exon_coding_region 464def: "The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm] 465subset: SOFA 466synonym: "five prime exon coding region" EXACT [] 467is_a: SO:0001215 ! coding_region_of_exon 468relationship: part_of SO:0000200 ! five_prime_coding_exon 469 470[Term] 471id: SO:0000197 472name: three_prime_coding_exon_coding_region 473def: "The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm] 474subset: SOFA 475synonym: "three prime exon coding region" EXACT [] 476is_a: SO:0001215 ! coding_region_of_exon 477 478[Term] 479id: SO:0000198 480name: noncoding_exon 481def: "An exon that does not contain any codons." [SO:ke] 482subset: SOFA 483synonym: "noncoding exon" EXACT [] 484is_a: SO:0000147 ! exon 485 486[Term] 487id: SO:0000200 488name: five_prime_coding_exon 489def: "The 5' most coding exon." [SO:ke] 490subset: SOFA 491synonym: "5' coding exon" EXACT [] 492synonym: "five prime coding exon" EXACT [] 493is_a: SO:0000195 ! coding_exon 494 495[Term] 496id: SO:0000203 497name: UTR 498def: "Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke] 499subset: SOFA 500synonym: "untranslated region" EXACT [] 501is_a: SO:0000836 ! mRNA_region 502 503[Term] 504id: SO:0000204 505name: five_prime_UTR 506def: "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] 507subset: SOFA 508synonym: "5' UTR" EXACT [] 509synonym: "five prime UTR" EXACT [] 510synonym: "five_prime_untranslated_region" EXACT [] 511xref: http://en.wikipedia.org/wiki/5'_UTR "wiki" 512is_a: SO:0000203 ! UTR 513 514[Term] 515id: SO:0000205 516name: three_prime_UTR 517def: "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] 518subset: SOFA 519synonym: "three prime untranslated region" EXACT [] 520synonym: "three prime UTR" EXACT [] 521xref: http://en.wikipedia.org/wiki/Three_prime_untranslated_region "wiki" 522is_a: SO:0000203 ! UTR 523 524[Term] 525id: SO:0000209 526name: rRNA_primary_transcript 527def: "A primary transcript encoding a ribosomal RNA." [SO:ke] 528subset: SOFA 529synonym: "ribosomal RNA primary transcript" EXACT [] 530synonym: "rRNA primary transcript" EXACT [] 531is_a: SO:0000483 ! nc_primary_transcript 532 533[Term] 534id: SO:0000233 535name: mature_transcript 536def: "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] 537comment: A processed transcript cannot contain introns. 538subset: SOFA 539synonym: "mature transcript" EXACT [] 540xref: http://en.wikipedia.org/wiki/Mature_transcript "wiki" 541is_a: SO:0000673 ! transcript 542relationship: derives_from SO:0000185 ! primary_transcript 543 544[Term] 545id: SO:0000234 546name: mRNA 547def: "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma] 548comment: 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. 549subset: SOFA 550synonym: "messenger RNA" EXACT [] 551xref: http://en.wikipedia.org/wiki/MRNA "wiki" 552is_a: SO:0000233 ! mature_transcript 553 554[Term] 555id: SO:0000235 556name: TF_binding_site 557def: "A region of a molecule that binds a TF complex [GO:0005667]." [SO:ke] 558subset: SOFA 559synonym: "TF binding site" EXACT [] 560synonym: "transcription factor binding site" EXACT [] 561is_a: SO:0000410 ! protein_binding_site 562is_a: SO:0005836 ! regulatory_region 563 564[Term] 565id: SO:0000236 566name: ORF 567def: "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] 568comment: 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. 569subset: SOFA 570synonym: "open reading frame" EXACT [] 571is_a: SO:0000717 ! reading_frame 572 573[Term] 574id: SO:0000239 575name: flanking_region 576def: "The sequences extending on either side of a specific region." [SO:ke] 577subset: SOFA 578synonym: "flanking region" EXACT [] 579is_a: SO:0001412 ! topologically_defined_region 580 581[Term] 582id: SO:0000252 583name: rRNA 584def: "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] 585subset: SOFA 586synonym: "ribosomal ribonucleic acid" EXACT [] 587synonym: "ribosomal RNA" EXACT [] 588xref: http://en.wikipedia.org/wiki/RRNA "wiki" 589is_a: SO:0000655 ! ncRNA 590relationship: derives_from SO:0000209 ! rRNA_primary_transcript 591 592[Term] 593id: SO:0000253 594name: tRNA 595def: "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] 596comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. 597subset: SOFA 598synonym: "transfer ribonucleic acid" RELATED [] 599synonym: "transfer RNA" RELATED [] 600xref: http://en.wikipedia.org/wiki/TRNA "wiki" 601is_a: SO:0000655 ! ncRNA 602 603[Term] 604id: SO:0000274 605name: snRNA 606def: "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] 607comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. 608subset: SOFA 609synonym: "small nuclear RNA" EXACT [] 610xref: http://en.wikipedia.org/wiki/SnRNA "wiki" 611is_a: SO:0000655 ! ncRNA 612 613[Term] 614id: SO:0000275 615name: snoRNA 616def: "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] 617subset: SOFA 618synonym: "small nucleolar RNA" EXACT [] 619xref: http://en.wikipedia.org/wiki/SnoRNA "wiki" 620is_a: SO:0000655 ! ncRNA 621 622[Term] 623id: SO:0000276 624name: miRNA 625def: "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] 626subset: SOFA 627synonym: "micro RNA" EXACT [] 628synonym: "microRNA" EXACT [] 629xref: http://en.wikipedia.org/wiki/MiRNA "wiki" 630is_a: SO:0000370 ! small_regulatory_ncRNA 631 632[Term] 633id: SO:0000289 634name: microsatellite 635def: "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] 636subset: SOFA 637synonym: "microsatellite locus" EXACT [] 638synonym: "microsatellite marker" EXACT [] 639synonym: "VNTR" EXACT [] 640xref: http://en.wikipedia.org/wiki/Microsatellite "wiki" 641is_a: SO:0000005 ! satellite_DNA 642 643[Term] 644id: SO:0000294 645name: inverted_repeat 646def: "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] 647subset: SOFA 648synonym: "inverted repeat" EXACT [] 649synonym: "inverted repeat sequence" EXACT [] 650xref: http://en.wikipedia.org/wiki/Inverted_repeat "wiki" 651is_a: SO:0000657 ! repeat_region 652 653[Term] 654id: SO:0000296 655name: origin_of_replication 656def: "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] 657subset: SOFA 658synonym: "ori" EXACT [] 659synonym: "origin of replication" EXACT [] 660xref: http://en.wikipedia.org/wiki/Origin_of_replication "wiki" 661is_a: SO:0001411 ! biological_region 662relationship: part_of SO:0001235 ! replicon 663 664[Term] 665id: SO:0000303 666name: clip 667def: "Part of the primary transcript that is clipped off during processing." [SO:ke] 668subset: SOFA 669is_a: SO:0000835 ! primary_transcript_region 670 671[Term] 672id: SO:0000305 673name: modified_base 674def: "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] 675comment: Modified base:<modified_base>. 676subset: SOFA 677synonym: "modified base site" EXACT [] 678is_a: SO:0001720 ! epigenetically_modified_region 679 680[Term] 681id: SO:0000306 682name: methylated_base_feature 683def: "A nucleotide modified by methylation." [SO:ke] 684subset: SOFA 685synonym: "methylated base feature" EXACT [] 686is_a: SO:0000305 ! modified_base 687 688[Term] 689id: SO:0000307 690name: CpG_island 691def: "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] 692subset: SOFA 693synonym: "CG island" EXACT [] 694synonym: "CpG island" EXACT [] 695xref: http://en.wikipedia.org/wiki/CpG_island "wiki" 696is_a: SO:0001411 ! biological_region 697 698[Term] 699id: SO:0000314 700name: direct_repeat 701def: "A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA." [SO:ke] 702subset: SOFA 703synonym: "direct repeat" EXACT [] 704xref: http://en.wikipedia.org/wiki/Direct_repeat "wiki" 705is_a: SO:0000657 ! repeat_region 706 707[Term] 708id: SO:0000315 709name: TSS 710def: "The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke] 711subset: SOFA 712synonym: "transcription start site" EXACT [] 713is_a: SO:0000835 ! primary_transcript_region 714 715[Term] 716id: SO:0000316 717name: CDS 718def: "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma] 719subset: SOFA 720synonym: "coding sequence" EXACT [] 721is_a: SO:0000836 ! mRNA_region 722 723[Term] 724id: SO:0000318 725name: start_codon 726def: "First codon to be translated by a ribosome." [SO:ke] 727subset: SOFA 728synonym: "initiation codon" EXACT [] 729synonym: "start codon" EXACT [] 730xref: http://en.wikipedia.org/wiki/Start_codon "wiki" 731is_a: SO:0000360 ! codon 732 733[Term] 734id: SO:0000319 735name: stop_codon 736def: "In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke] 737subset: SOFA 738synonym: "stop codon" EXACT [] 739xref: http://en.wikipedia.org/wiki/Stop_codon "wiki" 740is_a: SO:0000360 ! codon 741 742[Term] 743id: SO:0000324 744name: tag 745def: "A nucleotide sequence that may be used to identify a larger sequence." [SO:ke] 746subset: SOFA 747is_a: SO:0000696 ! oligo 748 749[Term] 750id: SO:0000325 751name: rRNA_large_subunit_primary_transcript 752def: "A primary transcript encoding a large ribosomal subunit RNA." [SO:ke] 753subset: SOFA 754synonym: "rRNA large subunit primary transcript" EXACT [] 755is_a: SO:0000209 ! rRNA_primary_transcript 756 757[Term] 758id: SO:0000326 759name: SAGE_tag 760def: "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] 761subset: SOFA 762synonym: "SAGE tag" EXACT [] 763is_a: SO:0000324 ! tag 764 765[Term] 766id: SO:0000330 767name: conserved_region 768def: "Region of sequence similarity by descent from a common ancestor." [SO:ke] 769subset: SOFA 770synonym: "conserved region" EXACT [] 771xref: http://en.wikipedia.org/wiki/Conserved_region "wiki" 772is_a: SO:0001410 ! experimental_feature 773 774[Term] 775id: SO:0000331 776name: STS 777def: "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] 778subset: SOFA 779synonym: "sequence tag site" EXACT [] 780is_a: SO:0000324 ! tag 781 782[Term] 783id: SO:0000332 784name: coding_conserved_region 785def: "Coding region of sequence similarity by descent from a common ancestor." [SO:ke] 786subset: SOFA 787synonym: "coding conserved region" EXACT [] 788is_a: SO:0000330 ! conserved_region 789 790[Term] 791id: SO:0000333 792name: exon_junction 793def: "The boundary between two exons in a processed transcript." [SO:ke] 794subset: SOFA 795synonym: "exon junction" EXACT [] 796is_a: SO:0000699 ! junction 797relationship: part_of SO:0000233 ! mature_transcript 798 799[Term] 800id: SO:0000334 801name: nc_conserved_region 802def: "Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke] 803subset: SOFA 804synonym: "nc conserved region" EXACT [] 805synonym: "noncoding conserved region" EXACT [] 806is_a: SO:0000330 ! conserved_region 807 808[Term] 809id: SO:0000336 810name: pseudogene 811def: "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] 812subset: SOFA 813xref: http://en.wikipedia.org/wiki/Pseudogene "wiki" 814is_a: SO:0000462 ! pseudogenic_region 815relationship: non_functional_homolog_of SO:0000704 ! gene 816 817[Term] 818id: SO:0000337 819name: RNAi_reagent 820def: "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd] 821subset: SOFA 822synonym: "RNAi reagent" EXACT [] 823is_a: SO:0000442 ! ds_oligo 824 825[Term] 826id: SO:0000340 827name: chromosome 828def: "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] 829comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. 830subset: SOFA 831xref: http://en.wikipedia.org/wiki/Chromosome "wiki" 832is_a: SO:0001235 ! replicon 833 834[Term] 835id: SO:0000341 836name: chromosome_band 837def: "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma] 838subset: SOFA 839synonym: "chromosome band" EXACT [] 840synonym: "cytoband" EXACT [] 841synonym: "cytological band" EXACT [] 842xref: http://en.wikipedia.org/wiki/Cytological_band "wiki" 843is_a: SO:0000830 ! chromosome_part 844 845[Term] 846id: SO:0000343 847name: match 848def: "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke] 849subset: SOFA 850is_a: SO:0001410 ! experimental_feature 851 852[Term] 853id: SO:0000344 854name: splice_enhancer 855def: "Region of a transcript that regulates splicing." [SO:ke] 856subset: SOFA 857synonym: "splice enhancer" EXACT [] 858is_a: SO:0001056 ! splicing_regulatory_region 859 860[Term] 861id: SO:0000345 862name: EST 863def: "A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke] 864comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. 865subset: SOFA 866synonym: "expressed sequence tag" EXACT [] 867is_a: SO:0000324 ! tag 868relationship: derives_from SO:0000234 ! mRNA 869 870[Term] 871id: SO:0000347 872name: nucleotide_match 873def: "A match against a nucleotide sequence." [SO:ke] 874subset: SOFA 875synonym: "nucleotide match" EXACT [] 876is_a: SO:0000343 ! match 877 878[Term] 879id: SO:0000349 880name: protein_match 881def: "A match against a protein sequence." [SO:ke] 882subset: SOFA 883synonym: "protein match" EXACT [] 884is_a: SO:0000343 ! match 885 886[Term] 887id: SO:0000353 888name: sequence_assembly 889def: "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma] 890subset: SOFA 891synonym: "sequence assembly" EXACT [] 892xref: http://en.wikipedia.org/wiki/Sequence_assembly "wiki" 893is_a: SO:0001248 ! assembly 894 895[Term] 896id: SO:0000360 897name: codon 898def: "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] 899subset: SOFA 900xref: http://en.wikipedia.org/wiki/Codon "wiki" 901is_a: SO:0000851 ! CDS_region 902 903[Term] 904id: SO:0000366 905name: insertion_site 906def: "The junction where an insertion occurred." [SO:ke] 907subset: SOFA 908synonym: "insertion site" EXACT [] 909is_a: SO:0000699 ! junction 910 911[Term] 912id: SO:0000368 913name: transposable_element_insertion_site 914def: "The junction in a genome where a transposable_element has inserted." [SO:ke] 915subset: SOFA 916synonym: "transposable element insertion site" EXACT [] 917is_a: SO:0000366 ! insertion_site 918 919[Term] 920id: SO:0000370 921name: small_regulatory_ncRNA 922def: "A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma] 923subset: SOFA 924synonym: "small regulatory ncRNA" EXACT [] 925is_a: SO:0000655 ! ncRNA 926 927[Term] 928id: SO:0000372 929name: enzymatic_RNA 930def: "An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb] 931comment: 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. 932subset: SOFA 933synonym: "enzymatic RNA" EXACT [] 934is_a: SO:0000673 ! implied link automatically realized ! transcript 935intersection_of: SO:0000673 ! transcript 936 937[Term] 938id: SO:0000374 939name: ribozyme 940def: "An RNA with catalytic activity." [SO:ma] 941subset: SOFA 942xref: http://en.wikipedia.org/wiki/Ribozyme "wiki" 943is_a: SO:0000372 ! implied link automatically realized ! enzymatic_RNA 944intersection_of: SO:0000372 ! enzymatic_RNA 945 946[Term] 947id: SO:0000375 948name: rRNA_5_8S 949def: "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] 950subset: SOFA 951synonym: "5.8S LSU rRNA" EXACT [] 952synonym: "5.8S ribosomal RNA" EXACT [] 953synonym: "5.8S rRNA" EXACT [] 954synonym: "rRNA 5 8S" EXACT [] 955xref: http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA "wiki" 956is_a: SO:0000651 ! large_subunit_rRNA 957 958[Term] 959id: SO:0000380 960name: hammerhead_ribozyme 961def: "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] 962subset: SOFA 963synonym: "hammerhead ribozyme" EXACT [] 964xref: http://en.wikipedia.org/wiki/Hammerhead_ribozyme "wiki" 965is_a: SO:0000715 ! implied link automatically realized ! RNA_motif 966intersection_of: SO:0000715 ! RNA_motif 967 968[Term] 969id: SO:0000385 970name: RNase_MRP_RNA 971def: "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] 972subset: SOFA 973synonym: "RNase MRP RNA" EXACT [] 974is_a: SO:0000655 ! ncRNA 975 976[Term] 977id: SO:0000386 978name: RNase_P_RNA 979def: "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] 980subset: SOFA 981synonym: "RNase P RNA" EXACT [] 982is_a: SO:0000655 ! ncRNA 983 984[Term] 985id: SO:0000390 986name: telomerase_RNA 987def: "The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025] 988subset: SOFA 989synonym: "telomerase RNA" EXACT [] 990xref: http://en.wikipedia.org/wiki/Telomerase_RNA "wiki" 991is_a: SO:0000655 ! ncRNA 992 993[Term] 994id: SO:0000391 995name: U1_snRNA 996def: "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] 997subset: SOFA 998synonym: "small nuclear RNA U1" EXACT [RSC:cb] 999synonym: "snRNA U1" EXACT [RSC:cb] 1000synonym: "U1 small nuclear RNA" EXACT [RSC:cb] 1001synonym: "U1 snRNA" EXACT [] 1002xref: http://en.wikipedia.org/wiki/U1_snRNA "wiki" 1003is_a: SO:0000274 ! snRNA 1004 1005[Term] 1006id: SO:0000392 1007name: U2_snRNA 1008def: "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] 1009subset: SOFA 1010synonym: "small nuclear RNA U2" EXACT [RSC:CB] 1011synonym: "snRNA U2" EXACT [RSC:CB] 1012synonym: "U2 small nuclear RNA" EXACT [RSC:CB] 1013synonym: "U2 snRNA" EXACT [] 1014xref: http://en.wikipedia.org/wiki/U2_snRNA "wiki" 1015is_a: SO:0000274 ! snRNA 1016 1017[Term] 1018id: SO:0000393 1019name: U4_snRNA 1020def: "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] 1021subset: SOFA 1022synonym: "small nuclear RNA U4" EXACT [RSC:cb] 1023synonym: "snRNA U4" EXACT [RSC:cb] 1024synonym: "U4 small nuclear RNA" EXACT [RSC:cb] 1025synonym: "U4 snRNA" EXACT [] 1026xref: http://en.wikipedia.org/wiki/U4_snRNA "wiki" 1027is_a: SO:0000274 ! snRNA 1028 1029[Term] 1030id: SO:0000394 1031name: U4atac_snRNA 1032def: "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] 1033subset: SOFA 1034synonym: "small nuclear RNA U4atac" EXACT [RSC:cb] 1035synonym: "snRNA U4atac" EXACT [RSC:cb] 1036synonym: "U4atac small nuclear RNA" EXACT [RSC:cb] 1037synonym: "U4atac snRNA" EXACT [] 1038is_a: SO:0000274 ! snRNA 1039 1040[Term] 1041id: SO:0000395 1042name: U5_snRNA 1043def: "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] 1044subset: SOFA 1045synonym: "small nuclear RNA U5" EXACT [RSC:cb] 1046synonym: "snRNA U5" EXACT [RSC:cb] 1047synonym: "U5 small nuclear RNA" EXACT [RSC:cb] 1048synonym: "U5 snRNA" EXACT [] 1049xref: http://en.wikipedia.org/wiki/U5_snRNA "wiki" 1050is_a: SO:0000274 ! snRNA 1051 1052[Term] 1053id: SO:0000396 1054name: U6_snRNA 1055def: "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] 1056subset: SOFA 1057synonym: "small nuclear RNA U6" EXACT [RSC:cb] 1058synonym: "snRNA U6" EXACT [RSC:cb] 1059synonym: "U6 small nuclear RNA" EXACT [RSC:cb] 1060synonym: "U6 snRNA" EXACT [] 1061xref: http://en.wikipedia.org/wiki/U6_snRNA "wiki" 1062is_a: SO:0000274 ! snRNA 1063 1064[Term] 1065id: SO:0000397 1066name: U6atac_snRNA 1067def: "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] 1068subset: SOFA 1069synonym: "snRNA U6atac" EXACT [RSC:cb] 1070synonym: "U6atac small nuclear RNA" EXACT [RSC:cb] 1071synonym: "U6atac snRNA" EXACT [RSC:cb] 1072is_a: SO:0000274 ! snRNA 1073 1074[Term] 1075id: SO:0000398 1076name: U11_snRNA 1077def: "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] 1078subset: SOFA 1079synonym: "small nuclear RNA U11" EXACT [RSC:cb] 1080synonym: "snRNA U11" EXACT [RSC:cb] 1081synonym: "U11 small nuclear RNA" EXACT [RSC:cb] 1082synonym: "U11 snRNA" EXACT [] 1083xref: http://en.wikipedia.org/wiki/U11_snRNA "wiki" 1084is_a: SO:0000274 ! snRNA 1085 1086[Term] 1087id: SO:0000399 1088name: U12_snRNA 1089def: "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] 1090subset: SOFA 1091synonym: "small nuclear RNA U12" EXACT [RSC:cb] 1092synonym: "snRNA U12" EXACT [RSC:cb] 1093synonym: "U12 small nuclear RNA" EXACT [RSC:cb] 1094synonym: "U12 snRNA" EXACT [] 1095xref: http://en.wikipedia.org/wiki/U12_snRNA "wiki" 1096is_a: SO:0000274 ! snRNA 1097 1098[Term] 1099id: SO:0000403 1100name: U14_snoRNA 1101alt_id: SO:0005839 1102def: "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] 1103comment: An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA. 1104subset: SOFA 1105synonym: "small nucleolar RNA U14" EXACT [] 1106synonym: "snoRNA U14" EXACT [] 1107synonym: "U14 small nucleolar RNA" EXACT [] 1108synonym: "U14 snoRNA" EXACT [] 1109is_a: SO:0000593 ! C_D_box_snoRNA 1110 1111[Term] 1112id: SO:0000404 1113name: vault_RNA 1114def: "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] 1115subset: SOFA 1116synonym: "vault RNA" EXACT [] 1117xref: http://en.wikipedia.org/wiki/Vault_RNA "wiki" 1118is_a: SO:0000655 ! ncRNA 1119 1120[Term] 1121id: SO:0000405 1122name: Y_RNA 1123def: "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] 1124subset: SOFA 1125synonym: "Y RNA" EXACT [] 1126xref: http://en.wikipedia.org/wiki/Y_RNA "wiki" 1127is_a: SO:0000655 ! ncRNA 1128 1129[Term] 1130id: SO:0000407 1131name: rRNA_18S 1132def: "A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke] 1133subset: SOFA 1134synonym: "18S ribosomal RNA" EXACT [] 1135synonym: "18S rRNA" EXACT [] 1136synonym: "rRNA 18S" EXACT [] 1137xref: http://en.wikipedia.org/wiki/18S_ribosomal_RNA "wiki" 1138is_a: SO:0000650 ! small_subunit_rRNA 1139 1140[Term] 1141id: SO:0000409 1142name: binding_site 1143alt_id: BS:00033 1144def: "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] 1145comment: Discrete. 1146subset: biosapiens 1147subset: SOFA 1148synonym: "binding_or_interaction_site" EXACT [] 1149synonym: "site" RELATED [] 1150xref: http://en.wikipedia.org/wiki/Binding_site "wiki" 1151is_a: SO:0001411 ! biological_region 1152 1153[Term] 1154id: SO:0000410 1155name: protein_binding_site 1156def: "A region of a molecule that binds to a protein." [SO:ke] 1157subset: SOFA 1158synonym: "protein binding site" EXACT [] 1159is_a: SO:0000409 ! binding_site 1160 1161[Term] 1162id: SO:0000412 1163name: restriction_fragment 1164def: "A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke] 1165subset: SOFA 1166synonym: "restriction fragment" EXACT [] 1167xref: http://en.wikipedia.org/wiki/Restriction_fragment "wiki" 1168is_a: SO:0000143 ! assembly_component 1169 1170[Term] 1171id: SO:0000413 1172name: sequence_difference 1173def: "A region where the sequence differs from that of a specified sequence." [SO:ke] 1174subset: SOFA 1175synonym: "sequence difference" EXACT [] 1176is_a: SO:0000700 ! remark 1177 1178[Term] 1179id: SO:0000418 1180name: signal_peptide 1181alt_id: BS:00159 1182def: "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] 1183comment: 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. 1184subset: biosapiens 1185subset: SOFA 1186synonym: "signal" RELATED [uniprot:feature_type] 1187synonym: "signal peptide" EXACT [] 1188synonym: "signal peptide coding sequence" EXACT [] 1189xref: http://en.wikipedia.org/wiki/Signal_peptide "wiki" 1190is_a: SO:0001527 ! peptide_localization_signal 1191 1192[Term] 1193id: SO:0000419 1194name: mature_protein_region 1195alt_id: BS:00149 1196def: "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] 1197comment: 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. 1198subset: biosapiens 1199subset: SOFA 1200synonym: "chain" RELATED [uniprot:feature_type] 1201synonym: "mature peptide" RELATED [] 1202synonym: "mature protein region" EXACT [] 1203is_a: SO:0000839 ! polypeptide_region 1204relationship: part_of SO:0001063 ! immature_peptide_region 1205 1206[Term] 1207id: SO:0000436 1208name: ARS 1209def: "A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma] 1210subset: SOFA 1211synonym: "autonomously replicating sequence" EXACT [] 1212is_a: SO:0000296 ! origin_of_replication 1213 1214[Term] 1215id: SO:0000441 1216name: ss_oligo 1217def: "A single stranded oligonucleotide." [SO:ke] 1218comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. 1219subset: SOFA 1220synonym: "single strand oligo" EXACT [] 1221synonym: "single strand oligonucleotide" EXACT [] 1222synonym: "single stranded oligonucleotide" EXACT [] 1223synonym: "ss oligo" EXACT [] 1224synonym: "ss oligonucleotide" EXACT [] 1225is_a: SO:0000696 ! oligo 1226 1227[Term] 1228id: SO:0000442 1229name: ds_oligo 1230def: "A double stranded oligonucleotide." [SO:ke] 1231comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. 1232subset: SOFA 1233synonym: "double stranded oligonucleotide" EXACT [] 1234synonym: "ds oligo" EXACT [] 1235synonym: "ds-oligonucleotide" EXACT [] 1236is_a: SO:0000696 ! oligo 1237 1238[Term] 1239id: SO:0000454 1240name: rasiRNA 1241def: "A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284] 1242subset: SOFA 1243synonym: "repeat associated small interfering RNA" EXACT [] 1244xref: http://en.wikipedia.org/wiki/RasiRNA "wiki" 1245is_a: SO:0000655 ! ncRNA 1246 1247[Term] 1248id: SO:0000462 1249name: pseudogenic_region 1250def: "A non-functional descendent of a functional entity." [SO:cjm] 1251subset: SOFA 1252synonym: "pseudogenic region" EXACT [] 1253is_a: SO:0001411 ! biological_region 1254 1255[Term] 1256id: SO:0000464 1257name: decayed_exon 1258def: "A non-functional descendant of an exon." [SO:ke] 1259subset: SOFA 1260synonym: "decayed exon" EXACT [] 1261is_a: SO:0000462 ! pseudogenic_region 1262relationship: non_functional_homolog_of SO:0000147 ! exon 1263 1264[Term] 1265id: SO:0000468 1266name: golden_path_fragment 1267def: "One of the pieces of sequence that make up a golden path." [SO:rd] 1268subset: SOFA 1269synonym: "golden path fragment" EXACT [] 1270is_a: SO:0000143 ! assembly_component 1271relationship: part_of SO:0000688 ! golden_path 1272 1273[Term] 1274id: SO:0000472 1275name: tiling_path 1276def: "A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm] 1277subset: SOFA 1278synonym: "tiling path" EXACT [] 1279is_a: SO:0000353 ! sequence_assembly 1280 1281[Term] 1282id: SO:0000474 1283name: tiling_path_fragment 1284def: "A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke] 1285subset: SOFA 1286synonym: "tiling path fragment" EXACT [] 1287is_a: SO:0000143 ! assembly_component 1288relationship: part_of SO:0000472 ! tiling_path 1289 1290[Term] 1291id: SO:0000483 1292name: nc_primary_transcript 1293def: "A primary transcript that is never translated into a protein." [SO:ke] 1294subset: SOFA 1295synonym: "nc primary transcript" EXACT [] 1296synonym: "noncoding primary transcript" EXACT [] 1297is_a: SO:0000185 ! primary_transcript 1298 1299[Term] 1300id: SO:0000484 1301name: three_prime_coding_exon_noncoding_region 1302def: "The sequence of the 3' exon that is not coding." [SO:ke] 1303subset: SOFA 1304synonym: "three prime coding exon noncoding region" EXACT [] 1305synonym: "three_prime_exon_noncoding_region" EXACT [] 1306is_a: SO:0001214 ! noncoding_region_of_exon 1307 1308[Term] 1309id: SO:0000486 1310name: five_prime_coding_exon_noncoding_region 1311def: "The sequence of the 5' exon preceding the start codon." [SO:ke] 1312subset: SOFA 1313synonym: "five prime coding exon noncoding region" EXACT [] 1314synonym: "five_prime_exon_noncoding_region" EXACT [] 1315is_a: SO:0001214 ! noncoding_region_of_exon 1316relationship: part_of SO:0000200 ! five_prime_coding_exon 1317 1318[Term] 1319id: SO:0000499 1320name: virtual_sequence 1321def: "A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke] 1322subset: SOFA 1323synonym: "virtual sequence" EXACT [] 1324is_a: SO:0000353 ! sequence_assembly 1325 1326[Term] 1327id: SO:0000502 1328name: transcribed_region 1329def: "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] 1330comment: 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. 1331subset: SOFA 1332is_obsolete: true 1333 1334[Term] 1335id: SO:0000551 1336name: polyA_signal_sequence 1337def: "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] 1338subset: SOFA 1339synonym: "poly(A) signal" EXACT [] 1340synonym: "polyA signal sequence" EXACT [] 1341synonym: "polyadenylation termination signal" EXACT [] 1342is_a: SO:0005836 ! regulatory_region 1343 1344[Term] 1345id: SO:0000553 1346name: polyA_site 1347def: "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] 1348subset: SOFA 1349synonym: "polyA cleavage site" EXACT [] 1350synonym: "polyA site" EXACT [] 1351synonym: "polyadenylation site" RELATED [] 1352is_a: SO:0000837 ! UTR_region 1353relationship: part_of SO:0000205 ! three_prime_UTR 1354relationship: part_of SO:0000233 ! mature_transcript 1355 1356[Term] 1357id: SO:0000577 1358name: centromere 1359def: "A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke] 1360subset: SOFA 1361xref: http://en.wikipedia.org/wiki/Centromere "wiki" 1362is_a: SO:0000628 ! chromosomal_structural_element 1363 1364[Term] 1365id: SO:0000581 1366name: cap 1367def: "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] 1368subset: SOFA 1369xref: http://en.wikipedia.org/wiki/5%27_cap "wiki" 1370is_a: SO:0001411 ! biological_region 1371 1372[Term] 1373id: SO:0000587 1374name: group_I_intron 1375def: "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] 1376comment: GO:0000372. 1377subset: SOFA 1378synonym: "group I intron" EXACT [] 1379xref: http://en.wikipedia.org/wiki/Group_I_intron "wiki" 1380is_a: SO:0000588 ! autocatalytically_spliced_intron 1381 1382[Term] 1383id: SO:0000588 1384name: autocatalytically_spliced_intron 1385def: "A self spliced intron." [SO:ke] 1386subset: SOFA 1387synonym: "autocatalytically spliced intron" EXACT [] 1388is_a: SO:0000188 ! implied link automatically realized ! intron 1389intersection_of: SO:0000188 ! intron 1390 1391[Term] 1392id: SO:0000590 1393name: SRP_RNA 1394def: "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] 1395subset: SOFA 1396synonym: "7S RNA" RELATED [] 1397synonym: "signal recognition particle RNA" RELATED [] 1398synonym: "SRP RNA" EXACT [] 1399is_a: SO:0000655 ! ncRNA 1400 1401[Term] 1402id: SO:0000593 1403name: C_D_box_snoRNA 1404def: "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] 1405subset: SOFA 1406synonym: "box C/D snoRNA" EXACT [] 1407synonym: "C D box snoRNA" EXACT [] 1408synonym: "C/D box snoRNA" EXACT [] 1409is_a: SO:0000275 ! snoRNA 1410 1411[Term] 1412id: SO:0000602 1413name: guide_RNA 1414def: "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] 1415subset: SOFA 1416synonym: "gRNA" EXACT [] 1417synonym: "guide RNA" EXACT [] 1418xref: http://en.wikipedia.org/wiki/Guide_RNA "wiki" 1419is_a: SO:0000655 ! ncRNA 1420 1421[Term] 1422id: SO:0000603 1423name: group_II_intron 1424def: "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] 1425comment: GO:0000373. 1426subset: SOFA 1427synonym: "group II intron" EXACT [] 1428xref: http://en.wikipedia.org/wiki/Group_II_intron "wiki" 1429is_a: SO:0000588 ! autocatalytically_spliced_intron 1430 1431[Term] 1432id: SO:0000605 1433name: intergenic_region 1434def: "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] 1435comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. 1436subset: SOFA 1437synonym: "intergenic region" EXACT [] 1438xref: http://en.wikipedia.org/wiki/Intergenic_region "wiki" 1439is_a: SO:0001411 ! biological_region 1440 1441[Term] 1442id: SO:0000610 1443name: polyA_sequence 1444def: "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke] 1445subset: SOFA 1446synonym: "polyA sequence" EXACT [] 1447is_a: SO:0001411 ! biological_region 1448relationship: adjacent_to SO:0000234 ! mRNA 1449 1450[Term] 1451id: SO:0000611 1452name: branch_site 1453def: "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] 1454subset: SOFA 1455synonym: "branch point" EXACT [] 1456synonym: "branch site" EXACT [] 1457synonym: "branch_point" EXACT [] 1458is_a: SO:0000841 ! spliceosomal_intron_region 1459 1460[Term] 1461id: SO:0000612 1462name: polypyrimidine_tract 1463def: "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] 1464subset: SOFA 1465synonym: "polypyrimidine tract" EXACT [] 1466xref: http://en.wikipedia.org/wiki/Polypyrimidine_tract "wiki" 1467is_a: SO:0000841 ! spliceosomal_intron_region 1468 1469[Term] 1470id: SO:0000616 1471name: transcription_end_site 1472def: "The base where transcription ends." [SO:ke] 1473subset: SOFA 1474synonym: "transcription end site" EXACT [] 1475is_a: SO:0000835 ! primary_transcript_region 1476 1477[Term] 1478id: SO:0000624 1479name: telomere 1480def: "A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma] 1481subset: SOFA 1482synonym: "telomeric DNA" EXACT [] 1483synonym: "telomeric sequence" EXACT [] 1484xref: http://en.wikipedia.org/wiki/Telomere "wiki" 1485is_a: SO:0000628 ! chromosomal_structural_element 1486 1487[Term] 1488id: SO:0000625 1489name: silencer 1490def: "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke] 1491subset: SOFA 1492xref: http://en.wikipedia.org/wiki/Silencer_(DNA) "wiki" 1493is_a: SO:0000727 ! CRM 1494 1495[Term] 1496id: SO:0000627 1497name: insulator 1498def: "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] 1499subset: SOFA 1500synonym: "insulator element" EXACT [] 1501xref: http://en.wikipedia.org/wiki/Insulator_(genetics) "wiki" 1502is_a: SO:0001055 ! transcriptional_cis_regulatory_region 1503 1504[Term] 1505id: SO:0000628 1506name: chromosomal_structural_element 1507subset: SOFA 1508synonym: "chromosomal structural element" EXACT [] 1509is_a: SO:0000830 ! chromosome_part 1510 1511[Term] 1512id: SO:0000643 1513name: minisatellite 1514def: "A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml] 1515subset: SOFA 1516xref: http://en.wikipedia.org/wiki/Minisatellite "wiki" 1517is_a: SO:0000005 ! satellite_DNA 1518 1519[Term] 1520id: SO:0000644 1521name: antisense_RNA 1522def: "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] 1523subset: SOFA 1524synonym: "antisense RNA" EXACT [] 1525xref: http://en.wikipedia.org/wiki/Antisense_RNA "wiki" 1526is_a: SO:0000655 ! ncRNA 1527relationship: derives_from SO:0000645 ! antisense_primary_transcript 1528 1529[Term] 1530id: SO:0000645 1531name: antisense_primary_transcript 1532def: "The reverse complement of the primary transcript." [SO:ke] 1533subset: SOFA 1534synonym: "antisense primary transcript" EXACT [] 1535is_a: SO:0000185 ! primary_transcript 1536 1537[Term] 1538id: SO:0000646 1539name: siRNA 1540def: "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] 1541subset: SOFA 1542synonym: "small interfering RNA" EXACT [] 1543xref: http://en.wikipedia.org/wiki/SiRNA "wiki" 1544is_a: SO:0000655 ! ncRNA 1545 1546[Term] 1547id: SO:0000649 1548name: stRNA 1549def: "Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans." [PMID:11081512] 1550subset: SOFA 1551synonym: "small temporal RNA" EXACT [] 1552xref: http://en.wikipedia.org/wiki/StRNA "wiki" 1553is_a: SO:0000655 ! ncRNA 1554 1555[Term] 1556id: SO:0000650 1557name: small_subunit_rRNA 1558def: "Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke] 1559subset: SOFA 1560synonym: "small subunit rRNA" EXACT [] 1561synonym: "SSU RNA" EXACT [RSC:cb] 1562synonym: "SSU rRNA" EXACT [RSC:cb] 1563is_a: SO:0000252 ! rRNA 1564 1565[Term] 1566id: SO:0000651 1567name: large_subunit_rRNA 1568def: "Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke] 1569subset: SOFA 1570synonym: "large subunit rRNA" EXACT [] 1571synonym: "LSU RNA" EXACT [RSC:cb] 1572synonym: "LSU rRNA" EXACT [RSC:cb] 1573is_a: SO:0000252 ! rRNA 1574relationship: derives_from SO:0000325 ! rRNA_large_subunit_primary_transcript 1575 1576[Term] 1577id: SO:0000652 1578name: rRNA_5S 1579def: "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] 1580subset: SOFA 1581synonym: "5S LSU rRNA" EXACT [] 1582synonym: "5S ribosomal RNA" EXACT [] 1583synonym: "5S rRNA" EXACT [] 1584synonym: "rRNA 5S" EXACT [] 1585xref: http://en.wikipedia.org/wiki/5S_ribosomal_RNA "wiki" 1586is_a: SO:0000651 ! large_subunit_rRNA 1587 1588[Term] 1589id: SO:0000653 1590name: rRNA_28S 1591def: "A component of the large ribosomal subunit." [SO:ke] 1592subset: SOFA 1593synonym: "28S LSU rRNA" EXACT [] 1594synonym: "28S ribosomal RNA" EXACT [] 1595synonym: "28S rRNA" EXACT [] 1596synonym: "rRNA 28S" EXACT [] 1597xref: http://en.wikipedia.org/wiki/28S_ribosomal_RNA "wiki" 1598is_a: SO:0000651 ! large_subunit_rRNA 1599 1600[Term] 1601id: SO:0000655 1602name: ncRNA 1603def: "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke] 1604comment: 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. 1605subset: SOFA 1606synonym: "noncoding RNA" EXACT [] 1607xref: http://en.wikipedia.org/wiki/NcRNA "wiki" 1608is_a: SO:0000233 ! mature_transcript 1609 1610[Term] 1611id: SO:0000657 1612name: repeat_region 1613def: "A region of sequence containing one or more repeat units." [SO:ke] 1614subset: SOFA 1615synonym: "repeat region" EXACT [] 1616is_a: SO:0001412 ! topologically_defined_region 1617 1618[Term] 1619id: SO:0000658 1620name: dispersed_repeat 1621def: "A repeat that is located at dispersed sites in the genome." [SO:ke] 1622subset: SOFA 1623synonym: "dispersed repeat" EXACT [] 1624synonym: "interspersed repeat" EXACT [] 1625xref: http://en.wikipedia.org/wiki/Interspersed_repeat "wiki" 1626is_a: SO:0000657 ! repeat_region 1627 1628[Term] 1629id: SO:0000662 1630name: spliceosomal_intron 1631def: "An intron which is spliced by the spliceosome." [SO:ke] 1632comment: GO:0000398. 1633subset: SOFA 1634synonym: "spliceosomal intron" EXACT [] 1635is_a: SO:0000188 ! intron 1636 1637[Term] 1638id: SO:0000667 1639name: insertion 1640alt_id: SO:1000034 1641def: "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke] 1642subset: SOFA 1643synonym: "nucleotide insertion" EXACT [] 1644synonym: "nucleotide_insertion" EXACT [] 1645is_a: SO:0001059 ! sequence_alteration 1646is_a: SO:0001411 ! biological_region 1647 1648[Term] 1649id: SO:0000668 1650name: EST_match 1651def: "A match against an EST sequence." [SO:ke] 1652subset: SOFA 1653synonym: "EST match" EXACT [] 1654is_a: SO:0000102 ! expressed_sequence_match 1655 1656[Term] 1657id: SO:0000673 1658name: transcript 1659def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma] 1660subset: SOFA 1661xref: http://en.wikipedia.org/wiki/RNA "wiki" 1662is_a: SO:0000831 ! gene_member_region 1663 1664[Term] 1665id: SO:0000684 1666name: nuclease_sensitive_site 1667def: "A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma] 1668subset: SOFA 1669synonym: "nuclease sensitive site" EXACT [] 1670is_a: SO:0000059 ! nuclease_binding_site 1671 1672[Term] 1673id: SO:0000687 1674name: deletion_junction 1675def: "The space between two bases in a sequence which marks the position where a deletion has occurred." [SO:ke] 1676subset: SOFA 1677synonym: "deletion junction" EXACT [] 1678is_a: SO:0000699 ! junction 1679 1680[Term] 1681id: SO:0000688 1682name: golden_path 1683def: "A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls] 1684subset: SOFA 1685synonym: "golden path" EXACT [] 1686is_a: SO:0000353 ! sequence_assembly 1687 1688[Term] 1689id: SO:0000689 1690name: cDNA_match 1691def: "A match against cDNA sequence." [SO:ke] 1692subset: SOFA 1693synonym: "cDNA match" EXACT [] 1694is_a: SO:0000102 ! expressed_sequence_match 1695 1696[Term] 1697id: SO:0000694 1698name: SNP 1699def: "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] 1700subset: SOFA 1701synonym: "single nucleotide polymorphism" EXACT [] 1702is_a: SO:0001483 ! SNV 1703 1704[Term] 1705id: SO:0000695 1706name: reagent 1707def: "A sequence used in experiment." [SO:ke] 1708comment: Requested by Lynn Crosby, jan 2006. 1709subset: SOFA 1710is_a: SO:0001409 ! biomaterial_region 1711 1712[Term] 1713id: SO:0000696 1714name: oligo 1715def: "A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma] 1716subset: SOFA 1717synonym: "oligonucleotide" EXACT [] 1718xref: http://en.wikipedia.org/wiki/Oligonucleotide "wiki" 1719is_a: SO:0000695 ! reagent 1720 1721[Term] 1722id: SO:0000699 1723name: junction 1724def: "A sequence_feature with an extent of zero." [SO:ke] 1725comment: A junction is a boundary between regions. A boundary has an extent of zero. 1726subset: SOFA 1727synonym: "boundary" EXACT [] 1728synonym: "breakpoint" EXACT [] 1729is_a: SO:0000110 ! sequence_feature 1730disjoint_from: SO:0000001 ! region 1731 1732[Term] 1733id: SO:0000700 1734name: remark 1735def: "A comment about the sequence." [SO:ke] 1736subset: SOFA 1737is_a: SO:0001410 ! experimental_feature 1738 1739[Term] 1740id: SO:0000701 1741name: possible_base_call_error 1742def: "A region of sequence where the validity of the base calling is questionable." [SO:ke] 1743subset: SOFA 1744synonym: "possible base call error" EXACT [] 1745is_a: SO:0000413 ! sequence_difference 1746 1747[Term] 1748id: SO:0000702 1749name: possible_assembly_error 1750def: "A region of sequence where there may have been an error in the assembly." [SO:ke] 1751subset: SOFA 1752synonym: "possible assembly error" EXACT [] 1753is_a: SO:0000413 ! sequence_difference 1754 1755[Term] 1756id: SO:0000703 1757name: experimental_result_region 1758def: "A region of sequence implicated in an experimental result." [SO:ke] 1759subset: SOFA 1760synonym: "experimental result region" EXACT [] 1761is_a: SO:0000700 ! remark 1762 1763[Term] 1764id: SO:0000704 1765name: gene 1766def: "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] 1767comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance. 1768subset: SOFA 1769xref: http://en.wikipedia.org/wiki/Gene "wiki" 1770is_a: SO:0001411 ! biological_region 1771relationship: member_of SO:0005855 ! gene_group 1772 1773[Term] 1774id: SO:0000705 1775name: tandem_repeat 1776def: "Two or more adjcent copies of a region (of length greater than 1)." [SO:ke] 1777subset: SOFA 1778synonym: "tandem repeat" EXACT [] 1779xref: http://en.wikipedia.org/wiki/Tandem_repeat "wiki" 1780xref: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html 1781is_a: SO:0000657 ! repeat_region 1782 1783[Term] 1784id: SO:0000706 1785name: trans_splice_acceptor_site 1786def: "The 3' splice site of the acceptor primary transcript." [SO:ke] 1787comment: This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans. 1788subset: SOFA 1789synonym: "3' trans splice site" RELATED [] 1790synonym: "trans splice acceptor site" EXACT [] 1791is_a: SO:0001420 ! trans_splice_site 1792 1793[Term] 1794id: SO:0000714 1795name: nucleotide_motif 1796def: "A region of nucleotide sequence corresponding to a known motif." [SO:ke] 1797subset: SOFA 1798synonym: "nucleotide motif" EXACT [] 1799is_a: SO:0001411 ! biological_region 1800 1801[Term] 1802id: SO:0000715 1803name: RNA_motif 1804def: "A motif that is active in RNA sequence." [SO:ke] 1805subset: SOFA 1806synonym: "RNA motif" EXACT [] 1807is_a: SO:0000714 ! nucleotide_motif 1808 1809[Term] 1810id: SO:0000717 1811name: reading_frame 1812def: "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] 1813comment: This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop. 1814subset: SOFA 1815synonym: "reading frame" EXACT [] 1816xref: http://en.wikipedia.org/wiki/Reading_frame "wiki" 1817is_a: SO:0001410 ! experimental_feature 1818 1819[Term] 1820id: SO:0000719 1821name: ultracontig 1822def: "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] 1823subset: SOFA 1824is_a: SO:0000353 ! sequence_assembly 1825 1826[Term] 1827id: SO:0000724 1828name: oriT 1829def: "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] 1830subset: SOFA 1831synonym: "origin of transfer" EXACT [] 1832xref: http://en.wikipedia.org/wiki/Origin_of_transfer "wiki" 1833is_a: SO:0000296 ! origin_of_replication 1834 1835[Term] 1836id: SO:0000725 1837name: transit_peptide 1838alt_id: BS:00055 1839def: "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] 1840comment: 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. 1841subset: biosapiens 1842subset: SOFA 1843synonym: "signal" RELATED [] 1844synonym: "transit" RELATED [uniprot:feature_type] 1845synonym: "transit peptide" EXACT [] 1846is_a: SO:0001527 ! peptide_localization_signal 1847 1848[Term] 1849id: SO:0000727 1850name: CRM 1851def: "A regulatory_region where more than 1 TF_binding_site together are regulatorily active." [SO:SG] 1852comment: Requested by Stepen Grossmann Dec 2004. 1853subset: SOFA 1854synonym: "cis regulatory module" EXACT [] 1855synonym: "TF module" EXACT [] 1856is_a: SO:0001055 ! implied link automatically realized ! transcriptional_cis_regulatory_region 1857intersection_of: SO:0001055 ! transcriptional_cis_regulatory_region 1858intersection_of: has_part SO:0000235 ! TF_binding_site 1859 1860[Term] 1861id: SO:0000730 1862name: gap 1863def: "A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke] 1864subset: SOFA 1865is_a: SO:0000143 ! assembly_component 1866relationship: part_of SO:0000353 ! sequence_assembly 1867 1868[Term] 1869id: SO:0000752 1870name: gene_group_regulatory_region 1871subset: SOFA 1872synonym: "gene group regulatory region" EXACT [] 1873is_a: SO:0005836 ! regulatory_region 1874relationship: member_of SO:0005855 ! gene_group 1875 1876[Term] 1877id: SO:0000753 1878name: clone_insert 1879def: "The region of sequence that has been inserted and is being propogated by the clone." [SO:ke] 1880subset: SOFA 1881synonym: "clone insert" EXACT [] 1882is_a: SO:0000695 ! reagent 1883relationship: part_of SO:0000151 ! clone 1884 1885[Term] 1886id: SO:0000777 1887name: pseudogenic_rRNA 1888def: "A non functional descendent of an rRNA." [SO:ke] 1889comment: 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. 1890subset: SOFA 1891synonym: "pseudogenic rRNA" EXACT [] 1892is_a: SO:0000462 ! pseudogenic_region 1893 1894[Term] 1895id: SO:0000778 1896name: pseudogenic_tRNA 1897def: "A non functional descendent of a tRNA." [SO:ke] 1898comment: 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. 1899subset: SOFA 1900synonym: "pseudogenic tRNA" EXACT [] 1901is_a: SO:0000462 ! pseudogenic_region 1902 1903[Term] 1904id: SO:0000830 1905name: chromosome_part 1906def: "A region of a chromosome." [SO:ke] 1907comment: 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. 1908subset: SOFA 1909synonym: "chromosome part" EXACT [] 1910is_a: SO:0001411 ! biological_region 1911relationship: part_of SO:0000340 ! chromosome 1912 1913[Term] 1914id: SO:0000831 1915name: gene_member_region 1916def: "A region of a gene." [SO:ke] 1917comment: A manufactured term used to allow the parts of a gene to have an is_a path to the root. 1918subset: SOFA 1919synonym: "gene member region" EXACT [] 1920is_a: SO:0001411 ! biological_region 1921relationship: member_of SO:0000704 ! gene 1922 1923[Term] 1924id: SO:0000833 1925name: transcript_region 1926def: "A region of a transcript." [SO:ke] 1927comment: 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. 1928subset: SOFA 1929synonym: "transcript region" EXACT [] 1930is_a: SO:0001411 ! biological_region 1931relationship: part_of SO:0000673 ! transcript 1932 1933[Term] 1934id: SO:0000834 1935name: mature_transcript_region 1936def: "A region of a mature transcript." [SO:ke] 1937comment: A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root. 1938subset: SOFA 1939synonym: "mature transcript region" EXACT [] 1940is_a: SO:0000833 ! transcript_region 1941 1942[Term] 1943id: SO:0000835 1944name: primary_transcript_region 1945def: "A part of a primary transcript." [SO:ke] 1946comment: 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. 1947subset: SOFA 1948synonym: "primary transcript region" EXACT [] 1949is_a: SO:0000833 ! transcript_region 1950relationship: part_of SO:0000185 ! primary_transcript 1951 1952[Term] 1953id: SO:0000836 1954name: mRNA_region 1955def: "A region of an mRNA." [SO:cb] 1956comment: 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. 1957subset: SOFA 1958synonym: "mRNA region" EXACT [] 1959is_a: SO:0000834 ! mature_transcript_region 1960relationship: part_of SO:0000234 ! mRNA 1961 1962[Term] 1963id: SO:0000837 1964name: UTR_region 1965def: "A region of UTR." [SO:ke] 1966comment: 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. 1967subset: SOFA 1968synonym: "UTR region" EXACT [] 1969is_a: SO:0000836 ! mRNA_region 1970 1971[Term] 1972id: SO:0000839 1973name: polypeptide_region 1974alt_id: BS:00124 1975alt_id: BS:00331 1976def: "Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke] 1977comment: Added to allow the polypeptide regions to have is_a paths back to the root. 1978subset: biosapiens 1979subset: SOFA 1980synonym: "positional" RELATED [] 1981synonym: "positional polypeptide feature" RELATED [] 1982synonym: "region" NARROW [uniprot:feature_type] 1983synonym: "region or site annotation" RELATED [] 1984synonym: "site" NARROW [uniprot:feature_type] 1985is_a: SO:0001411 ! biological_region 1986relationship: part_of SO:0000104 ! polypeptide 1987 1988[Term] 1989id: SO:0000841 1990name: spliceosomal_intron_region 1991def: "A region within an intron." [SO:ke] 1992comment: A terms added to allow the parts of introns to have is_a paths to the root. 1993subset: SOFA 1994synonym: "spliceosomal intron region" EXACT [] 1995is_a: SO:0000835 ! primary_transcript_region 1996relationship: part_of SO:0000662 ! spliceosomal_intron 1997 1998[Term] 1999id: SO:0000842 2000name: gene_component_region 2001subset: SOFA 2002synonym: "gene component region" EXACT [] 2003is_a: SO:0001411 ! biological_region 2004relationship: part_of SO:0000704 ! gene 2005 2006[Term] 2007id: SO:0000851 2008name: CDS_region 2009def: "A region of a CDS." [SO:cb] 2010subset: SOFA 2011synonym: "CDS region" EXACT [] 2012is_a: SO:0000836 ! mRNA_region 2013relationship: part_of SO:0000316 ! CDS 2014 2015[Term] 2016id: SO:0000852 2017name: exon_region 2018def: "A region of an exon." [RSC:cb] 2019subset: SOFA 2020synonym: "exon region" EXACT [] 2021is_a: SO:0000833 ! transcript_region 2022relationship: part_of SO:0000147 ! exon 2023 2024[Term] 2025id: SO:0001000 2026name: rRNA_16S 2027def: "A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke] 2028subset: SOFA 2029synonym: "16S ribosomal RNA" EXACT [] 2030synonym: "16S rRNA" RELATED [] 2031synonym: "16S SSU RNA" EXACT [] 2032synonym: "rRNA 16S" EXACT [] 2033xref: http://en.wikipedia.org/wiki/16S_ribosomal_RNA "wiki" 2034is_a: SO:0000650 ! small_subunit_rRNA 2035 2036[Term] 2037id: SO:0001001 2038name: rRNA_23S 2039def: "A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke] 2040subset: SOFA 2041synonym: "23S LSU rRNA" EXACT [] 2042synonym: "23S ribosomal RNA" RELATED [] 2043synonym: "23S rRNA" EXACT [] 2044synonym: "rRNA 23S" EXACT [] 2045is_a: SO:0000651 ! large_subunit_rRNA 2046 2047[Term] 2048id: SO:0001002 2049name: rRNA_25S 2050def: "A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb] 2051subset: SOFA 2052synonym: "25S LSU rRNA" EXACT [] 2053synonym: "25S ribosomal RNA" EXACT [] 2054synonym: "25S rRNA" EXACT [] 2055synonym: "rRNA 25S" EXACT [] 2056is_a: SO:0000651 ! large_subunit_rRNA 2057 2058[Term] 2059id: SO:0001019 2060name: copy_number_variation 2061def: "A variation that increases or decreases the copy number of a given region." [SO:ke] 2062subset: SOFA 2063synonym: "CNP" EXACT [] 2064synonym: "CNV" EXACT [] 2065synonym: "copy number polymorphism" EXACT [] 2066synonym: "copy number variation" EXACT [] 2067xref: http://en.wikipedia.org/wiki/Copy_number_variation "wiki" 2068is_a: SO:0001059 ! sequence_alteration 2069 2070[Term] 2071id: SO:0001037 2072name: mobile_genetic_element 2073def: "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] 2074subset: SOFA 2075synonym: "MGE" EXACT [] 2076synonym: "mobile genetic element" EXACT [] 2077xref: http://en.wikipedia.org/wiki/Mobile_genetic_element "wiki" 2078is_a: SO:0001411 ! biological_region 2079intersection_of: SO:0000001 ! region 2080 2081[Term] 2082id: SO:0001039 2083name: integrated_mobile_genetic_element 2084def: "An MGE that is integrated into the host chromosome." [SO:ke] 2085subset: SOFA 2086synonym: "integrated mobile genetic element" EXACT [] 2087is_a: SO:0001037 ! mobile_genetic_element 2088 2089[Term] 2090id: SO:0001055 2091name: transcriptional_cis_regulatory_region 2092def: "A regulatory_region that modulates the transcription of a gene or genes." [SO:regcreative] 2093subset: SOFA 2094synonym: "transcriptional cis regulatory region" EXACT [] 2095is_a: SO:0005836 ! regulatory_region 2096 2097[Term] 2098id: SO:0001056 2099name: splicing_regulatory_region 2100def: "A regulatory_region that modulates splicing." [SO:ke] 2101subset: SOFA 2102synonym: "splicing regulatory region" EXACT [] 2103is_a: SO:0005836 ! regulatory_region 2104 2105[Term] 2106id: SO:0001059 2107name: sequence_alteration 2108alt_id: SO:1000004 2109alt_id: SO:1000007 2110def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke] 2111comment: Merged with partially characterized change in nucleotide sequence. 2112subset: SOFA 2113synonym: "partially characterised change in DNA sequence" EXACT [] 2114synonym: "partially_characterised_change_in_DNA_sequence" EXACT [] 2115synonym: "sequence alteration" EXACT [] 2116is_a: SO:0000110 ! sequence_feature 2117 2118[Term] 2119id: SO:0001063 2120name: immature_peptide_region 2121alt_id: BS:00129 2122def: "An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR] 2123comment: Range. 2124subset: biosapiens 2125subset: SOFA 2126synonym: "immature_peptide_region" EXACT [] 2127is_a: SO:0000839 ! polypeptide_region 2128 2129[Term] 2130id: SO:0001214 2131name: noncoding_region_of_exon 2132def: "The maximal intersection of exon and UTR." [SO:ke] 2133comment: 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. 2134subset: SOFA 2135synonym: "noncoding region of exon" EXACT [] 2136is_a: SO:0000852 ! exon_region 2137 2138[Term] 2139id: SO:0001215 2140name: coding_region_of_exon 2141def: "The region of an exon that encodes for protein sequence." [SO:ke] 2142comment: An exon containing either a start or stop codon will be partially coding and partially non coding. 2143subset: SOFA 2144synonym: "coding region of exon" EXACT [] 2145is_a: SO:0000852 ! exon_region 2146 2147[Term] 2148id: SO:0001235 2149name: replicon 2150def: "A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207] 2151subset: SOFA 2152xref: http://en.wikipedia.org/wiki/Replicon_(genetics) "wiki" 2153is_a: SO:0001411 ! biological_region 2154 2155[Term] 2156id: SO:0001236 2157name: base 2158def: "A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke] 2159subset: SOFA 2160xref: http://en.wikipedia.org/wiki/Nucleobase "wiki" 2161is_a: SO:0001411 ! biological_region 2162 2163[Term] 2164id: SO:0001248 2165name: assembly 2166def: "A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke] 2167subset: SOFA 2168xref: http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly "wiki" 2169is_a: SO:0001410 ! experimental_feature 2170 2171[Term] 2172id: SO:0001409 2173name: biomaterial_region 2174def: "A region which is intended for use in an experiment." [SO:cb] 2175subset: SOFA 2176synonym: "biomaterial region" EXACT [] 2177is_a: SO:0000001 ! region 2178 2179[Term] 2180id: SO:0001410 2181name: experimental_feature 2182def: "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] 2183subset: SOFA 2184synonym: "analysis feature" RELATED [] 2185synonym: "experimental output artefact" EXACT [] 2186synonym: "experimental_output_artefact" EXACT [] 2187is_a: SO:0000001 ! region 2188 2189[Term] 2190id: SO:0001411 2191name: biological_region 2192def: "A region defined by its disposition to be involved in a biological process." [SO:cb] 2193subset: SOFA 2194synonym: "biological region" EXACT [] 2195is_a: SO:0000001 ! region 2196 2197[Term] 2198id: SO:0001412 2199name: topologically_defined_region 2200def: "A region that is defined according to its relations with other regions within the same sequence." [SO:cb] 2201subset: SOFA 2202synonym: "topologically defined region" EXACT [] 2203is_a: SO:0000001 ! region 2204 2205[Term] 2206id: SO:0001419 2207name: cis_splice_site 2208def: "Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke] 2209subset: SOFA 2210synonym: "cis splice site" EXACT [] 2211is_a: SO:0000162 ! splice_site 2212 2213[Term] 2214id: SO:0001420 2215name: trans_splice_site 2216def: "Primary transcript region bordering trans-splice junction." [SO:ke] 2217subset: SOFA 2218synonym: "trans splice site" EXACT [] 2219is_a: SO:0000162 ! splice_site 2220 2221[Term] 2222id: SO:0001483 2223name: SNV 2224def: "SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist." [SO:bm] 2225subset: SOFA 2226synonym: "single nucleotide variant" EXACT [] 2227is_a: SO:1000002 ! substitution 2228created_by: kareneilbeck 2229creation_date: 2009-10-08T11:37:49Z 2230 2231[Term] 2232id: SO:0001527 2233name: peptide_localization_signal 2234def: "A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke] 2235subset: SOFA 2236synonym: "localization signal" RELATED [] 2237synonym: "peptide localization signal" EXACT [] 2238is_a: SO:0000839 ! polypeptide_region 2239created_by: kareneilbeck 2240creation_date: 2010-03-11T02:15:05Z 2241 2242[Term] 2243id: SO:0001720 2244name: epigenetically_modified_region 2245def: "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] 2246subset: SOFA 2247synonym: "epigenetically modified region" RELATED [] 2248is_a: SO:0001411 ! biological_region 2249intersection_of: SO:0001411 ! biological_region 2250created_by: kareneilbeck 2251creation_date: 2010-03-27T12:02:29Z 2252 2253[Term] 2254id: SO:0005836 2255name: regulatory_region 2256def: "A DNA sequence that controls the expression of a gene." [SO:ke] 2257subset: SOFA 2258synonym: "regulatory region" EXACT [] 2259xref: http://en.wikipedia.org/wiki/Regulatory_region "wiki" 2260is_a: SO:0000831 ! gene_member_region 2261 2262[Term] 2263id: SO:0005855 2264name: gene_group 2265def: "A collection of related genes." [SO:ma] 2266subset: SOFA 2267synonym: "gene group" EXACT [] 2268is_a: SO:0001411 ! biological_region 2269 2270[Term] 2271id: SO:0100011 2272name: cleaved_peptide_region 2273def: "The cleaved_peptide_regon is the a region of peptide sequence that is cleaved during maturation." [EBIBS:GAR] 2274comment: Range. 2275subset: biosapiens 2276subset: SOFA 2277synonym: "cleaved peptide region" EXACT [] 2278is_a: SO:0000839 ! polypeptide_region 2279relationship: part_of SO:0001063 ! immature_peptide_region 2280 2281[Term] 2282id: SO:1000002 2283name: substitution 2284def: "Any change in genomic DNA caused by a single event." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] 2285subset: SOFA 2286is_a: SO:0001059 ! sequence_alteration 2287is_a: SO:0001411 ! biological_region 2288 2289[Term] 2290id: SO:1000005 2291name: complex_substitution 2292def: "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] 2293subset: SOFA 2294synonym: "complex substitution" EXACT [] 2295is_a: SO:1000002 ! substitution 2296 2297[Term] 2298id: SO:1000008 2299name: point_mutation 2300def: "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop] 2301subset: SOFA 2302synonym: "point mutation" EXACT [] 2303xref: http://en.wikipedia.org/wiki/Point_mutation "wiki" 2304is_a: SO:0001483 ! SNV 2305 2306[Term] 2307id: SO:1000036 2308name: inversion 2309def: "A continuous nucleotide sequence is inverted in the same position." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] 2310subset: SOFA 2311is_a: SO:0001059 ! sequence_alteration 2312is_a: SO:0001411 ! biological_region 2313 2314[Term] 2315id: SO:1001284 2316name: regulon 2317def: "A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732] 2318subset: SOFA 2319xref: http://en.wikipedia.org/wiki/Regulon "wiki" 2320is_a: SO:0005855 ! gene_group 2321 2322[Term] 2323id: SO:2000061 2324name: databank_entry 2325def: "The sequence referred to by an entry in a databank such as Genbank or SwissProt." [SO:ke] 2326subset: SOFA 2327synonym: "accession" RELATED [] 2328synonym: "databank entry" EXACT [] 2329is_a: SO:0000695 ! reagent 2330 2331[Typedef] 2332id: adjacent_to 2333name: adjacent_to 2334def: "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence." [SO:ke] 2335subset: SOFA 2336 2337[Typedef] 2338id: associated_with 2339name: associated_with 2340comment: This relationship is vague and up for discussion. 2341 2342[Typedef] 2343id: complete_evidence_for_feature 2344name: complete_evidence_for_feature 2345def: "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] 2346comment: 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. 2347is_transitive: true 2348is_a: evidence_for_feature ! evidence_for_feature 2349 2350[Typedef] 2351id: derives_from 2352name: derives_from 2353subset: SOFA 2354is_transitive: true 2355 2356[Typedef] 2357id: edited_from 2358name: edited_from 2359created_by: kareneilbeck 2360creation_date: 2009-08-19T02:19:45Z 2361 2362[Typedef] 2363id: edited_to 2364name: edited_to 2365created_by: kareneilbeck 2366creation_date: 2009-08-19T02:19:11Z 2367 2368[Typedef] 2369id: evidence_for_feature 2370name: evidence_for_feature 2371def: "B is evidence_for_feature A, if an instance of B supports the existence of A." [SO:ke] 2372comment: 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. 2373is_transitive: true 2374 2375[Typedef] 2376id: exemplar_of 2377name: exemplar_of 2378def: "X is exemplar of Y if X is the best evidence for Y." [SO:ke] 2379comment: Tracker id: 2594157. 2380 2381[Typedef] 2382id: genome_of 2383name: genome_of 2384 2385[Typedef] 2386id: guided_by 2387name: guided_by 2388created_by: kareneilbeck 2389creation_date: 2009-08-19T02:27:04Z 2390 2391[Typedef] 2392id: guides 2393name: guides 2394created_by: kareneilbeck 2395creation_date: 2009-08-19T02:27:24Z 2396 2397[Typedef] 2398id: has_genome_location 2399name: has_genome_location 2400is_obsolete: true 2401 2402[Typedef] 2403id: has_intergral_part 2404name: has_integral_part 2405def: "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] 2406comment: Example: mRNA has_integral_part CDS. 2407created_by: kareneilbeck 2408creation_date: 2009-08-19T12:01:46Z 2409 2410[Typedef] 2411id: has_origin 2412name: has_origin 2413 2414[Typedef] 2415id: has_part 2416name: has_part 2417def: "Inverse of part_of." [http://precedings.nature.com/documents/3495/version/1] 2418comment: Example: operon has_part gene. 2419 2420[Typedef] 2421id: has_quality 2422name: has_quality 2423comment: The relationship between a feature and an attribute. 2424 2425[Typedef] 2426id: homologous_to 2427name: homologous_to 2428subset: SOFA 2429is_symmetric: true 2430is_a: similar_to ! similar_to 2431 2432[Typedef] 2433id: integral_part_of 2434name: integral_part_of 2435def: "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] 2436comment: Example: exon integral_part_of transcript. 2437created_by: kareneilbeck 2438creation_date: 2009-08-19T12:03:28Z 2439 2440[Typedef] 2441id: member_of 2442name: member_of 2443comment: 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. 2444subset: SOFA 2445is_transitive: true 2446 2447[Typedef] 2448id: non_functional_homolog_of 2449name: non_functional_homolog_of 2450def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke] 2451subset: SOFA 2452is_a: homologous_to ! homologous_to 2453 2454[Typedef] 2455id: orthologous_to 2456name: orthologous_to 2457subset: SOFA 2458is_symmetric: true 2459is_a: homologous_to ! homologous_to 2460 2461[Typedef] 2462id: paralogous_to 2463name: paralogous_to 2464subset: SOFA 2465is_symmetric: true 2466is_a: homologous_to ! homologous_to 2467 2468[Typedef] 2469id: part_of 2470name: part_of 2471def: "X part_of Y if X is a subregion of Y." [http://precedings.nature.com/documents/3495/version/1] 2472comment: Example: amino_acid part_of polypeptide. 2473subset: SOFA 2474is_transitive: true 2475 2476[Typedef] 2477id: partial_evidence_for_feature 2478name: partial_evidence_for_feature 2479def: "B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A." [SO:ke] 2480is_a: evidence_for_feature ! evidence_for_feature 2481 2482[Typedef] 2483id: position_of 2484name: position_of 2485 2486[Typedef] 2487id: processed_from 2488name: processed_from 2489def: "Inverse of processed_into." [http://precedings.nature.com/documents/3495/version/1] 2490comment: Example: miRNA processed_from miRNA_primary_transcript. 2491created_by: kareneilbeck 2492creation_date: 2009-08-19T12:14:00Z 2493 2494[Typedef] 2495id: processed_into 2496name: processed_into 2497def: "X is processed_into Y if a region X is modified to create Y." [http://precedings.nature.com/documents/3495/version/1] 2498comment: Example: miRNA_primary_transcript processed into miRNA. 2499created_by: kareneilbeck 2500creation_date: 2009-08-19T12:15:02Z 2501 2502[Typedef] 2503id: recombined_from 2504name: recombined_from 2505created_by: kareneilbeck 2506creation_date: 2009-08-19T02:21:03Z 2507 2508[Typedef] 2509id: recombined_to 2510name: recombined_to 2511created_by: kareneilbeck 2512creation_date: 2009-08-19T02:20:07Z 2513 2514[Typedef] 2515id: regulated_by 2516name: regulated_by 2517is_obsolete: true 2518 2519[Typedef] 2520id: sequence_of 2521name: sequence_of 2522 2523[Typedef] 2524id: similar_to 2525name: similar_to 2526subset: SOFA 2527is_symmetric: true 2528 2529[Typedef] 2530id: trans_spliced_from 2531name: trans_spliced_from 2532created_by: kareneilbeck 2533creation_date: 2009-08-19T02:22:14Z 2534 2535[Typedef] 2536id: trans_spliced_to 2537name: trans_spliced_to 2538created_by: kareneilbeck 2539creation_date: 2009-08-19T02:22:00Z 2540 2541[Typedef] 2542id: transcribed_from 2543name: transcribed_from 2544def: "X is transcribed_from Y if X is synthesized from template Y." [http://precedings.nature.com/documents/3495/version/1] 2545comment: Example: primary_transcript transcribed_from gene. 2546created_by: kareneilbeck 2547creation_date: 2009-08-19T12:05:39Z 2548 2549[Typedef] 2550id: transcribed_to 2551name: transcribed_to 2552def: "Inverse of transcribed_from." [http://precedings.nature.com/documents/3495/version/1] 2553comment: Example: gene transcribed_to primary_transcript. 2554created_by: kareneilbeck 2555creation_date: 2009-08-19T12:08:24Z 2556 2557[Typedef] 2558id: translates_to 2559name: translates_to 2560def: "Inverse of translation _of." [http://precedings.nature.com/documents/3495/version/1] 2561comment: Example: codon translates_to amino_acid. 2562created_by: kareneilbeck 2563creation_date: 2009-08-19T12:11:53Z 2564 2565[Typedef] 2566id: translation_of 2567name: translation_of 2568def: "X is translation of Y if X is translated by ribosome to create Y." [http://precedings.nature.com/documents/3495/version/1] 2569comment: Example: Polypeptide translation_of CDS. 2570created_by: kareneilbeck 2571creation_date: 2009-08-19T12:09:59Z 2572 2573[Typedef] 2574id: variant_of 2575name: variant_of 2576def: "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] 2577comment: Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith. 2578 2579