BioPerl
view release on metacpan or search on metacpan
t/data/so.obo view on Meta::CPAN
id: SO:0000177
name: cross_genome_match
def: "A nucleotide match against a sequence from another organism." [SO:ma]
subset: SOFA
is_a: SO:0000347 ! nucleotide_match
[Term]
id: SO:0000178
name: operon
def: "A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma]
subset: SOFA
is_a: SO:0005855 ! gene_group
[Term]
id: SO:0000179
name: clone_insert_start
def: "The start of the clone insert." [SO:ke]
subset: SOFA
is_a: SO:0000699 ! junction
relationship: part_of SO:0000753 ! clone_insert
[Term]
id: SO:0000180
name: retrotransposon
def: "A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.genpromag.com/scripts/glossary.asp?LETTER=R]
is_a: SO:0000101 ! transposable_element
[Term]
id: SO:0000181
name: translated_nucleotide_match
def: "A match against a translated sequence." [SO:ke]
subset: SOFA
is_a: SO:0000347 ! nucleotide_match
[Term]
id: SO:0000182
name: DNA_transposon
def: "A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]
is_a: SO:0000101 ! transposable_element
[Term]
id: SO:0000183
name: non_transcribed_region
def: "A region of the gene which is not transcribed." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region
relationship: part_of SO:0000704 ! gene
[Term]
id: SO:0000184
name: U2_intron
def: "A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]
comment: May have either GT-AG or AT-AG 5' and 3' boundaries.
is_a: SO:0000662 ! spliceosomal_intron
[Term]
id: SO:0000185
name: primary_transcript
def: "The primary (initial, unprocessed) transcript; includes five_prime_clip (SO:0000555), five_prime_untranslated_region (SO:0000204), open reading frames (SO:0000236), introns (SO:0000188) and three_prime_ untranslated_region (three_prime_UTR), an...
subset: SOFA
synonym: "precursor_RNA" RELATED []
is_a: SO:0000673 ! transcript
[Term]
id: SO:0000186
name: LTR_retrotransposon
def: "A retrotransposon flanked by long terminal repeat sequences." [SO:ke]
is_a: SO:0000180 ! retrotransposon
[Term]
id: SO:0000187
name: repeat_family
def: "A group of characterized repeat sequences." [SO:ke]
subset: SOFA
is_a: SO:0000657 ! repeat_region
[Term]
id: SO:0000188
name: intron
def: "A segment of DNA 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#line_types]
subset: SOFA
relationship: part_of SO:0000185 ! primary_transcript
[Term]
id: SO:0000189
name: non_LTR_retrotransposon
def: "A retrotransposon without long terminal repeat sequences." [SO:ke]
is_a: SO:0000180 ! retrotransposon
[Term]
id: SO:0000190
name: five_prime_intron
is_a: SO:0000188 ! intron
[Term]
id: SO:0000191
name: interior_intron
is_a: SO:0000188 ! intron
[Term]
id: SO:0000192
name: three_prime_intron
is_a: SO:0000188 ! intron
[Term]
id: SO:0000193
name: RFLP_fragment
def: "A polymorphism detectable by the size differences in DNA fragments generated by a restriction enzyme." [PMID:6247908]
subset: SOFA
synonym: "restriction_fragment_length_polymorphism" RELATED []
is_a: SO:0000412 ! restriction_fragment
[Term]
id: SO:0000194
name: LINE_element
def: "A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [h...
synonym: "Long interspersed element" RELATED []
synonym: "Long interspersed nuclear element" RELATED []
is_a: SO:0000189 ! non_LTR_retrotransposon
[Term]
t/data/so.obo view on Meta::CPAN
[Term]
id: SO:0000266
name: methionyl_tRNA
is_a: SO:0000253 ! tRNA
[Term]
id: SO:0000267
name: phenylalanyl_tRNA
is_a: SO:0000253 ! tRNA
[Term]
id: SO:0000268
name: prolyl_tRNA
is_a: SO:0000253 ! tRNA
[Term]
id: SO:0000269
name: seryl_tRNA
is_a: SO:0000253 ! tRNA
[Term]
id: SO:0000270
name: threonyl_tRNA
is_a: SO:0000253 ! tRNA
[Term]
id: SO:0000271
name: tryptophanyl_tRNA
is_a: SO:0000253 ! tRNA
[Term]
id: SO:0000272
name: tyrosyl_tRNA
is_a: SO:0000253 ! tRNA
[Term]
id: SO:0000273
name: valyl_tRNA
is_a: SO:0000253 ! tRNA
[Term]
id: SO:0000274
name: snRNA
def: "Small non-coding RNA in the nucleoplasm. A small nuclear RNA molecule involved in pre-mRNA splicing and processing" [ems:WB, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types, PMID:11733745]
subset: SOFA
synonym: "small_nuclear_RNA" RELATED []
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000275
name: snoRNA
def: "Small nucleolar RNAs (snoRNAs) are involved in the processing and modification of rRNA in the nucleolus. There are two main classes of snoRNAs: the box C/D class, and the box H/ACA class. U3 snoRNA is a member of the box C/D class. Indeed, the ...
subset: SOFA
synonym: "small_nucleolar_RNA" RELATED []
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000276
name: miRNA
def: "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. miRNAs are produced from precursor molecules (SO:0000647) that can form local hairpin strcutures, which ordinarily are processed (via the Dicer pathway) such that a ...
subset: SOFA
synonym: "micro_RNA" RELATED []
is_a: SO:0000370 ! small_regulatory_ncRNA
[Term]
id: SO:0000277
name: transcript_by_bound_factor
is_a: SO:0000237 ! transcript_attribute
[Term]
id: SO:0000278
name: transcript_by_bound_nucleic_acid
is_a: SO:0000277 ! transcript_by_bound_factor
[Term]
id: SO:0000279
name: transcript_by_bound_protein
is_a: SO:0000277 ! transcript_by_bound_factor
[Term]
id: SO:0000280
name: engineered_gene
is_a: SO:0000009 ! gene_class
[Term]
id: SO:0000281
name: engineered_foreign_gene
is_a: SO:0000280 ! engineered_gene
is_a: SO:0000285 ! foreign_gene
[Term]
id: SO:0000282
name: mRNA_with_minus_1_frameshift
is_a: SO:0000108 ! mRNA_with_frameshift
[Term]
id: SO:0000283
name: engineered_foreign_transposable_element_gene
is_a: SO:0000111 ! transposable_element_gene
is_a: SO:0000280 ! engineered_gene
[Term]
id: SO:0000284
name: type_I_enzyme_restriction_site
def: "The recognition site is bipartate and interupted." [http://www.promega.com]
is_obsolete: true
[Term]
id: SO:0000285
name: foreign_gene
is_a: SO:0000452 ! transgene
[Term]
id: SO:0000286
name: long_terminal_repeat
def: "A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
synonym: "LTR" RELATED []
synonym: "direct_terminal _repeat" RELATED []
is_a: SO:0000657 ! repeat_region
relationship: part_of SO:0000186 ! LTR_retrotransposon
t/data/so.obo view on Meta::CPAN
id: SO:0000366
name: insertion_site
def: "The junction where an insertion occurred." [SO:ke]
subset: SOFA
is_a: SO:0000109 ! sequence_variant
is_a: SO:0000699 ! junction
relationship: position_of SO:0000046 ! insert
[Term]
id: SO:0000367
name: attI_site
relationship: part_of SO:0000365 ! integron
[Term]
id: SO:0000368
name: transposable_element_insertion_site
def: "The junction in a genome where a transposable_element has inserted." [SO:ke]
subset: SOFA
is_a: SO:0000366 ! insertion_site
[Term]
id: SO:0000369
name: integrase_coding_region
relationship: part_of SO:0000365 ! integron
[Term]
id: SO:0000370
name: small_regulatory_ncRNA
def: "A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]
subset: SOFA
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000371
name: conjugative_transposon
def: "A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/ ~ smaloy/Glossary/C.html]
is_a: SO:0000182 ! DNA_transposon
[Term]
id: SO:0000372
name: enzymatic_RNA
def: "A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]
subset: SOFA
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000373
name: recombinationally_inverted
is_a: SO:0000456 ! recombinationally_rearranged_gene
[Term]
id: SO:0000374
name: ribozyme
def: "An RNA with catalytic activity." [SO:ma]
subset: SOFA
is_a: SO:0000372 ! enzymatic_RNA
[Term]
id: SO:0000375
name: rRNA_5.8S
def: "5.8S ribosomal RNA (5.8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA ma...
subset: SOFA
synonym: "5.8S_rRNA" RELATED []
is_a: SO:0000252 ! rRNA
[Term]
id: SO:0000376
name: RNA_6S
def: "A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.a...
synonym: "6S_RNA" RELATED []
is_a: SO:0000370 ! small_regulatory_ncRNA
[Term]
id: SO:0000377
name: CsrB_RsmB_RNA
def: "An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glyco...
synonym: "CsrB-RsmB_RNA" RELATED []
is_a: SO:0000370 ! small_regulatory_ncRNA
[Term]
id: SO:0000378
name: DsrA_RNA
def: "DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be se...
is_a: SO:0000370 ! small_regulatory_ncRNA
[Term]
id: SO:0000379
name: GcvB_RNA
def: "A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022]
is_a: SO:0000378 ! DsrA_RNA
[Term]
id: SO:0000380
name: hammerhead_ribozyme
def: "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs."...
subset: SOFA
is_a: SO:0000374 ! ribozyme
[Term]
id: SO:0000381
name: group_IIA_intron
is_a: SO:0000603 ! group_II_intron
[Term]
id: SO:0000382
name: group_IIB_intron
is_a: SO:0000603 ! group_II_intron
[Term]
id: SO:0000383
name: MicF_RNA
def: "A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033]
is_a: SO:0000644 ! antisense_RNA
[Term]
id: SO:0000384
name: OxyS_RNA
def: "A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the...
is_a: SO:0000370 ! small_regulatory_ncRNA
[Term]
id: SO:0000385
name: RNase_MRP_RNA
def: "The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In t...
subset: SOFA
is_a: SO:0000372 ! enzymatic_RNA
[Term]
id: SO:0000386
name: RNase_P_RNA
def: "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterised activity is the generation of mature 5 prime ends of tRNAs by ...
subset: SOFA
is_a: SO:0000374 ! ribozyme
[Term]
id: SO:0000387
name: RprA_RNA
def: "Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones car...
is_a: SO:0000370 ! small_regulatory_ncRNA
[Term]
id: SO:0000388
name: RRE_RNA
def: "The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export a...
is_a: SO:0000370 ! small_regulatory_ncRNA
[Term]
id: SO:0000389
name: spot_42_RNA
def: "A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021]
is_a: SO:0000370 ! small_regulatory_ncRNA
[Term]
id: SO:0000390
name: telomerase_RNA
def: "The RNA component of telomerase, a reverse transcriptase that synthesises telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]
subset: SOFA
is_a: SO:0000372 ! enzymatic_RNA
[Term]
id: SO:0000391
name: U1_snRNA
def: "U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differenc...
subset: SOFA
is_a: SO:0000274 ! snRNA
[Term]
id: SO:0000392
name: U2_snRNA
def: "U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron re...
subset: SOFA
is_a: SO:0000274 ! snRNA
[Term]
id: SO:0000393
name: U4_snRNA
def: "U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and c...
subset: SOFA
is_a: SO:0000274 ! snRNA
[Term]
id: SO:0000394
name: U4atac_snRNA
def: "An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455]
subset: SOFA
is_a: SO:0000274 ! snRNA
[Term]
id: SO:0000395
name: U5_snRNA
def: "U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm si...
subset: SOFA
is_a: SO:0000274 ! snRNA
[Term]
id: SO:0000396
name: U6_snRNA
def: "U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions wit...
subset: SOFA
is_a: SO:0000274 ! snRNA
[Term]
id: SO:0000397
name: U6atac_snRNA
def: "U6atac_snRNA -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)." [https://www.ncbi.nlm.nih.gov/pubmed/12409455]
subset: SOFA
is_a: SO:0000274 ! snRNA
[Term]
id: SO:0000398
name: U11_snRNA
def: "U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129]
subset: SOFA
is_a: SO:0000274 ! snRNA
[Term]
id: SO:0000399
name: U12_snRNA
def: "The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007]
subset: SOFA
is_a: SO:0000274 ! snRNA
[Term]
id: SO:0000400
name: sequence_attribute
is_a: SO:0000000 ! Sequence_Ontology
[Term]
id: SO:0000401
name: gene_attribute
is_a: SO:0000400 ! sequence_attribute
[Term]
id: SO:0000402
name: enhancer_attribute
is_a: SO:0000401 ! gene_attribute
[Term]
id: SO:0000403
name: U14_snRNA
def: "U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a dif...
subset: SOFA
is_a: SO:0000274 ! snRNA
[Term]
id: SO:0000404
name: vault_RNA
def: "A family of RNAs are found as part of the enigmatic vault ribonuceoprotein 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 sugges...
subset: SOFA
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000405
name: Y_RNA
def: "Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can ...
subset: SOFA
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000406
name: twintron
def: "An intron within an intron." [PMID:1899376]
is_a: SO:0000188 ! intron
[Term]
id: SO:0000407
name: rRNA_18S
def: "18S_rRNA -A large polynucleotide which functions as a part of the small subunit of the ribosome" [SO:ke]
subset: SOFA
synonym: "16S_rRNA" RELATED []
is_a: SO:0000252 ! rRNA
[Term]
id: SO:0000408
name: site
def: "The interbase position where something (eg an aberration) occurred." [SO:ke]
is_obsolete: true
[Term]
id: SO:0000409
name: binding_site
def: "A region on the surface of a molecule that may interact with another molecule." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region
[Term]
id: SO:0000410
name: protein_binding_site
def: "A region of a molecule that binds to a protein." [SO:ke]
is_a: SO:0000409 ! binding_site
[Term]
id: SO:0000411
name: rescue_fragment
is_a: SO:0000695 ! reagent
[Term]
id: SO:0000412
name: restriction_fragment
def: "Any of the individual polynucleotide sequences produced by digestion of DNA with a restriction endonuclease." [http://www.agron.missouri.edu/cgi-bin/sybgw_mdb/mdb3/Term/119]
subset: SOFA
t/data/so.obo view on Meta::CPAN
[Term]
id: SO:0000546
name: designed_sequence
is_a: SO:0000351 ! synthetic_sequence
[Term]
id: SO:0000547
name: inversion_derived_bipartite_duplication
def: "A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]
is_a: SO:1000038 ! intrachromosomal_duplication
[Term]
id: SO:0000548
name: gene_with_edited_transcript
is_a: SO:0000064 ! gene_by_transcript_attribute
[Term]
id: SO:0000549
name: inversion_derived_duplication_plus_aneuploid
def: "A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]
is_a: SO:1000038 ! intrachromosomal_duplication
[Term]
id: SO:0000550
name: aneuploid_chromosome
is_a: SO:1000183 ! chromosome_structure_variation
[Term]
id: SO:0000551
name: polyA_signal_sequence
def: "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
is_a: SO:0005836 ! regulatory_region
[Term]
id: SO:0000552
name: Shine_Dalgarno_sequence
def: "Region in 5' UTR where ribosome assembles on mRNA." [SO:ke]
synonym: "RBS" RELATED []
synonym: "Shine-Dalgarno_sequence" RELATED []
synonym: "five_prime_ribosome_binding_site" RELATED []
is_a: SO:0000139 ! ribosome_entry_site
[Term]
id: SO:0000553
name: polyA_site
def: "The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
is_a: SO:0000699 ! junction
relationship: part_of SO:0000233 ! processed_transcript
[Term]
id: SO:0000554
name: assortment_derived_deficiency_plus_duplication
is_obsolete: true
[Term]
id: SO:0000555
name: five_prime_clip
def: "5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
synonym: "five_prime_-clip" RELATED []
is_a: SO:0000303 ! clip
[Term]
id: SO:0000556
name: five_prime_D_recombination_signal_sequence
def: "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://i...
synonym: "5'RS" RELATED []
synonym: "five_prime_D-recombination_signal_sequence" RELATED []
is_a: SO:0000492 ! D_gene_recombination_feature
[Term]
id: SO:0000557
name: three_prime_clip
def: "3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
synonym: "3'-clip" RELATED []
is_a: SO:0000303 ! clip
[Term]
id: SO:0000558
name: C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#C-CLUSTER]
synonym: "C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
[Term]
id: SO:0000559
name: D_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#D-CLUSTER]
synonym: "D-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
[Term]
id: SO:0000560
name: D_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#D-J-CLUSTER]
synonym: "D-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
[Term]
id: SO:0000561
name: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
def: " 7 nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin/T-cell receptor gene" [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#HEPTAMER]
synonym: "HEPTAMER" RELATED []
is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene
[Term]
id: SO:0000562
name: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene
[Term]
id: SO:0000563
name: spacer_of_recombination_feature_of_vertebrate_immune_system_gene
is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene
[Term]
id: SO:0000564
name: V_DJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(DJ)-J-C-CLUSTER]
synonym: "V-(DJ)-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
[Term]
id: SO:0000565
name: V_VDJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(VDJ)-J-C-CLUSTER]
synonym: "V-(VDJ)-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
[Term]
id: SO:0000566
name: V_VJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(VJ)-J-C-CLUSTER]
synonym: "V-(VJ)-J-C-CLUSTER" RELATED []
t/data/so.obo view on Meta::CPAN
id: SO:0000578
name: snoRNA_gene
is_a: SO:0000011 ! non_protein_coding_gene
[Term]
id: SO:0000579
name: edited_transcript_feature
def: "A locatable feature on a transcript that is edited." [SO:ma]
relationship: part_of SO:0000673 ! transcript
[Term]
id: SO:0000580
name: methylation_guide_snoRNA_primary_transcript
def: "A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke]
is_a: SO:0000232 ! snoRNA_primary_transcript
[Term]
id: SO:0000581
name: cap
def: "A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/m...
subset: SOFA
relationship: adjacent_to SO:0000234 ! mRNA
[Term]
id: SO:0000582
name: rRNA_cleavage_snoRNA_primary_transcript
def: "A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke]
is_a: SO:0000232 ! snoRNA_primary_transcript
[Term]
id: SO:0000583
name: pre_edited_region
def: "The region of a transcript that will be edited." [http://www.rna.ucla.edu]
synonym: "pre-edited_region" RELATED []
is_a: SO:0000579 ! edited_transcript_feature
[Term]
id: SO:0000584
name: tmRNA
def: "tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads ...
synonym: "10Sa_RNA" RELATED []
synonym: "ssrA" RELATED []
is_a: SO:0000370 ! small_regulatory_ncRNA
[Term]
id: SO:0000585
name: C_D_box_snoRNA_gene
is_a: SO:0000578 ! snoRNA_gene
[Term]
id: SO:0000586
name: tmRNA_primary_transcript
def: "A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke]
synonym: "10Sa_RNA_primary_transcript" RELATED []
synonym: "ssrA_RNA_primary_transcript" RELATED []
is_a: SO:0000483 ! nc_primary_transcript
[Term]
id: SO:0000587
name: group_I_intron
def: "Group I catalytic introns are large self-splicing ribozymes. They catalyse 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 ess...
subset: SOFA
is_a: SO:0000188 ! intron
[Term]
id: SO:0000588
name: autocatalytically_spliced_intron
def: "A self spliced intron." [SO:ke]
subset: SOFA
is_a: SO:0000188 ! intron
is_a: SO:0000374 ! ribozyme
[Term]
id: SO:0000589
name: SRP_RNA_primary_transcript
def: "A primary transcript encoding a signal recognition particle RNA." [SO:ke]
is_a: SO:0000483 ! nc_primary_transcript
[Term]
id: SO:0000590
name: SRP_RNA
def: "The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68,...
subset: SOFA
synonym: "7S RNA" RELATED []
synonym: "signal_recognition_particle_RNA" RELATED []
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000591
name: pseudoknot
def: "A stem-loop RNA structure where nucleotides in the loop participate in complementary interactions with a region of RNA downstream of the stem-loop." [https://www.ncbi.nlm.nih.gov/pubmed/12519954]
is_a: SO:0000002 ! sequence_secondary_structure
[Term]
id: SO:0000592
name: H_pseudoknot
def: "A pseudoknot which contains two stems and at least two loops." [https://www.ncbi.nlm.nih.gov/pubmed/10334330]
synonym: "H-pseudoknot" RELATED []
is_a: SO:0000591 ! pseudoknot
[Term]
id: SO:0000593
name: C_D_box_snoRNA
def: "Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for sno...
synonym: "C/D_box_snoRNA" RELATED []
is_a: SO:0000275 ! snoRNA
[Term]
id: SO:0000594
name: H_ACA_box_snoRNA
def: "Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesi...
synonym: "H/ACA_box_snoRNA" RELATED []
is_a: SO:0000275 ! snoRNA
[Term]
id: SO:0000595
name: C_D_box_snoRNA_primary_transcript
def: "A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke]
is_a: SO:0000232 ! snoRNA_primary_transcript
[Term]
t/data/so.obo view on Meta::CPAN
subset: SOFA
is_a: SO:0000705 ! tandem_repeat
[Term]
id: SO:0000644
name: antisense_RNA
def: "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke]
subset: SOFA
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000645
name: antisense_primary_transcript
def: "The reverse complement of the primary transcript." [SO:ke]
subset: SOFA
is_a: SO:0000185 ! primary_transcript
[Term]
id: SO:0000646
name: siRNA
def: "Small RNA molecule that is the product of a longerexogenous or endogenous dsRNA, which is either a bimolecular duplexe or very longhairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulatefrom both strands of the dsRNA. sR...
subset: SOFA
synonym: "small_interfering_RNA" RELATED []
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000647
name: miRNA_primary_transcript
def: "A primary transcript encoding a micro RNA." [SO:ke]
synonym: "micro_RNA_primary_transcript" RELATED []
is_a: SO:0000483 ! nc_primary_transcript
[Term]
id: SO:0000648
name: stRNA_primary_transcript
def: "A primary transcript encoding a small temporal mRNA (SO:0000649)." [SO:ke]
synonym: "small_temporal_RNA_primary_transcript" RELATED []
is_a: SO:0000647 ! miRNA_primary_transcript
[Term]
id: SO:0000649
name: stRNA
def: "Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans." [PMID:11081512]
subset: SOFA
synonym: "small_temporal_RNA" RELATED []
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000650
name: small_subunit_rRNA
is_a: SO:0000252 ! rRNA
[Term]
id: SO:0000651
name: large_subunit_rRNA
is_a: SO:0000252 ! rRNA
[Term]
id: SO:0000652
name: rRNA_5S
def: "5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA ...
subset: SOFA
is_a: SO:0000252 ! rRNA
[Term]
id: SO:0000653
name: rRNA_28S
def: "A component of the large ribosomal subunit." [SO:ke]
subset: SOFA
synonym: "23S_rRNA" RELATED []
synonym: "28S_rRNA" RELATED []
is_a: SO:0000252 ! rRNA
[Term]
id: SO:0000654
name: maxi_circle_gene
synonym: "maxi-circle" RELATED []
is_a: SO:0000088 ! mt_gene
[Term]
id: SO:0000655
name: ncRNA
def: "An mRNA sequence that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]
comment: ncRNA is a processed_transcript so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript.
subset: SOFA
synonym: "noncoding_RNA" RELATED []
is_a: SO:0000233 ! processed_transcript
[Term]
id: SO:0000656
name: stRNA_gene
is_a: SO:0000011 ! non_protein_coding_gene
[Term]
id: SO:0000657
name: repeat_region
def: "A region of sequence containing one or more repeat units." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region
[Term]
id: SO:0000658
name: dispersed_repeat
def: "A repeat that is located at dispersed sites in the genome." [SO:ke]
subset: SOFA
synonym: "interspersed_repeat" RELATED []
is_a: SO:0000657 ! repeat_region
[Term]
id: SO:0000659
name: tmRNA_gene
is_a: SO:0000011 ! non_protein_coding_gene
[Term]
id: SO:0000660
name: DNA_invertase_target_sequence
is_a: SO:0000342 ! site_specific_recombination_target_region
[Term]
id: SO:0000661
name: intron_attribute
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