format-version: 1.2
subsetdef: biosapiens "biosapiens protein feature ontology"
subsetdef: DBVAR "database of genomic structural variation"
subsetdef: SOFA "SO feature annotation"
synonymtypedef: aa1 "amino acid 1 letter code"
synonymtypedef: aa3 "amino acid 3 letter code"
synonymtypedef: AAMOD "amino acid modification"
synonymtypedef: BS "biosapiens"
synonymtypedef: dbsnp "dbsnp variant terms"
synonymtypedef: dbvar "DBVAR"
synonymtypedef: ebi_variants "ensembl variant terms"
synonymtypedef: RNAMOD "RNA modification" EXACT
synonymtypedef: VAR "variant annotation term"
ontology: so/subsets/SOFA

[Term]
id: SO:0000000
name: Sequence_Ontology
namespace: sequence
subset: SOFA
is_obsolete: true

[Term]
id: SO:0000001
name: region
namespace: sequence
def: "A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]
subset: SOFA
synonym: "sequence" EXACT []
is_a: SO:0000110 ! sequence_feature

[Term]
id: SO:0000004
name: interior_coding_exon
namespace: sequence
subset: SOFA
synonym: "interior coding exon" EXACT []
is_a: SO:0000195 ! coding_exon

[Term]
id: SO:0000005
name: satellite_DNA
namespace: sequence
def: "The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "INSDC_feature:repeat_region" BROAD []
synonym: "INSDC_qualifier:satellite" EXACT []
synonym: "satellite DNA" EXACT []
xref: http://en.wikipedia.org/wiki/Satellite_DNA "wiki"
is_a: SO:0000705 ! tandem_repeat

[Term]
id: SO:0000006
name: PCR_product
namespace: sequence
def: "A region amplified by a PCR reaction." [SO:ke]
comment: This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406.
subset: SOFA
synonym: "amplicon" RELATED []
synonym: "PCR product" EXACT []
xref: http://en.wikipedia.org/wiki/RAPD "wiki"
is_a: SO:0000695 ! reagent

[Term]
id: SO:0000007
name: read_pair
namespace: sequence
def: "One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]
subset: SOFA
synonym: "mate pair" EXACT []
synonym: "read-pair" EXACT []
is_a: SO:0000150 ! read
relationship: part_of SO:0000149 ! contig
relationship: part_of SO:0001790 ! paired_end_fragment

[Term]
id: SO:0000013
name: scRNA
namespace: sequence
def: "A small non coding RNA sequence, present in the cytoplasm." [SO:ke]
subset: SOFA
synonym: "INSDC_feature:ncRNA" BROAD []
synonym: "INSDC_qualifier:scRNA" EXACT []
synonym: "small cytoplasmic RNA" EXACT []
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000038
name: match_set
namespace: sequence
def: "A collection of match parts." [SO:ke]
subset: SOFA
is_obsolete: true

[Term]
id: SO:0000039
name: match_part
namespace: sequence
def: "A part of a match, for example an hsp from blast is a match_part." [SO:ke]
subset: SOFA
synonym: "match part" EXACT []
is_a: SO:0001410 ! experimental_feature
relationship: part_of SO:0000343 ! match

[Term]
id: SO:0000050
name: gene_part
namespace: sequence
def: "A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene." [SO:ke]
subset: SOFA
is_obsolete: true

[Term]
id: SO:0000057
name: operator
namespace: sequence
def: "A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma]
subset: SOFA
synonym: "operator segment" EXACT []
xref: http://en.wikipedia.org/wiki/Operator_(biology)#Operator "wiki"
is_a: SO:0000752 ! gene_group_regulatory_region

[Term]
id: SO:0000059
name: nuclease_binding_site
namespace: sequence
def: "A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb]
subset: SOFA
synonym: "nuclease binding site" EXACT []
is_a: SO:0001654 ! nucleotide_to_protein_binding_site

[Term]
id: SO:0000101
name: transposable_element
namespace: sequence
def: "A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]
subset: SOFA
synonym: "transposable element" EXACT []
synonym: "transposon" EXACT []
xref: http://en.wikipedia.org/wiki/Transposable_element "wiki"
is_a: SO:0001039 ! integrated_mobile_genetic_element

[Term]
id: SO:0000102
name: expressed_sequence_match
namespace: sequence
def: "A match to an EST or cDNA sequence." [SO:ke]
subset: SOFA
synonym: "expressed sequence match" EXACT []
is_a: SO:0000347 ! nucleotide_match

[Term]
id: SO:0000103
name: clone_insert_end
namespace: sequence
def: "The end of the clone insert." [SO:ke]
subset: SOFA
synonym: "clone insert end" EXACT []
is_a: SO:0000699 ! junction
relationship: part_of SO:0000753 ! clone_insert

[Term]
id: SO:0000104
name: polypeptide
namespace: sequence
alt_id: SO:0000358
def: "A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute.
subset: SOFA
synonym: "protein" EXACT []
xref: http://en.wikipedia.org/wiki/Polypeptide "wiki"
is_a: SO:0001411 ! biological_region
relationship: derives_from SO:0000316 ! CDS

[Term]
id: SO:0000109
name: sequence_variant_obs
namespace: sequence
def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]
subset: SOFA
synonym: "mutation" RELATED []
is_obsolete: true

[Term]
id: SO:0000110
name: sequence_feature
namespace: sequence
def: "Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]
subset: SOFA
synonym: "INSDC_feature:misc_feature" EXACT []
synonym: "INSDC_note:other" EXACT []
synonym: "INSDC_note:sequence_feature" EXACT []
synonym: "located sequence feature" RELATED []
synonym: "located_sequence_feature" EXACT []
synonym: "sequence feature" EXACT []

[Term]
id: SO:0000112
name: primer
namespace: sequence
def: "An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke]
subset: SOFA
synonym: "DNA primer" EXACT []
synonym: "primer oligonucleotide" EXACT []
synonym: "primer polynucleotide" EXACT []
synonym: "primer sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Primer_(molecular_biology) "wiki"
is_a: SO:0000441 ! ss_oligo

[Term]
id: SO:0000113
name: proviral_region
namespace: sequence
def: "A viral sequence which has integrated into a host genome." [SO:ke]
subset: SOFA
synonym: "proviral region" EXACT []
synonym: "proviral sequence" RELATED []
is_a: SO:0001039 ! integrated_mobile_genetic_element

[Term]
id: SO:0000114
name: methylated_cytosine
namespace: sequence
def: "A methylated deoxy-cytosine." [SO:ke]
subset: SOFA
synonym: "methylated C" EXACT []
synonym: "methylated cytosine" EXACT []
synonym: "methylated cytosine base" EXACT []
synonym: "methylated cytosine residue" EXACT []
synonym: "methylated_C" EXACT []
is_a: SO:0000306 ! methylated_DNA_base_feature

[Term]
id: SO:0000120
name: protein_coding_primary_transcript
namespace: sequence
def: "A primary transcript that, at least in part, encodes one or more proteins." [SO:ke]
comment: May contain introns.
subset: SOFA
synonym: "pre mRNA" RELATED []
synonym: "protein coding primary transcript" EXACT []
is_a: SO:0000185 ! primary_transcript

[Term]
id: SO:0000139
name: ribosome_entry_site
namespace: sequence
def: "Region in mRNA where ribosome assembles." [SO:ke]
subset: SOFA
synonym: "INSDC_feature:regulatory" BROAD []
synonym: "INSDC_qualifier:ribosome_binding_site" EXACT []
synonym: "ribosome entry site" EXACT []
is_a: SO:0000836 ! mRNA_region
relationship: part_of SO:0000204 ! five_prime_UTR

[Term]
id: SO:0000140
name: attenuator
namespace: sequence
def: "A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as]
subset: SOFA
synonym: "attenuator sequence" EXACT []
synonym: "INSDC_feature:regulatory" BROAD []
synonym: "INSDC_qualifier:attenuator" EXACT []
xref: http://en.wikipedia.org/wiki/Attenuator "wiki"
is_a: SO:0005836 ! regulatory_region
relationship: part_of SO:0000234 ! mRNA

[Term]
id: SO:0000141
name: terminator
namespace: sequence
def: "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "INSDC_feature:regulatory" BROAD []
synonym: "INSDC_qualifier:terminator" EXACT []
synonym: "terminator sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Terminator_(genetics) "wiki"
is_a: SO:0001679 ! transcription_regulatory_region
relationship: part_of SO:0000673 ! transcript

[Term]
id: SO:0000143
name: assembly_component
namespace: sequence
def: "A region of known length which may be used to manufacture a longer region." [SO:ke]
subset: SOFA
synonym: "assembly component" EXACT []
is_a: SO:0001410 ! experimental_feature

[Term]
id: SO:0000147
name: exon
namespace: sequence
def: "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "INSDC_feature:exon" EXACT []
xref: http://en.wikipedia.org/wiki/Exon "wiki"
is_a: SO:0000833 ! transcript_region

[Term]
id: SO:0000148
name: supercontig
namespace: sequence
def: "One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]
subset: SOFA
synonym: "scaffold" RELATED []
is_a: SO:0000353 ! sequence_assembly
relationship: part_of SO:0000719 ! ultracontig

[Term]
id: SO:0000149
name: contig
namespace: sequence
def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Contig "wiki"
is_a: SO:0000143 ! assembly_component
is_a: SO:0000353 ! sequence_assembly
relationship: part_of SO:0000148 ! supercontig

[Term]
id: SO:0000150
name: read
namespace: sequence
def: "A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]
subset: SOFA
is_a: SO:0000143 ! assembly_component
relationship: part_of SO:0000149 ! contig

[Term]
id: SO:0000151
name: clone
namespace: sequence
def: "A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]
subset: SOFA
xref: http:http\://en.wikipedia.org/wiki/Clone_(genetics) "wiki"
is_a: SO:0000695 ! reagent

[Term]
id: SO:0000159
name: deletion
namespace: sequence
alt_id: SO:1000033
def: "The point at which one or more contiguous nucleotides were excised." [SO:ke]
subset: SOFA
synonym: "deleted_sequence" EXACT []
synonym: "nucleotide deletion" EXACT []
synonym: "nucleotide_deletion" EXACT []
xref: http://en.wikipedia.org/wiki/Nucleotide_deletion "wiki"
xref: loinc:LA6692-3 "Deletion"
is_a: SO:0001059 ! sequence_alteration
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0000161
name: methylated_adenine
namespace: sequence
def: "A modified  base in which adenine has been methylated." [SO:ke]
subset: SOFA
synonym: "methylated A" EXACT []
synonym: "methylated adenine" EXACT []
synonym: "methylated adenine base" EXACT []
synonym: "methylated adenine residue" EXACT []
synonym: "methylated_A" EXACT []
is_a: SO:0000306 ! methylated_DNA_base_feature

[Term]
id: SO:0000162
name: splice_site
namespace: sequence
def: "Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]
comment: With spliceosomal introns, the splice sites bind the spliceosomal machinery.
subset: SOFA
synonym: "splice site" EXACT []
xref: http://en.wikipedia.org/wiki/Splice_site "wiki"
is_a: SO:0000835 ! primary_transcript_region

[Term]
id: SO:0000163
name: five_prime_cis_splice_site
namespace: sequence
def: "Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]
subset: SOFA
synonym: "5' splice site" EXACT []
synonym: "donor" RELATED []
synonym: "donor splice site" EXACT []
synonym: "five prime splice site" EXACT []
synonym: "splice donor site" EXACT []
is_a: SO:0001419 ! cis_splice_site

[Term]
id: SO:0000164
name: three_prime_cis_splice_site
namespace: sequence
def: "Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]
subset: SOFA
synonym: "3' splice site" RELATED []
synonym: "acceptor" RELATED []
synonym: "acceptor splice site" EXACT []
synonym: "splice acceptor site" EXACT []
synonym: "three prime splice site" EXACT []
is_a: SO:0001419 ! cis_splice_site

[Term]
id: SO:0000165
name: enhancer
namespace: sequence
def: "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO.
subset: SOFA
synonym: "INSDC_feature:regulatory" BROAD []
synonym: "INSDC_qualifier:enhancer" EXACT []
xref: http://en.wikipedia.org/wiki/Enhancer_(genetics) "wiki"
is_a: SO:0000727 ! CRM

[Term]
id: SO:0000167
name: promoter
namespace: sequence
def: "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription.
subset: SOFA
synonym: "INSDC_feature:regulatory" BROAD []
synonym: "INSDC_qualifier:promoter" EXACT []
synonym: "promoter sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Promoter "wiki"
is_a: SO:0001055 ! transcriptional_cis_regulatory_region

[Term]
id: SO:0000177
name: cross_genome_match
namespace: sequence
def: "A nucleotide match against a sequence from another organism." [SO:ma]
subset: SOFA
synonym: "cross genome match" EXACT []
is_a: SO:0000347 ! nucleotide_match

[Term]
id: SO:0000178
name: operon
namespace: sequence
def: "A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "INSDC_feature:operon" EXACT []
xref: http://en.wikipedia.org/wiki/Operon "wiki"
is_a: SO:0005855 ! gene_group

[Term]
id: SO:0000179
name: clone_insert_start
namespace: sequence
def: "The start of the clone insert." [SO:ke]
subset: SOFA
synonym: "clone insert start" EXACT []
is_a: SO:0000699 ! junction
relationship: part_of SO:0000753 ! clone_insert

[Term]
id: SO:0000181
name: translated_nucleotide_match
namespace: sequence
def: "A match against a translated sequence." [SO:ke]
subset: SOFA
synonym: "translated nucleotide match" EXACT []
is_a: SO:0000347 ! nucleotide_match

[Term]
id: SO:0000183
name: non_transcribed_region
namespace: sequence
def: "A region of the gene which is not transcribed." [SO:ke]
subset: SOFA
synonym: "non transcribed region" EXACT []
synonym: "non-transcribed sequence" EXACT []
synonym: "nontranscribed region" EXACT []
synonym: "nontranscribed sequence" EXACT []
is_a: SO:0000842 ! gene_component_region

[Term]
id: SO:0000185
name: primary_transcript
namespace: sequence
def: "A transcript that in its initial state requires modification to be functional." [SO:ma]
subset: SOFA
synonym: "INSDC_feature:precursor_RNA" EXACT []
synonym: "INSDC_feature:prim_transcript" EXACT []
synonym: "precursor RNA" EXACT []
synonym: "primary transcript" EXACT []
xref: http://en.wikipedia.org/wiki/Primary_transcript "wiki"
is_a: SO:0000673 ! transcript

[Term]
id: SO:0000187
name: repeat_family
namespace: sequence
def: "A group of characterized repeat sequences." [SO:ke]
subset: SOFA
is_obsolete: true

[Term]
id: SO:0000188
name: intron
namespace: sequence
def: "A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "INSDC_feature:intron" EXACT []
xref: http://en.wikipedia.org/wiki/Intron "wiki"
is_a: SO:0000835 ! primary_transcript_region

[Term]
id: SO:0000193
name: RFLP_fragment
namespace: sequence
def: "A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme." [GOC:pj]
subset: SOFA
synonym: "restriction fragment length polymorphism" EXACT []
synonym: "RFLP" EXACT []
synonym: "RFLP fragment" EXACT []
xref: http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism "wiki"
is_a: SO:0000412 ! restriction_fragment

[Term]
id: SO:0000195
name: coding_exon
namespace: sequence
def: "An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]
subset: SOFA
synonym: "coding exon" EXACT []
is_a: SO:0000147 ! exon

[Term]
id: SO:0000196
name: five_prime_coding_exon_coding_region
namespace: sequence
def: "The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]
subset: SOFA
synonym: "five prime exon coding region" EXACT []
is_a: SO:0001215 ! coding_region_of_exon
relationship: part_of SO:0000200 ! five_prime_coding_exon

[Term]
id: SO:0000197
name: three_prime_coding_exon_coding_region
namespace: sequence
def: "The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]
subset: SOFA
synonym: "three prime exon coding region" EXACT []
is_a: SO:0001215 ! coding_region_of_exon
relationship: part_of SO:0000195 ! coding_exon

[Term]
id: SO:0000198
name: noncoding_exon
namespace: sequence
def: "An exon that does not contain any codons." [SO:ke]
subset: SOFA
synonym: "noncoding exon" EXACT []
is_a: SO:0000147 ! exon

[Term]
id: SO:0000200
name: five_prime_coding_exon
namespace: sequence
def: "The 5' most coding exon." [SO:ke]
subset: SOFA
synonym: "5' coding exon" EXACT []
synonym: "five prime coding exon" EXACT []
is_a: SO:0000195 ! coding_exon

[Term]
id: SO:0000203
name: UTR
namespace: sequence
def: "Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]
subset: SOFA
synonym: "untranslated region" EXACT []
is_a: SO:0000836 ! mRNA_region

[Term]
id: SO:0000204
name: five_prime_UTR
namespace: sequence
def: "A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "5' UTR" EXACT []
synonym: "five prime UTR" EXACT []
synonym: "five_prime_untranslated_region" EXACT []
synonym: "INSDC_feature:5'UTR" EXACT []
xref: http://en.wikipedia.org/wiki/5'_UTR "wiki"
is_a: SO:0000203 ! UTR

[Term]
id: SO:0000205
name: three_prime_UTR
namespace: sequence
def: "A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "INSDC_feature:3'UTR" EXACT []
synonym: "three prime untranslated region" EXACT []
synonym: "three prime UTR" EXACT []
xref: http://en.wikipedia.org/wiki/Three_prime_untranslated_region "wiki"
is_a: SO:0000203 ! UTR

[Term]
id: SO:0000209
name: rRNA_primary_transcript
namespace: sequence
def: "A primary transcript encoding a ribosomal RNA." [SO:ke]
subset: SOFA
synonym: "ribosomal RNA primary transcript" EXACT []
synonym: "rRNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000233
name: mature_transcript
namespace: sequence
def: "A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]
comment: A processed transcript cannot contain introns.
subset: SOFA
synonym: "mature transcript" EXACT []
xref: http://en.wikipedia.org/wiki/Mature_transcript "wiki"
is_a: SO:0000673 ! transcript
relationship: derives_from SO:0000185 ! primary_transcript

[Term]
id: SO:0000234
name: mRNA
namespace: sequence
def: "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]
comment: An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "INSDC_feature:mRNA" EXACT []
synonym: "messenger RNA" EXACT []
synonym: "protein_coding_transcript" EXACT []
xref: http://en.wikipedia.org/wiki/MRNA "wiki"
xref: http://www.gencodegenes.org/gencode_biotypes.html "GENCODE"
is_a: SO:0000233 ! mature_transcript

[Term]
id: SO:0000235
name: TF_binding_site
namespace: sequence
def: "A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke]
subset: SOFA
synonym: "TF binding site" EXACT []
synonym: "transcription factor binding site" EXACT []
is_a: SO:0001654 ! nucleotide_to_protein_binding_site
is_a: SO:0001679 ! transcription_regulatory_region

[Term]
id: SO:0000236
name: ORF
namespace: sequence
def: "The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma]
comment: The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "open reading frame" EXACT []
is_a: SO:0000717 ! reading_frame

[Term]
id: SO:0000239
name: flanking_region
namespace: sequence
def: "The sequences extending on either side of a specific region." [SO:ke]
subset: SOFA
synonym: "flanking region" EXACT []
is_a: SO:0001412 ! topologically_defined_region

[Term]
id: SO:0000252
name: rRNA
namespace: sequence
def: "RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]
subset: SOFA
synonym: "INSDC_feature:rRNA" EXACT []
synonym: "INSDC_qualifier:unknown" BROAD []
synonym: "ribosomal ribonucleic acid" EXACT []
synonym: "ribosomal RNA" EXACT []
xref: http://en.wikipedia.org/wiki/RRNA "wiki"
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000209 ! rRNA_primary_transcript

[Term]
id: SO:0000253
name: tRNA
namespace: sequence
def: "Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "INSDC_feature:tRNA" EXACT []
synonym: "INSDC_qualifier:unknown" BROAD []
synonym: "transfer ribonucleic acid" RELATED []
synonym: "transfer RNA" RELATED []
xref: http://en.wikipedia.org/wiki/TRNA "wiki"
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000274
name: snRNA
namespace: sequence
def: "A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "INSDC_feature:ncRNA" BROAD []
synonym: "INSDC_qualifier:snRNA" EXACT []
synonym: "small nuclear RNA" EXACT []
xref: http://en.wikipedia.org/wiki/SnRNA "wiki"
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000275
name: snoRNA
namespace: sequence
def: "A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc]
subset: SOFA
synonym: "INSDC_feature:ncRNA" BROAD []
synonym: "INSDC_qualifier:snoRNA" EXACT []
synonym: "small nucleolar RNA" EXACT []
xref: http://en.wikipedia.org/wiki/SnoRNA "wiki"
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000276
name: miRNA
namespace: sequence
alt_id: SO:0000649
def: "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:11081512, PMID:12592000]
subset: SOFA
synonym: "INSDC_feature:ncRNA" BROAD []
synonym: "INSDC_qualifier:miRNA" EXACT []
synonym: "micro RNA" EXACT []
synonym: "microRNA" EXACT []
synonym: "small temporal RNA" EXACT []
synonym: "stRNA" EXACT []
xref: http://en.wikipedia.org/wiki/MiRNA "wiki"
xref: http://en.wikipedia.org/wiki/StRNA "wiki"
is_a: SO:0000370 ! small_regulatory_ncRNA
relationship: part_of SO:0000835 ! primary_transcript_region

[Term]
id: SO:0000289
name: microsatellite
namespace: sequence
def: "A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th]
subset: SOFA
synonym: "INSDC_feature:repeat_region" BROAD []
synonym: "INSDC_qualifier:microsatellite" EXACT []
synonym: "microsatellite locus" EXACT []
synonym: "microsatellite marker" EXACT []
synonym: "short tandem repeat" EXACT []
synonym: "STR" EXACT [http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9651/]
xref: http://en.wikipedia.org/wiki/Microsatellite "wiki"
is_a: SO:0000005 ! satellite_DNA

[Term]
id: SO:0000294
name: inverted_repeat
namespace: sequence
def: "The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:ke]
subset: SOFA
synonym: "INSDC_feature:repeat_region" BROAD []
synonym: "INSDC_qualifier:inverted" EXACT []
synonym: "inverted repeat" EXACT []
synonym: "inverted repeat sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Inverted_repeat "wiki"
is_a: SO:0000657 ! repeat_region

[Term]
id: SO:0000296
name: origin_of_replication
namespace: sequence
def: "A region of nucleic acid from which replication initiates; includes sequences that are recognized by replication proteins, the site from which the first separation of complementary strands occurs, and specific replication start sites." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, NCBI:cf]
subset: SOFA
synonym: "INSDC_feature:rep_origin" EXACT []
synonym: "ori" EXACT []
synonym: "origin of replication" EXACT []
xref: http://en.wikipedia.org/wiki/Origin_of_replication "wiki"
is_a: SO:0001411 ! biological_region
relationship: part_of SO:0001235 ! replicon

[Term]
id: SO:0000303
name: clip
namespace: sequence
def: "Part of the primary transcript that is clipped off during processing." [SO:ke]
subset: SOFA
is_a: SO:0000835 ! primary_transcript_region

[Term]
id: SO:0000305
name: modified_DNA_base
namespace: sequence
def: "A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: Modified base:<modified_base>.
subset: SOFA
synonym: "INSDC_feature:modified_base" EXACT []
synonym: "modified base site" EXACT []
is_a: SO:0001236 ! base
is_a: SO:0001720 ! epigenetically_modified_region

[Term]
id: SO:0000306
name: methylated_DNA_base_feature
namespace: sequence
def: "A nucleotide modified by methylation." [SO:ke]
subset: SOFA
synonym: "methylated base feature" EXACT []
is_a: SO:0000305 ! modified_DNA_base

[Term]
id: SO:0000307
name: CpG_island
namespace: sequence
def: "Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." [SO:rd]
subset: SOFA
synonym: "CG island" EXACT []
synonym: "CpG island" EXACT []
xref: http://en.wikipedia.org/wiki/CpG_island "wiki"
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0000314
name: direct_repeat
namespace: sequence
def: "A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA." [SO:ke]
subset: SOFA
synonym: "direct repeat" EXACT []
synonym: "INSDC_feature:repeat_region" BROAD []
synonym: "INSDC_qualifier:direct" EXACT []
xref: http://en.wikipedia.org/wiki/Direct_repeat "wiki"
is_a: SO:0000657 ! repeat_region

[Term]
id: SO:0000315
name: TSS
namespace: sequence
def: "The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]
subset: SOFA
synonym: "INSDC_feature:misc_feature" BROAD []
synonym: "INSDC_note:transcription_start_site" EXACT []
synonym: "transcription start site" EXACT []
synonym: "transcription_start_site" EXACT []
is_a: SO:0000835 ! primary_transcript_region

[Term]
id: SO:0000316
name: CDS
namespace: sequence
def: "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]
subset: SOFA
synonym: "coding sequence" EXACT []
synonym: "coding_sequence" EXACT []
synonym: "INSDC_feature:CDS" EXACT []
is_a: SO:0000836 ! mRNA_region

[Term]
id: SO:0000318
name: start_codon
namespace: sequence
def: "First codon to be translated by a ribosome." [SO:ke]
subset: SOFA
synonym: "initiation codon" EXACT []
synonym: "start codon" EXACT []
xref: http://en.wikipedia.org/wiki/Start_codon "wiki"
is_a: SO:0000360 ! codon

[Term]
id: SO:0000319
name: stop_codon
namespace: sequence
def: "In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]
subset: SOFA
synonym: "stop codon" EXACT []
xref: http://en.wikipedia.org/wiki/Stop_codon "wiki"
is_a: SO:0000360 ! codon

[Term]
id: SO:0000324
name: tag
namespace: sequence
def: "A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]
subset: SOFA
is_a: SO:0000696 ! oligo

[Term]
id: SO:0000325
name: rRNA_large_subunit_primary_transcript
namespace: sequence
def: "A primary transcript encoding a large ribosomal subunit RNA." [SO:ke]
subset: SOFA
synonym: "35S rRNA primary transcript" EXACT []
synonym: "rRNA large subunit primary transcript" EXACT []
is_a: SO:0000209 ! rRNA_primary_transcript

[Term]
id: SO:0000326
name: SAGE_tag
namespace: sequence
def: "A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract]
subset: SOFA
synonym: "SAGE tag" EXACT []
is_a: SO:0000324 ! tag

[Term]
id: SO:0000330
name: conserved_region
namespace: sequence
def: "Region of sequence similarity by descent from a common ancestor." [SO:ke]
subset: SOFA
synonym: "conserved region" EXACT []
synonym: "INSDC_feature:misc_feature" BROAD []
synonym: "INSDC_note:conserved_region" EXACT []
xref: http://en.wikipedia.org/wiki/Conserved_region "wiki"
is_a: SO:0001410 ! experimental_feature

[Term]
id: SO:0000331
name: STS
namespace: sequence
def: "Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com]
subset: SOFA
synonym: "INSDC_feature:STS" EXACT []
synonym: "sequence tag site" EXACT []
is_a: SO:0000324 ! tag

[Term]
id: SO:0000332
name: coding_conserved_region
namespace: sequence
def: "Coding region of sequence similarity by descent from a common ancestor." [SO:ke]
subset: SOFA
synonym: "coding conserved region" EXACT []
is_a: SO:0000330 ! conserved_region

[Term]
id: SO:0000333
name: exon_junction
namespace: sequence
def: "The boundary between two exons in a processed transcript." [SO:ke]
subset: SOFA
synonym: "exon junction" EXACT []
is_a: SO:0000699 ! junction
relationship: part_of SO:0000233 ! mature_transcript

[Term]
id: SO:0000334
name: nc_conserved_region
namespace: sequence
def: "Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke]
subset: SOFA
synonym: "conserved non-coding element" EXACT []
synonym: "conserved non-coding sequence" EXACT []
synonym: "nc conserved region" EXACT []
synonym: "noncoding conserved region" EXACT []
is_a: SO:0000330 ! conserved_region

[Term]
id: SO:0000336
name: pseudogene
namespace: sequence
def: "A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]
subset: SOFA
synonym: "INSDC_feature:gene" BROAD []
synonym: "INSDC_qualifier:pseudo" EXACT []
synonym: "INSDC_qualifier:unknown" EXACT []
xref: http://en.wikipedia.org/wiki/Pseudogene "wiki"
is_a: SO:0001411 ! biological_region
relationship: non_functional_homolog_of SO:0000704 ! gene

[Term]
id: SO:0000337
name: RNAi_reagent
namespace: sequence
def: "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd]
subset: SOFA
synonym: "RNAi reagent" EXACT []
is_a: SO:0000442 ! ds_oligo

[Term]
id: SO:0000340
name: chromosome
namespace: sequence
def: "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
xref: http://en.wikipedia.org/wiki/Chromosome "wiki"
is_a: SO:0001235 ! replicon

[Term]
id: SO:0000341
name: chromosome_band
namespace: sequence
def: "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma]
subset: SOFA
synonym: "chromosome band" EXACT []
synonym: "cytoband" EXACT []
synonym: "cytological band" EXACT []
xref: http://en.wikipedia.org/wiki/Cytological_band "wiki"
is_a: SO:0000830 ! chromosome_part

[Term]
id: SO:0000343
name: match
namespace: sequence
def: "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]
subset: SOFA
is_a: SO:0001410 ! experimental_feature

[Term]
id: SO:0000344
name: splice_enhancer
namespace: sequence
def: "Region of a transcript that regulates splicing." [SO:ke]
subset: SOFA
synonym: "splice enhancer" EXACT []
is_a: SO:0000165 ! enhancer
is_a: SO:0001056 ! splicing_regulatory_region

[Term]
id: SO:0000345
name: EST
namespace: sequence
def: "A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "expressed sequence tag" EXACT []
is_a: SO:0000324 ! tag
relationship: derives_from SO:0000234 ! mRNA

[Term]
id: SO:0000347
name: nucleotide_match
namespace: sequence
def: "A match against a nucleotide sequence." [SO:ke]
subset: SOFA
synonym: "nucleotide match" EXACT []
is_a: SO:0000343 ! match

[Term]
id: SO:0000349
name: protein_match
namespace: sequence
def: "A match against a protein sequence." [SO:ke]
subset: SOFA
synonym: "protein match" EXACT []
is_a: SO:0000343 ! match

[Term]
id: SO:0000353
name: sequence_assembly
namespace: sequence
def: "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]
subset: SOFA
synonym: "sequence assembly" EXACT []
xref: http://en.wikipedia.org/wiki/Sequence_assembly "wiki"
is_a: SO:0001248 ! assembly

[Term]
id: SO:0000360
name: codon
namespace: sequence
def: "A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [SO:ke]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Codon "wiki"
is_a: SO:0000851 ! CDS_region

[Term]
id: SO:0000366
name: insertion_site
namespace: sequence
def: "The junction where an insertion occurred." [SO:ke]
subset: SOFA
synonym: "insertion site" EXACT []
is_a: SO:0000699 ! junction

[Term]
id: SO:0000368
name: transposable_element_insertion_site
namespace: sequence
def: "The junction in a genome where a transposable_element has inserted." [SO:ke]
subset: SOFA
synonym: "transposable element insertion site" EXACT []
is_a: SO:0000366 ! insertion_site

[Term]
id: SO:0000370
name: small_regulatory_ncRNA
namespace: sequence
def: "A non-coding RNA less than 200 nucleotides long, usually with a specific secondary structure, that acts to regulate gene expression. These include short ncRNAs such as piRNA, miRNA and siRNAs (among others)." [PMID:28541282, PomBase:al, SO:ma]
subset: SOFA
synonym: "small regulatory ncRNA" EXACT []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000372
name: enzymatic_RNA
namespace: sequence
def: "An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]
comment: This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts.
subset: SOFA
synonym: "enzymatic RNA" EXACT []
is_a: SO:0000673 ! transcript

[Term]
id: SO:0000374
name: ribozyme
namespace: sequence
def: "An RNA with catalytic activity." [SO:ma]
subset: SOFA
synonym: "INSDC_feature:ncRNA" BROAD []
synonym: "INSDC_qualifier:ribozyme" EXACT []
xref: http://en.wikipedia.org/wiki/Ribozyme "wiki"
is_a: SO:0000372 ! enzymatic_RNA

[Term]
id: SO:0000375
name: rRNA_5_8S
namespace: sequence
def: "5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002]
subset: SOFA
synonym: "5.8S LSU rRNA" EXACT []
synonym: "5.8S ribosomal RNA" EXACT []
synonym: "5.8S rRNA" EXACT []
synonym: "rRNA 5 8S" EXACT []
xref: http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA "wiki"
is_a: SO:0000651 ! large_subunit_rRNA

[Term]
id: SO:0000380
name: hammerhead_ribozyme
namespace: sequence
def: "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [PMID:2436805]
subset: SOFA
synonym: "hammerhead ribozyme" EXACT []
synonym: "INSDC_feature:ncRNA" BROAD []
synonym: "INSDC_qualifier:hammerhead_ribozyme" EXACT []
xref: http://en.wikipedia.org/wiki/Hammerhead_ribozyme "wiki"
is_a: SO:0000715 ! RNA_motif

[Term]
id: SO:0000385
name: RNase_MRP_RNA
namespace: sequence
def: "The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030]
subset: SOFA
synonym: "INSDC_feature:ncRNA" BROAD []
synonym: "INSDC_qualifier:RNase_MRP_RNA" EXACT []
synonym: "RNase MRP RNA" EXACT []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000386
name: RNase_P_RNA
namespace: sequence
def: "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010]
subset: SOFA
synonym: "INSDC_feature:ncRNA" BROAD []
synonym: "INSDC_qualifier:RNase_P_RNA" EXACT []
synonym: "RNase P RNA" EXACT []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000390
name: telomerase_RNA
namespace: sequence
def: "The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]
subset: SOFA
synonym: "INSDC_feature:ncRNA" BROAD []
synonym: "INSDC_qualifier:telomerase_RNA" EXACT []
synonym: "telomerase RNA" EXACT []
xref: http://en.wikipedia.org/wiki/Telomerase_RNA "wiki"
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000391
name: U1_snRNA
namespace: sequence
def: "U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003]
subset: SOFA
synonym: "small nuclear RNA U1" EXACT [RSC:cb]
synonym: "snRNA U1" EXACT [RSC:cb]
synonym: "U1 small nuclear RNA" EXACT [RSC:cb]
synonym: "U1 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U1_snRNA "wiki"
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000392
name: U2_snRNA
namespace: sequence
def: "U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004]
subset: SOFA
synonym: "small nuclear RNA U2" EXACT [RSC:CB]
synonym: "snRNA U2" EXACT [RSC:CB]
synonym: "U2 small nuclear RNA" EXACT [RSC:CB]
synonym: "U2 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U2_snRNA "wiki"
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000393
name: U4_snRNA
namespace: sequence
def: "U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]
subset: SOFA
synonym: "small nuclear RNA U4" EXACT [RSC:cb]
synonym: "snRNA U4" EXACT [RSC:cb]
synonym: "U4 small nuclear RNA" EXACT [RSC:cb]
synonym: "U4 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U4_snRNA "wiki"
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000394
name: U4atac_snRNA
namespace: sequence
def: "An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455]
subset: SOFA
synonym: "small nuclear RNA U4atac" EXACT [RSC:cb]
synonym: "snRNA U4atac" EXACT [RSC:cb]
synonym: "U4atac small nuclear RNA" EXACT [RSC:cb]
synonym: "U4atac snRNA" EXACT []
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000395
name: U5_snRNA
namespace: sequence
def: "U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020]
subset: SOFA
synonym: "small nuclear RNA U5" EXACT [RSC:cb]
synonym: "snRNA U5" EXACT [RSC:cb]
synonym: "U5 small nuclear RNA" EXACT [RSC:cb]
synonym: "U5 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U5_snRNA "wiki"
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000396
name: U6_snRNA
namespace: sequence
def: "U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]
subset: SOFA
synonym: "small nuclear RNA U6" EXACT [RSC:cb]
synonym: "snRNA U6" EXACT [RSC:cb]
synonym: "U6 small nuclear RNA" EXACT [RSC:cb]
synonym: "U6 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U6_snRNA "wiki"
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000397
name: U6atac_snRNA
namespace: sequence
def: "U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract]
subset: SOFA
synonym: "snRNA U6atac" EXACT [RSC:cb]
synonym: "U6atac small nuclear RNA" EXACT [RSC:cb]
synonym: "U6atac snRNA" EXACT [RSC:cb]
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000398
name: U11_snRNA
namespace: sequence
def: "U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129]
subset: SOFA
synonym: "small nuclear RNA U11" EXACT [RSC:cb]
synonym: "snRNA U11" EXACT [RSC:cb]
synonym: "U11 small nuclear RNA" EXACT [RSC:cb]
synonym: "U11 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U11_snRNA "wiki"
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000399
name: U12_snRNA
namespace: sequence
def: "The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007]
subset: SOFA
synonym: "small nuclear RNA U12" EXACT [RSC:cb]
synonym: "snRNA U12" EXACT [RSC:cb]
synonym: "U12 small nuclear RNA" EXACT [RSC:cb]
synonym: "U12 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U12_snRNA "wiki"
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000403
name: U14_snoRNA
namespace: sequence
alt_id: SO:0005839
def: "U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119]
comment: An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.
subset: SOFA
synonym: "small nucleolar RNA U14" EXACT []
synonym: "snoRNA U14" EXACT []
synonym: "U14 small nucleolar RNA" EXACT []
synonym: "U14 snoRNA" EXACT []
is_a: SO:0000593 ! C_D_box_snoRNA

[Term]
id: SO:0000404
name: vault_RNA
namespace: sequence
def: "A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006]
subset: SOFA
synonym: "INSDC_feature:ncRNA" BROAD []
synonym: "INSDC_qualifier:vault_RNA" EXACT []
synonym: "vault RNA" EXACT []
xref: http://en.wikipedia.org/wiki/Vault_RNA "wiki"
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000405
name: Y_RNA
namespace: sequence
def: "Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019]
subset: SOFA
synonym: "INSDC_feature:ncRNA" BROAD []
synonym: "INSDC_qualifier:Y_RNA" EXACT []
synonym: "Y RNA" EXACT []
xref: http://en.wikipedia.org/wiki/Y_RNA "wiki"
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000407
name: rRNA_18S
namespace: sequence
def: "A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke]
subset: SOFA
synonym: "18S ribosomal RNA" EXACT []
synonym: "18S rRNA" EXACT []
synonym: "rRNA 18S" EXACT []
xref: http://en.wikipedia.org/wiki/18S_ribosomal_RNA "wiki"
is_a: SO:0000650 ! small_subunit_rRNA

[Term]
id: SO:0000409
name: binding_site
namespace: sequence
alt_id: BS:00033
def: "A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]
comment: See GO:0005488 : binding.
subset: biosapiens
subset: SOFA
synonym: "binding site" EXACT []
synonym: "binding_or_interaction_site" EXACT []
synonym: "INSDC_feature:misc_binding" EXACT []
synonym: "site" RELATED []
xref: http://en.wikipedia.org/wiki/Binding_site "wiki"
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0000410
name: protein_binding_site
namespace: sequence
def: "A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]
comment: See GO:0042277 : peptide binding.
subset: SOFA
synonym: "INSDC_feature:protein_bind" EXACT []
synonym: "protein binding site" EXACT []
is_a: SO:0000409 ! binding_site

[Term]
id: SO:0000412
name: restriction_fragment
namespace: sequence
def: "A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke]
subset: SOFA
synonym: "restriction fragment" EXACT []
xref: http://en.wikipedia.org/wiki/Restriction_fragment "wiki"
is_a: SO:0000143 ! assembly_component

[Term]
id: SO:0000413
name: sequence_difference
namespace: sequence
def: "A region where the sequence differs from that of a specified sequence." [SO:ke]
subset: SOFA
synonym: "INSDC_feature:misc_difference" EXACT []
synonym: "sequence difference" EXACT []
is_a: SO:0000700 ! remark

[Term]
id: SO:0000418
name: signal_peptide
namespace: sequence
alt_id: BS:00159
def: "The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence.
subset: biosapiens
subset: SOFA
synonym: "INSDC_feature:sig_peptide" EXACT []
synonym: "signal" RELATED [uniprot:feature_type]
synonym: "signal peptide" EXACT []
synonym: "signal peptide coding sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Signal_peptide "wiki"
is_a: SO:0001527 ! peptide_localization_signal
relationship: part_of SO:0100011 ! cleaved_peptide_region

[Term]
id: SO:0000419
name: mature_protein_region
namespace: sequence
alt_id: BS:00149
def: "The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb]
comment: This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification.
subset: biosapiens
subset: SOFA
synonym: "chain" RELATED [uniprot:feature_type]
synonym: "INSDC_feature:mat_peptide" EXACT []
synonym: "mature peptide" RELATED []
synonym: "mature protein region" EXACT []
is_a: SO:0000839 ! polypeptide_region
relationship: part_of SO:0001063 ! immature_peptide_region

[Term]
id: SO:0000436
name: ARS
namespace: sequence
def: "A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma]
subset: SOFA
synonym: "autonomously replicating sequence" EXACT []
is_a: SO:0000296 ! origin_of_replication

[Term]
id: SO:0000441
name: ss_oligo
namespace: sequence
def: "A single stranded oligonucleotide." [SO:ke]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "single strand oligo" EXACT []
synonym: "single strand oligonucleotide" EXACT []
synonym: "single stranded oligonucleotide" EXACT []
synonym: "ss oligo" EXACT []
synonym: "ss oligonucleotide" EXACT []
is_a: SO:0000696 ! oligo

[Term]
id: SO:0000442
name: ds_oligo
namespace: sequence
def: "A double stranded oligonucleotide." [SO:ke]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "double stranded oligonucleotide" EXACT []
synonym: "ds oligo" EXACT []
synonym: "ds-oligonucleotide" EXACT []
is_a: SO:0000696 ! oligo

[Term]
id: SO:0000454
name: rasiRNA
namespace: sequence
def: "A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284]
subset: SOFA
synonym: "INSDC_feature:ncRNA" BROAD []
synonym: "INSDC_qualifier:rasiRNA" EXACT []
synonym: "repeat associated small interfering RNA" EXACT []
xref: http://en.wikipedia.org/wiki/RasiRNA "wiki"
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000462
name: pseudogenic_region
namespace: sequence
def: "A non-functional descendant of a functional entity." [SO:cjm]
subset: SOFA
synonym: "pseudogenic region" EXACT []
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0000464
name: decayed_exon
namespace: sequence
def: "A non-functional descendant of an exon." [SO:ke]
comment: Does not have to be part of a pseudogene.
subset: SOFA
synonym: "decayed exon" EXACT []
is_a: SO:0000462 ! pseudogenic_region
relationship: non_functional_homolog_of SO:0000147 ! exon

[Term]
id: SO:0000468
name: golden_path_fragment
namespace: sequence
def: "One of the pieces of sequence that make up a golden path." [SO:rd]
subset: SOFA
synonym: "golden path fragment" EXACT []
is_a: SO:0000143 ! assembly_component
relationship: part_of SO:0000688 ! golden_path

[Term]
id: SO:0000472
name: tiling_path
namespace: sequence
def: "A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm]
subset: SOFA
synonym: "tiling path" EXACT []
is_a: SO:0000353 ! sequence_assembly

[Term]
id: SO:0000474
name: tiling_path_fragment
namespace: sequence
def: "A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke]
subset: SOFA
synonym: "tiling path fragment" EXACT []
is_a: SO:0000143 ! assembly_component
relationship: part_of SO:0000472 ! tiling_path

[Term]
id: SO:0000483
name: nc_primary_transcript
namespace: sequence
def: "A primary transcript that is never translated into a protein." [SO:ke]
subset: SOFA
synonym: "nc primary transcript" EXACT []
synonym: "noncoding primary transcript" EXACT []
is_a: SO:0000185 ! primary_transcript

[Term]
id: SO:0000484
name: three_prime_coding_exon_noncoding_region
namespace: sequence
def: "The sequence of the 3' exon that is not coding." [SO:ke]
subset: SOFA
synonym: "three prime coding exon noncoding region" EXACT []
synonym: "three_prime_exon_noncoding_region" EXACT []
is_a: SO:0001214 ! noncoding_region_of_exon
relationship: part_of SO:0000195 ! coding_exon

[Term]
id: SO:0000486
name: five_prime_coding_exon_noncoding_region
namespace: sequence
def: "The sequence of the 5' exon preceding the start codon." [SO:ke]
subset: SOFA
synonym: "five prime coding exon noncoding region" EXACT []
synonym: "five_prime_exon_noncoding_region" EXACT []
is_a: SO:0001214 ! noncoding_region_of_exon
relationship: part_of SO:0000200 ! five_prime_coding_exon

[Term]
id: SO:0000499
name: virtual_sequence
namespace: sequence
def: "A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke]
subset: SOFA
synonym: "virtual sequence" EXACT []
is_a: SO:0000353 ! sequence_assembly

[Term]
id: SO:0000502
name: transcribed_region
namespace: sequence
def: "A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes." [SO:ke]
comment: This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being.
subset: SOFA
is_obsolete: true

[Term]
id: SO:0000551
name: polyA_signal_sequence
namespace: sequence
def: "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "INSDC_feature:regulatory" BROAD []
synonym: "INSDC_qualifier:polyA_signal_sequence" EXACT []
synonym: "poly(A) signal" EXACT []
synonym: "polyA signal sequence" EXACT []
synonym: "polyadenylation termination signal" EXACT []
is_a: SO:0001679 ! transcription_regulatory_region

[Term]
id: SO:0000553
name: polyA_site
namespace: sequence
alt_id: SO:0001430
def: "The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "INSDC_feature:polyA_site" EXACT []
synonym: "polyA cleavage site" EXACT []
synonym: "polyA junction" EXACT []
synonym: "polyA site" EXACT []
synonym: "polyA_junction" EXACT []
synonym: "polyadenylation site" RELATED []
is_a: SO:0000699 ! junction
relationship: part_of SO:0000205 ! three_prime_UTR
relationship: part_of SO:0000233 ! mature_transcript

[Term]
id: SO:0000577
name: centromere
namespace: sequence
def: "A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]
subset: SOFA
synonym: "INSDC_feature:centromere" EXACT []
xref: http://en.wikipedia.org/wiki/Centromere "wiki"
is_a: SO:0000628 ! chromosomal_structural_element

[Term]
id: SO:0000581
name: cap
namespace: sequence
def: "A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]
subset: SOFA
xref: http://en.wikipedia.org/wiki/5%27_cap "wiki"
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0000587
name: group_I_intron
namespace: sequence
def: "Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]
comment: GO:0000372.
subset: SOFA
synonym: "group I intron" EXACT []
xref: http://en.wikipedia.org/wiki/Group_I_intron "wiki"
is_a: SO:0000588 ! autocatalytically_spliced_intron

[Term]
id: SO:0000588
name: autocatalytically_spliced_intron
namespace: sequence
def: "A self spliced intron." [SO:ke]
subset: SOFA
synonym: "autocatalytically spliced intron" EXACT []
synonym: "INSDC_feature:ncRNA" BROAD []
synonym: "INSDC_qualifier:autocatalytically_spliced_intron" EXACT []
is_a: SO:0000188 ! intron

[Term]
id: SO:0000590
name: SRP_RNA
namespace: sequence
def: "The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017]
subset: SOFA
synonym: "7S RNA" RELATED []
synonym: "INSDC_feature:ncRNA" BROAD []
synonym: "INSDC_qualifier:SRP_RNA" EXACT []
synonym: "signal recognition particle RNA" RELATED []
synonym: "SRP RNA" EXACT []
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000593
name: C_D_box_snoRNA
namespace: sequence
def: "Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]
subset: SOFA
synonym: "box C/D snoRNA" EXACT []
synonym: "C D box snoRNA" EXACT []
synonym: "C/D box snoRNA" EXACT []
is_a: SO:0000275 ! snoRNA

[Term]
id: SO:0000602
name: guide_RNA
namespace: sequence
def: "A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html]
subset: SOFA
synonym: "gRNA" EXACT []
synonym: "guide RNA" EXACT []
synonym: "INSDC_feature:ncRNA" BROAD []
synonym: "INSDC_qualifier:guide_RNA" EXACT []
xref: http://en.wikipedia.org/wiki/Guide_RNA "wiki"
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000603
name: group_II_intron
namespace: sequence
def: "Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron to intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]
comment: GO:0000373.
subset: SOFA
synonym: "group II intron" EXACT []
xref: http://en.wikipedia.org/wiki/Group_II_intron "wiki"
is_a: SO:0000588 ! autocatalytically_spliced_intron

[Term]
id: SO:0000605
name: intergenic_region
namespace: sequence
def: "A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome." [SO:cjm]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "intergenic region" EXACT []
xref: http://en.wikipedia.org/wiki/Intergenic_region "wiki"
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0000610
name: polyA_sequence
namespace: sequence
def: "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke]
subset: SOFA
synonym: "polyA sequence" EXACT []
is_a: SO:0001411 ! biological_region
relationship: adjacent_to SO:0000234 ! mRNA

[Term]
id: SO:0000611
name: branch_site
namespace: sequence
def: "A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]
subset: SOFA
synonym: "branch point" EXACT []
synonym: "branch site" EXACT []
synonym: "branch_point" EXACT []
is_a: SO:0000841 ! spliceosomal_intron_region

[Term]
id: SO:0000612
name: polypyrimidine_tract
namespace: sequence
def: "The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]
subset: SOFA
synonym: "polypyrimidine tract" EXACT []
xref: http://en.wikipedia.org/wiki/Polypyrimidine_tract "wiki"
is_a: SO:0000841 ! spliceosomal_intron_region

[Term]
id: SO:0000616
name: transcription_end_site
namespace: sequence
def: "The base where transcription ends." [SO:ke]
subset: SOFA
synonym: "transcription end site" EXACT []
is_a: SO:0000835 ! primary_transcript_region

[Term]
id: SO:0000624
name: telomere
namespace: sequence
def: "A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]
subset: SOFA
synonym: "INSDC_feature:telomere" EXACT []
synonym: "telomeric DNA" EXACT []
synonym: "telomeric sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Telomere "wiki"
is_a: SO:0000628 ! chromosomal_structural_element

[Term]
id: SO:0000625
name: silencer
namespace: sequence
def: "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke]
subset: SOFA
synonym: "INSDC_feature:regulatory" BROAD []
synonym: "INSDC_qualifier:silencer" EXACT []
xref: http://en.wikipedia.org/wiki/Silencer_(DNA) "wiki"
is_a: SO:0000727 ! CRM

[Term]
id: SO:0000627
name: insulator
namespace: sequence
def: "A regulatory region that 1) when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression and 2) acts as a chromatin boundary element or barrier that can block the encroachment of condensed chromatin from an adjacent region." [NCBI:cf, PMID:12154228, SO:regcreative]
subset: SOFA
synonym: "INSDC_feature:regulatory" BROAD []
synonym: "INSDC_qualifier:insulator" EXACT []
synonym: "insulator element" EXACT []
xref: http://en.wikipedia.org/wiki/Insulator_(genetics) "wiki"
is_a: SO:0001055 ! transcriptional_cis_regulatory_region

[Term]
id: SO:0000628
name: chromosomal_structural_element
namespace: sequence
subset: SOFA
synonym: "chromosomal structural element" EXACT []
is_a: SO:0000830 ! chromosome_part

[Term]
id: SO:0000643
name: minisatellite
namespace: sequence
def: "A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml]
subset: SOFA
synonym: "INSDC_feature:repeat_region" BROAD []
synonym: "INSDC_qualifier:minisatellite" EXACT []
synonym: "VNTR" EXACT [http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9655/]
xref: http://en.wikipedia.org/wiki/Minisatellite "wiki"
is_a: SO:0000005 ! satellite_DNA

[Term]
id: SO:0000644
name: antisense_RNA
namespace: sequence
def: "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke]
subset: SOFA
synonym: "antisense RNA" EXACT []
synonym: "INSDC_feature:ncRNA" BROAD []
synonym: "INSDC_qualifier:antisense_RNA" EXACT []
xref: http://en.wikipedia.org/wiki/Antisense_RNA "wiki"
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000645 ! antisense_primary_transcript

[Term]
id: SO:0000645
name: antisense_primary_transcript
namespace: sequence
def: "The reverse complement of the primary transcript." [SO:ke]
subset: SOFA
synonym: "antisense primary transcript" EXACT []
is_a: SO:0000185 ! primary_transcript

[Term]
id: SO:0000646
name: siRNA
namespace: sequence
def: "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000]
subset: SOFA
synonym: "INSDC_feature:ncRNA" BROAD []
synonym: "INSDC_qualifier:siRNA" EXACT []
synonym: "small interfering RNA" EXACT []
xref: http://en.wikipedia.org/wiki/SiRNA "wiki"
is_a: SO:0000370 ! small_regulatory_ncRNA

[Term]
id: SO:0000650
name: small_subunit_rRNA
namespace: sequence
def: "Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke]
subset: SOFA
synonym: "small subunit rRNA" EXACT []
synonym: "SSU RNA" EXACT [RSC:cb]
synonym: "SSU rRNA" EXACT [RSC:cb]
is_a: SO:0000252 ! rRNA

[Term]
id: SO:0000651
name: large_subunit_rRNA
namespace: sequence
def: "Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]
subset: SOFA
synonym: "large subunit rRNA" EXACT []
synonym: "LSU RNA" EXACT [RSC:cb]
synonym: "LSU rRNA" EXACT [RSC:cb]
is_a: SO:0000252 ! rRNA
relationship: derives_from SO:0000325 ! rRNA_large_subunit_primary_transcript

[Term]
id: SO:0000652
name: rRNA_5S
namespace: sequence
def: "5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001]
subset: SOFA
synonym: "5S LSU rRNA" EXACT []
synonym: "5S ribosomal RNA" EXACT []
synonym: "5S rRNA" EXACT []
synonym: "rRNA 5S" EXACT []
xref: http://en.wikipedia.org/wiki/5S_ribosomal_RNA "wiki"
is_a: SO:0000651 ! large_subunit_rRNA

[Term]
id: SO:0000653
name: rRNA_28S
namespace: sequence
def: "A component of the large ribosomal subunit." [SO:ke]
subset: SOFA
synonym: "28S LSU rRNA" EXACT []
synonym: "28S ribosomal RNA" EXACT []
synonym: "28S rRNA" EXACT []
synonym: "rRNA 28S" EXACT []
xref: http://en.wikipedia.org/wiki/28S_ribosomal_RNA "wiki"
is_a: SO:0000651 ! large_subunit_rRNA

[Term]
id: SO:0000655
name: ncRNA
namespace: sequence
def: "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]
comment: A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript.
subset: SOFA
synonym: "INSDC_qualifier:other" BROAD []
synonym: "known_ncrna" EXACT []
synonym: "noncoding RNA" EXACT []
xref: http://en.wikipedia.org/wiki/NcRNA "wiki"
xref: http://www.gencodegenes.org/gencode_biotypes.html "GENCODE"
is_a: SO:0000233 ! mature_transcript

[Term]
id: SO:0000657
name: repeat_region
namespace: sequence
def: "A region of sequence containing one or more repeat units." [SO:ke]
subset: SOFA
synonym: "INSDC_feature:repeat_region" BROAD []
synonym: "INSDC_qualifier:other" EXACT []
synonym: "repeat region" EXACT []
is_a: SO:0001411 ! biological_region
relationship: has_part SO:0001411 ! biological_region

[Term]
id: SO:0000658
name: dispersed_repeat
namespace: sequence
def: "A repeat that is located at dispersed sites in the genome." [SO:ke]
subset: SOFA
synonym: "dispersed repeat" EXACT []
synonym: "INSDC_feature:repeat_region" BROAD []
synonym: "INSDC_qualifier:dispersed" EXACT []
synonym: "interspersed repeat" EXACT []
xref: http://en.wikipedia.org/wiki/Interspersed_repeat "wiki"
is_a: SO:0000657 ! repeat_region

[Term]
id: SO:0000662
name: spliceosomal_intron
namespace: sequence
def: "An intron which is spliced by the spliceosome." [SO:ke]
comment: GO:0000398.
subset: SOFA
synonym: "spliceosomal intron" EXACT []
is_a: SO:0000188 ! intron

[Term]
id: SO:0000667
name: insertion
namespace: sequence
alt_id: SO:1000034
def: "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]
subset: DBVAR
subset: SOFA
synonym: "insertion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
synonym: "nucleotide insertion" EXACT []
synonym: "nucleotide_insertion" EXACT []
xref: loinc:LA6687-3 "Insertion"
is_a: SO:0001059 ! sequence_alteration
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0000668
name: EST_match
namespace: sequence
def: "A match against an EST sequence." [SO:ke]
subset: SOFA
synonym: "EST match" EXACT []
is_a: SO:0000102 ! expressed_sequence_match

[Term]
id: SO:0000673
name: transcript
namespace: sequence
def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]
subset: SOFA
synonym: "INSDC_feature:misc_RNA" BROAD []
xref: http://en.wikipedia.org/wiki/RNA "wiki"
is_a: SO:0000831 ! gene_member_region

[Term]
id: SO:0000684
name: nuclease_sensitive_site
namespace: sequence
def: "A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma]
subset: SOFA
synonym: "nuclease sensitive site" EXACT []
is_a: SO:0000059 ! nuclease_binding_site

[Term]
id: SO:0000687
name: deletion_junction
namespace: sequence
def: "The space between two bases in a sequence which marks the position where a deletion has occurred." [SO:ke]
subset: SOFA
synonym: "deletion junction" EXACT []
is_a: SO:0000699 ! junction

[Term]
id: SO:0000688
name: golden_path
namespace: sequence
def: "A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls]
subset: SOFA
synonym: "golden path" EXACT []
is_a: SO:0000353 ! sequence_assembly

[Term]
id: SO:0000689
name: cDNA_match
namespace: sequence
def: "A match against cDNA sequence." [SO:ke]
subset: SOFA
synonym: "cDNA match" EXACT []
is_a: SO:0000102 ! expressed_sequence_match

[Term]
id: SO:0000694
name: SNP
namespace: sequence
def: "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb]
subset: SOFA
synonym: "single nucleotide polymorphism" EXACT []
is_a: SO:0001483 ! SNV

[Term]
id: SO:0000695
name: reagent
namespace: sequence
def: "A sequence used in experiment." [SO:ke]
comment: Requested by Lynn Crosby, jan 2006.
subset: SOFA
is_a: SO:0001409 ! biomaterial_region

[Term]
id: SO:0000696
name: oligo
namespace: sequence
def: "A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]
subset: SOFA
synonym: "oligonucleotide" EXACT []
xref: http://en.wikipedia.org/wiki/Oligonucleotide "wiki"
is_a: SO:0000695 ! reagent

[Term]
id: SO:0000699
name: junction
namespace: sequence
def: "A sequence_feature with an extent of zero." [SO:ke]
comment: A junction is a boundary between regions. A boundary has an extent of zero.
subset: SOFA
synonym: "boundary" EXACT []
synonym: "breakpoint" EXACT []
is_a: SO:0000110 ! sequence_feature

[Term]
id: SO:0000700
name: remark
namespace: sequence
def: "A comment about the sequence." [SO:ke]
subset: SOFA
is_a: SO:0001410 ! experimental_feature

[Term]
id: SO:0000701
name: possible_base_call_error
namespace: sequence
def: "A region of sequence where the validity of the base calling is questionable." [SO:ke]
subset: SOFA
synonym: "possible base call error" EXACT []
is_a: SO:0000413 ! sequence_difference

[Term]
id: SO:0000702
name: possible_assembly_error
namespace: sequence
def: "A region of sequence where there may have been an error in the assembly." [SO:ke]
subset: SOFA
synonym: "possible assembly error" EXACT []
is_a: SO:0000413 ! sequence_difference

[Term]
id: SO:0000703
name: experimental_result_region
namespace: sequence
def: "A region of sequence implicated in an experimental result." [SO:ke]
subset: SOFA
synonym: "experimental result region" EXACT []
is_a: SO:0000700 ! remark

[Term]
id: SO:0000704
name: gene
namespace: sequence
def: "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.
subset: SOFA
synonym: "INSDC_feature:gene" EXACT []
xref: http://en.wikipedia.org/wiki/Gene "wiki"
is_a: SO:0001411 ! biological_region
relationship: member_of SO:0005855 ! gene_group

[Term]
id: SO:0000705
name: tandem_repeat
namespace: sequence
def: "Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]
subset: SOFA
synonym: "INSDC_feature:repeat_region" BROAD []
synonym: "INSDC_qualifier:tandem" EXACT []
synonym: "tandem repeat" EXACT []
xref: http://en.wikipedia.org/wiki/Tandem_repeat "wiki"
xref: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html
is_a: SO:0000657 ! repeat_region

[Term]
id: SO:0000706
name: trans_splice_acceptor_site
namespace: sequence
def: "The 3' splice site of the acceptor primary transcript." [SO:ke]
comment: This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans.
subset: SOFA
synonym: "3' trans splice site" RELATED []
synonym: "trans splice acceptor site" EXACT []
is_a: SO:0001420 ! trans_splice_site

[Term]
id: SO:0000714
name: nucleotide_motif
namespace: sequence
def: "A region of nucleotide sequence corresponding to a known motif." [SO:ke]
subset: SOFA
synonym: "INSDC_feature:misc_feature" BROAD []
synonym: "INSDC_note:nucleotide_motif" EXACT []
synonym: "nucleotide motif" EXACT []
is_a: SO:0001683 ! sequence_motif

[Term]
id: SO:0000715
name: RNA_motif
namespace: sequence
def: "A motif that is active in RNA sequence." [SO:ke]
subset: SOFA
synonym: "RNA motif" EXACT []
is_a: SO:0000714 ! nucleotide_motif

[Term]
id: SO:0000717
name: reading_frame
namespace: sequence
def: "A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb]
comment: This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop.
subset: SOFA
synonym: "reading frame" EXACT []
xref: http://en.wikipedia.org/wiki/Reading_frame "wiki"
is_a: SO:0001410 ! experimental_feature

[Term]
id: SO:0000719
name: ultracontig
namespace: sequence
def: "An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]
subset: SOFA
synonym: "pseudochromosome" EXACT []
synonym: "superscaffold" RELATED []
is_a: SO:0000353 ! sequence_assembly

[Term]
id: SO:0000724
name: oriT
namespace: sequence
def: "A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "INSDC_feature:oriT" EXACT []
synonym: "origin of transfer" EXACT []
xref: http://en.wikipedia.org/wiki/Origin_of_transfer "wiki"
is_a: SO:0000296 ! origin_of_replication

[Term]
id: SO:0000725
name: transit_peptide
namespace: sequence
alt_id: BS:00055
def: "The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: Added to bring SO inline with the EMBL, DDBJ, GenBank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle.
subset: biosapiens
subset: SOFA
synonym: "INSDC_feature:transit_peptide" EXACT []
synonym: "signal" RELATED []
synonym: "transit" RELATED [uniprot:feature_type]
synonym: "transit peptide" EXACT []
is_a: SO:0001527 ! peptide_localization_signal

[Term]
id: SO:0000727
name: CRM
namespace: sequence
def: "A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG]
comment: Requested by Stephen Grossmann Dec 2004.
subset: SOFA
synonym: "cis regulatory module" EXACT []
synonym: "TF module" EXACT []
synonym: "transcription factor module" EXACT []
is_a: SO:0001055 ! transcriptional_cis_regulatory_region
intersection_of: SO:0001055 ! transcriptional_cis_regulatory_region
intersection_of: has_part SO:0000235 ! TF_binding_site
relationship: has_part SO:0000235 ! TF_binding_site

[Term]
id: SO:0000730
name: gap
namespace: sequence
def: "A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke]
subset: SOFA
synonym: "INSDC_feature:assembly_gap" NARROW []
synonym: "INSDC_feature:gap" EXACT []
is_a: SO:0000143 ! assembly_component
relationship: part_of SO:0000353 ! sequence_assembly

[Term]
id: SO:0000752
name: gene_group_regulatory_region
namespace: sequence
subset: SOFA
synonym: "gene group regulatory region" EXACT []
is_a: SO:0001679 ! transcription_regulatory_region
relationship: member_of SO:0005855 ! gene_group

[Term]
id: SO:0000753
name: clone_insert
namespace: sequence
def: "The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]
subset: SOFA
synonym: "clone insert" EXACT []
is_a: SO:0000695 ! reagent
relationship: part_of SO:0000151 ! clone

[Term]
id: SO:0000777
name: pseudogenic_rRNA
namespace: sequence
def: "A non functional descendant of an rRNA." [SO:ke]
comment: Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
subset: SOFA
synonym: "INSDC_feature:rRNA" BROAD []
synonym: "INSDC_qualifier:pseudo" EXACT []
synonym: "pseudogenic rRNA" EXACT []
is_a: SO:0000462 ! pseudogenic_region
relationship: non_functional_homolog_of SO:0000673 ! transcript
relationship: part_of SO:0000336 ! pseudogene

[Term]
id: SO:0000778
name: pseudogenic_tRNA
namespace: sequence
def: "A non functional descendent of a tRNA." [SO:ke]
comment: Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
subset: SOFA
synonym: "INSDC_feature:tRNA" BROAD []
synonym: "INSDC_qualifier:pseudo" EXACT []
synonym: "pseudogenic tRNA" EXACT []
is_a: SO:0000462 ! pseudogenic_region
relationship: non_functional_homolog_of SO:0000673 ! transcript
relationship: part_of SO:0000336 ! pseudogene

[Term]
id: SO:0000830
name: chromosome_part
namespace: sequence
def: "A region of a chromosome." [SO:ke]
comment: This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root.
subset: SOFA
synonym: "chromosome part" EXACT []
is_a: SO:0001411 ! biological_region
relationship: part_of SO:0000340 ! chromosome

[Term]
id: SO:0000831
name: gene_member_region
namespace: sequence
def: "A region of a gene." [SO:ke]
comment: A manufactured term used to allow the parts of a gene to have an is_a path to the root.
subset: SOFA
synonym: "gene member region" EXACT []
is_a: SO:0001411 ! biological_region
relationship: member_of SO:0000704 ! gene

[Term]
id: SO:0000833
name: transcript_region
namespace: sequence
def: "A region of a transcript." [SO:ke]
comment: This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root.
subset: SOFA
synonym: "transcript region" EXACT []
is_a: SO:0001411 ! biological_region
relationship: part_of SO:0000673 ! transcript

[Term]
id: SO:0000834
name: mature_transcript_region
namespace: sequence
def: "A region of a mature transcript." [SO:ke]
comment: A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root.
subset: SOFA
synonym: "mature transcript region" EXACT []
is_a: SO:0000833 ! transcript_region

[Term]
id: SO:0000835
name: primary_transcript_region
namespace: sequence
def: "A part of a primary transcript." [SO:ke]
comment: This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root.
subset: SOFA
synonym: "primary transcript region" EXACT []
is_a: SO:0000833 ! transcript_region
relationship: part_of SO:0000185 ! primary_transcript

[Term]
id: SO:0000836
name: mRNA_region
namespace: sequence
def: "A region of an mRNA." [SO:cb]
comment: This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root.
subset: SOFA
synonym: "mRNA region" EXACT []
is_a: SO:0000834 ! mature_transcript_region
relationship: part_of SO:0000234 ! mRNA

[Term]
id: SO:0000837
name: UTR_region
namespace: sequence
def: "A region of UTR." [SO:ke]
comment: A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root.
subset: SOFA
synonym: "UTR region" EXACT []
is_a: SO:0000836 ! mRNA_region

[Term]
id: SO:0000839
name: polypeptide_region
namespace: sequence
alt_id: BS:00124
alt_id: BS:00331
def: "Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]
comment: Added to allow the polypeptide regions to have is_a paths back to the root.
subset: biosapiens
subset: SOFA
synonym: "positional" RELATED []
synonym: "positional polypeptide feature" RELATED []
synonym: "region" NARROW [uniprot:feature_type]
synonym: "region or site annotation" RELATED []
synonym: "site" NARROW [uniprot:feature_type]
is_a: SO:0001411 ! biological_region
relationship: part_of SO:0000104 ! polypeptide

[Term]
id: SO:0000841
name: spliceosomal_intron_region
namespace: sequence
def: "A region within an intron." [SO:ke]
comment: A terms added to allow the parts of introns to have is_a paths to the root.
subset: SOFA
synonym: "spliceosomal intron region" EXACT []
is_a: SO:0000835 ! primary_transcript_region
relationship: part_of SO:0000662 ! spliceosomal_intron

[Term]
id: SO:0000842
name: gene_component_region
namespace: sequence
subset: SOFA
synonym: "gene component region" EXACT []
is_a: SO:0001411 ! biological_region
relationship: part_of SO:0000704 ! gene

[Term]
id: SO:0000851
name: CDS_region
namespace: sequence
def: "A region of a CDS." [SO:cb]
subset: SOFA
synonym: "CDS region" EXACT []
is_a: SO:0000836 ! mRNA_region
relationship: part_of SO:0000316 ! CDS

[Term]
id: SO:0000852
name: exon_region
namespace: sequence
def: "A region of an exon." [RSC:cb]
subset: SOFA
synonym: "exon region" EXACT []
is_a: SO:0000833 ! transcript_region
relationship: part_of SO:0000147 ! exon

[Term]
id: SO:0001000
name: rRNA_16S
namespace: sequence
def: "A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke]
subset: SOFA
synonym: "16S ribosomal RNA" EXACT []
synonym: "16S rRNA" RELATED []
synonym: "16S SSU RNA" EXACT []
synonym: "rRNA 16S" EXACT []
xref: http://en.wikipedia.org/wiki/16S_ribosomal_RNA "wiki"
is_a: SO:0000650 ! small_subunit_rRNA

[Term]
id: SO:0001001
name: rRNA_23S
namespace: sequence
def: "A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke]
subset: SOFA
synonym: "23S LSU rRNA" EXACT []
synonym: "23S ribosomal RNA" RELATED []
synonym: "23S rRNA" EXACT []
synonym: "rRNA 23S" EXACT []
is_a: SO:0000651 ! large_subunit_rRNA

[Term]
id: SO:0001002
name: rRNA_25S
namespace: sequence
def: "A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb]
subset: SOFA
synonym: "25S LSU rRNA" EXACT []
synonym: "25S ribosomal RNA" EXACT []
synonym: "25S rRNA" EXACT []
synonym: "rRNA 25S" EXACT []
is_a: SO:0000651 ! large_subunit_rRNA

[Term]
id: SO:0001019
name: copy_number_variation
namespace: sequence
def: "A variation that increases or decreases the copy number of a given region." [SO:ke]
subset: SOFA
synonym: "CNP" EXACT []
synonym: "CNV" EXACT []
synonym: "copy number polymorphism" EXACT []
synonym: "copy number variation" EXACT []
xref: http://en.wikipedia.org/wiki/Copy_number_variation "wiki"
is_a: SO:0001059 ! sequence_alteration

[Term]
id: SO:0001037
name: mobile_genetic_element
namespace: sequence
def: "A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]
subset: SOFA
synonym: "INSDC_feature:mobile_element" EXACT []
synonym: "MGE" EXACT []
synonym: "mobile genetic element" EXACT []
xref: http://en.wikipedia.org/wiki/Mobile_genetic_element "wiki"
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0001039
name: integrated_mobile_genetic_element
namespace: sequence
def: "An MGE that is integrated into the host chromosome." [SO:ke]
subset: SOFA
synonym: "integrated mobile genetic element" EXACT []
is_a: SO:0001037 ! mobile_genetic_element

[Term]
id: SO:0001055
name: transcriptional_cis_regulatory_region
namespace: sequence
def: "A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]
subset: SOFA
synonym: "INSDC_feature:regulatory" BROAD []
synonym: "INSDC_qualifier:transcriptional_cis_regulatory_region" EXACT []
synonym: "transcription-control region" EXACT []
synonym: "transcriptional cis regulatory region" EXACT []
is_a: SO:0001679 ! transcription_regulatory_region

[Term]
id: SO:0001056
name: splicing_regulatory_region
namespace: sequence
def: "A regulatory_region that modulates splicing." [SO:ke]
subset: SOFA
synonym: "splicing regulatory region" EXACT []
is_a: SO:0001679 ! transcription_regulatory_region

[Term]
id: SO:0001059
name: sequence_alteration
namespace: sequence
alt_id: SO:1000004
alt_id: SO:1000007
def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]
comment: Merged with partially characterized change in nucleotide sequence.
subset: SOFA
synonym: "INSDC_feature:misc_feature" BROAD []
synonym: "INSDC_feature:variation" EXACT []
synonym: "INSDC_note:sequence_alteration" EXACT []
synonym: "partially characterised change in DNA sequence" NARROW []
synonym: "partially_characterised_change_in_DNA_sequence" NARROW []
synonym: "sequence alteration" EXACT []
synonym: "sequence variation" RELATED []
synonym: "uncharacterised_change_in_nucleotide_sequence" NARROW []
is_a: SO:0000110 ! sequence_feature

[Term]
id: SO:0001063
name: immature_peptide_region
namespace: sequence
alt_id: BS:00129
def: "An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]
comment: Range.
subset: biosapiens
subset: SOFA
synonym: "immature peptide region" EXACT []
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:0001214
name: noncoding_region_of_exon
namespace: sequence
def: "The maximal intersection of exon and UTR." [SO:ke]
comment: An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding.
subset: SOFA
synonym: "noncoding region of exon" EXACT []
is_a: SO:0000852 ! exon_region

[Term]
id: SO:0001215
name: coding_region_of_exon
namespace: sequence
def: "The region of an exon that encodes for protein sequence." [SO:ke]
comment: An exon containing either a start or stop codon will be partially coding and partially non coding.
subset: SOFA
synonym: "coding region of exon" EXACT []
is_a: SO:0000852 ! exon_region

[Term]
id: SO:0001235
name: replicon
namespace: sequence
def: "A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Replicon_(genetics) "wiki"
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0001236
name: base
namespace: sequence
def: "A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Nucleobase "wiki"
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0001248
name: assembly
namespace: sequence
def: "A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly "wiki"
is_a: SO:0001410 ! experimental_feature

[Term]
id: SO:0001409
name: biomaterial_region
namespace: sequence
def: "A region which is intended for use in an experiment." [SO:cb]
subset: SOFA
synonym: "biomaterial region" EXACT []
is_a: SO:0000001 ! region

[Term]
id: SO:0001410
name: experimental_feature
namespace: sequence
def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]
subset: SOFA
synonym: "analysis feature" RELATED []
synonym: "experimental output artefact" EXACT []
synonym: "experimental_output_artefact" EXACT []
is_a: SO:0000001 ! region

[Term]
id: SO:0001411
name: biological_region
namespace: sequence
def: "A region defined by its disposition to be involved in a biological process." [SO:cb]
subset: SOFA
synonym: "biological region" EXACT []
synonym: "INSDC_misc_feature" BROAD []
synonym: "INSDC_note:biological_region" EXACT []
is_a: SO:0000001 ! region

[Term]
id: SO:0001412
name: topologically_defined_region
namespace: sequence
def: "A region that is defined according to its relations with other regions within the same sequence." [SO:cb]
subset: SOFA
synonym: "topologically defined region" EXACT []
is_a: SO:0000001 ! region

[Term]
id: SO:0001419
name: cis_splice_site
namespace: sequence
def: "Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]
subset: SOFA
synonym: "cis splice site" EXACT []
is_a: SO:0000162 ! splice_site

[Term]
id: SO:0001420
name: trans_splice_site
namespace: sequence
def: "Primary transcript region bordering trans-splice junction." [SO:ke]
subset: SOFA
synonym: "trans splice site" EXACT []
is_a: SO:0000162 ! splice_site

[Term]
id: SO:0001483
name: SNV
namespace: sequence
def: "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]
subset: SOFA
synonym: "single nucleotide variant" EXACT []
is_a: SO:1000002 ! substitution
created_by: kareneilbeck
creation_date: 2009-10-08T11:37:49Z

[Term]
id: SO:0001527
name: peptide_localization_signal
namespace: sequence
def: "A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]
subset: SOFA
synonym: "localization signal" RELATED []
synonym: "peptide localization signal" EXACT []
is_a: SO:0000839 ! polypeptide_region
created_by: kareneilbeck
creation_date: 2010-03-11T02:15:05Z

[Term]
id: SO:0001647
name: kozak_sequence
namespace: sequence
def: "A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]
subset: SOFA
synonym: "kozak consensus" EXACT []
synonym: "kozak consensus sequence" EXACT []
synonym: "kozak sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Kozak_consensus_sequence "wikipedia"
is_a: SO:0000139 ! ribosome_entry_site
created_by: kareneilbeck
creation_date: 2010-06-07T03:12:20Z

[Term]
id: SO:0001654
name: nucleotide_to_protein_binding_site
namespace: sequence
def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]
subset: SOFA
synonym: "nucleotide to protein binding site" RELATED []
is_a: SO:0000410 ! protein_binding_site
created_by: kareneilbeck
creation_date: 2010-08-03T12:26:05Z

[Term]
id: SO:0001679
name: transcription_regulatory_region
namespace: sequence
def: "A regulatory region that is involved in the control of the process of transcription." [SO:ke]
subset: SOFA
synonym: "transcription regulatory region" EXACT []
is_a: SO:0005836 ! regulatory_region
created_by: kareneilbeck
creation_date: 2010-10-12T03:49:35Z

[Term]
id: SO:0001683
name: sequence_motif
namespace: sequence
def: "A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]
subset: SOFA
synonym: "sequence motif" RELATED []
xref: http://en.wikipedia.org/wiki/Sequence_motif "wikipedia"
is_a: SO:0001411 ! biological_region
created_by: kareneilbeck
creation_date: 2010-10-14T04:13:22Z

[Term]
id: SO:0001720
name: epigenetically_modified_region
namespace: sequence
def: "A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]
subset: SOFA
synonym: "epigenetically modified region" RELATED []
is_a: SO:0001411 ! biological_region
created_by: kareneilbeck
creation_date: 2010-03-27T12:02:29Z

[Term]
id: SO:0001790
name: paired_end_fragment
namespace: sequence
def: "An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair)." [SO:ke]
subset: SOFA
synonym: "paired end fragment" EXACT []
is_a: SO:0000143 ! assembly_component
created_by: kareneilbeck
creation_date: 2011-04-14T01:48:20Z

[Term]
id: SO:0005836
name: regulatory_region
namespace: sequence
def: "A region of sequence that is involved in the control of a biological process." [SO:ke]
subset: SOFA
synonym: "INSDC_feature:regulatory" BROAD []
synonym: "INSDC_qualifier:other" EXACT []
synonym: "regulatory region" EXACT []
xref: http://en.wikipedia.org/wiki/Regulatory_region "wiki"
is_a: SO:0000831 ! gene_member_region

[Term]
id: SO:0005855
name: gene_group
namespace: sequence
def: "A collection of related genes." [SO:ma]
subset: SOFA
synonym: "gene group" EXACT []
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0100011
name: cleaved_peptide_region
namespace: sequence
def: "The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]
comment: Range.
subset: biosapiens
subset: SOFA
synonym: "cleaved peptide region" EXACT []
is_a: SO:0000839 ! polypeptide_region
relationship: part_of SO:0001063 ! immature_peptide_region

[Term]
id: SO:1000002
name: substitution
namespace: sequence
def: "A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]
subset: SOFA
xref: loinc:LA6690-7 "Substitution"
is_a: SO:0001059 ! sequence_alteration
is_a: SO:0001411 ! biological_region

[Term]
id: SO:1000005
name: complex_substitution
namespace: sequence
def: "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
subset: SOFA
synonym: "complex substitution" EXACT []
is_a: SO:1000002 ! substitution

[Term]
id: SO:1000008
name: point_mutation
namespace: sequence
def: "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop]
subset: SOFA
synonym: "point mutation" EXACT []
xref: http://en.wikipedia.org/wiki/Point_mutation "wiki"
is_a: SO:0001483 ! SNV

[Term]
id: SO:1000036
name: inversion
namespace: sequence
def: "A continuous nucleotide sequence is inverted in the same position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
subset: DBVAR
subset: SOFA
synonym: "inversion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
xref: loinc:LA6689-9 "Inversion"
is_a: SO:0001059 ! sequence_alteration
is_a: SO:0001411 ! biological_region

[Term]
id: SO:1001284
name: regulon
namespace: sequence
def: "A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Regulon "wiki"
is_a: SO:0005855 ! gene_group

[Term]
id: SO:2000061
name: databank_entry
namespace: sequence
def: "The sequence referred to by an entry in a databank such as GenBank or SwissProt." [SO:ke]
subset: SOFA
synonym: "accession" RELATED []
synonym: "databank entry" EXACT []
is_a: SO:0000695 ! reagent

[Typedef]
id: adjacent_to
name: adjacent_to
namespace: sequence
def: "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap." [PMID:20226267, SO:ke]
subset: SOFA

[Typedef]
id: associated_with
name: associated_with
namespace: sequence
comment: This relationship is vague and up for discussion.

[Typedef]
id: complete_evidence_for_feature
name: complete_evidence_for_feature
namespace: sequence
def: "B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A." [SO:ke]
comment: If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
is_transitive: true
is_a: evidence_for_feature ! evidence_for_feature

[Typedef]
id: connects_on
name: connects_on
namespace: sequence
def: "X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z." [PMID:20226267]
comment: Example: A splice_junction connects_on exon, exon, mature_transcript.
created_by: kareneilbeck
creation_date: 2010-10-14T01:38:51Z

[Typedef]
id: contained_by
name: contained_by
namespace: sequence
def: "X contained_by Y iff X starts after start of Y and X ends before end of Y." [PMID:20226267]
comment: The inverse is contains. Example: intein contained_by immature_peptide_region.
is_transitive: true
created_by: kareneilbeck
creation_date: 2010-10-14T01:26:16Z

[Typedef]
id: contains
name: contains
namespace: sequence
def: "The inverse of contained_by." [PMID:20226267]
comment: Example: pre_miRNA contains miRNA_loop.
is_transitive: true
created_by: kareneilbeck
creation_date: 2010-10-14T01:32:15Z

[Typedef]
id: derives_from
name: derives_from
namespace: sequence
subset: SOFA
is_transitive: true

[Typedef]
id: disconnected_from
name: disconnected_from
namespace: sequence
def: "X is disconnected_from Y iff it is not the case that X overlaps Y." [PMID:20226267]
created_by: kareneilbeck
creation_date: 2010-10-14T01:42:10Z

[Typedef]
id: edited_from
name: edited_from
namespace: sequence
created_by: kareneilbeck
creation_date: 2009-08-19T02:19:45Z

[Typedef]
id: edited_to
name: edited_to
namespace: sequence
created_by: kareneilbeck
creation_date: 2009-08-19T02:19:11Z

[Typedef]
id: evidence_for_feature
name: evidence_for_feature
namespace: sequence
def: "B is evidence_for_feature A, if an instance of B supports the existence of A." [SO:ke]
comment: This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
is_transitive: true

[Typedef]
id: exemplar_of
name: exemplar_of
namespace: sequence
def: "X is exemplar of Y if X is the best evidence for Y." [SO:ke]
comment: Tracker id: 2594157.

[Typedef]
id: finished_by
name: finished_by
namespace: sequence
def: "Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary." [PMID:20226267]
comment: Example CDS finished_by stop_codon.
created_by: kareneilbeck
creation_date: 2010-10-14T01:45:45Z

[Typedef]
id: finishes
name: finishes
namespace: sequence
def: "X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary." [PMID:20226267]
comment: Example: stop_codon finishes CDS.
created_by: kareneilbeck
creation_date: 2010-10-14T02:17:53Z

[Typedef]
id: gained
name: gained
namespace: sequence
def: "X gained Y if X is a variant_of X' and Y part of X but not X'." [SO:ke]
comment: A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may gain a stop codon not present in the reference sequence.
created_by: kareneilbeck
creation_date: 2011-06-28T12:51:10Z

[Typedef]
id: genome_of
name: genome_of
namespace: sequence

[Typedef]
id: guided_by
name: guided_by
namespace: sequence
created_by: kareneilbeck
creation_date: 2009-08-19T02:27:04Z

[Typedef]
id: guides
name: guides
namespace: sequence
created_by: kareneilbeck
creation_date: 2009-08-19T02:27:24Z

[Typedef]
id: has_integral_part
name: has_integral_part
namespace: sequence
def: "X has_integral_part Y if and only if: X has_part Y and Y part_of X." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: mRNA has_integral_part CDS.
is_a: has_part ! has_part
created_by: kareneilbeck
creation_date: 2009-08-19T12:01:46Z

[Typedef]
id: has_origin
name: has_origin
namespace: sequence

[Typedef]
id: has_part
name: has_part
namespace: sequence
def: "Inverse of part_of." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: operon has_part gene.

[Typedef]
id: has_quality
name: has_quality
namespace: sequence
comment: The relationship between a feature and an attribute.

[Typedef]
id: homologous_to
name: homologous_to
namespace: sequence
subset: SOFA
is_symmetric: true
is_a: similar_to ! similar_to

[Typedef]
id: integral_part_of
name: integral_part_of
namespace: sequence
def: "X integral_part_of Y if and only if: X part_of Y and Y has_part X." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: exon integral_part_of transcript.
is_a: part_of ! part_of
created_by: kareneilbeck
creation_date: 2009-08-19T12:03:28Z

[Typedef]
id: is_consecutive_sequence_of
name: is_consecutive_sequence_of
namespace: sequence
def: "R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical)." [PMID:20226267]
comment: Example: region is consecutive_sequence of base.
created_by: kareneilbeck
creation_date: 2010-10-14T02:19:48Z

[Typedef]
id: lost
name: lost
namespace: sequence
def: "X lost Y if X is a variant_of X' and Y part of X' but not X." [SO:ke]
comment: A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may have lost a stop codon present in the reference sequence.
created_by: kareneilbeck
creation_date: 2011-06-28T12:53:16Z

[Typedef]
id: maximally_overlaps
name: maximally_overlaps
namespace: sequence
def: "A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y." [PMID:20226267]
comment: Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR.
created_by: kareneilbeck
creation_date: 2010-10-14T01:34:48Z

[Typedef]
id: member_of
name: member_of
namespace: sequence
comment: A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.
subset: SOFA
is_transitive: true
is_a: part_of ! part_of

[Typedef]
id: non_functional_homolog_of
name: non_functional_homolog_of
namespace: sequence
def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke]
subset: SOFA
is_a: homologous_to ! homologous_to

[Typedef]
id: orthologous_to
name: orthologous_to
namespace: sequence
subset: SOFA
is_symmetric: true
is_a: homologous_to ! homologous_to

[Typedef]
id: overlaps
name: overlaps
namespace: sequence
def: "X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y." [PMID:20226267]
comment: Example: coding_exon overlaps CDS.
created_by: kareneilbeck
creation_date: 2010-10-14T01:33:15Z

[Typedef]
id: paralogous_to
name: paralogous_to
namespace: sequence
subset: SOFA
is_symmetric: true
is_a: homologous_to ! homologous_to

[Typedef]
id: part_of
name: part_of
namespace: sequence
def: "X part_of Y if X is a subregion of Y." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: amino_acid part_of polypeptide.
subset: SOFA
is_transitive: true

[Typedef]
id: partial_evidence_for_feature
name: partial_evidence_for_feature
namespace: sequence
def: "B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A." [SO:ke]
is_a: evidence_for_feature ! evidence_for_feature

[Typedef]
id: position_of
name: position_of
namespace: sequence

[Typedef]
id: processed_from
name: processed_from
namespace: sequence
def: "Inverse of processed_into." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: miRNA processed_from miRNA_primary_transcript.
created_by: kareneilbeck
creation_date: 2009-08-19T12:14:00Z

[Typedef]
id: processed_into
name: processed_into
namespace: sequence
def: "X is processed_into Y if a region X is modified to create Y." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: miRNA_primary_transcript processed into miRNA.
created_by: kareneilbeck
creation_date: 2009-08-19T12:15:02Z

[Typedef]
id: recombined_from
name: recombined_from
namespace: sequence
created_by: kareneilbeck
creation_date: 2009-08-19T02:21:03Z

[Typedef]
id: recombined_to
name: recombined_to
namespace: sequence
created_by: kareneilbeck
creation_date: 2009-08-19T02:20:07Z

[Typedef]
id: sequence_of
name: sequence_of
namespace: sequence

[Typedef]
id: similar_to
name: similar_to
namespace: sequence
subset: SOFA
is_symmetric: true

[Typedef]
id: started_by
name: started_by
namespace: sequence
def: "X is strted_by Y if Y is part_of X and X and Y share a 5' boundary." [PMID:20226267]
comment: Example: CDS started_by start_codon.
created_by: kareneilbeck
creation_date: 2010-10-14T01:43:55Z

[Typedef]
id: starts
name: starts
namespace: sequence
def: "X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary." [PMID:20226267]
comment: Example: start_codon starts CDS.
created_by: kareneilbeck
creation_date: 2010-10-14T01:47:53Z

[Typedef]
id: trans_spliced_from
name: trans_spliced_from
namespace: sequence
created_by: kareneilbeck
creation_date: 2009-08-19T02:22:14Z

[Typedef]
id: trans_spliced_to
name: trans_spliced_to
namespace: sequence
created_by: kareneilbeck
creation_date: 2009-08-19T02:22:00Z

[Typedef]
id: transcribed_from
name: transcribed_from
namespace: sequence
def: "X is transcribed_from Y if X is synthesized from template Y." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: primary_transcript transcribed_from gene.
created_by: kareneilbeck
creation_date: 2009-08-19T12:05:39Z

[Typedef]
id: transcribed_to
name: transcribed_to
namespace: sequence
def: "Inverse of transcribed_from." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: gene transcribed_to primary_transcript.
created_by: kareneilbeck
creation_date: 2009-08-19T12:08:24Z

[Typedef]
id: translates_to
name: translates_to
namespace: sequence
def: "Inverse of translation _of." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: codon translates_to amino_acid.
created_by: kareneilbeck
creation_date: 2009-08-19T12:11:53Z

[Typedef]
id: translation_of
name: translation_of
namespace: sequence
def: "X is translation of Y if Y is translated by ribosome to create X." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: Polypeptide translation_of CDS.
created_by: kareneilbeck
creation_date: 2009-08-19T12:09:59Z

[Typedef]
id: variant_of
name: variant_of
namespace: sequence
def: "A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A." [SO:immuno_workshop]
comment: Added to SO during the immunology workshop, June 2007.  This relationship was approved by Barry Smith.

