17:01:2012 15:28 kareneilbeck sequence autogenerated-by\: DAG-Edit version 1.417\nsaved-by\: eilbeck\ndate\: Tue May 11 15\:18\:44 PDT 2004\nversion\: $Revision\: 1.45 $ biosapiens protein feature ontology database of genomic structural variation SO feature annotation sequence This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi Sequence_Ontology sequence region 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 http://purl.org/obo/owl/SO#SO_ke sequence sequence sequence_secondary_structure A folded sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence secondary structure sequence G_quartet G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet. URL:http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract G quartet G tetrad G-quadruplex G-quartet G-tetrad G_quadruplex guanine tetrad sequence URL:http://en.wikipedia.org/wiki/G-quadruplex http://en.wikipedia.org/wiki/G-quadruplex interior_coding_exon interior coding exon sequence satellite_DNA 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. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html satellite DNA sequence URL:http://en.wikipedia.org/wiki/Satellite_DNA http://en.wikipedia.org/wiki/Satellite_DNA PCR_product This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406. A region amplified by a PCR reaction. SO:ke http://purl.org/obo/owl/SO#SO_ke amplicon PCR product sequence URL:http://en.wikipedia.org/wiki/RAPD http://en.wikipedia.org/wiki/RAPD read_pair 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 http://purl.org/obo/owl/SO#SO_ls mate pair read-pair sequence gene_sensu_your_favorite_organism sequence gene_class sequence protein_coding protein-coding sequence non_protein_coding non protein-coding sequence scRNA_primary_transcript The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a eukaryote. URL:http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html scRNA primary transcript scRNA transcript small cytoplasmic RNA small cytoplasmic RNA transcript small_cytoplasmic_RNA sequence scRNA A small non coding RNA sequence, present in the cytoplasm. SO:ke http://purl.org/obo/owl/SO#SO_ke small cytoplasmic RNA sequence INR_motif Binds TAF1, TAF2. A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element. PMID:12651739 http://purl.org/obo/owl/PMID#PMID_12651739 PMID:16858867 http://purl.org/obo/owl/PMID#PMID_16858867 DMp2 initiator initiator motif INR motif sequence DPE_motif Binds TAF6, TAF9. A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C). PMID:12651739:12537576 http://purl.org/obo/owl/PMID#PMID_12651739:12537576 PMID:16858867 http://purl.org/obo/owl/PMID#PMID_16858867 CRWMGCGWKCGCTTS downstream core promoter element DPE motif sequence BREu_motif Binds TFIIB. A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB. PMID:12651739 http://purl.org/obo/owl/PMID#PMID_12651739 PMID:16858867 http://purl.org/obo/owl/PMID#PMID_16858867 B-recognition element BRE motif BREu BREu motif TFIIB recognition element transcription factor B-recognition element sequence PSE_motif A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G). PMID:12651739 http://purl.org/obo/owl/PMID#PMID_12651739 proximal sequence element PSE motif sequence linkage_group A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned. ISBN:038752046 http://purl.org/obo/owl/ISBN#ISBN_038752046 linkage group sequence URL:http://en.wikipedia.org/wiki/Linkage_group http://en.wikipedia.org/wiki/Linkage_group RNA_internal_loop A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge. SO:ke http://purl.org/obo/owl/SO#SO_ke RNA internal loop sequence asymmetric_RNA_internal_loop An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand. SO:ke http://purl.org/obo/owl/SO#SO_ke asymmetric RNA internal loop sequence A_minor_RNA_motif A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix. SO:ke http://purl.org/obo/owl/SO#SO_ke A minor RNA motif sequence K_turn_RNA_motif The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices. SO:ke http://purl.org/obo/owl/SO#SO_ke K turn RNA motif K-turn kink turn kink-turn motif sequence URL:http://en.wikipedia.org/wiki/K-turn http://en.wikipedia.org/wiki/K-turn sarcin_like_RNA_motif A loop in ribosomal RNA containing the sites of attack for ricin and sarcin. URL:http://www.ncbi.nlm.nih.gov/pubmed/7897662 http://www.ncbi.nlm.nih.gov/pubmed/7897662 sarcin like RNA motif sarcin/ricin domain sarcin/ricin loop sarcin/ricin RNA domain sequence symmetric_RNA_internal_loop An internal RNA loop where the extent of the loop on both stands is the same size. SO:ke http://purl.org/obo/owl/SO#SO_ke A-minor RNA motif sequence RNA_junction_loop RNA junction loop sequence RNA_hook_turn hook turn hook-turn motif RNA hook turn sequence base_pair base pair sequence URL:http://en.wikipedia.org/wiki/Base_pair http://en.wikipedia.org/wiki/Base_pair WC_base_pair The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation. PMID:12177293 http://purl.org/obo/owl/PMID#PMID_12177293 canonical base pair Watson Crick base pair Watson-Crick base pair Watson-Crick pair WC base pair sequence sugar_edge_base_pair A type of non-canonical base-pairing. PMID:12177293 http://purl.org/obo/owl/PMID#PMID_12177293 sugar edge base pair sequence aptamer DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. URL:http://aptamer.icmb.utexas.edu http://aptamer.icmb.utexas.edu sequence URL:http://en.wikipedia.org/wiki/Aptamer http://en.wikipedia.org/wiki/Aptamer DNA_aptamer DNA molecules that have been selected from random pools based on their ability to bind other molecules. http:aptamer.icmb.utexas.edu http://purl.org/obo/owl/http#http_aptamer.icmb.utexas.edu DNA aptamer sequence RNA_aptamer RNA molecules that have been selected from random pools based on their ability to bind other molecules. URL:http://aptamer.icmb.utexas.edu http://aptamer.icmb.utexas.edu RNA aptamer sequence morpholino_oligo Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino. URL:http://www.gene-tools.com/ http://www.gene-tools.com/ morphant morpholino morpholino oligo sequence riboswitch A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites. PMID:2820954 http://purl.org/obo/owl/PMID#PMID_2820954 riboswitch RNA sequence URL:http://en.wikipedia.org/wiki/Riboswitch http://en.wikipedia.org/wiki/Riboswitch matrix_attachment_site A DNA region that is required for the binding of chromatin to the nuclear matrix. SO:ma http://purl.org/obo/owl/SO#SO_ma MAR matrix association region matrix attachment region matrix attachment site nuclear matrix association region nuclear matrix attachment site S/MAR S/MAR element scaffold attachment site scaffold matrix attachment region SMAR sequence URL:http://en.wikipedia.org/wiki/Matrix_attachment_site http://en.wikipedia.org/wiki/Matrix_attachment_site locus_control_region A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene. SO:ma http://purl.org/obo/owl/SO#SO_ma LCR locus control element locus control region sequence URL:http://en.wikipedia.org/wiki/Locus_control_region http://en.wikipedia.org/wiki/Locus_control_region match_set A collection of match parts. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence match_part A part of a match, for example an hsp from blast is a match_part. SO:ke http://purl.org/obo/owl/SO#SO_ke match part sequence genomic_clone A clone of a DNA region of a genome. SO:ma http://purl.org/obo/owl/SO#SO_ma genomic clone sequence sequence_operation An operation that can be applied to a sequence, that results in a change. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence operation sequence pseudogene_attribute An attribute of a pseudogene (SO:0000336). SO:ma http://purl.org/obo/owl/SO#SO_ma pseudogene attribute sequence processed_pseudogene Please not the synonym R psi M uses the spelled out form of the greek letter. A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail. SO:xp http://purl.org/obo/owl/SO#SO_xp processed pseudogene pseudogene by reverse transcription R psi G retropseudogene sequence pseudogene_by_unequal_crossing_over A pseudogene caused by unequal crossing over at recombination. SO:ke http://purl.org/obo/owl/SO#SO_ke pseudogene by unequal crossing over sequence delete To remove a subsection of sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence insert To insert a subsection of sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence invert To invert a subsection of sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence substitute To substitute a subsection of sequence for another. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence translocate To translocate a subsection of sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence gene_part 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 http://purl.org/obo/owl/SO#SO_ke sequence probe A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence URL:http://en.wikipedia.org/wiki/Hybridization_probe http://en.wikipedia.org/wiki/Hybridization_probe assortment_derived_deficiency assortment-derived_deficiency sequence sequence_variant_affecting_regulatory_region OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A sequence_variant_effect which changes the regulatory region of a gene. SO:ke http://purl.org/obo/owl/SO#SO_ke mutation affecting regulatory region sequence variant affecting regulatory region sequence aneuploid A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Aneuploid http://en.wikipedia.org/wiki/Aneuploid hyperploid A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Hyperploid http://en.wikipedia.org/wiki/Hyperploid hypoploid A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Hypoploid http://en.wikipedia.org/wiki/Hypoploid operator A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon. SO:ma http://purl.org/obo/owl/SO#SO_ma operator segment sequence URL:http://en.wikipedia.org/wiki/Operator_(biology)#Operator http://en.wikipedia.org/wiki/Operator_(biology)#Operator assortment_derived_aneuploid assortment-derived_aneuploid sequence nuclease_binding_site A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease. SO:cb http://purl.org/obo/owl/SO#SO_cb nuclease binding site sequence compound_chromosome_arm FLAG - this term is should probably be a part of rather than an is_a. compound chromosome arm sequence restriction_enzyme_binding_site A region of a molecule that binds to a restriction enzyme. A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme. SO:cb http://purl.org/obo/owl/SO#SO_cb restriction endonuclease binding site restriction enzyme binding site sequence deficient_intrachromosomal_transposition An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual deficient intrachromosomal transposition sequence deficient_interchromosomal_transposition An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining. SO:ke http://purl.org/obo/owl/SO#SO_ke deficient interchromosomal transposition sequence gene_by_transcript_attribute This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004. sequence free_chromosome_arm A chromosome structure variation whereby an arm exists as an individual chromosome element. SO:ke http://purl.org/obo/owl/SO#SO_ke free chromosome arm sequence gene_by_polyadenylation_attribute sequence gene_to_gene_feature gene to gene feature sequence overlapping An attribute describing a gene that has a sequence that overlaps the sequence of another gene. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence inside_intron An attribute to describe a gene when it is located within the intron of another gene. SO:ke http://purl.org/obo/owl/SO#SO_ke inside intron sequence inside_intron_antiparallel An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand. SO:ke http://purl.org/obo/owl/SO#SO_ke inside intron antiparallel sequence inside_intron_parallel An attribute to describe a gene when it is located within the intron of another gene and on the same strand. SO:ke http://purl.org/obo/owl/SO#SO_ke inside intron parallel sequence end_overlapping_gene sequence five_prime_three_prime_overlap An attribute to describe a gene when the five prime region overlaps with another gene's 3' region. SO:ke http://purl.org/obo/owl/SO#SO_ke five prime-three prime overlap sequence five_prime_five_prime_overlap An attribute to describe a gene when the five prime region overlaps with another gene's five prime region. SO:ke http://purl.org/obo/owl/SO#SO_ke five prime-five prime overlap sequence three_prime_three_prime_overlap An attribute to describe a gene when the 3' region overlaps with another gene's 3' region. SO:ke http://purl.org/obo/owl/SO#SO_ke three prime-three prime overlap sequence three_prime_five_prime_overlap An attribute to describe a gene when the 3' region overlaps with another gene's 5' region. SO:ke http://purl.org/obo/owl/SO#SO_ke 5' 3' overlap three prime five prime overlap sequence antisense A region sequence that is complementary to a sequence of messenger RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Antisense http://en.wikipedia.org/wiki/Antisense polycistronic_transcript A transcript that is polycistronic. SO:xp http://purl.org/obo/owl/SO#SO_xp polycistronic transcript sequence dicistronic_transcript A transcript that is dicistronic. SO:ke http://purl.org/obo/owl/SO#SO_ke dicistronic transcript sequence operon_member operon member sequence gene_array_member gene array member sequence processed_transcript_attribute sequence macronuclear_sequence macronuclear sequence sequence micronuclear_sequence micronuclear sequence sequence gene_by_genome_location sequence gene_by_organelle_of_genome sequence nuclear_gene A gene from nuclear sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp nuclear gene sequence URL:http://en.wikipedia.org/wiki/Nuclear_gene http://en.wikipedia.org/wiki/Nuclear_gene mt_gene A gene located in mitochondrial sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp mitochondrial gene mt gene sequence URL:http://en.wikipedia.org/wiki/Mitochondrial_gene http://en.wikipedia.org/wiki/Mitochondrial_gene kinetoplast_gene A gene located in kinetoplast sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp kinetoplast gene sequence plastid_gene A gene from plastid sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp plastid gene sequence apicoplast_gene A gene from apicoplast sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp apicoplast gene sequence ct_gene A gene from chloroplast sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp chloroplast gene ct gene sequence chromoplast_gene A gene from chromoplast_sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp chromoplast gene sequence cyanelle_gene A gene from cyanelle sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp cyanelle gene sequence leucoplast_gene A plastid gene from leucoplast sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp leucoplast gene sequence proplastid_gene A gene from proplastid sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke proplastid gene sequence nucleomorph_gene A gene from nucleomorph sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp nucleomorph gene sequence plasmid_gene A gene from plasmid sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp plasmid gene sequence proviral_gene A gene from proviral sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp proviral gene sequence endogenous_retroviral_gene A proviral gene with origin endogenous retrovirus. SO:xp http://purl.org/obo/owl/SO#SO_xp endogenous retroviral gene sequence transposable_element A transposon or insertion sequence. An element that can insert in a variety of DNA sequences. URL:http://www.sci.sdsu.edu/~smaloy/Glossary/T.html http://www.sci.sdsu.edu/~smaloy/Glossary/T.html transposable element transposon sequence URL:http://en.wikipedia.org/wiki/Transposable_element http://en.wikipedia.org/wiki/Transposable_element expressed_sequence_match A match to an EST or cDNA sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke expressed sequence match sequence clone_insert_end The end of the clone insert. SO:ke http://purl.org/obo/owl/SO#SO_ke clone insert end sequence polypeptide 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. 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 http://purl.org/obo/owl/SO#SO_ma protein sequence SO:0000358 URL:http://en.wikipedia.org/wiki/Polypeptide http://en.wikipedia.org/wiki/Polypeptide chromosome_arm A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere. URL:http://www.medterms.com/script/main/art.asp?articlekey=5152 http://www.medterms.com/script/main/art.asp?articlekey=5152 chromosome arm sequence non_capped_primary_transcript sequence sequencing_primer sequencing primer sequence mRNA_with_frameshift An mRNA with a frameshift. SO:xp http://purl.org/obo/owl/SO#SO_xp frameshifted mRNA mRNA with frameshift sequence sequence_variant_obs A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. SO:ke http://purl.org/obo/owl/SO#SO_ke mutation sequence sequence_feature An extent of biological sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke located sequence feature located_sequence_feature sequence feature sequence transposable_element_gene A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast. SO:ke http://purl.org/obo/owl/SO#SO_ke transposable element gene sequence primer An oligo to which new deoxyribonucleotides can be added by DNA polymerase. SO:ke http://purl.org/obo/owl/SO#SO_ke DNA primer primer oligonucleotide primer polynucleotide primer sequence sequence URL:http://en.wikipedia.org/wiki/Primer_(molecular_biology) http://en.wikipedia.org/wiki/Primer_(molecular_biology) proviral_region A viral sequence which has integrated into a host genome. SO:ke http://purl.org/obo/owl/SO#SO_ke proviral region proviral sequence sequence methylated_C A methylated deoxy-cytosine. SO:ke http://purl.org/obo/owl/SO#SO_ke methylated C methylated cytosine methylated cytosine base methylated cytosine residue sequence transcript_feature sequence edited An attribute describing a sequence that is modified by editing. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence transcript_with_readthrough_stop_codon sequence transcript_with_translational_frameshift A transcript with a translational frameshift. SO:xp http://purl.org/obo/owl/SO#SO_xp transcript with translational frameshift sequence regulated An attribute to describe a sequence that is regulated. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence protein_coding_primary_transcript May contain introns. A primary transcript that, at least in part, encodes one or more proteins. SO:ke http://purl.org/obo/owl/SO#SO_ke pre mRNA protein coding primary transcript sequence forward_primer This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A single stranded oligo used for polymerase chain reaction. URL:http://mged.sourceforge.net/ontologies/MGEDontology.php http://mged.sourceforge.net/ontologies/MGEDontology.php DNA forward primer forward DNA primer forward primer forward primer oligo forward primer oligonucleotide forward primer polynucleotide forward primer sequence sequence RNA_sequence_secondary_structure A folded RNA sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke RNA sequence secondary structure sequence transcriptionally_regulated By:<protein_id>. An attribute describing a gene that is regulated at transcription. SO:ma http://purl.org/obo/owl/SO#SO_ma transcriptionally regulated sequence transcriptionally_constitutive Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate. SO:ke http://purl.org/obo/owl/SO#SO_ke transcriptionally constitutive sequence transcriptionally_induced An inducer molecule is required for transcription to occur. SO:ke http://purl.org/obo/owl/SO#SO_ke transcriptionally induced sequence transcriptionally_repressed A repressor molecule is required for transcription to stop. SO:ke http://purl.org/obo/owl/SO#SO_ke transcriptionally repressed sequence silenced_gene A gene that is silenced. SO:xp http://purl.org/obo/owl/SO#SO_xp silenced gene sequence gene_silenced_by_DNA_modification A gene that is silenced by DNA modification. SO:xp http://purl.org/obo/owl/SO#SO_xp gene silenced by DNA modification sequence gene_silenced_by_DNA_methylation A gene that is silenced by DNA methylation. SO:xp http://purl.org/obo/owl/SO#SO_xp gene silenced by DNA methylation methylation-silenced gene sequence post_translationally_regulated An attribute describing a gene that is regulated after it has been translated. SO:ke http://purl.org/obo/owl/SO#SO_ke post translationally regulated post-translationally regulated sequence translationally_regulated An attribute describing a gene that is regulated as it is translated. SO:ke http://purl.org/obo/owl/SO#SO_ke translationally regulated sequence reverse_primer This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A single stranded oligo used for polymerase chain reaction. URL:http://mged.sourceforge.net/ontologies/MGEDontology.php http://mged.sourceforge.net/ontologies/MGEDontology.php DNA reverse primer reverse DNA primer reverse primer reverse primer oligo reverse primer oligonucleotide reverse primer sequence sequence epigenetically_modified This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones. SO:ke http://purl.org/obo/owl/SO#SO_ke epigenetically modified sequence imprinted Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence http:http://en.wikipedia.org/wiki/Genomic_imprinting http://purl.org/obo/owl/http#http_http://en.wikipedia.org/wiki/Genomic_imprinting maternally_imprinted The maternal copy of the gene is modified, rendering it transcriptionally silent. SO:ke http://purl.org/obo/owl/SO#SO_ke maternally imprinted sequence paternally_imprinted The paternal copy of the gene is modified, rendering it transcriptionally silent. SO:ke http://purl.org/obo/owl/SO#SO_ke paternally imprinted sequence allelically_excluded Examples are x-inactivation and immunoglobulin formation. Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell. SO:ke http://purl.org/obo/owl/SO#SO_ke allelically excluded sequence gene_rearranged_at_DNA_level An epigenetically modified gene, rearranged at the DNA level. SO:xp http://purl.org/obo/owl/SO#SO_xp gene rearranged at DNA level sequence ribosome_entry_site Region in mRNA where ribosome assembles. SO:ke http://purl.org/obo/owl/SO#SO_ke ribosome entry site sequence attenuator A sequence segment located within the five prime end of an mRNA that causes premature termination of translation. SO:as http://purl.org/obo/owl/SO#SO_as attenuator sequence sequence URL:http://en.wikipedia.org/wiki/Attenuator http://en.wikipedia.org/wiki/Attenuator terminator The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html terminator sequence sequence URL:http://en.wikipedia.org/wiki/Terminator_(genetics) http://en.wikipedia.org/wiki/Terminator_(genetics) DNA_sequence_secondary_structure A folded DNA sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke DNA sequence secondary structure sequence assembly_component A region of known length which may be used to manufacture a longer region. SO:ke http://purl.org/obo/owl/SO#SO_ke assembly component sequence primary_transcript_attribute sequence recoded_codon A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough. SO:xp http://purl.org/obo/owl/SO#SO_xp recoded codon sequence capped An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence exon This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Exon http://en.wikipedia.org/wiki/Exon supercontig One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's. SO:ls http://purl.org/obo/owl/SO#SO_ls scaffold sequence contig A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. SO:ls http://purl.org/obo/owl/SO#SO_ls sequence URL:http://en.wikipedia.org/wiki/Contig http://en.wikipedia.org/wiki/Contig read 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 http://purl.org/obo/owl/SO#SO_rd sequence clone 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 http://purl.org/obo/owl/SO#SO_ke sequence http:http://en.wikipedia.org/wiki/Clone_(genetics) http://purl.org/obo/owl/http#http_http://en.wikipedia.org/wiki/Clone_(genetics) YAC This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells. SO:ma http://purl.org/obo/owl/SO#SO_ma yeast artificial chromosome sequence BAC This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host. SO:ma http://purl.org/obo/owl/SO#SO_ma bacterial artificial chromosome sequence PAC This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Drosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome. The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells. URL:http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome P1 P1 artificial chromosome sequence URL:http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome plasmid This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism. SO:ma http://purl.org/obo/owl/SO#SO_ma plasmid sequence sequence cosmid Paper: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1):9-20. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites. SO:ma http://purl.org/obo/owl/SO#SO_ma cosmid vector sequence URL:http://en.wikipedia.org/wiki/Cosmid http://en.wikipedia.org/wiki/Cosmid phagemid A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with "helper" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids. SO:ma http://purl.org/obo/owl/SO#SO_ma phagemid vector sequence URL:http://en.wikipedia.org/wiki/Phagemid http://en.wikipedia.org/wiki/Phagemid fosmid Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996. A cloning vector that utilizes the E. coli F factor. SO:ma http://purl.org/obo/owl/SO#SO_ma fosmid vector sequence URL:http://en.wikipedia.org/wiki/Fosmid http://en.wikipedia.org/wiki/Fosmid deletion The point at which one or more contiguous nucleotides were excised. SO:ke http://purl.org/obo/owl/SO#SO_ke deleted_sequence nucleotide deletion nucleotide_deletion sequence SO:1000033 URL:http://en.wikipedia.org/wiki/Nucleotide_deletion http://en.wikipedia.org/wiki/Nucleotide_deletion lambda_clone A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome. ISBN:0-1767-2380-8 http://purl.org/obo/owl/ISBN#ISBN_0-1767-2380-8 sequence methylated_A A modified RNA base in which adenine has been methylated. SO:ke http://purl.org/obo/owl/SO#SO_ke methylated A methylated adenine methylated adenine base methylated adenine residue sequence splice_site With spliceosomal introns, the splice sites bind the spliceosomal machinery. Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction. SO:cjm http://purl.org/obo/owl/SO#SO_cjm SO:ke http://purl.org/obo/owl/SO#SO_ke splice site sequence URL:http://en.wikipedia.org/wiki/Splice_site http://en.wikipedia.org/wiki/Splice_site five_prime_cis_splice_site 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. URL:http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html SO:cjm http://purl.org/obo/owl/SO#SO_cjm SO:ke http://purl.org/obo/owl/SO#SO_ke 5' splice site donor donor splice site five prime splice site splice donor site sequence three_prime_cis_splice_site 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. URL:http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html SO:cjm http://purl.org/obo/owl/SO#SO_cjm SO:ke http://purl.org/obo/owl/SO#SO_ke 3' splice site acceptor acceptor splice site splice acceptor site three prime splice site sequence enhancer 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. 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. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html sequence URL:http://en.wikipedia.org/wiki/Enhancer_(genetics) http://en.wikipedia.org/wiki/Enhancer_(genetics) enhancer_bound_by_factor An enhancer bound by a factor. SO:xp http://purl.org/obo/owl/SO#SO_xp enhancer bound by factor sequence promoter 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. A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery. SO:regcreative http://purl.org/obo/owl/SO#SO_regcreative promoter sequence sequence URL:http://en.wikipedia.org/wiki/Promoter http://en.wikipedia.org/wiki/Promoter restriction_enzyme_cut_site A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence RNApol_I_promoter A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription. SO:ke http://purl.org/obo/owl/SO#SO_ke pol I promoter polymerase I promoter RNA polymerase A promoter RNApol I promoter sequence RNApol_II_promoter A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription. SO:ke http://purl.org/obo/owl/SO#SO_ke pol II promoter polymerase II promoter RNA polymerase B promoter RNApol II promoter sequence RNApol_III_promoter A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription. SO:ke http://purl.org/obo/owl/SO#SO_ke pol III promoter polymerase III promoter RNA polymerase C promoter RNApol III promoter sequence CAAT_signal Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html CAAT box CAAT signal CAAT-box sequence URL:http://en.wikipedia.org/wiki/CAAT_box http://en.wikipedia.org/wiki/CAAT_box GC_rich_promoter_region A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html GC rich promoter region GC-rich region sequence TATA_box Binds TBP. A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T). URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html PMID:16858867 http://purl.org/obo/owl/PMID#PMID_16858867 Goldstein-Hogness box TATA box sequence URL:http://en.wikipedia.org/wiki/TATA_box http://en.wikipedia.org/wiki/TATA_box minus_10_signal A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html -10 signal minus 10 signal Pribnow box Pribnow Schaller box Pribnow-Schaller box sequence URL:http://en.wikipedia.org/wiki/Pribnow_box http://en.wikipedia.org/wiki/Pribnow_box minus_35_signal A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html -35 signal minus 35 signal sequence cross_genome_match A nucleotide match against a sequence from another organism. SO:ma http://purl.org/obo/owl/SO#SO_ma cross genome match sequence operon This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence URL:http://en.wikipedia.org/wiki/Operon http://en.wikipedia.org/wiki/Operon clone_insert_start The start of the clone insert. SO:ke http://purl.org/obo/owl/SO#SO_ke clone insert start sequence retrotransposon A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase. URL:http://www.dddmag.com/Glossary.aspx#r http://www.dddmag.com/Glossary.aspx#r class I class I transposon retrotransposon element sequence URL:http://en.wikipedia.org/wiki/Retrotransposon http://en.wikipedia.org/wiki/Retrotransposon translated_nucleotide_match A match against a translated sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke translated nucleotide match sequence DNA_transposon A transposon where the mechanism of transposition is via a DNA intermediate. SO:ke http://purl.org/obo/owl/SO#SO_ke class II class II transposon DNA transposon sequence non_transcribed_region A region of the gene which is not transcribed. SO:ke http://purl.org/obo/owl/SO#SO_ke non transcribed region non-transcribed sequence nontranscribed region nontranscribed sequence sequence U2_intron May have either GT-AG or AT-AG 5' and 3' boundaries. A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs. PMID:9428511 http://purl.org/obo/owl/PMID#PMID_9428511 U2 intron sequence primary_transcript A transcript that in its initial state requires modification to be functional. SO:ma http://purl.org/obo/owl/SO#SO_ma precursor RNA primary transcript sequence URL:http://en.wikipedia.org/wiki/Primary_transcript http://en.wikipedia.org/wiki/Primary_transcript LTR_retrotransposon A retrotransposon flanked by long terminal repeat sequences. SO:ke http://purl.org/obo/owl/SO#SO_ke long terminal repeat retrotransposon LTR retrotransposon sequence repeat_family A group of characterized repeat sequences. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence intron This term is mapped to MGED. Do not obsolete without consulting MGED ontology. 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. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html sequence URL:http://en.wikipedia.org/wiki/Intron http://en.wikipedia.org/wiki/Intron non_LTR_retrotransposon A retrotransposon without long terminal repeat sequences. SO:ke http://purl.org/obo/owl/SO#SO_ke non LTR retrotransposon sequence five_prime_intron 5' intron 5' intron sequence five prime intron sequence interior_intron interior intron sequence three_prime_intron 3' intron 3' intron sequence three prime intron sequence RFLP_fragment 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 http://purl.org/obo/owl/GOC#GOC_pj restriction fragment length polymorphism RFLP RFLP fragment sequence URL:http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism LINE_element A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats. URL:http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html LINE LINE element Long interspersed element Long interspersed nuclear element sequence coding_exon An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon). SO:ke http://purl.org/obo/owl/SO#SO_ke coding exon sequence five_prime_coding_exon_coding_region The sequence of the five_prime_coding_exon that codes for protein. SO:cjm http://purl.org/obo/owl/SO#SO_cjm five prime exon coding region sequence three_prime_coding_exon_coding_region The sequence of the three_prime_coding_exon that codes for protein. SO:cjm http://purl.org/obo/owl/SO#SO_cjm three prime exon coding region sequence noncoding_exon An exon that does not contain any codons. SO:ke http://purl.org/obo/owl/SO#SO_ke noncoding exon sequence translocation A region of nucleotide sequence that has translocated to a new position. SO:ke http://purl.org/obo/owl/SO#SO_ke transchr URL:http://www.ncbi.nlm.nih.gov/dbvar/ http://www.ncbi.nlm.nih.gov/dbvar/ translocated sequence sequence five_prime_coding_exon The 5' most coding exon. SO:ke http://purl.org/obo/owl/SO#SO_ke 5' coding exon five prime coding exon sequence interior_exon An exon that is bounded by 5' and 3' splice sites. PMID:10373547 http://purl.org/obo/owl/PMID#PMID_10373547 interior exon sequence three_prime_coding_exon The coding exon that is most 3-prime on a given transcript. SO:ma http://purl.org/obo/owl/SO#SO_ma 3' coding exon three prime coding exon sequence UTR Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated. SO:ke http://purl.org/obo/owl/SO#SO_ke untranslated region sequence five_prime_UTR A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html 5' UTR five prime UTR five_prime_untranslated_region sequence URL:http://en.wikipedia.org/wiki/5'_UTR http://en.wikipedia.org/wiki/5'_UTR three_prime_UTR A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html three prime untranslated region three prime UTR sequence URL:http://en.wikipedia.org/wiki/Three_prime_untranslated_region http://en.wikipedia.org/wiki/Three_prime_untranslated_region SINE_element A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element. SO:ke http://purl.org/obo/owl/SO#SO_ke Short interspersed element Short interspersed nuclear element SINE element sequence URL:http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element simple_sequence_length_variation simple sequence length polymorphism simple sequence length variation SSLP sequence terminal_inverted_repeat_element A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long. URL:http://www.genetics.org/cgi/reprint/156/4/1983.pdf http://www.genetics.org/cgi/reprint/156/4/1983.pdf terminal inverted repeat element TIR element sequence rRNA_primary_transcript A primary transcript encoding a ribosomal RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke ribosomal RNA primary transcript rRNA primary transcript sequence tRNA_primary_transcript A primary transcript encoding a transfer RNA (SO:0000253). SO:ke http://purl.org/obo/owl/SO#SO_ke tRNA primary transcript sequence alanine_tRNA_primary_transcript A primary transcript encoding alanyl tRNA. SO:ke http://purl.org/obo/owl/SO#SO_ke alanine tRNA primary transcript sequence arginine_tRNA_primary_transcript A primary transcript encoding arginyl tRNA (SO:0000255). SO:ke http://purl.org/obo/owl/SO#SO_ke arginine tRNA primary transcript sequence asparagine_tRNA_primary_transcript A primary transcript encoding asparaginyl tRNA (SO:0000256). SO:ke http://purl.org/obo/owl/SO#SO_ke asparagine tRNA primary transcript sequence aspartic_acid_tRNA_primary_transcript A primary transcript encoding aspartyl tRNA (SO:0000257). SO:ke http://purl.org/obo/owl/SO#SO_ke aspartic acid tRNA primary transcript sequence cysteine_tRNA_primary_transcript A primary transcript encoding cysteinyl tRNA (SO:0000258). SO:ke http://purl.org/obo/owl/SO#SO_ke cysteine tRNA primary transcript sequence glutamic_acid_tRNA_primary_transcript A primary transcript encoding glutaminyl tRNA (SO:0000260). SO:ke http://purl.org/obo/owl/SO#SO_ke glutamic acid tRNA primary transcript sequence glutamine_tRNA_primary_transcript A primary transcript encoding glutamyl tRNA (SO:0000260). SO:ke http://purl.org/obo/owl/SO#SO_ke glutamine tRNA primary transcript sequence glycine_tRNA_primary_transcript A primary transcript encoding glycyl tRNA (SO:0000263). SO:ke http://purl.org/obo/owl/SO#SO_ke glycine tRNA primary transcript sequence histidine_tRNA_primary_transcript A primary transcript encoding histidyl tRNA (SO:0000262). SO:ke http://purl.org/obo/owl/SO#SO_ke histidine tRNA primary transcript sequence isoleucine_tRNA_primary_transcript A primary transcript encoding isoleucyl tRNA (SO:0000263). SO:ke http://purl.org/obo/owl/SO#SO_ke isoleucine tRNA primary transcript sequence leucine_tRNA_primary_transcript A primary transcript encoding leucyl tRNA (SO:0000264). SO:ke http://purl.org/obo/owl/SO#SO_ke leucine tRNA primary transcript sequence lysine_tRNA_primary_transcript A primary transcript encoding lysyl tRNA (SO:0000265). SO:ke http://purl.org/obo/owl/SO#SO_ke lysine tRNA primary transcript sequence methionine_tRNA_primary_transcript A primary transcript encoding methionyl tRNA (SO:0000266). SO:ke http://purl.org/obo/owl/SO#SO_ke methionine tRNA primary transcript sequence phenylalanine_tRNA_primary_transcript A primary transcript encoding phenylalanyl tRNA (SO:0000267). SO:ke http://purl.org/obo/owl/SO#SO_ke phenylalanine tRNA primary transcript sequence proline_tRNA_primary_transcript A primary transcript encoding prolyl tRNA (SO:0000268). SO:ke http://purl.org/obo/owl/SO#SO_ke proline tRNA primary transcript sequence serine_tRNA_primary_transcript A primary transcript encoding seryl tRNA (SO:000269). SO:ke http://purl.org/obo/owl/SO#SO_ke serine tRNA primary transcript sequence threonine_tRNA_primary_transcript A primary transcript encoding threonyl tRNA (SO:000270). SO:ke http://purl.org/obo/owl/SO#SO_ke threonine tRNA primary transcript sequence tryptophan_tRNA_primary_transcript A primary transcript encoding tryptophanyl tRNA (SO:000271). SO:ke http://purl.org/obo/owl/SO#SO_ke tryptophan tRNA primary transcript sequence tyrosine_tRNA_primary_transcript A primary transcript encoding tyrosyl tRNA (SO:000272). SO:ke http://purl.org/obo/owl/SO#SO_ke tyrosine tRNA primary transcript sequence valine_tRNA_primary_transcript A primary transcript encoding valyl tRNA (SO:000273). SO:ke http://purl.org/obo/owl/SO#SO_ke valine tRNA primary transcript sequence snRNA_primary_transcript A primary transcript encoding a small nuclear RNA (SO:0000274). SO:ke http://purl.org/obo/owl/SO#SO_ke snRNA primary transcript sequence snoRNA_primary_transcript A primary transcript encoding a small nucleolar mRNA (SO:0000275). SO:ke http://purl.org/obo/owl/SO#SO_ke snoRNA primary transcript sequence mature_transcript A processed transcript cannot contain introns. 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 http://purl.org/obo/owl/SO#SO_ke mature transcript sequence URL:http://en.wikipedia.org/wiki/Mature_transcript http://en.wikipedia.org/wiki/Mature_transcript mRNA 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. Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns. SO:ma http://purl.org/obo/owl/SO#SO_ma messenger RNA sequence URL:http://en.wikipedia.org/wiki/MRNA http://en.wikipedia.org/wiki/MRNA TF_binding_site A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]. SO:ke http://purl.org/obo/owl/SO#SO_ke TF binding site transcription factor binding site sequence ORF 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. 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 http://purl.org/obo/owl/SGD#SGD_rb SO:ma http://purl.org/obo/owl/SO#SO_ma open reading frame sequence transcript_attribute transcript attribute sequence foldback_element A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats. URL:http://www.genetics.org/cgi/reprint/156/4/1983.pdf http://www.genetics.org/cgi/reprint/156/4/1983.pdf foldback element long inverted repeat element LVR element sequence flanking_region The sequences extending on either side of a specific region. SO:ke http://purl.org/obo/owl/SO#SO_ke flanking region sequence chromosome_variation chromosome variation sequence internal_UTR A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal. SO:cjm http://purl.org/obo/owl/SO#SO_cjm internal UTR sequence untranslated_region_polycistronic_mRNA The untranslated sequence separating the 'cistrons' of multicistronic mRNA. SO:ke http://purl.org/obo/owl/SO#SO_ke untranslated region polycistronic mRNA sequence internal_ribosome_entry_site Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation. SO:ke http://purl.org/obo/owl/SO#SO_ke internal ribosomal entry sequence internal ribosomal entry site internal ribosome entry sequence internal ribosome entry site IRES sequence URL:http://en.wikipedia.org/wiki/Internal_ribosome_entry_site http://en.wikipedia.org/wiki/Internal_ribosome_entry_site four_cutter_restriction_site 4-cutter_restriction_site four-cutter_restriction_sit sequence mRNA_by_polyadenylation_status sequence polyadenylated A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence mRNA_not_polyadenylated sequence sequence_length_variation sequence length variation sequence six_cutter_restriction_site 6-cutter_restriction_site six-cutter_restriction_site sequence modified_RNA_base_feature A post_transcriptionally modified base. SO:ke http://purl.org/obo/owl/SO#SO_ke modified RNA base feature sequence eight_cutter_restriction_site 8-cutter_restriction_site eight-cutter_restriction_site sequence rRNA RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html ISBN:0198506732 http://purl.org/obo/owl/ISBN#ISBN_0198506732 ribosomal ribonucleic acid ribosomal RNA sequence URL:http://en.wikipedia.org/wiki/RRNA http://en.wikipedia.org/wiki/RRNA tRNA This term is mapped to MGED. Do not obsolete without consulting MGED ontology. 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. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005 ISBN:0198506732 http://purl.org/obo/owl/ISBN#ISBN_0198506732 transfer ribonucleic acid transfer RNA sequence URL:http://en.wikipedia.org/wiki/TRNA http://en.wikipedia.org/wiki/TRNA alanyl_tRNA A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke alanyl tRNA alanyl-transfer ribonucleic acid alanyl-transfer RNA sequence rRNA_small_subunit_primary_transcript A primary transcript encoding a small ribosomal subunit RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke rRNA small subunit primary transcript sequence asparaginyl_tRNA A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke asparaginyl tRNA asparaginyl-transfer ribonucleic acid asparaginyl-transfer RNA sequence aspartyl_tRNA A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke aspartyl tRNA aspartyl-transfer ribonucleic acid aspartyl-transfer RNA sequence cysteinyl_tRNA A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke cysteinyl tRNA cysteinyl-transfer ribonucleic acid cysteinyl-transfer RNA sequence glutaminyl_tRNA A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke glutaminyl tRNA glutaminyl-transfer ribonucleic acid glutaminyl-transfer RNA sequence glutamyl_tRNA A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke glutamyl tRNA glutamyl-transfer ribonucleic acid glutamyl-transfer RNA sequence glycyl_tRNA A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke glycyl tRNA glycyl-transfer ribonucleic acid glycyl-transfer RNA sequence histidyl_tRNA A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke histidyl tRNA histidyl-transfer ribonucleic acid histidyl-transfer RNA sequence isoleucyl_tRNA A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke isoleucyl tRNA isoleucyl-transfer ribonucleic acid isoleucyl-transfer RNA sequence leucyl_tRNA A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke leucyl tRNA leucyl-transfer ribonucleic acid leucyl-transfer RNA sequence lysyl_tRNA A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke lysyl tRNA lysyl-transfer ribonucleic acid lysyl-transfer RNA sequence methionyl_tRNA A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke methionyl tRNA methionyl-transfer ribonucleic acid methionyl-transfer RNA sequence phenylalanyl_tRNA A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke phenylalanyl tRNA phenylalanyl-transfer ribonucleic acid phenylalanyl-transfer RNA sequence prolyl_tRNA A tRNA sequence that has a proline anticodon, and a 3' proline binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke prolyl tRNA prolyl-transfer ribonucleic acid prolyl-transfer RNA sequence seryl_tRNA A tRNA sequence that has a serine anticodon, and a 3' serine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke seryl tRNA seryl-transfer ribonucleic acid seryl-transfer RNA sequence threonyl_tRNA A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke threonyl tRNA threonyl-transfer ribonucleic acid threonyl-transfer RNA sequence tryptophanyl_tRNA A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke tryptophanyl tRNA tryptophanyl-transfer ribonucleic acid tryptophanyl-transfer RNA sequence tyrosyl_tRNA A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke tyrosyl tRNA tyrosyl-transfer ribonucleic acid tyrosyl-transfer RNA sequence valyl_tRNA A tRNA sequence that has a valine anticodon, and a 3' valine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke valyl tRNA valyl-transfer ribonucleic acid valyl-transfer RNA sequence snRNA This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A small nuclear RNA molecule involved in pre-mRNA splicing and processing. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html PMID:11733745 http://purl.org/obo/owl/PMID#PMID_11733745 WB:ems http://purl.org/obo/owl/WB#WB_ems small nuclear RNA sequence URL:http://en.wikipedia.org/wiki/SnRNA http://en.wikipedia.org/wiki/SnRNA snoRNA 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 http://purl.org/obo/owl/GOC#GOC_kgc small nucleolar RNA sequence URL:http://en.wikipedia.org/wiki/SnoRNA http://en.wikipedia.org/wiki/SnoRNA miRNA Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. PMID:12592000 http://purl.org/obo/owl/PMID#PMID_12592000 micro RNA microRNA sequence URL:http://en.wikipedia.org/wiki/MiRNA http://en.wikipedia.org/wiki/MiRNA bound_by_factor Formerly called transcript_by_bound_factor. An attribute describing a sequence that is bound by another molecule. SO:ke http://purl.org/obo/owl/SO#SO_ke bound by factor sequence transcript_bound_by_nucleic_acid Formerly called transcript_by_bound_nucleic_acid. A transcript that is bound by a nucleic acid. SO:xp http://purl.org/obo/owl/SO#SO_xp transcript bound by nucleic acid sequence transcript_bound_by_protein Formerly called transcript_by_bound_protein. A transcript that is bound by a protein. SO:xp http://purl.org/obo/owl/SO#SO_xp transcript bound by protein sequence engineered_gene A gene that is engineered. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered gene sequence engineered_foreign_gene A gene that is engineered and foreign. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered foreign gene sequence mRNA_with_minus_1_frameshift An mRNA with a minus 1 frameshift. SO:xp http://purl.org/obo/owl/SO#SO_xp mRNA with minus 1 frameshift sequence engineered_foreign_transposable_element_gene A transposable_element that is engineered and foreign. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered foreign transposable element gene sequence type_I_enzyme_restriction_site The recognition site is bipartite and interrupted. URL:http://www.promega.com http://www.promega.com sequence foreign_gene A gene that is foreign. SO:xp http://purl.org/obo/owl/SO#SO_xp foreign gene sequence long_terminal_repeat A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html direct terminal repeat long terminal repeat LTR sequence URL:http://en.wikipedia.org/wiki/Long_terminal_repeat http://en.wikipedia.org/wiki/Long_terminal_repeat fusion_gene A gene that is a fusion. SO:xp http://purl.org/obo/owl/SO#SO_xp fusion gene sequence URL:http://en.wikipedia.org/wiki/Fusion_gene http://en.wikipedia.org/wiki/Fusion_gene engineered_fusion_gene A fusion gene that is engineered. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered fusion gene sequence microsatellite A repeat_region containing repeat_units (2 to 4 bp) that is repeated multiple times in tandem. URL:http://www.informatics.jax.org/silver/glossary.shtml http://www.informatics.jax.org/silver/glossary.shtml microsatellite locus microsatellite marker VNTR sequence URL:http://en.wikipedia.org/wiki/Microsatellite http://en.wikipedia.org/wiki/Microsatellite dinucleotide_repeat_microsatellite_feature dinucleotide repeat microsatellite dinucleotide repeat microsatellite feature dinucleotide repeat microsatellite locus dinucleotide repeat microsatellite marker sequence trinucleotide_repeat_microsatellite_feature dinucleotide repeat microsatellite marker rinucleotide repeat microsatellite trinucleotide repeat microsatellite feature trinucleotide repeat microsatellite locus sequence repetitive_element sequence engineered_foreign_repetitive_element A repetitive element that is engineered and foreign. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered foreign repetitive element sequence inverted_repeat 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 http://purl.org/obo/owl/SO#SO_ke inverted repeat inverted repeat sequence sequence URL:http://en.wikipedia.org/wiki/Inverted_repeat http://en.wikipedia.org/wiki/Inverted_repeat U12_intron May have either GT-AC or AT-AC 5' and 3' boundaries. A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs. PMID:9428511 http://purl.org/obo/owl/PMID#PMID_9428511 U12 intron U12-dependent intron sequence origin_of_replication The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html ori origin of replication sequence URL:http://en.wikipedia.org/wiki/Origin_of_replication http://en.wikipedia.org/wiki/Origin_of_replication D_loop Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html D-loop displacement loop sequence URL:http://en.wikipedia.org/wiki/D_loop http://en.wikipedia.org/wiki/D_loop recombination_feature recombination feature sequence specific_recombination_site specific recombination site sequence recombination_feature_of_rearranged_gene recombination feature of rearranged gene sequence vertebrate_immune_system_gene_recombination_feature vertebrate immune system gene recombination feature sequence J_gene_recombination_feature Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# J gene recombination feature J-RS sequence clip Part of the primary transcript that is clipped off during processing. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence type_II_enzyme_restriction_site The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site. URL:http://www.promega.com http://www.promega.com sequence modified_base Modified base:<modified_base>. A modified nucleotide, i.e. a nucleotide other than A, T, C. G. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html modified base site sequence methylated_base_feature A nucleotide modified by methylation. SO:ke http://purl.org/obo/owl/SO#SO_ke methylated base feature sequence CpG_island 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 http://purl.org/obo/owl/SO#SO_rd CG island CpG island sequence URL:http://en.wikipedia.org/wiki/CpG_island http://en.wikipedia.org/wiki/CpG_island sequence_feature_locating_method sequence computed_feature sequence predicted_ab_initio_computation sequence computed_feature_by_similarity similar to:<sequence_id> . SO:ma http://purl.org/obo/owl/SO#SO_ma sequence experimentally_determined Attribute to describe a feature that has been experimentally verified. SO:ke http://purl.org/obo/owl/SO#SO_ke experimentally determined sequence stem_loop A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html RNA_hairpin_loop stem loop stem-loop sequence SO:0000019 URL:http://en.wikipedia.org/wiki/Stem_loop http://en.wikipedia.org/wiki/Stem_loop direct_repeat A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA. SO:ke http://purl.org/obo/owl/SO#SO_ke direct repeat sequence URL:http://en.wikipedia.org/wiki/Direct_repeat http://en.wikipedia.org/wiki/Direct_repeat TSS The first base where RNA polymerase begins to synthesize the RNA transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke transcription start site sequence CDS A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon. SO:ma http://purl.org/obo/owl/SO#SO_ma coding sequence sequence cDNA_clone This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host. URL:http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html cDNA clone sequence start_codon First codon to be translated by a ribosome. SO:ke http://purl.org/obo/owl/SO#SO_ke initiation codon start codon sequence URL:http://en.wikipedia.org/wiki/Start_codon http://en.wikipedia.org/wiki/Start_codon stop_codon In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis. SO:ke http://purl.org/obo/owl/SO#SO_ke stop codon sequence URL:http://en.wikipedia.org/wiki/Stop_codon http://en.wikipedia.org/wiki/Stop_codon intronic_splice_enhancer Sequences within the intron that modulate splice site selection for some introns. SO:ke http://purl.org/obo/owl/SO#SO_ke intronic splice enhancer sequence mRNA_with_plus_1_frameshift An mRNA with a plus 1 frameshift. SO:ke http://purl.org/obo/owl/SO#SO_ke mRNA with plus 1 frameshift sequence nuclease_hypersensitive_site nuclease hypersensitive site sequence coding_start The first base to be translated into protein. SO:ke http://purl.org/obo/owl/SO#SO_ke coding start translation initiation site translation start sequence tag A nucleotide sequence that may be used to identify a larger sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence rRNA_large_subunit_primary_transcript A primary transcript encoding a large ribosomal subunit RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke rRNA large subunit primary transcript sequence SAGE_tag A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts. URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=7570003&amp;dopt=Abstract http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=7570003&amp;dopt=Abstract SAGE tag sequence coding_end The last base to be translated into protein. It does not include the stop codon. SO:ke http://purl.org/obo/owl/SO#SO_ke coding end translation termination site translation_end sequence microarray_oligo microarray oligo microarray oligonucleotide sequence mRNA_with_plus_2_frameshift An mRNA with a plus 2 frameshift. SO:xp http://purl.org/obo/owl/SO#SO_xp mRNA with plus 2 frameshift sequence conserved_region Region of sequence similarity by descent from a common ancestor. SO:ke http://purl.org/obo/owl/SO#SO_ke conserved region sequence URL:http://en.wikipedia.org/wiki/Conserved_region http://en.wikipedia.org/wiki/Conserved_region STS 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. URL:http://www.biospace.com http://www.biospace.com sequence tag site sequence coding_conserved_region Coding region of sequence similarity by descent from a common ancestor. SO:ke http://purl.org/obo/owl/SO#SO_ke coding conserved region sequence exon_junction The boundary between two exons in a processed transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke exon junction sequence nc_conserved_region Non-coding region of sequence similarity by descent from a common ancestor. SO:ke http://purl.org/obo/owl/SO#SO_ke nc conserved region noncoding conserved region sequence mRNA_with_minus_2_frameshift A mRNA with a minus 2 frameshift. SO:ke http://purl.org/obo/owl/SO#SO_ke mRNA with minus 2 frameshift sequence pseudogene 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). URL:http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html sequence URL:http://en.wikipedia.org/wiki/Pseudogene http://en.wikipedia.org/wiki/Pseudogene RNAi_reagent A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference. SO:rd http://purl.org/obo/owl/SO#SO_rd RNAi reagent sequence MITE A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins. URL:http://www.pnas.org/cgi/content/full/97/18/10083 http://www.pnas.org/cgi/content/full/97/18/10083 miniature inverted repeat transposable element sequence recombination_hotspot A region in a genome which promotes recombination. SO:rd http://purl.org/obo/owl/SO#SO_rd recombination hotspot sequence URL:http://en.wikipedia.org/wiki/Recombination_hotspot http://en.wikipedia.org/wiki/Recombination_hotspot chromosome This term is mapped to MGED. Do not obsolete without consulting MGED ontology. 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 http://purl.org/obo/owl/SO#SO_ma sequence URL:http://en.wikipedia.org/wiki/Chromosome http://en.wikipedia.org/wiki/Chromosome chromosome_band A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark. SO:ma http://purl.org/obo/owl/SO#SO_ma chromosome band cytoband cytological band sequence URL:http://en.wikipedia.org/wiki/Cytological_band http://en.wikipedia.org/wiki/Cytological_band site_specific_recombination_target_region site specific recombination target region sequence match A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence splice_enhancer Region of a transcript that regulates splicing. SO:ke http://purl.org/obo/owl/SO#SO_ke splice enhancer sequence EST This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long. SO:ke http://purl.org/obo/owl/SO#SO_ke expressed sequence tag sequence loxP_site Cre-recombination target region loxP site sequence nucleotide_match A match against a nucleotide sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke nucleotide match sequence nucleic_acid An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. CHEBI:33696 http://purl.org/obo/owl/CHEBI#CHEBI_33696 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb nucleic acid sequence URL:http://en.wikipedia.org/wiki/Nucleic_acid http://en.wikipedia.org/wiki/Nucleic_acid protein_match A match against a protein sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke protein match sequence FRT_site An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid. SO:ma http://purl.org/obo/owl/SO#SO_ma FLP recombination target region FRT site sequence synthetic_sequence An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence. SO:ma http://purl.org/obo/owl/SO#SO_ma synthetic sequence sequence DNA An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb sequence sequence_assembly A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence assembly sequence URL:http://en.wikipedia.org/wiki/Sequence_assembly http://en.wikipedia.org/wiki/Sequence_assembly group_1_intron_homing_endonuclease_target_region A region of intronic nucleotide sequence targeted by a nuclease enzyme. SO:ke http://purl.org/obo/owl/SO#SO_ke group 1 intron homing endonuclease target region sequence haplotype_block A region of the genome which is co-inherited as the result of the lack of historic recombination within it. SO:ma http://purl.org/obo/owl/SO#SO_ma haplotype block sequence RNA This term is mapped to MGED. Do not obsolete without consulting MGED ontology. An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb sequence flanked An attribute describing a region that is bounded either side by a particular kind of region. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence floxed An attribute describing sequence that is flanked by Lox-P sites. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Floxed http://en.wikipedia.org/wiki/Floxed codon 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. URL:http://www.everythingbio.com/glos/definition.php?word=codon http://www.everythingbio.com/glos/definition.php?word=codon SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Codon http://en.wikipedia.org/wiki/Codon FRT_flanked An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT. SO:ke http://purl.org/obo/owl/SO#SO_ke FRT flanked sequence invalidated_by_chimeric_cDNA A cDNA clone constructed from more than one mRNA. Usually an experimental artifact. SO:ma http://purl.org/obo/owl/SO#SO_ma invalidated by chimeric cDNA sequence floxed_gene A transgene that is floxed. SO:xp http://purl.org/obo/owl/SO#SO_xp floxed gene sequence transposable_element_flanking_region The region of sequence surrounding a transposable element. SO:ke http://purl.org/obo/owl/SO#SO_ke transposable element flanking region sequence integron A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site. SO:as http://purl.org/obo/owl/SO#SO_as sequence URL:http://en.wikipedia.org/wiki/Integron http://en.wikipedia.org/wiki/Integron insertion_site The junction where an insertion occurred. SO:ke http://purl.org/obo/owl/SO#SO_ke insertion site sequence attI_site A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place. SO:as http://purl.org/obo/owl/SO#SO_as attI site sequence transposable_element_insertion_site The junction in a genome where a transposable_element has inserted. SO:ke http://purl.org/obo/owl/SO#SO_ke transposable element insertion site sequence integrase_coding_region sequence small_regulatory_ncRNA A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression. SO:ma http://purl.org/obo/owl/SO#SO_ma small regulatory ncRNA sequence conjugative_transposon A transposon that encodes function required for conjugation. URL:http://www.sci.sdsu.edu/~smaloy/Glossary/C.html http://www.sci.sdsu.edu/~smaloy/Glossary/C.html conjugative transposon sequence enzymatic_RNA 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. An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb enzymatic RNA sequence recombinationally_inverted_gene A recombinationally rearranged gene by inversion. SO:xp http://purl.org/obo/owl/SO#SO_xp recombinationally inverted gene sequence ribozyme An RNA with catalytic activity. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence URL:http://en.wikipedia.org/wiki/Ribozyme http://en.wikipedia.org/wiki/Ribozyme rRNA_5_8S 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. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002 5.8S LSU rRNA 5.8S ribosomal RNA 5.8S rRNA rRNA 5 8S sequence URL:http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA RNA_6S A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013 6S RNA RNA 6S sequence URL:http://en.wikipedia.org/wiki/6S_RNA http://en.wikipedia.org/wiki/6S_RNA CsrB_RsmB_RNA An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018 CsrB RsmB RNA CsrB-RsmB RNA sequence DsrA_RNA DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014 DsrA RNA sequence URL:http://en.wikipedia.org/wiki/DsrA_RNA http://en.wikipedia.org/wiki/DsrA_RNA GcvB_RNA A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022 GcvB RNA sequence URL:http://en.wikipedia.org/wiki/GcvB_RNA http://en.wikipedia.org/wiki/GcvB_RNA hammerhead_ribozyme 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 http://purl.org/obo/owl/PMID#PMID_2436805 hammerhead ribozyme sequence URL:http://en.wikipedia.org/wiki/Hammerhead_ribozyme http://en.wikipedia.org/wiki/Hammerhead_ribozyme group_IIA_intron group IIA intron sequence group_IIB_intron group IIB intron sequence MicF_RNA A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033 MicF RNA sequence URL:http://en.wikipedia.org/wiki/MicF_RNA http://en.wikipedia.org/wiki/MicF_RNA OxyS_RNA A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035 OxyS RNA sequence URL:http://en.wikipedia.org/wiki/OxyS_RNA http://en.wikipedia.org/wiki/OxyS_RNA RNase_MRP_RNA 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. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030 RNase MRP RNA sequence RNase_P_RNA 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. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010 RNase P RNA sequence RprA_RNA Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034 RprA RNA sequence URL:http://en.wikipedia.org/wiki/RprA_RNA http://en.wikipedia.org/wiki/RprA_RNA RRE_RNA The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036 RRE RNA sequence spot_42_RNA A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021 spot-42 RNA sequence URL:http://en.wikipedia.org/wiki/Spot_42_RNA http://en.wikipedia.org/wiki/Spot_42_RNA telomerase_RNA The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025 telomerase RNA sequence URL:http://en.wikipedia.org/wiki/Telomerase_RNA http://en.wikipedia.org/wiki/Telomerase_RNA U1_snRNA 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. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003 small nuclear RNA U1 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb snRNA U1 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U1 small nuclear RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U1 snRNA sequence URL:http://en.wikipedia.org/wiki/U1_snRNA http://en.wikipedia.org/wiki/U1_snRNA U2_snRNA 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. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004 small nuclear RNA U2 RSC:CB http://purl.org/obo/owl/RSC#RSC_CB snRNA U2 RSC:CB http://purl.org/obo/owl/RSC#RSC_CB U2 small nuclear RNA RSC:CB http://purl.org/obo/owl/RSC#RSC_CB U2 snRNA sequence URL:http://en.wikipedia.org/wiki/U2_snRNA http://en.wikipedia.org/wiki/U2_snRNA U4_snRNA 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. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015 small nuclear RNA U4 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb snRNA U4 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U4 small nuclear RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U4 snRNA sequence URL:http://en.wikipedia.org/wiki/U4_snRNA http://en.wikipedia.org/wiki/U4_snRNA U4atac_snRNA 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 http://purl.org/obo/owl/PMID#PMID_=12409455 small nuclear RNA U4atac RSC:cb http://purl.org/obo/owl/RSC#RSC_cb snRNA U4atac RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U4atac small nuclear RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U4atac snRNA sequence U5_snRNA 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. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020 small nuclear RNA U5 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb snRNA U5 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U5 small nuclear RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U5 snRNA sequence URL:http://en.wikipedia.org/wiki/U5_snRNA http://en.wikipedia.org/wiki/U5_snRNA U6_snRNA 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. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015 small nuclear RNA U6 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb snRNA U6 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U6 small nuclear RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U6 snRNA sequence URL:http://en.wikipedia.org/wiki/U6_snRNA http://en.wikipedia.org/wiki/U6_snRNA U6atac_snRNA 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). URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&amp;db=pubmed&amp;list_uids=12409455&amp;dopt=Abstract http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&amp;db=pubmed&amp;list_uids=12409455&amp;dopt=Abstract snRNA U6atac RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U6atac small nuclear RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U6atac snRNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb sequence U11_snRNA 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 http://purl.org/obo/owl/PMID#PMID_9622129 small nuclear RNA U11 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb snRNA U11 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U11 small nuclear RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U11 snRNA sequence URL:http://en.wikipedia.org/wiki/U11_snRNA http://en.wikipedia.org/wiki/U11_snRNA U12_snRNA 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. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007 small nuclear RNA U12 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb snRNA U12 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U12 small nuclear RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U12 snRNA sequence URL:http://en.wikipedia.org/wiki/U12_snRNA http://en.wikipedia.org/wiki/U12_snRNA sequence_attribute An attribute describes a quality of sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence attribute sequence gene_attribute gene attribute sequence enhancer_attribute sequence U14_snoRNA An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA. 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. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016 PMID:2551119 http://purl.org/obo/owl/PMID#PMID_2551119 small nucleolar RNA U14 snoRNA U14 U14 small nucleolar RNA U14 snoRNA sequence SO:0005839 vault_RNA 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. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006 vault RNA sequence URL:http://en.wikipedia.org/wiki/Vault_RNA http://en.wikipedia.org/wiki/Vault_RNA Y_RNA 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. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019 Y RNA sequence URL:http://en.wikipedia.org/wiki/Y_RNA http://en.wikipedia.org/wiki/Y_RNA twintron An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed. PMID:1899376 http://purl.org/obo/owl/PMID#PMID_1899376 PMID:7823908 http://purl.org/obo/owl/PMID#PMID_7823908 sequence URL:http://en.wikipedia.org/wiki/Twintron http://en.wikipedia.org/wiki/Twintron rRNA_18S A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome. SO:ke http://purl.org/obo/owl/SO#SO_ke 18S ribosomal RNA 18S rRNA rRNA 18S sequence URL:http://en.wikipedia.org/wiki/18S_ribosomal_RNA http://en.wikipedia.org/wiki/18S_ribosomal_RNA site The interbase position where something (eg an aberration) occurred. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence binding_site See GO:0005488 : binding. 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 http://purl.org/obo/owl/EBIBS#EBIBS_GAR SO:ke http://purl.org/obo/owl/SO#SO_ke binding_or_interaction_site site sequence BS:00033 URL:http://en.wikipedia.org/wiki/Binding_site http://en.wikipedia.org/wiki/Binding_site protein_binding_site See GO:0042277 : peptide binding. A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules. SO:ke http://purl.org/obo/owl/SO#SO_ke protein binding site sequence rescue_region A region that rescues. SO:xp http://purl.org/obo/owl/SO#SO_xp rescue fragment rescue region rescue segment sequence restriction_fragment A region of polynucleotide sequence produced by digestion with a restriction endonuclease. SO:ke http://purl.org/obo/owl/SO#SO_ke restriction fragment sequence URL:http://en.wikipedia.org/wiki/Restriction_fragment http://en.wikipedia.org/wiki/Restriction_fragment sequence_difference A region where the sequence differs from that of a specified sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence difference sequence invalidated_by_genomic_contamination An attribute to describe a feature that is invalidated due to genomic contamination. SO:ke http://purl.org/obo/owl/SO#SO_ke invalidated by genomic contamination sequence invalidated_by_genomic_polyA_primed_cDNA An attribute to describe a feature that is invalidated due to polyA priming. SO:ke http://purl.org/obo/owl/SO#SO_ke invalidated by genomic polyA primed cDNA sequence invalidated_by_partial_processing An attribute to describe a feature that is invalidated due to partial processing. SO:ke http://purl.org/obo/owl/SO#SO_ke invalidated by partial processing sequence polypeptide_domain Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains. A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR ca_bind uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type DNA_bind uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type domain uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type np_bind uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type polypeptide domain polypeptide_structural_domain structural domain zn_fing uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type sequence BS:00012 BS:00134 SO:0001069 signal_peptide 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. 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. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html signal uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type signal peptide signal peptide coding sequence sequence BS:00159 URL:http://en.wikipedia.org/wiki/Signal_peptide http://en.wikipedia.org/wiki/Signal_peptide mature_protein_region 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. The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html SO:cb http://purl.org/obo/owl/SO#SO_cb chain uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type mature peptide mature protein region sequence BS:00149 five_prime_terminal_inverted_repeat 5' TIR five prime terminal inverted repeat sequence three_prime_terminal_inverted_repeat 3' TIR three prime terminal inverted repeat sequence U5_LTR_region U5 long terminal repeat region U5 LTR region sequence R_LTR_region R long terminal repeat region R LTR region sequence U3_LTR_region U3 long terminal repeat region U3 LTR region sequence five_prime_LTR 5' long terminal repeat 5' LTR five prime LTR sequence three_prime_LTR 3' long terminal repeat 3' LTR three prime LTR sequence R_five_prime_LTR_region R 5' long term repeat region R five prime LTR region sequence U5_five_prime_LTR_region U5 5' long terminal repeat region U5 five prime LTR region sequence U3_five_prime_LTR_region U3 5' long term repeat region U3 five prime LTR region sequence R_three_prime_LTR_region R 3' long terminal repeat region R three prime LTR region sequence U3_three_prime_LTR_region U3 3' long terminal repeat region U3 three prime LTR region sequence U5_three_prime_LTR_region U5 3' long terminal repeat region U5 three prime LTR region sequence non_LTR_retrotransposon_polymeric_tract A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon. SO:ke http://purl.org/obo/owl/SO#SO_ke non LTR retrotransposon polymeric tract sequence target_site_duplication A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion. URL:http://www.koko.gov.my/CocoaBioTech/Glossaryt.html http://www.koko.gov.my/CocoaBioTech/Glossaryt.html target site duplication sequence RR_tract A polypurine tract within an LTR_retrotransposon. SO:ke http://purl.org/obo/owl/SO#SO_ke LTR retrotransposon poly purine tract RR tract sequence ARS A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host. SO:ma http://purl.org/obo/owl/SO#SO_ma autonomously replicating sequence sequence assortment_derived_duplication sequence gene_not_polyadenylated sequence inverted_ring_chromosome inverted ring chromosome sequence vector_replicon This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A replicon that has been modified to act as a vector for foreign sequence. SO:ma http://purl.org/obo/owl/SO#SO_ma vector vector replicon sequence URL:http://en.wikipedia.org/wiki/Vector_(molecular_biology) http://en.wikipedia.org/wiki/Vector_(molecular_biology) ss_oligo This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A single stranded oligonucleotide. SO:ke http://purl.org/obo/owl/SO#SO_ke single strand oligo single strand oligonucleotide single stranded oligonucleotide ss oligo ss oligonucleotide sequence ds_oligo This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A double stranded oligonucleotide. SO:ke http://purl.org/obo/owl/SO#SO_ke double stranded oligonucleotide ds oligo ds-oligonucleotide sequence polymer_attribute An attribute to describe the kind of biological sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke polymer attribute sequence three_prime_noncoding_exon Non-coding exon in the 3' UTR. SO:ke http://purl.org/obo/owl/SO#SO_ke three prime noncoding exon sequence five_prime_noncoding_exon Non-coding exon in the 5' UTR. SO:ke http://purl.org/obo/owl/SO#SO_ke 5' nc exon 5' non coding exon five prime noncoding exon sequence UTR_intron Intron located in the untranslated region. SO:ke http://purl.org/obo/owl/SO#SO_ke UTR intron sequence five_prime_UTR_intron An intron located in the 5' UTR. SO:ke http://purl.org/obo/owl/SO#SO_ke five prime UTR intron sequence three_prime_UTR_intron An intron located in the 3' UTR. SO:ke http://purl.org/obo/owl/SO#SO_ke three prime UTR intron sequence random_sequence A sequence of nucleotides or amino acids which, by design, has a "random" order of components, given a predetermined input frequency of these components. SO:ma http://purl.org/obo/owl/SO#SO_ma random sequence sequence interband A light region between two darkly staining bands in a polytene chromosome. SO:ma http://purl.org/obo/owl/SO#SO_ma chromosome interband sequence gene_with_polyadenylated_mRNA A gene that encodes a polyadenylated mRNA. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with polyadenylated mRNA sequence transgene_attribute sequence chromosomal_transposition A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual SO:ke http://purl.org/obo/owl/SO#SO_ke chromosomal transposition transposition sequence rasiRNA A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements. URL:http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284 http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284 repeat associated small interfering RNA sequence URL:http://en.wikipedia.org/wiki/RasiRNA http://en.wikipedia.org/wiki/RasiRNA gene_with_mRNA_with_frameshift A gene that encodes an mRNA with a frameshift. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with mRNA with frameshift sequence recombinationally_rearranged_gene A gene that is recombinationally rearranged. SO:ke http://purl.org/obo/owl/SO#SO_ke recombinationally rearranged gene sequence interchromosomal_duplication A chromosome duplication involving an insertion from another chromosome. SO:ke http://purl.org/obo/owl/SO#SO_ke interchromosomal duplication sequence D_gene_segment Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# D gene D-GENE sequence gene_with_trans_spliced_transcript A gene with a transcript that is trans-spliced. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with trans spliced transcript sequence vertebrate_immunoglobulin_T_cell_receptor_segment I am using the term segment instead of gene here to avoid confusion with the region 'gene'. vertebrate immunoglobulin T cell receptor segment vertebrate_immunoglobulin/T-cell receptor gene sequence inversion_derived_bipartite_deficiency A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion. FB:km http://purl.org/obo/owl/FB#FB_km inversion derived bipartite deficiency sequence pseudogenic_region A non-functional descendent of a functional entity. SO:cjm http://purl.org/obo/owl/SO#SO_cjm pseudogenic region sequence encodes_alternately_spliced_transcripts A gene that encodes more than one transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke encodes alternately spliced transcripts sequence decayed_exon A non-functional descendant of an exon. SO:ke http://purl.org/obo/owl/SO#SO_ke decayed exon sequence inversion_derived_deficiency_plus_duplication A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion. FB:km http://purl.org/obo/owl/FB#FB_km inversion derived deficiency plus duplication sequence V_gene_segment Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V gene V-GENE variable_gene sequence post_translationally_regulated_by_protein_stability An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein. SO:ke http://purl.org/obo/owl/SO#SO_ke post translationally regulated by protein stability post-translationally regulated by protein stability sequence golden_path_fragment One of the pieces of sequence that make up a golden path. SO:rd http://purl.org/obo/owl/SO#SO_rd golden path fragment sequence post_translationally_regulated_by_protein_modification An attribute describing a gene sequence where the resulting protein is modified to regulate it. SO:ke http://purl.org/obo/owl/SO#SO_ke post translationally regulated by protein modification post-translationally regulated by protein modification sequence J_gene_segment Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# J gene J-GENE sequence autoregulated The gene product is involved in its own transcriptional regulation. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence tiling_path A set of regions which overlap with minimal polymorphism to form a linear sequence. SO:cjm http://purl.org/obo/owl/SO#SO_cjm tiling path sequence negatively_autoregulated The gene product is involved in its own transcriptional regulation where it decreases transcription. SO:ke http://purl.org/obo/owl/SO#SO_ke negatively autoregulated sequence tiling_path_fragment A piece of sequence that makes up a tiling_path (SO:0000472). SO:ke http://purl.org/obo/owl/SO#SO_ke tiling path fragment sequence positively_autoregulated The gene product is involved in its own transcriptional regulation, where it increases transcription. SO:ke http://purl.org/obo/owl/SO#SO_ke positively autoregulated sequence contig_read A DNA sequencer read which is part of a contig. SO:ke http://purl.org/obo/owl/SO#SO_ke contig read sequence polycistronic_gene A gene that is polycistronic. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence C_gene_segment Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205). URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# C gene C_GENE constant gene sequence trans_spliced_transcript A transcript that is trans-spliced. SO:xp http://purl.org/obo/owl/SO#SO_xp trans spliced transcript trans-spliced transcript sequence tiling_path_clone A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly. SO:ke http://purl.org/obo/owl/SO#SO_ke tiling path clone sequence terminal_inverted_repeat An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon. SO:ke http://purl.org/obo/owl/SO#SO_ke terminal inverted repeat TIR sequence vertebrate_immunoglobulin_T_cell_receptor_gene_cluster vertebrate immunoglobulin T cell receptor gene cluster vertebrate_immunoglobulin/T-cell receptor gene cluster sequence nc_primary_transcript A primary transcript that is never translated into a protein. SO:ke http://purl.org/obo/owl/SO#SO_ke nc primary transcript noncoding primary transcript sequence three_prime_coding_exon_noncoding_region The sequence of the 3' exon that is not coding. SO:ke http://purl.org/obo/owl/SO#SO_ke three prime coding exon noncoding region three_prime_exon_noncoding_region sequence DJ_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# (DJ)-J-CLUSTER DJ J cluster sequence five_prime_coding_exon_noncoding_region The sequence of the 5' exon preceding the start codon. SO:ke http://purl.org/obo/owl/SO#SO_ke five prime coding exon noncoding region five_prime_exon_noncoding_region sequence VDJ_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# (VDJ)-J-C-CLUSTER VDJ J C cluster sequence VDJ_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# (VDJ)-J-CLUSTER VDJ J cluster sequence VJ_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# (VJ)-C-CLUSTER VJ C cluster sequence VJ_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# (VJ)-J-C-CLUSTER VJ J C cluster sequence VJ_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# (VJ)-J-CLUSTER VJ J cluster sequence D_gene_recombination_feature D gene recombination feature sequence three_prime_D_heptamer 7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# 3'D-HEPTAMER three prime D heptamer sequence three_prime_D_nonamer A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# 3'D-NOMAMER three prime D nonamer sequence three_prime_D_spacer A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# 3'D-SPACER three prime D spacer sequence five_prime_D_heptamer 7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# 5'D-HEPTAMER five prime D heptamer sequence five_prime_D_nonamer 9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# 5'D-NONAMER five prime D nonamer sequence five_prime_D_spacer 12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# 5'-SPACER five prime D spacer five prime D-spacer sequence virtual_sequence A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database. SO:ke http://purl.org/obo/owl/SO#SO_ke virtual sequence sequence Hoogsteen_base_pair A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds. PMID:12177293 http://purl.org/obo/owl/PMID#PMID_12177293 Hoogsteen base pair sequence URL:http://en.wikipedia.org/wiki/Hoogsteen_base_pair http://en.wikipedia.org/wiki/Hoogsteen_base_pair reverse_Hoogsteen_base_pair A type of non-canonical base-pairing. SO:ke http://purl.org/obo/owl/SO#SO_ke reverse Hoogsteen base pair sequence transcribed_region 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. 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 http://purl.org/obo/owl/SO#SO_ke sequence alternately_spliced_gene_encodeing_one_transcript sequence D_DJ_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# D DJ C cluster D-(DJ)-C-CLUSTER sequence D_DJ_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# D DJ cluster D-(DJ)-CLUSTER sequence D_DJ_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# D DJ J C cluster D-(DJ)-J-C-CLUSTER sequence pseudogenic_exon This is the analog of the exon of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations. A non functional descendant of an exon, part of a pseudogene. SO:ke http://purl.org/obo/owl/SO#SO_ke pseudogenic exon sequence D_DJ_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# D DJ J cluster D-(DJ)-J-CLUSTER sequence D_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# D J C cluster D-J-C-CLUSTER sequence VD_gene_segment Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205). URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V_D_GENE VD gene sequence J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# J C cluster J-C-CLUSTER sequence inversion_derived_deficiency_plus_aneuploid A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion. FB:km http://purl.org/obo/owl/FB#FB_km inversion derived deficiency plus aneuploid sequence J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# J cluster J-CLUSTER sequence J_nonamer 9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# J nonamer J-NONAMER sequence J_heptamer 7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# J heptamer J-HEPTAMER sequence pseudogenic_transcript This is the analog of the transcript of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations. A non functional descendant of a transcript, part of a pseudogene. SO:ke http://purl.org/obo/owl/SO#SO_ke pseudogenic transcript sequence J_spacer 12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# J spacer J-SPACER sequence V_DJ_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V DJ cluster V-(DJ)-CLUSTER sequence V_DJ_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V DJ J cluster V-(DJ)-J-CLUSTER sequence V_VDJ_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V VDJ C cluster V-(VDJ)-C-CLUSTER sequence V_VDJ_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V VDJ cluster V-(VDJ)-CLUSTER sequence V_VDJ_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V VDJ J cluster V-(VDJ)-J-CLUSTER sequence V_VJ_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V VJ C cluster V-(VJ)-C-CLUSTER sequence V_VJ_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V VJ cluster V-(VJ)-CLUSTER sequence V_VJ_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V VJ J cluster V-(VJ)-J-CLUSTER sequence V_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V cluster V-CLUSTER sequence V_D_DJ_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V D DJ C cluster V-D-(DJ)-C-CLUSTER sequence V_D_DJ_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V D DJ cluster V-D-(DJ)-CLUSTER sequence V_D_DJ_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V D DJ J C cluster V-D-(DJ)-J-C-CLUSTER sequence V_D_DJ_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V D DJ J cluster V-D-(DJ)-J-CLUSTER sequence V_D_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V D J C cluster V-D-J-C-CLUSTER sequence V_D_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V D J cluster V-D-J-CLUSTER sequence V_heptamer 7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V heptamer V-HEPTAMER sequence V_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V J cluster V-J-CLUSTER sequence V_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V J C cluster V-J-C-CLUSTER sequence V_nonamer 9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V nonamer V-NONAMER sequence V_spacer 12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V spacer V-SPACER sequence V_gene_recombination_feature Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V gene recombination feature V-RS sequence DJ_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# (DJ)-C-CLUSTER DJ C cluster sequence DJ_J_C_cluster Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# (DJ)-J-C-CLUSTER DJ J C cluster sequence VDJ_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# (VDJ)-C-CLUSTER VDJ C cluster sequence V_DJ_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V DJ C cluster V-(DJ)-C-CLUSTER sequence alternately_spliced_gene_encoding_greater_than_one_transcript sequence helitron A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons. URL:http://www.pnas.org/cgi/content/full/100/11/6569 http://www.pnas.org/cgi/content/full/100/11/6569 ISCR sequence URL:http://en.wikipedia.org/wiki/Helitron http://en.wikipedia.org/wiki/Helitron recoding_pseudoknot The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding. URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937 recoding pseudoknot sequence designed_sequence designed sequence sequence inversion_derived_bipartite_duplication A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion. FB:km http://purl.org/obo/owl/FB#FB_km inversion derived bipartite duplication sequence gene_with_edited_transcript A gene that encodes a transcript that is edited. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with edited transcript sequence inversion_derived_duplication_plus_aneuploid A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion. FB:km http://purl.org/obo/owl/FB#FB_km inversion derived duplication plus aneuploid sequence aneuploid_chromosome Examples are Nullo-4, Haplo-4 and triplo-4 in Drosophila. A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking. SO:ke http://purl.org/obo/owl/SO#SO_ke aneuploid chromosome sequence polyA_signal_sequence The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html poly(A) signal polyA signal sequence polyadenylation termination signal sequence Shine_Dalgarno_sequence Not found in Eukaryotic sequence. A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex. SO:jh http://purl.org/obo/owl/SO#SO_jh five prime ribosome binding site RBS Shine Dalgarno sequence Shine-Dalgarno sequence sequence URL:http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence polyA_site 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. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html polyA cleavage site polyA junction polyA site polyA_junction polyadenylation site sequence SO:0001430 assortment_derived_deficiency_plus_duplication sequence five_prime_clip 5' most region of a precursor transcript that is clipped off during processing. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html 5' clip five prime clip sequence five_prime_D_recombination_signal_sequence Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# 5'RS five prime D recombination signal sequence five prime D-recombination signal sequence sequence three_prime_clip 3'-most region of a precursor transcript that is clipped off during processing. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html 3'-clip three prime clip sequence C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# C cluster C-CLUSTER sequence D_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# D cluster D-CLUSTER sequence D_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# D J cluster D-J-CLUSTER sequence heptamer_of_recombination_feature_of_vertebrate_immune_system_gene Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# HEPTAMER heptamer of recombination feature of vertebrate immune system gene sequence nonamer_of_recombination_feature_of_vertebrate_immune_system_gene nonamer of recombination feature of vertebrate immune system gene sequence vertebrate_immune_system_gene_recombination_spacer vertebrate immune system gene recombination spacer sequence V_DJ_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V DJ J C cluster V-(DJ)-J-C-CLUSTER sequence V_VDJ_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V VDJ J C cluster V-(VDJ)-J-C-CLUSTER sequence V_VJ_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V VJ J C cluster V-(VJ)-J-C-CLUSTER sequence inversion_derived_aneuploid_chromosome A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion. FB:km http://purl.org/obo/owl/FB#FB_km inversion derived aneuploid chromosome sequence bidirectional_promoter bidirectional promoter sequence retrotransposed GO:0003964 RNA-directed DNA polymerase activity. An attribute of a feature that occurred as the product of a reverse transcriptase mediated event. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence SO:0100042 URL:http://en.wikipedia.org/wiki/Retrotransposed http://en.wikipedia.org/wiki/Retrotransposed three_prime_D_recombination_signal_sequence Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# 3'D-RS three prime D recombination signal sequence three_prime_D-recombination_signal_sequence sequence miRNA_encoding miRNA encoding sequence DJ_gene_segment Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# D-J-GENE DJ gene sequence rRNA_encoding rRNA encoding sequence VDJ_gene_segment Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205). URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V-D-J-GENE VDJ gene sequence scRNA_encoding scRNA encoding sequence VJ_gene_segment Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205). URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V-J-GENE VJ gene sequence centromere A region of chromosome where the spindle fibers attach during mitosis and meiosis. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Centromere http://en.wikipedia.org/wiki/Centromere snoRNA_encoding snoRNA encoding sequence edited_transcript_feature A locatable feature on a transcript that is edited. SO:ma http://purl.org/obo/owl/SO#SO_ma edited transcript feature sequence methylation_guide_snoRNA_primary_transcript A primary transcript encoding a methylation guide small nucleolar RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke methylation guide snoRNA primary transcript sequence cap 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. URL:http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html sequence URL:http://en.wikipedia.org/wiki/5%27_cap http://en.wikipedia.org/wiki/5%27_cap rRNA_cleavage_snoRNA_primary_transcript A primary transcript encoding an rRNA cleavage snoRNA. SO:ke http://purl.org/obo/owl/SO#SO_ke rRNA cleavage snoRNA primary transcript sequence pre_edited_region The region of a transcript that will be edited. URL:http://dna.kdna.ucla.edu/rna/index.aspx http://dna.kdna.ucla.edu/rna/index.aspx pre edited region pre-edited region sequence tmRNA A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023 10Sa RNA ssrA sequence URL:http://en.wikipedia.org/wiki/TmRNA http://en.wikipedia.org/wiki/TmRNA C_D_box_snoRNA_encoding C/D box snoRNA encoding sequence tmRNA_primary_transcript A primary transcript encoding a tmRNA (SO:0000584). SO:ke http://purl.org/obo/owl/SO#SO_ke 10Sa RNA primary transcript ssrA RNA primary transcript tmRNA primary transcript sequence group_I_intron GO:0000372. 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. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028 group I intron sequence URL:http://en.wikipedia.org/wiki/Group_I_intron http://en.wikipedia.org/wiki/Group_I_intron autocatalytically_spliced_intron A self spliced intron. SO:ke http://purl.org/obo/owl/SO#SO_ke autocatalytically spliced intron sequence SRP_RNA_primary_transcript A primary transcript encoding a signal recognition particle RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke SRP RNA primary transcript sequence SRP_RNA 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. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017 7S RNA signal recognition particle RNA SRP RNA sequence pseudoknot A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb sequence URL:http://en.wikipedia.org/wiki/Pseudoknot http://en.wikipedia.org/wiki/Pseudoknot H_pseudoknot A pseudoknot which contains two stems and at least two loops. URL:http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=10334330&amp;dopt=Abstract http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=10334330&amp;dopt=Abstract classical pseudoknot H pseudoknot H-pseudoknot H-type pseudoknot hairpin-type pseudoknot sequence C_D_box_snoRNA 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'. URL:http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html box C/D snoRNA C D box snoRNA C/D box snoRNA sequence H_ACA_box_snoRNA Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains. URL:http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html box H/ACA snoRNA H ACA box snoRNA H/ACA box snoRNA sequence C_D_box_snoRNA_primary_transcript A primary transcript encoding a small nucleolar RNA of the box C/D family. SO:ke http://purl.org/obo/owl/SO#SO_ke C/D box snoRNA primary transcript sequence H_ACA_box_snoRNA_primary_transcript A primary transcript encoding a small nucleolar RNA of the box H/ACA family. SO:ke http://purl.org/obo/owl/SO#SO_ke H ACA box snoRNA primary transcript sequence transcript_edited_by_U_insertion/deletion The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa. URL:http://www.rna.ucla.edu/index.html http://www.rna.ucla.edu/index.html sequence edited_by_C_insertion_and_dinucleotide_insertion transcript_edited_by_C-insertion_and_dinucleotide_insertion sequence edited_by_C_to_U_substitution sequence edited_by_A_to_I_substitution sequence edited_by_G_addition sequence guide_RNA 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. URL:http://www.rna.ucla.edu/index.html http://www.rna.ucla.edu/index.html gRNA guide RNA sequence URL:http://en.wikipedia.org/wiki/Guide_RNA http://en.wikipedia.org/wiki/Guide_RNA group_II_intron GO:0000373. Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny. URL:http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml group II intron sequence URL:http://en.wikipedia.org/wiki/Group_II_intron http://en.wikipedia.org/wiki/Group_II_intron editing_block Edited mRNA sequence mediated by a single guide RNA (SO:0000602). URL:http://dna.kdna.ucla.edu/rna/index.aspx http://dna.kdna.ucla.edu/rna/index.aspx editing block sequence intergenic_region This term is mapped to MGED. Do not obsolete without consulting MGED ontology. 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 http://purl.org/obo/owl/SO#SO_cjm intergenic region sequence URL:http://en.wikipedia.org/wiki/Intergenic_region http://en.wikipedia.org/wiki/Intergenic_region editing_domain Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602). URL:http://dna.kdna.ucla.edu/rna/index.aspx http://dna.kdna.ucla.edu/rna/index.aspx editing domain sequence unedited_region The region of an edited transcript that will not be edited. URL:http://dna.kdna.ucla.edu/rna/index.aspx http://dna.kdna.ucla.edu/rna/index.aspx unedited region sequence H_ACA_box_snoRNA_encoding H ACA box snoRNA encoding sequence oligo_U_tail The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602). URL:http://www.rna.ucla.edu/ http://www.rna.ucla.edu/ oligo U tail sequence polyA_sequence Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs. SO:ke http://purl.org/obo/owl/SO#SO_ke polyA sequence sequence branch_site 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 http://purl.org/obo/owl/SO#SO_ke branch point branch site branch_point sequence polypyrimidine_tract The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing. URL:http://nar.oupjournals.org/cgi/content/full/25/4/888 http://nar.oupjournals.org/cgi/content/full/25/4/888 polypyrimidine tract sequence URL:http://en.wikipedia.org/wiki/Polypyrimidine_tract http://en.wikipedia.org/wiki/Polypyrimidine_tract bacterial_RNApol_promoter A DNA sequence to which bacterial RNA polymerase binds, to begin transcription. SO:ke http://purl.org/obo/owl/SO#SO_ke bacterial RNApol promoter sequence bacterial_terminator A terminator signal for bacterial transcription. SO:ke http://purl.org/obo/owl/SO#SO_ke bacterial terminator sequence terminator_of_type_2_RNApol_III_promoter A terminator signal for RNA polymerase III transcription. SO:ke http://purl.org/obo/owl/SO#SO_ke terminator of type 2 RNApol III promoter sequence transcription_end_site The base where transcription ends. SO:ke http://purl.org/obo/owl/SO#SO_ke transcription end site sequence RNApol_III_promoter_type_1 RNApol III promoter type 1 sequence RNApol_III_promoter_type_2 RNApol III promoter type 2 tRNA promoter sequence A_box Binds TFIIIC. A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG. SO:ke http://purl.org/obo/owl/SO#SO_ke A-box sequence URL:http://en.wikipedia.org/wiki/A-box http://en.wikipedia.org/wiki/A-box B_box Binds TFIIIC. A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC. SO:ke http://purl.org/obo/owl/SO#SO_ke B-box sequence RNApol_III_promoter_type_3 RNApol III promoter type 3 sequence C_box An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn. SO:ke http://purl.org/obo/owl/SO#SO_ke C-box sequence snRNA_encoding snRNA encoding sequence telomere A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end. SO:ma http://purl.org/obo/owl/SO#SO_ma telomeric DNA telomeric sequence sequence URL:http://en.wikipedia.org/wiki/Telomere http://en.wikipedia.org/wiki/Telomere silencer A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Silencer_(DNA) http://en.wikipedia.org/wiki/Silencer_(DNA) chromosomal_regulatory_element chromosomal regulatory element sequence insulator A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression. SO:regcreative http://purl.org/obo/owl/SO#SO_regcreative insulator element sequence URL:http://en.wikipedia.org/wiki/Insulator_(genetics) http://en.wikipedia.org/wiki/Insulator_(genetics) chromosomal_structural_element chromosomal structural element sequence five_prime_open_reading_frame five prime open reading frame sequence upstream_AUG_codon A start codon upstream of the ORF. SO:ke http://purl.org/obo/owl/SO#SO_ke upstream AUG codon sequence polycistronic_primary_transcript A primary transcript encoding for more than one gene product. SO:ke http://purl.org/obo/owl/SO#SO_ke polycistronic primary transcript sequence monocistronic_primary_transcript A primary transcript encoding for one gene product. SO:ke http://purl.org/obo/owl/SO#SO_ke monocistronic primary transcript sequence monocistronic_mRNA An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap. SO:rd http://purl.org/obo/owl/SO#SO_rd monocistronic mRNA monocistronic processed transcript sequence URL:http://en.wikipedia.org/wiki/Monocistronic_mRNA http://en.wikipedia.org/wiki/Monocistronic_mRNA polycistronic_mRNA An mRNA that encodes multiple proteins from at least two non-overlapping regions. SO:rd http://purl.org/obo/owl/SO#SO_rd polycistronic mRNA polycistronic processed transcript sequence URL:http://en.wikipedia.org/wiki/Polycistronic_mRNA http://en.wikipedia.org/wiki/Polycistronic_mRNA mini_exon_donor_RNA A primary transcript that donates the spliced leader to other mRNA. SO:ke http://purl.org/obo/owl/SO#SO_ke mini exon donor RNA mini-exon donor RNA sequence spliced_leader_RNA mini-exon spliced leader RNA sequence engineered_plasmid A plasmid that is engineered. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered plasmid engineered plasmid gene sequence transcribed_spacer_region Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA. URL:http://oregonstate.edu/instruction/bb492/general/glossary.html http://oregonstate.edu/instruction/bb492/general/glossary.html transcribed spacer region sequence internal_transcribed_spacer_region Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs. SO:ke http://purl.org/obo/owl/SO#SO_ke internal transcribed spacer region sequence external_transcribed_spacer_region Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke external transcribed spacer region sequence tetranucleotide_repeat_microsatellite_feature tetranucleotide repeat microsatellite feature sequence SRP_RNA_encoding SRP RNA encoding sequence minisatellite A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp. URL:http://www.informatics.jax.org/silver/glossary.shtml http://www.informatics.jax.org/silver/glossary.shtml sequence URL:http://en.wikipedia.org/wiki/Minisatellite http://en.wikipedia.org/wiki/Minisatellite antisense_RNA 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 http://purl.org/obo/owl/SO#SO_ke antisense RNA sequence URL:http://en.wikipedia.org/wiki/Antisense_RNA http://en.wikipedia.org/wiki/Antisense_RNA antisense_primary_transcript The reverse complement of the primary transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke antisense primary transcript sequence siRNA 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 http://purl.org/obo/owl/PMID#PMID_12592000 small interfering RNA sequence URL:http://en.wikipedia.org/wiki/SiRNA http://en.wikipedia.org/wiki/SiRNA miRNA_primary_transcript A primary transcript encoding a micro RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke micro RNA primary transcript miRNA primary transcript sequence stRNA_primary_transcript A primary transcript encoding a small temporal mRNA (SO:0000649). SO:ke http://purl.org/obo/owl/SO#SO_ke small temporal RNA primary transcript stRNA primary transcript sequence stRNA Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans. PMID:11081512 http://purl.org/obo/owl/PMID#PMID_11081512 small temporal RNA sequence URL:http://en.wikipedia.org/wiki/StRNA http://en.wikipedia.org/wiki/StRNA small_subunit_rRNA Ribosomal RNA transcript that structures the small subunit of the ribosome. SO:ke http://purl.org/obo/owl/SO#SO_ke small subunit rRNA SSU RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb SSU rRNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb sequence large_subunit_rRNA Ribosomal RNA transcript that structures the large subunit of the ribosome. SO:ke http://purl.org/obo/owl/SO#SO_ke large subunit rRNA LSU RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb LSU rRNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb sequence rRNA_5S 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. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001 5S LSU rRNA 5S ribosomal RNA 5S rRNA rRNA 5S sequence URL:http://en.wikipedia.org/wiki/5S_ribosomal_RNA http://en.wikipedia.org/wiki/5S_ribosomal_RNA rRNA_28S A component of the large ribosomal subunit. SO:ke http://purl.org/obo/owl/SO#SO_ke 28S LSU rRNA 28S ribosomal RNA 28S rRNA rRNA 28S sequence URL:http://en.wikipedia.org/wiki/28S_ribosomal_RNA http://en.wikipedia.org/wiki/28S_ribosomal_RNA maxicircle_gene A mitochondrial gene located in a maxicircle. SO:xp http://purl.org/obo/owl/SO#SO_xp maxi-circle gene maxicircle gene sequence ncRNA 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. An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product. SO:ke http://purl.org/obo/owl/SO#SO_ke noncoding RNA sequence URL:http://en.wikipedia.org/wiki/NcRNA http://en.wikipedia.org/wiki/NcRNA stRNA_encoding stRNA encoding sequence repeat_region A region of sequence containing one or more repeat units. SO:ke http://purl.org/obo/owl/SO#SO_ke repeat region sequence dispersed_repeat A repeat that is located at dispersed sites in the genome. SO:ke http://purl.org/obo/owl/SO#SO_ke dispersed repeat interspersed repeat sequence URL:http://en.wikipedia.org/wiki/Interspersed_repeat http://en.wikipedia.org/wiki/Interspersed_repeat tmRNA_encoding tmRNA encoding sequence DNA_invertase_target_sequence sequence intron_attribute sequence spliceosomal_intron GO:0000398. An intron which is spliced by the spliceosome. SO:ke http://purl.org/obo/owl/SO#SO_ke spliceosomal intron sequence tRNA_encoding tRNA encoding sequence introgressed_chromosome_region introgressed chromosome region sequence monocistronic_transcript A transcript that is monocistronic. SO:xp http://purl.org/obo/owl/SO#SO_xp monocistronic transcript sequence mobile_intron An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility. SO:ke http://purl.org/obo/owl/SO#SO_ke mobile intron sequence insertion The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke insertion URL:http://www.ncbi.nlm.nih.gov/dbvar/ http://www.ncbi.nlm.nih.gov/dbvar/ nucleotide insertion nucleotide_insertion sequence SO:1000034 EST_match A match against an EST sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke EST match sequence sequence_rearrangement_feature sequence rearrangement feature sequence chromosome_breakage_sequence A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation. SO:ma http://purl.org/obo/owl/SO#SO_ma chromosome breakage sequence sequence internal_eliminated_sequence A sequence eliminated from the genome of ciliates during nuclear differentiation. SO:ma http://purl.org/obo/owl/SO#SO_ma internal eliminated sequence sequence macronucleus_destined_segment A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome. SO:ma http://purl.org/obo/owl/SO#SO_ma macronucleus destined segment sequence transcript An RNA synthesized on a DNA or RNA template by an RNA polymerase. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence URL:http://en.wikipedia.org/wiki/RNA http://en.wikipedia.org/wiki/RNA non_canonical_splice_site A splice site where the donor and acceptor sites differ from the canonical form. SO:ke http://purl.org/obo/owl/SO#SO_ke non canonical splice site non-canonical splice site sequence canonical_splice_site The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively. SO:ke http://purl.org/obo/owl/SO#SO_ke canonical splice site sequence canonical_three_prime_splice_site The canonical 3' splice site has the sequence "AG". SO:ke http://purl.org/obo/owl/SO#SO_ke canonical 3' splice site canonical three prime splice site sequence canonical_five_prime_splice_site The canonical 5' splice site has the sequence "GT". SO:ke http://purl.org/obo/owl/SO#SO_ke canonical 5' splice site canonical five prime splice site sequence non_canonical_three_prime_splice_site A 3' splice site that does not have the sequence "AG". SO:ke http://purl.org/obo/owl/SO#SO_ke non canonical 3' splice site non canonical three prime splice site non-canonical three prime splice site sequence non_canonical_five_prime_splice_site A 5' splice site which does not have the sequence "GT". SO:ke http://purl.org/obo/owl/SO#SO_ke non canonical 5' splice site non canonical five prime splice site non-canonical five prime splice site sequence non_canonical_start_codon A start codon that is not the usual AUG sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke non ATG start codon non canonical start codon non-canonical start codon sequence aberrant_processed_transcript A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons. SO:ke http://purl.org/obo/owl/SO#SO_ke aberrant processed transcript sequence splicing_feature sequence exonic_splice_enhancer Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron. URL:http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=12403462&amp;dopt=Abstract http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=12403462&amp;dopt=Abstract exonic splice enhancer sequence nuclease_sensitive_site A region of nucleotide sequence targeted by a nuclease enzyme. SO:ma http://purl.org/obo/owl/SO#SO_ma nuclease sensitive site sequence DNAseI_hypersensitive_site DHS DNAseI hypersensitive site sequence translocation_element A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations. SO:ma http://purl.org/obo/owl/SO#SO_ma translocation element sequence deletion_junction The space between two bases in a sequence which marks the position where a deletion has occurred. SO:ke http://purl.org/obo/owl/SO#SO_ke deletion junction sequence golden_path A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence. SO:ls http://purl.org/obo/owl/SO#SO_ls golden path sequence cDNA_match A match against cDNA sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke cDNA match sequence gene_with_polycistronic_transcript A gene that encodes a polycistronic transcript. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with polycistronic transcript sequence cleaved_initiator_methionine The initiator methionine that has been cleaved from a mature polypeptide sequence. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR cleaved initiator methionine init_met uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type initiator methionine sequence BS:00067 gene_with_dicistronic_transcript A gene that encodes a dicistronic transcript. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with dicistronic transcript sequence gene_with_recoded_mRNA A gene that encodes an mRNA that is recoded. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with recoded mRNA sequence SNP 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 http://purl.org/obo/owl/SO#SO_cb single nucleotide polymorphism sequence reagent Requested by Lynn Crosby, jan 2006. A sequence used in experiment. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence oligo A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. SO:ma http://purl.org/obo/owl/SO#SO_ma oligonucleotide sequence URL:http://en.wikipedia.org/wiki/Oligonucleotide http://en.wikipedia.org/wiki/Oligonucleotide gene_with_stop_codon_read_through A gene that encodes a transcript with stop codon readthrough. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with stop codon read through sequence gene_with_stop_codon_redefined_as_pyrrolysine A gene encoding an mRNA that has the stop codon redefined as pyrrolysine. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with stop codon redefined as pyrrolysine sequence junction A junction is a boundary between regions. A boundary has an extent of zero. A sequence_feature with an extent of zero. SO:ke http://purl.org/obo/owl/SO#SO_ke boundary breakpoint sequence remark A comment about the sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence possible_base_call_error A region of sequence where the validity of the base calling is questionable. SO:ke http://purl.org/obo/owl/SO#SO_ke possible base call error sequence possible_assembly_error A region of sequence where there may have been an error in the assembly. SO:ke http://purl.org/obo/owl/SO#SO_ke possible assembly error sequence experimental_result_region A region of sequence implicated in an experimental result. SO:ke http://purl.org/obo/owl/SO#SO_ke experimental result region sequence gene This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance. 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 http://purl.org/obo/owl/SO#SO_immuno_workshop sequence URL:http://en.wikipedia.org/wiki/Gene http://en.wikipedia.org/wiki/Gene tandem_repeat Two or more adjcent copies of a region (of length greater than 1). SO:ke http://purl.org/obo/owl/SO#SO_ke tandem repeat sequence URL:http://en.wikipedia.org/wiki/Tandem_repeat http://en.wikipedia.org/wiki/Tandem_repeat URL:http://www.sci.sdsu.edu/~smaloy/Glossary/T.html http://www.sci.sdsu.edu/~smaloy/Glossary/T.html trans_splice_acceptor_site This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans. The 3' splice site of the acceptor primary transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke 3' trans splice site trans splice acceptor site sequence trans_splice_donor_site SL RNA contains a donor site. The 5' five prime splice site region of the donor RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke 5 prime trans splice site trans splice donor site trans-splice donor site sequence SL1_acceptor_site A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs. SO:nlw http://purl.org/obo/owl/SO#SO_nlw SL1 acceptor site sequence SL2_acceptor_site A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:nlw http://purl.org/obo/owl/SO#SO_nlw SL2 acceptor site sequence gene_with_stop_codon_redefined_as_selenocysteine A gene encoding an mRNA that has the stop codon redefined as selenocysteine. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with stop codon redefined as selenocysteine sequence gene_with_mRNA_recoded_by_translational_bypass A gene with mRNA recoded by translational bypass. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with mRNA recoded by translational bypass sequence gene_with_transcript_with_translational_frameshift A gene encoding a transcript that has a translational frameshift. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with transcript with translational frameshift sequence DNA_motif A motif that is active in the DNA form of the sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke DNA motif sequence URL:http://en.wikipedia.org/wiki/DNA_motif http://en.wikipedia.org/wiki/DNA_motif nucleotide_motif A region of nucleotide sequence corresponding to a known motif. SO:ke http://purl.org/obo/owl/SO#SO_ke nucleotide motif sequence RNA_motif A motif that is active in RNA sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke RNA motif sequence dicistronic_mRNA An mRNA that has the quality dicistronic. SO:ke http://purl.org/obo/owl/SO#SO_ke dicistronic mRNA dicistronic processed transcript sequence reading_frame This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop. 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 http://purl.org/obo/owl/SGD#SGD_rb reading frame sequence URL:http://en.wikipedia.org/wiki/Reading_frame http://en.wikipedia.org/wiki/Reading_frame blocked_reading_frame Term requested by Rama from SGD. A reading_frame that is interrupted by one or more stop codons; usually identified through intergenomic sequence comparisons. SGD:rb http://purl.org/obo/owl/SGD#SGD_rb blocked reading frame sequence ultracontig 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 http://purl.org/obo/owl/FB#FB_WG superscaffold sequence foreign_transposable_element requested by Michael on 19 Nov 2004. A transposable element that is foreign. SO:ke http://purl.org/obo/owl/SO#SO_ke foreign transposable element sequence gene_with_dicistronic_primary_transcript Requested by Michael, 19 nov 2004. A gene that encodes a dicistronic primary transcript. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with dicistronic primary transcript sequence gene_with_dicistronic_mRNA Requested by MA nov 19 2004. A gene that encodes a polycistronic mRNA. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with dicistronic mRNA gene with dicistronic processed transcript sequence iDNA Genomic sequence removed from the genome, as a normal event, by a process of recombination. SO:ma http://purl.org/obo/owl/SO#SO_ma intervening DNA sequence URL:http://en.wikipedia.org/wiki/IDNA http://en.wikipedia.org/wiki/IDNA oriT A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html origin of transfer sequence URL:http://en.wikipedia.org/wiki/Origin_of_transfer http://en.wikipedia.org/wiki/Origin_of_transfer transit_peptide 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. 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). URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html signal transit uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type transit peptide sequence BS:00055 repeat_unit Added to comply with the feature table. A single repeat. The simplest repeated component of a repeat region. A single repeat. SO:ke http://purl.org/obo/owl/SO#SO_ke repeat unit sequence URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html CRM Requested by Stepen Grossmann Dec 2004. A regulatory_region where more than 1 TF_binding_site together are regulatorily active. SO:SG http://purl.org/obo/owl/SO#SO_SG cis regulatory module TF module sequence intein Intein-mediated protein splicing occurs after mRNA has been translated into a protein. A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond. SO:ke http://purl.org/obo/owl/SO#SO_ke protein intron sequence URL:http://en.wikipedia.org/wiki/Intein http://en.wikipedia.org/wiki/Intein intein_containing An attribute of protein-coding genes where the initial protein product contains an intein. SO:ke http://purl.org/obo/owl/SO#SO_ke intein containing sequence gap A gap in the sequence of known length. The unknown bases are filled in with N's. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence fragmentary Term added because of request by MO people. An attribute to describe a feature that is incomplete. SO:ke http://purl.org/obo/owl/SO#SO_ke fragment sequence predicted An attribute describing an unverified region. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Predicted http://en.wikipedia.org/wiki/Predicted feature_attribute An attribute describing a located_sequence_feature. SO:ke http://purl.org/obo/owl/SO#SO_ke feature attribute sequence exemplar_mRNA Added for the MO people. An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group. URL:http://mged.sourceforge.net/ontologies/MGEDontology.php http://mged.sourceforge.net/ontologies/MGEDontology.php exemplar mRNA sequence sequence_location sequence location sequence organelle_sequence organelle sequence sequence mitochondrial_sequence This term is mapped to MGED. Do not obsolete without consulting MGED ontology. mitochondrial sequence sequence nuclear_sequence nuclear sequence sequence nucleomorphic_sequence nucleomorphic sequence sequence plastid_sequence plastid sequence sequence kinetoplast A kinetoplast is an interlocked network of thousands of minicircles and tens of maxi circles, located near the base of the flagellum of some protozoan species. PMID:8395055 http://purl.org/obo/owl/PMID#PMID_8395055 kinetoplast_chromosome sequence SO:0000826 URL:http://en.wikipedia.org/wiki/Kinetoplast http://en.wikipedia.org/wiki/Kinetoplast maxicircle A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method. PMID:8395055 http://purl.org/obo/owl/PMID#PMID_8395055 maxicircle_chromosome sequence SO:0000827 apicoplast_sequence apicoplast sequence sequence chromoplast_sequence chromoplast sequence sequence chloroplast_sequence chloroplast sequence sequence cyanelle_sequence cyanelle sequence sequence leucoplast_sequence leucoplast sequence sequence proplastid_sequence proplastid sequence sequence plasmid_location plasmid location sequence amplification_origin An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence. SO:ma http://purl.org/obo/owl/SO#SO_ma amplification origin sequence proviral_location proviral location sequence gene_group_regulatory_region gene group regulatory region sequence clone_insert The region of sequence that has been inserted and is being propagated by the clone. SO:ke http://purl.org/obo/owl/SO#SO_ke clone insert sequence lambda_vector The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome. ISBN:0-1767-2380-8 http://purl.org/obo/owl/ISBN#ISBN_0-1767-2380-8 lambda vector sequence plasmid_vector plasmid vector sequence URL:http://en.wikipedia.org/wiki/Plasmid_vector#Vectors http://en.wikipedia.org/wiki/Plasmid_vector#Vectors cDNA DNA synthesized by reverse transcriptase using RNA as a template. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence URL:http://en.wikipedia.org/wiki/CDNA http://en.wikipedia.org/wiki/CDNA single_stranded_cDNA single strand cDNA single stranded cDNA single-strand cDNA sequence double_stranded_cDNA double strand cDNA double stranded cDNA double-strand cDNA sequence plasmid_clone sequence YAC_clone sequence phagemid_clone sequence PAC_clone P1_clone sequence fosmid_clone sequence BAC_clone sequence cosmid_clone sequence pyrrolysyl_tRNA A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke pyrrolysyl tRNA pyrrolysyl-transfer ribonucleic acid pyrrolysyl-transfer RNA sequence clone_insert_start sequence episome A plasmid that may integrate with a chromosome. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence tmRNA_coding_piece Added in response to comment from Kelly Williams from Indiana. Nov 2005. The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together. doi:10.1093/nar/gkh795 http://purl.org/obo/owl/doi#doi_10.1093/nar/gkh795 Indiana:kw http://purl.org/obo/owl/Indiana#Indiana_kw issn:1362-4962 http://purl.org/obo/owl/issn#issn_1362-4962 tmRNA coding piece sequence tmRNA_acceptor_piece Added in response to Kelly Williams from Indiana. Date: Nov 2005. The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together. doi:10.1093/nar/gkh795 http://purl.org/obo/owl/doi#doi_10.1093/nar/gkh795 Indiana:kw http://purl.org/obo/owl/Indiana#Indiana_kw tmRNA acceptor piece sequence QTL Added in respose to request by Simon Twigger November 14th 2005. A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. URL:http://rgd.mcw.edu/tu/qtls/ http://rgd.mcw.edu/tu/qtls/ quantitative trait locus sequence genomic_island Genomic islands are transmissible elements characterized by large size (>10kb). A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility. Phigo:at http://purl.org/obo/owl/Phigo#Phigo_at SO:ke http://purl.org/obo/owl/SO#SO_ke genomic island sequence URL:http://en.wikipedia.org/wiki/Genomic_island http://en.wikipedia.org/wiki/Genomic_island pathogenic_island Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker. Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species. SO:ke http://purl.org/obo/owl/SO#SO_ke pathogenic island sequence metabolic_island Genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands. A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria. SO:ke http://purl.org/obo/owl/SO#SO_ke metabolic island sequence adaptive_island The iron-uptake ability of many pathogens are conveyed by adaptive islands. Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker. An adaptive island is a genomic island that provides an adaptive advantage to the host. SO:ke http://purl.org/obo/owl/SO#SO_ke adaptive island sequence symbiosis_island Nitrogen fixation in Rhizobiaceae species is encoded by symbiosis islands. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. John T. Sullivan and Clive W. Ronso PNAS 1998 Apr 28 95 (9) 5145-5149. A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria. SO:ke http://purl.org/obo/owl/SO#SO_ke symbiosis island sequence pseudogenic_rRNA 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. A non functional descendent of an rRNA. SO:ke http://purl.org/obo/owl/SO#SO_ke pseudogenic rRNA sequence pseudogenic_tRNA 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. A non functional descendent of a tRNA. SO:ke http://purl.org/obo/owl/SO#SO_ke pseudogenic tRNA sequence engineered_episome Requested by Lynn Crosby Jan 2006. An episome that is engineered. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered episome sequence transposable_element_attribute Added by KE Jan 2006 to capture the kinds of attributes of TEs sequence transgenic Attribute describing sequence that has been integrated with foreign sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence natural An attribute describing a feature that occurs in nature. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence engineered An attribute to describe a region that was modified in vitro. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence foreign An attribute to describe a region from another species. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence cloned_region Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions. cloned region cloned segment sequence reagent_attribute Added jan 2006 by KE. reagent attribute sequence clone_attribute sequence cloned sequence validated An attribute to describe a feature that has been proven. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence invalidated An attribute describing a feature that is invalidated. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence cloned_genomic sequence cloned_cDNA sequence engineered_DNA sequence engineered_rescue_region A rescue region that is engineered. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered rescue fragment engineered rescue region engineered rescue segment sequence rescue_mini_gene A mini_gene that rescues. SO:xp http://purl.org/obo/owl/SO#SO_xp rescue mini gene rescue mini-gene sequence transgenic_transposable_element Modified as requested by Lynn - FB. May 2007. TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE. FB:mc http://purl.org/obo/owl/FB#FB_mc transgenic transposable element sequence natural_transposable_element TE that exists (or existed) in nature. FB:mc http://purl.org/obo/owl/FB#FB_mc natural transposable element sequence engineered_transposable_element TE that has been modified by manipulations in vitro. FB:mc http://purl.org/obo/owl/FB#FB_mc engineered transposable element sequence engineered_foreign_transposable_element A transposable_element that is engineered and foreign. FB:mc http://purl.org/obo/owl/FB#FB_mc engineered foreign transposable element sequence assortment_derived_duplication A multi-chromosome duplication aberration generated by reassortment of other aberration components. FB:gm http://purl.org/obo/owl/FB#FB_gm assortment derived duplication sequence assortment_derived_deficiency_plus_duplication A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication. FB:gm http://purl.org/obo/owl/FB#FB_gm assortment derived deficiency plus duplication sequence assortment_derived_deficiency A multi-chromosome deficiency aberration generated by reassortment of other aberration components. FB:gm http://purl.org/obo/owl/FB#FB_gm assortment-derived deficiency sequence assortment_derived_aneuploid A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication. FB:gm http://purl.org/obo/owl/FB#FB_gm assortment derived aneuploid sequence engineered_region A region that is engineered. SO:xp http://purl.org/obo/owl/SO#SO_xp construct engineered region engineered sequence sequence engineered_foreign_region A region that is engineered and foreign. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered foreign region sequence fusion sequence engineered_tag A tag that is engineered. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered tag sequence validated_cDNA_clone A cDNA clone that has been validated. SO:xp http://purl.org/obo/owl/SO#SO_xp validated cDNA clone sequence invalidated_cDNA_clone A cDNA clone that is invalid. SO:xp http://purl.org/obo/owl/SO#SO_xp invalidated cDNA clone sequence chimeric_cDNA_clone A cDNA clone invalidated because it is chimeric. SO:xp http://purl.org/obo/owl/SO#SO_xp chimeric cDNA clone sequence genomically_contaminated_cDNA_clone A cDNA clone invalidated by genomic contamination. SO:xp http://purl.org/obo/owl/SO#SO_xp genomically contaminated cDNA clone sequence polyA_primed_cDNA_clone A cDNA clone invalidated by polyA priming. SO:xp http://purl.org/obo/owl/SO#SO_xp polyA primed cDNA clone sequence partially_processed_cDNA_clone A cDNA invalidated clone by partial processing. SO:xp http://purl.org/obo/owl/SO#SO_xp partially processed cDNA clone sequence rescue An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence mini_gene By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA. PMID:15992143 http://purl.org/obo/owl/PMID#PMID_15992143 mini gene sequence rescue_gene A gene that rescues. SO:xp http://purl.org/obo/owl/SO#SO_xp rescue gene sequence wild_type An attribute describing sequence with the genotype found in nature and/or standard laboratory stock. SO:ke http://purl.org/obo/owl/SO#SO_ke wild type sequence URL:http://en.wikipedia.org/wiki/Wild_type http://en.wikipedia.org/wiki/Wild_type wild_type_rescue_gene A gene that rescues. SO:xp http://purl.org/obo/owl/SO#SO_xp wild type rescue gene sequence mitochondrial_chromosome A chromosome originating in a mitochondria. SO:xp http://purl.org/obo/owl/SO#SO_xp mitochondrial chromosome sequence chloroplast_chromosome A chromosome originating in a chloroplast. SO:xp http://purl.org/obo/owl/SO#SO_xp chloroplast chromosome sequence chromoplast_chromosome A chromosome originating in a chromoplast. SO:xp http://purl.org/obo/owl/SO#SO_xp chromoplast chromosome sequence cyanelle_chromosome A chromosome originating in a cyanelle. SO:xp http://purl.org/obo/owl/SO#SO_xp cyanelle chromosome sequence leucoplast_chromosome A chromosome with origin in a leucoplast. SO:xp http://purl.org/obo/owl/SO#SO_xp leucoplast chromosome sequence macronuclear_chromosome A chromosome originating in a macronucleus. SO:xp http://purl.org/obo/owl/SO#SO_xp macronuclear chromosome sequence micronuclear_chromosome A chromosome originating in a micronucleus. SO:xp http://purl.org/obo/owl/SO#SO_xp micronuclear chromosome sequence nuclear_chromosome A chromosome originating in a nucleus. SO:xp http://purl.org/obo/owl/SO#SO_xp nuclear chromosome sequence nucleomorphic_chromosome A chromosome originating in a nucleomorph. SO:xp http://purl.org/obo/owl/SO#SO_xp nucleomorphic chromosome sequence chromosome_part 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. A region of a chromosome. SO:ke http://purl.org/obo/owl/SO#SO_ke chromosome part sequence gene_member_region A manufactured term used to allow the parts of a gene to have an is_a path to the root. A region of a gene. SO:ke http://purl.org/obo/owl/SO#SO_ke gene member region sequence promoter_region This is a manufactured term to allow the parts of promoter to have an is_a path back to the root. A region of sequence which is part of a promoter. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence transcript_region 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. A region of a transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke transcript region sequence mature_transcript_region A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root. A region of a mature transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke mature transcript region sequence primary_transcript_region 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. A part of a primary transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke primary transcript region sequence mRNA_region 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. A region of an mRNA. SO:cb http://purl.org/obo/owl/SO#SO_cb mRNA region sequence UTR_region 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. A region of UTR. SO:ke http://purl.org/obo/owl/SO#SO_ke UTR region sequence rRNA_primary_transcript_region To allow transcribed_spacer_region to have a path to the root. A region of an rRNA primary transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke rRNA primary transcript region sequence polypeptide_region Added to allow the polypeptide regions to have is_a paths back to the root. Biological sequence region that can be assigned to a specific subsequence of a polypeptide. SO:GAR http://purl.org/obo/owl/SO#SO_GAR SO:ke http://purl.org/obo/owl/SO#SO_ke positional positional polypeptide feature region uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type region or site annotation site uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type sequence BS:00124 BS:00331 repeat_component A manufactured to group the parts of repeats, to give them an is_a path back to the root. A region of a repeated sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke repeat component sequence spliceosomal_intron_region A terms added to allow the parts of introns to have is_a paths to the root. A region within an intron. SO:ke http://purl.org/obo/owl/SO#SO_ke spliceosomal intron region sequence gene_component_region gene component region sequence bacterial_RNApol_promoter_region This is a manufactured term to allow the parts of bacterial_RNApol_promoter to have an is_a path back to the root. A region which is part of a bacterial RNA polymerase promoter. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence RNApol_II_promoter_region This is a manufactured term to allow the parts of RNApol_II_promoter to have an is_a path back to the root. A region of sequence which is a promoter for RNA polymerase II. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence RNApol_III_promoter_type_1_region This is a manufactured term to allow the parts of RNApol_III_promoter_type_1 to have an is_a path back to the root. A region of sequence which is a promoter for RNA polymerase III type 1. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence RNApol_III_promoter_type_2_region This is a manufactured term to allow the parts of RNApol_III_promoter_type_2 to have an is_a path back to the root. A region of sequence which is a promoter for RNA polymerase III type 2. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence tmRNA_region This term was added to provide a grouping term for the region parts of tmRNA, thus giving them an is_a path back to the root. A region of a tmRNA. SO:cb http://purl.org/obo/owl/SO#SO_cb tmRNA region sequence LTR_component long term repeat component LTR component sequence three_prime_LTR_component 3' long terminal repeat component three prime LTR component sequence five_prime_LTR_component 5' long term repeat component five prime LTR component sequence CDS_region A region of a CDS. SO:cb http://purl.org/obo/owl/SO#SO_cb CDS region sequence exon_region A region of an exon. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb exon region sequence homologous_region A region that is homologous to another region. SO:ke http://purl.org/obo/owl/SO#SO_ke homolog homologous region homologue sequence URL:http://en.wikipedia.org/wiki/Homology_(biology) http://en.wikipedia.org/wiki/Homology_(biology) paralogous_region A term to be used in conjunction with the paralogous_to relationship. A homologous_region that is paralogous to another region. SO:ke http://purl.org/obo/owl/SO#SO_ke paralog paralogous region paralogue sequence URL:http://en.wikipedia.org/wiki/Paralog#Paralogy http://en.wikipedia.org/wiki/Paralog#Paralogy orthologous_region This term should be used in conjunction with the similarity relationships defined in SO. A homologous_region that is orthologous to another region. SO:ke http://purl.org/obo/owl/SO#SO_ke ortholog orthologous region orthologue sequence URL:http://en.wikipedia.org/wiki/Ortholog#Orthology http://en.wikipedia.org/wiki/Ortholog#Orthology conserved sequence homologous Similarity due to common ancestry. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence orthologous An attribute describing a kind of homology where divergence occured after a speciation event. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence paralogous An attribute describing a kind of homology where divergence occurred after a duplication event. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence syntenic Attribute describing sequence regions occurring in same order on chromosome of different species. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Syntenic http://en.wikipedia.org/wiki/Syntenic capped_primary_transcript A primary transcript that is capped. SO:xp http://purl.org/obo/owl/SO#SO_xp capped primary transcript sequence capped_mRNA An mRNA that is capped. SO:xp http://purl.org/obo/owl/SO#SO_xp capped mRNA sequence mRNA_attribute An attribute describing an mRNA feature. SO:ke http://purl.org/obo/owl/SO#SO_ke mRNA attribute sequence exemplar An attribute describing a sequence is representative of a class of similar sequences. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence frameshift An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Frameshift http://en.wikipedia.org/wiki/Frameshift minus_1_frameshift A frameshift caused by deleting one base. SO:ke http://purl.org/obo/owl/SO#SO_ke minus 1 frameshift sequence minus_2_frameshift A frameshift caused by deleting two bases. SO:ke http://purl.org/obo/owl/SO#SO_ke minus 2 frameshift sequence plus_1_frameshift A frameshift caused by inserting one base. SO:ke http://purl.org/obo/owl/SO#SO_ke plus 1 frameshift sequence plus_2_framshift A frameshift caused by inserting two bases. SO:ke http://purl.org/obo/owl/SO#SO_ke plus 2 framshift sequence trans_spliced An attribute describing transcript sequence that is created by splicing exons from diferent genes. SO:ke http://purl.org/obo/owl/SO#SO_ke trans-spliced sequence polyadenylated_mRNA An mRNA that is polyadenylated. SO:xp http://purl.org/obo/owl/SO#SO_xp polyadenylated mRNA sequence trans_spliced_mRNA An mRNA that is trans-spliced. SO:xp http://purl.org/obo/owl/SO#SO_xp trans-spliced mRNA sequence edited_transcript A transcript that is edited. SO:ke http://purl.org/obo/owl/SO#SO_ke edited transcript sequence edited_transcript_by_A_to_I_substitution A transcript that has been edited by A to I substitution. SO:ke http://purl.org/obo/owl/SO#SO_ke edited transcript by A to I substitution sequence bound_by_protein An attribute describing a sequence that is bound by a protein. SO:ke http://purl.org/obo/owl/SO#SO_ke bound by protein sequence bound_by_nucleic_acid An attribute describing a sequence that is bound by a nucleic acid. SO:ke http://purl.org/obo/owl/SO#SO_ke bound by nucleic acid sequence alternatively_spliced An attribute describing a situation where a gene may encode for more than 1 transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke alternatively spliced sequence monocistronic An attribute describing a sequence that contains the code for one gene product. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence dicistronic An attribute describing a sequence that contains the code for two gene products. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence polycistronic An attribute describing a sequence that contains the code for more than one gene product. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence recoded An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence codon_redefined An attribute describing the alteration of codon meaning. SO:ke http://purl.org/obo/owl/SO#SO_ke codon redefined sequence stop_codon_read_through A stop codon redefined to be a new amino acid. SO:ke http://purl.org/obo/owl/SO#SO_ke stop codon read through stop codon readthrough sequence stop_codon_redefined_as_pyrrolysine A stop codon redefined to be the new amino acid, pyrrolysine. SO:ke http://purl.org/obo/owl/SO#SO_ke stop codon redefined as pyrrolysine sequence stop_codon_redefined_as_selenocysteine A stop codon redefined to be the new amino acid, selenocysteine. SO:ke http://purl.org/obo/owl/SO#SO_ke stop codon redefined as selenocysteine sequence recoded_by_translational_bypass Recoded mRNA where a block of nucleotides is not translated. SO:ke http://purl.org/obo/owl/SO#SO_ke recoded by translational bypass sequence translationally_frameshifted Recoding by frameshifting a particular site. SO:ke http://purl.org/obo/owl/SO#SO_ke translationally frameshifted sequence maternally_imprinted_gene A gene that is maternally_imprinted. SO:xp http://purl.org/obo/owl/SO#SO_xp maternally imprinted gene sequence paternally_imprinted_gene A gene that is paternally imprinted. SO:xp http://purl.org/obo/owl/SO#SO_xp paternally imprinted gene sequence post_translationally_regulated_gene A gene that is post translationally regulated. SO:xp http://purl.org/obo/owl/SO#SO_xp post translationally regulated gene sequence negatively_autoregulated_gene A gene that is negatively autoreguated. SO:xp http://purl.org/obo/owl/SO#SO_xp negatively autoregulated gene sequence positively_autoregulated_gene A gene that is positively autoregulated. SO:xp http://purl.org/obo/owl/SO#SO_xp positively autoregulated gene sequence silenced An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Silenced http://en.wikipedia.org/wiki/Silenced silenced_by_DNA_modification An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription. SO:ke http://purl.org/obo/owl/SO#SO_ke silenced by DNA modification sequence silenced_by_DNA_methylation An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription. SO:ke http://purl.org/obo/owl/SO#SO_ke silenced by DNA methylation sequence translationally_regulated_gene A gene that is translationally regulated. SO:xp http://purl.org/obo/owl/SO#SO_xp translationally regulated gene sequence allelically_excluded_gene A gene that is allelically_excluded. SO:xp http://purl.org/obo/owl/SO#SO_xp allelically excluded gene sequence epigenetically_modified_gene A gene that is epigenetically modified. SO:ke http://purl.org/obo/owl/SO#SO_ke epigenetically modified gene sequence nuclear_mitochondrial An attribute describing a nuclear pseudogene of a mitochndrial gene. SO:ke http://purl.org/obo/owl/SO#SO_ke nuclear mitochondrial sequence processed An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence unequally_crossed_over An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination. SO:ke http://purl.org/obo/owl/SO#SO_ke unequally crossed over sequence transgene A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence URL:http://en.wikipedia.org/wiki/Transgene http://en.wikipedia.org/wiki/Transgene endogenous_retroviral_sequence endogenous retroviral sequence sequence rearranged_at_DNA_level An attribute to describe the sequence of a feature, where the DNA is rearranged. SO:ke http://purl.org/obo/owl/SO#SO_ke rearranged at DNA level sequence status This term is the hypernym of attributes and should not be annotated to. An attribute describing the status of a feature, based on the available evidence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence independently_known Attribute to describe a feature that is independently known - not predicted. SO:ke http://purl.org/obo/owl/SO#SO_ke independently known sequence supported_by_sequence_similarity An attribute to describe a feature that has been predicted using sequence similarity techniques. SO:ke http://purl.org/obo/owl/SO#SO_ke supported by sequence similarity sequence supported_by_domain_match An attribute to describe a feature that has been predicted using sequence similarity of a known domain. SO:ke http://purl.org/obo/owl/SO#SO_ke supported by domain match sequence supported_by_EST_or_cDNA An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data. SO:ke http://purl.org/obo/owl/SO#SO_ke supported by EST or cDNA sequence orphan sequence predicted_by_ab_initio_computation An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity. SO:ke http://purl.org/obo/owl/SO#SO_ke predicted by ab initio computation sequence asx_turn A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2). URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ asx turn sequence BS:00203 cloned_cDNA_insert A clone insert made from cDNA. SO:xp http://purl.org/obo/owl/SO#SO_xp cloned cDNA insert sequence cloned_genomic_insert A clone insert made from genomic DNA. SO:xp http://purl.org/obo/owl/SO#SO_xp cloned genomic insert sequence engineered_insert A clone insert that is engineered. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered insert sequence edit_operation edit operation sequence insert_U The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa. An edit to insert a U. SO:ke http://purl.org/obo/owl/SO#SO_ke insert U sequence delete_U The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa. An edit to delete a uridine. SO:ke http://purl.org/obo/owl/SO#SO_ke delete U sequence substitute_A_to_I An edit to substitute an I for an A. SO:ke http://purl.org/obo/owl/SO#SO_ke substitute A to I sequence insert_C An edit to insert a cytidine. SO:ke http://purl.org/obo/owl/SO#SO_ke insert C sequence insert_dinucleotide An edit to insert a dinucleotide. SO:ke http://purl.org/obo/owl/SO#SO_ke insert dinucleotide sequence substitute_C_to_U An edit to substitute an U for a C. SO:ke http://purl.org/obo/owl/SO#SO_ke substitute C to U sequence insert_G An edit to insert a G. SO:ke http://purl.org/obo/owl/SO#SO_ke insert G sequence insert_GC The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. An edit to insert a GC dinucleotide. SO:ke http://purl.org/obo/owl/SO#SO_ke insert GC sequence insert_GU The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. An edit to insert a GU dinucleotide. SO:ke http://purl.org/obo/owl/SO#SO_ke insert GU sequence insert_CU The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. An edit to insert a CU dinucleotide. SO:ke http://purl.org/obo/owl/SO#SO_ke insert CU sequence insert_AU The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. An edit to insert a AU dinucleotide. SO:ke http://purl.org/obo/owl/SO#SO_ke insert AU sequence insert_AA The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. An edit to insert a AA dinucleotide. SO:ke http://purl.org/obo/owl/SO#SO_ke insert AA sequence edited_mRNA An mRNA that is edited. SO:xp http://purl.org/obo/owl/SO#SO_xp edited mRNA sequence guide_RNA_region A region of guide RNA. SO:ma http://purl.org/obo/owl/SO#SO_ma guide RNA region sequence anchor_region A region of a guide_RNA that base-pairs to a target mRNA. SO:jk http://purl.org/obo/owl/SO#SO_jk anchor region sequence pre_edited_mRNA pre-edited mRNA sequence intermediate An attribute to describe a feature between stages of processing. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence miRNA_target_site A miRNA target site is a binding site where the molecule is a micro RNA. FB:cds http://purl.org/obo/owl/FB#FB_cds miRNA target site sequence edited_CDS A CDS that is edited. SO:xp http://purl.org/obo/owl/SO#SO_xp edited CDS sequence vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment vertebrate immunoglobulin T cell receptor rearranged segment sequence vertebrate_immune_system_feature sequence vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster vertebrate immunoglobulin T cell receptor rearranged gene cluster sequence vertebrate_immune_system_gene_recombination_signal_feature vertebrate immune system gene recombination signal feature sequence recombinationally_rearranged recombinationally rearranged sequence recombinationally_rearranged_vertebrate_immune_system_gene A recombinationally rearranged gene of the vertebrate immune system. SO:xp http://purl.org/obo/owl/SO#SO_xp recombinationally rearranged vertebrate immune system gene sequence attP_site An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome. SO:as http://purl.org/obo/owl/SO#SO_as attP site sequence attB_site An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site. SO:as http://purl.org/obo/owl/SO#SO_as attB site sequence attL_site A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site. SO:as http://purl.org/obo/owl/SO#SO_as attBP' attL site sequence attR_site A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site. SO:as http://purl.org/obo/owl/SO#SO_as attPB' attR site sequence integration_excision_site A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site. SO:as http://purl.org/obo/owl/SO#SO_as attachment site integration excision site sequence resolution_site A region specifically recognised by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles. SO:as http://purl.org/obo/owl/SO#SO_as res site resolution site sequence inversion_site A target region for site-specific inversion of a DNA region and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase. A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites. SO:ma http://purl.org/obo/owl/SO#SO_ma inversion site sequence dif_site A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase. SO:as http://purl.org/obo/owl/SO#SO_as dif site sequence attC_site An attC site is a sequence required for the integration of a DNA of an integron. SO:as http://purl.org/obo/owl/SO#SO_as attC site sequence eukaryotic_terminator eukaryotic terminator sequence oriV An origin of vegetative replication in plasmids and phages. SO:as http://purl.org/obo/owl/SO#SO_as origin of vegetative replication sequence oriC An origin of bacterial chromosome replication. SO:as http://purl.org/obo/owl/SO#SO_as origin of bacterial chromosome replication sequence DNA_chromosome Structural unit composed of a self-replicating, DNA molecule. SO:ma http://purl.org/obo/owl/SO#SO_ma DNA chromosome sequence double_stranded_DNA_chromosome Structural unit composed of a self-replicating, double-stranded DNA molecule. SO:ma http://purl.org/obo/owl/SO#SO_ma double stranded DNA chromosome sequence single_stranded_DNA_chromosome Structural unit composed of a self-replicating, single-stranded DNA molecule. SO:ma http://purl.org/obo/owl/SO#SO_ma single stranded DNA chromosome sequence linear_double_stranded_DNA_chromosome Structural unit composed of a self-replicating, double-stranded, linear DNA molecule. SO:ma http://purl.org/obo/owl/SO#SO_ma linear double stranded DNA chromosome sequence circular_double_stranded_DNA_chromosome Structural unit composed of a self-replicating, double-stranded, circular DNA molecule. SO:ma http://purl.org/obo/owl/SO#SO_ma circular double stranded DNA chromosome sequence linear_single_stranded_DNA_chromosome Structural unit composed of a self-replicating, single-stranded, linear DNA molecule. SO:ma http://purl.org/obo/owl/SO#SO_ma linear single stranded DNA chromosome sequence circular_single_stranded_DNA_chromosome Structural unit composed of a self-replicating, single-stranded, circular DNA molecule. SO:ma http://purl.org/obo/owl/SO#SO_ma circular single stranded DNA chromosome sequence RNA_chromosome Structural unit composed of a self-replicating, RNA molecule. SO:ma http://purl.org/obo/owl/SO#SO_ma RNA chromosome sequence single_stranded_RNA_chromosome Structural unit composed of a self-replicating, single-stranded RNA molecule. SO:ma http://purl.org/obo/owl/SO#SO_ma single stranded RNA chromosome sequence linear_single_stranded_RNA_chromosome Structural unit composed of a self-replicating, single-stranded, linear RNA molecule. SO:ma http://purl.org/obo/owl/SO#SO_ma linear single stranded RNA chromosome sequence linear_double_stranded_RNA_chromosome Structural unit composed of a self-replicating, double-stranded, linear RNA molecule. SO:ma http://purl.org/obo/owl/SO#SO_ma linear double stranded RNA chromosome sequence double_stranded_RNA_chromosome Structural unit composed of a self-replicating, double-stranded RNA molecule. SO:ma http://purl.org/obo/owl/SO#SO_ma double stranded RNA chromosome sequence circular_single_stranded_RNA_chromosome Structural unit composed of a self-replicating, single-stranded, circular DNA molecule. SO:ma http://purl.org/obo/owl/SO#SO_ma circular single stranded RNA chromosome sequence circular_double_stranded_RNA_chromosome Structural unit composed of a self-replicating, double-stranded, circular RNA molecule. SO:ma http://purl.org/obo/owl/SO#SO_ma circular double stranded RNA chromosome sequence sequence_replication_mode This has been obsoleted as it represents a process. replaced_by: GO:0034961. sequence replication mode sequence rolling_circle This has been obsoleted as it represents a process. replaced_by: GO:0070581. rolling circle sequence URL:http://en.wikipedia.org/wiki/Rolling_circle http://en.wikipedia.org/wiki/Rolling_circle theta_replication This has been obsoleted as it represents a process. replaced_by: GO:0070582 theta replication sequence DNA_replication_mode This has been obsoleted as it represents a process. replaced_by: GO:0006260. DNA replication mode sequence RNA_replication_mode This has been obsoleted as it represents a process. replaced_by: GO:0034961. RNA replication mode sequence insertion_sequence A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats. SO:as http://purl.org/obo/owl/SO#SO_as insertion sequence IS sequence URL:http://en.wikipedia.org/wiki/Insertion_sequence http://en.wikipedia.org/wiki/Insertion_sequence minicircle_gene minicircle gene sequence cryptic A feature_attribute describing a feature that is not manifest under normal conditions. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence anchor_binding_site Part of an edited transcript only. anchor binding site sequence template_region A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA. SO:jk http://purl.org/obo/owl/SO#SO_jk information region template region sequence gRNA_encoding A non-protein_coding gene that encodes a guide_RNA. SO:ma http://purl.org/obo/owl/SO#SO_ma gRNA encoding sequence minicircle A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs. PMID:8395055 http://purl.org/obo/owl/PMID#PMID_8395055 minicircle_chromosome sequence SO:0000974 URL:http://en.wikipedia.org/wiki/Minicircle http://en.wikipedia.org/wiki/Minicircle rho_dependent_bacterial_terminator rho dependent bacterial terminator sequence rho_independent_bacterial_terminator rho independent bacterial terminator sequence strand_attribute Attributes added to describe the different kinds of replicon. SO workshop, September 2006. strand attribute sequence single Attributes added to describe the different kinds of replicon. SO workshop, September 2006. sequence double Attributes added to describe the different kinds of replicon. SO workshop, September 2006. sequence topology_attribute Attributes added to describe the different kinds of replicon. SO workshop, September 2006. topology attribute sequence linear Attributes added to describe the different kinds of replicon. SO workshop, September 2006. A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue. SO:cb http://purl.org/obo/owl/SO#SO_cb two-ended sequence circular Attributes added to describe the different kinds of replicon. SO workshop, September 2006. A quality of a nucleotide polymer that has no terminal nucleotide residues. SO:cb http://purl.org/obo/owl/SO#SO_cb zero-ended sequence class_II_RNA Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm. PMID:15333696 http://purl.org/obo/owl/PMID#PMID_15333696 class II RNA sequence class_I_RNA Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577. Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm. PMID:15333696 http://purl.org/obo/owl/PMID#PMID_15333696 class I RNA sequence genomic_DNA This term is mapped to MGED. Do not obsolete without consulting MGED ontology. genomic DNA sequence BAC_cloned_genomic_insert Requested by Andy Schroder - Flybase Harvard, Nov 2006. BAC cloned genomic insert sequence consensus Term added Dec 06 to comply with mapping to MGED terms. It should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA. sequence consensus_region DO not obsolete without considering MGED mapping. consensus region sequence consensus_mRNA DO not obsolete without considering MGED mapping. consensus mRNA sequence predicted_gene This term is mapped to MGED. Do not obsolete without consulting MGED ontology. predicted gene sequence gene_fragment This term is mapped to MGED. Do not obsolete without consulting MGED ontology. gene fragment sequence recursive_splice_site A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons. URL:http://www.genetics.org/cgi/content/full/170/2/661 http://www.genetics.org/cgi/content/full/170/2/661 recursive splice site sequence BAC_end Requested by Keith Boroevich December, 2006. A region of sequence from the end of a BAC clone that may provide a highly specific marker. SO:ke http://purl.org/obo/owl/SO#SO_ke BAC end BAC end sequence BES sequence rRNA_16S A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome. SO:ke http://purl.org/obo/owl/SO#SO_ke 16S ribosomal RNA 16S rRNA 16S SSU RNA rRNA 16S sequence URL:http://en.wikipedia.org/wiki/16S_ribosomal_RNA http://en.wikipedia.org/wiki/16S_ribosomal_RNA rRNA_23S A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome. SO:ke http://purl.org/obo/owl/SO#SO_ke 23S LSU rRNA 23S ribosomal RNA 23S rRNA rRNA 23S sequence rRNA_25S A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb 25S LSU rRNA 25S ribosomal RNA 25S rRNA rRNA 25S sequence solo_LTR Requested by Hadi Quesneville January 2007. A recombination product between the 2 LTR of the same element. SO:ke http://purl.org/obo/owl/SO#SO_ke solo LTR sequence low_complexity low complexity sequence low_complexity_region low complexity region sequence prophage A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated "island". GOC:jl http://purl.org/obo/owl/GOC#GOC_jl sequence URL:http://en.wikipedia.org/wiki/Prophage http://en.wikipedia.org/wiki/Prophage cryptic_prophage This is not cryptic in the same sense as a cryptic gene or cryptic splice site. A remnant of an integrated prophage in the host genome or an "island" in the host genome that includes phage like-genes. GOC:jl http://purl.org/obo/owl/GOC#GOC_jl cryptic prophage sequence URL:http://ecoliwiki.net/colipedia/index.php/Category:Cryptic_Prophage.w http://ecoliwiki.net/colipedia/index.php/Category:Cryptic_Prophage.w tetraloop A base-paired stem with loop of 4 non-hydrogen bonded nucleotides. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Tetraloop http://en.wikipedia.org/wiki/Tetraloop DNA_constraint_sequence A double-stranded DNA used to control macromolecular structure and function. DNA constraint DNA constraint sequence sequence i_motif A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH. PMID:9753739 http://purl.org/obo/owl/PMID#PMID_9753739 i motif short intercalated motif sequence PNA_oligo Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds. SO:ke http://purl.org/obo/owl/SO#SO_ke peptide nucleic acid PNA oligo sequence URL:http://en.wikipedia.org/wiki/Peptide_nucleic_acid http://en.wikipedia.org/wiki/Peptide_nucleic_acid DNAzyme Added by request from Colin Batchelor. A DNA sequence with catalytic activity. SO:cb http://purl.org/obo/owl/SO#SO_cb catalytic DNA deoxyribozyme DNA enzyme sequence MNP A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT. URL:http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431 http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431 multiple nucleotide polymorphism sequence intron_domain Requested by Colin Batchelor, Feb 2007. intron domain sequence wobble_base_pair A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C. PMID:11256617 http://purl.org/obo/owl/PMID#PMID_11256617 wobble base pair wobble pair sequence URL:http://en.wikipedia.org/wiki/Wobble_base_pair http://en.wikipedia.org/wiki/Wobble_base_pair internal_guide_sequence A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity. SO:cb http://purl.org/obo/owl/SO#SO_cb IGS internal guide sequence sequence silent_mutation Added in March 2007 in after meeting with pharmgkb. Although this term is in common usage, it is better to annotate with the most specific term possible, such as synonymous codon, intron variant etc. A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation. SO:ke http://purl.org/obo/owl/SO#SO_ke silent mutation sequence URL:http://en.wikipedia.org/wiki/Silent_mutation http://en.wikipedia.org/wiki/Silent_mutation epitope Requested by Trish Whetzel. A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells. URL:http://en.wikipedia.org/wiki/Epitope http://en.wikipedia.org/wiki/Epitope SO:cb http://purl.org/obo/owl/SO#SO_cb sequence URL:http://en.wikipedia.org/wiki/Epitope http://en.wikipedia.org/wiki/Epitope copy_number_variation A variation that increases or decreases the copy number of a given region. SO:ke http://purl.org/obo/owl/SO#SO_ke CNP CNV copy number polymorphism copy number variation sequence URL:http://en.wikipedia.org/wiki/Copy_number_variation http://en.wikipedia.org/wiki/Copy_number_variation sequence_variant_affecting_copy_number OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation affecting copy number sequence variant affecting copy number sequence chromosome_breakpoint aberration breakpoint aberration_junction chromosome breakpoint sequence SO:0001242 inversion_breakpoint The point within a chromosome where an inversion begins or ends. SO:cb http://purl.org/obo/owl/SO#SO_cb inversion breakpoint sequence allele An allele is one of a set of coexisting sequence variants of a gene. SO:immuno_workshop http://purl.org/obo/owl/SO#SO_immuno_workshop allelomorph sequence URL:http://en.wikipedia.org/wiki/Allele http://en.wikipedia.org/wiki/Allele haplotype A haplotype is one of a set of coexisting sequence variants of a haplotype block. SO:immuno_workshop http://purl.org/obo/owl/SO#SO_immuno_workshop sequence URL:http://en.wikipedia.org/wiki/Haplotype http://en.wikipedia.org/wiki/Haplotype polymorphic_sequence_variant A sequence variant that is segregating in one or more natural populations of a species. SO:immuno_workshop http://purl.org/obo/owl/SO#SO_immuno_workshop polymorphic sequence variant sequence genome A genome is the sum of genetic material within a cell or virion. SO:immuno_workshop http://purl.org/obo/owl/SO#SO_immuno_workshop sequence URL:http://en.wikipedia.org/wiki/Genome http://en.wikipedia.org/wiki/Genome genotype A genotype is a variant genome, complete or incomplete. SO:immuno_workshop http://purl.org/obo/owl/SO#SO_immuno_workshop sequence URL:http://en.wikipedia.org/wiki/Genotype http://en.wikipedia.org/wiki/Genotype diplotype A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known. SO:immuno_workshop http://purl.org/obo/owl/SO#SO_immuno_workshop sequence direction_attribute direction attribute sequence forward Forward is an attribute of the feature, where the feature is in the 5' to 3' direction. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence reverse Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence mitochondrial_DNA This terms is used by MO. mitochondrial DNA sequence URL:http://en.wikipedia.org/wiki/Mitochondrial_DNA http://en.wikipedia.org/wiki/Mitochondrial_DNA chloroplast_DNA This term is used by MO. chloroplast DNA sequence mirtron Ruby et al. Nature 448:83 describe a new class of miRNAs that are derived from de-branched introns. A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage. PMID:17589500 http://purl.org/obo/owl/PMID#PMID_17589500 SO:ma http://purl.org/obo/owl/SO#SO_ma sequence piRNA A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements. SO:ke http://purl.org/obo/owl/SO#SO_ke piwi-associated RNA sequence URL:http://en.wikipedia.org/wiki/PiRNA http://en.wikipedia.org/wiki/PiRNA arginyl_tRNA A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke arginyl tRNA sequence mobile_genetic_element A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome. PMID:14681355 http://purl.org/obo/owl/PMID#PMID_14681355 MGE mobile genetic element sequence URL:http://en.wikipedia.org/wiki/Mobile_genetic_element http://en.wikipedia.org/wiki/Mobile_genetic_element extrachromosomal_mobile_genetic_element An MGE that is not integrated into the host chromosome. SO:ke http://purl.org/obo/owl/SO#SO_ke extrachromosomal mobile genetic element sequence integrated_mobile_genetic_element An MGE that is integrated into the host chromosome. SO:ke http://purl.org/obo/owl/SO#SO_ke integrated mobile genetic element sequence integrated_plasmid A plasmid sequence that is integrated within the host chromosome. SO:ke http://purl.org/obo/owl/SO#SO_ke integrated plasmid sequence viral_sequence The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct. The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell. SO:ke http://purl.org/obo/owl/SO#SO_ke viral sequence virus sequence sequence phage_sequence The nucleotide sequence of a virus that infects bacteria. SO:ke http://purl.org/obo/owl/SO#SO_ke bacteriophage phage phage sequence sequence URL:http://en.wikipedia.org/wiki/Bacteriophage http://en.wikipedia.org/wiki/Bacteriophage attCtn_site An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon. Phigo:at http://purl.org/obo/owl/Phigo#Phigo_at attCtn site sequence nuclear_mt_pseudogene Definition change requested by Val, 3172757. A nuclear pseudogene of either coding or non-coding mitochondria derived sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp nuclear mitochondrial pseudogene nuclear mt pseudogene NUMT sequence URL:http://en.wikipedia.org/wiki/Numt http://en.wikipedia.org/wiki/Numt cointegrated_plasmid A MGE region consisting of two fused plasmids resulting from a replicative transposition event. phigo:at http://purl.org/obo/owl/phigo#phigo_at cointegrated plasmid cointegrated replicon sequence IRLinv_site Component of the inversion site located at the left of a region susceptible to site-specific inversion. Phigo:at http://purl.org/obo/owl/Phigo#Phigo_at IRLinv site sequence IRRinv_site Component of the inversion site located at the right of a region susceptible to site-specific inversion. Phigo:at http://purl.org/obo/owl/Phigo#Phigo_at IRRinv site sequence inversion_site_part A term created to allow the parts of an inversion site have an is_a path back to the root. A region located within an inversion site. SO:ke http://purl.org/obo/owl/SO#SO_ke inversion site part sequence defective_conjugative_transposon An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon. Phigo:ariane http://purl.org/obo/owl/Phigo#Phigo_ariane defective conjugative transposon sequence repeat_fragment Requested by Chris Smith, and others at Flybase to help annotate nested repeats. A portion of a repeat, interrupted by the insertion of another element. SO:ke http://purl.org/obo/owl/SO#SO_ke repeat fragment sequence nested_region sequence nested_repeat sequence nested_transposon sequence transposon_fragment A portion of a transposon, interrupted by the insertion of another element. SO:ke http://purl.org/obo/owl/SO#SO_ke transposon fragment sequence transcriptional_cis_regulatory_region A regulatory_region that modulates the transcription of a gene or genes. SO:regcreative http://purl.org/obo/owl/SO#SO_regcreative transcriptional cis regulatory region sequence splicing_regulatory_region A regulatory_region that modulates splicing. SO:ke http://purl.org/obo/owl/SO#SO_ke splicing regulatory region sequence enhanceosome sequence promoter_targeting_sequence A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter. SO:regcreative http://purl.org/obo/owl/SO#SO_regcreative promoter targeting sequence sequence sequence_alteration Merged with partially characterized change in nucleotide sequence. A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke partially characterised change in DNA sequence partially_characterised_change_in_DNA_sequence sequence alteration uncharacterised_change_in_nucleotide_sequence sequence SO:1000004 SO:1000007 sequence_variant A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence variant sequence propeptide_cleavage_site Discrete. The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR propeptide cleavage site sequence BS:00063 propeptide Range. Part of a peptide chain which is cleaved off during the formation of the mature protein. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR propep uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type sequence BS:00077 URL:http://en.wikipedia.org/wiki/Propeptide http://en.wikipedia.org/wiki/Propeptide immature_peptide_region Range. An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR immature peptide region sequence BS:00129 active_peptide Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length. Active peptides are proteins which are biologically active, released from a precursor molecule. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:curation_manual http://purl.org/obo/owl/UniProt#UniProt_curation_manual active peptide peptide uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type sequence BS:00076 URL:http://en.wikipedia.org/wiki/Peptide http://en.wikipedia.org/wiki/Peptide compositionally_biased_region_of_peptide Range. Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:curation_manual http://purl.org/obo/owl/UniProt#UniProt_curation_manual compbias uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type compositional bias compositionally biased compositionally biased region of peptide compositionally_biased_region sequence BS:00068 polypeptide_motif Range. A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.). EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:curation_manual http://purl.org/obo/owl/UniProt#UniProt_curation_manual motif uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type polypeptide motif sequence BS:00032 polypeptide_repeat Range. A polypeptide_repeat is a single copy of an internal sequence repetition. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR polypeptide repeat repeat uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type sequence BS:00070 polypeptide_structural_region Range. Region of polypeptide with a given structural property. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR SO:cb http://purl.org/obo/owl/SO#SO_cb polypeptide structural region structural_region sequence BS:00337 membrane_structure Range. Arrangement of the polypeptide with respect to the lipid bilayer. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR membrane structure sequence BS:00128 extramembrane_polypeptide_region Range. Polypeptide region that is localized outside of a lipid bilayer. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR SO:cb http://purl.org/obo/owl/SO#SO_cb extramembrane extramembrane polypeptide region extramembrane_region topo_dom uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type sequence BS:00154 cytoplasmic_polypeptide_region Polypeptide region that is localized inside the cytoplasm. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR SO:cb http://purl.org/obo/owl/SO#SO_cb cytoplasm_location cytoplasmic polypeptide region inside sequence BS:00145 non_cytoplasmic_polypeptide_region This could be inside an organelle within the cell. Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR SO:cb http://purl.org/obo/owl/SO#SO_cb non cytoplasmic polypeptide region non_cytoplasm_location outside sequence BS:00144 intramembrane_polypeptide_region Polypeptide region present in the lipid bilayer. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR intramembrane intramembrane polypeptide region sequence BS:00156 membrane_peptide_loop Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR SO:cb http://purl.org/obo/owl/SO#SO_cb membrane peptide loop membrane_loop sequence BS:00155 transmembrane_polypeptide_region Polypeptide region traversing the lipid bilayer. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:curator_manual http://purl.org/obo/owl/UniProt#UniProt_curator_manual transmem uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type transmembrane transmembrane polypeptide region sequence BS:00158 polypeptide_secondary_structure Biosapien term was secondary_structure. A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR 2nary structure polypeptide secondary structure secondary structure secondary structure region secondary_structure sequence BS:00003 URL:http://en.wikipedia.org/wiki/Secondary_structure http://en.wikipedia.org/wiki/Secondary_structure polypeptide_structural_motif Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR polypeptide structural motif structural_motif sequence BS:0000338 URL:http://en.wikipedia.org/wiki/Structural_motif http://en.wikipedia.org/wiki/Structural_motif coiled_coil Range. A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:curation_manual http://purl.org/obo/owl/UniProt#UniProt_curation_manual coiled uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type coiled coil sequence BS:00041 URL:http://en.wikipedia.org/wiki/Coiled_coil http://en.wikipedia.org/wiki/Coiled_coil helix_turn_helix A motif comprising two helices separated by a turn. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR helix turn helix helix-turn-helix HTH sequence BS:00147 polypeptide_sequencing_information Range. Incompatibility in the sequence due to some experimental problem. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR sequencing_information sequence BS:00125 non_adjacent_residues Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:curation_manual http://purl.org/obo/owl/UniProt#UniProt_curation_manual non consecutive non_cons uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type sequence BS:00182 non_terminal_residue Discrete. The residue at an extremity of the sequence is not the terminal residue. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:curation_manual http://purl.org/obo/owl/UniProt#UniProt_curation_manual non terminal non_ter uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type sequence BS:00072 sequence_conflict Discrete. Different sources report differing sequences. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:curation_manual http://purl.org/obo/owl/UniProt#UniProt_curation_manual conflict uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type sequence BS:00069 sequence_uncertainty Describes the positions in a sequence where the authors are unsure about the sequence assignment. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:curation_manual http://purl.org/obo/owl/UniProt#UniProt_curation_manual unsure uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type sequence BS:00181 cross_link Posttranslationally formed amino acid bonds. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:curation_manual http://purl.org/obo/owl/UniProt#UniProt_curation_manual cross link crosslink sequence BS:00178 disulfide_bond 2 discreet & joined. The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:curation_manual http://purl.org/obo/owl/UniProt#UniProt_curation_manual disulfid disulfide disulfide bond disulphide disulphide bond sequence BS:00028 post_translationally_modified_region Discrete. A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:curation_manual http://purl.org/obo/owl/UniProt#UniProt_curation_manual mod_res uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type modified residue post_translational_modification sequence BS:00052 URL:http://en.wikipedia.org/wiki/Post_translational_modification http://en.wikipedia.org/wiki/Post_translational_modification covalent_binding_site Binding involving a covalent bond. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR covalent binding site sequence BS:00246 non_covalent_binding_site Discrete. Binding site for any chemical group (co-enzyme, prosthetic group, etc.). EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR binding uniprot:curation http://purl.org/obo/owl/uniprot#uniprot_curation binding site non covalent binding site sequence BS:00029 polypeptide_metal_contact Residue is part of a binding site for a metal ion. A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR SO:cb http://purl.org/obo/owl/SO#SO_cb UniProt:curation_manual http://purl.org/obo/owl/UniProt#UniProt_curation_manual metal_binding sequence BS:00027 protein_protein_contact A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:Curation_manual http://purl.org/obo/owl/UniProt#UniProt_Curation_manual protein protein contact protein protein contact site protein_protein_interaction sequence BS:00131 URL:http://en.wikipedia.org/wiki/Protein_protein_interaction http://en.wikipedia.org/wiki/Protein_protein_interaction polypeptide_calcium_ion_contact_site Residue involved in contact with calcium. A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR ca bind Ca_contact_site polypeptide calcium ion contact site sequence BS:00186 polypeptide_cobalt_ion_contact_site A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR SO:cb http://purl.org/obo/owl/SO#SO_cb Co_contact_site polypeptide cobalt ion contact site sequence BS:00136 polypeptide_copper_ion_contact_site A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR SO:cb http://purl.org/obo/owl/SO#SO_cb Cu_contact_site polypeptide copper ion contact site sequence BS:00146 polypeptide_iron_ion_contact_site A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR SO:cb http://purl.org/obo/owl/SO#SO_cb Fe_contact_site polypeptide iron ion contact site sequence BS:00137 polypeptide_magnesium_ion_contact_site A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR SO:cb http://purl.org/obo/owl/SO#SO_cb Mg_contact_site polypeptide magnesium ion contact site sequence BS:00187 polypeptide_manganese_ion_contact_site A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR SO:cb http://purl.org/obo/owl/SO#SO_cb Mn_contact_site polypeptide manganese ion contact site sequence BS:00140 polypeptide_molybdenum_ion_contact_site A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR SO:cb http://purl.org/obo/owl/SO#SO_cb Mo_contact_site polypeptide molybdenum ion contact site sequence BS:00141 polypeptide_nickel_ion_contact_site A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR Ni_contact_site polypeptide nickel ion contact site sequence BS:00142 polypeptide_tungsten_ion_contact_site A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR SO:cb http://purl.org/obo/owl/SO#SO_cb polypeptide tungsten ion contact site W_contact_site sequence BS:00143 polypeptide_zinc_ion_contact_site A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR SO:cb http://purl.org/obo/owl/SO#SO_cb polypeptide zinc ion contact site Zn_contact_site sequence BS:00185 catalytic_residue Discrete. Amino acid involved in the activity of an enzyme. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:curation_manual http://purl.org/obo/owl/UniProt#UniProt_curation_manual act_site uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type active site residue catalytic residue sequence BS:00026 polypeptide_ligand_contact Residues which interact with a ligand. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR polypeptide ligand contact protein-ligand interaction sequence BS:00157 asx_motif A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4). EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ asx motif sequence BS:00202 beta_bulge A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ beta bulge sequence BS:00208 URL:http://en.wikipedia.org/wiki/Beta_bulge http://en.wikipedia.org/wiki/Beta_bulge beta_bulge_loop A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR Http://www.ebi.ac.uk/msd-srv/msdmotif/ http://purl.org/obo/owl/Http#Http_//www.ebi.ac.uk/msd-srv/msdmotif/ beta bulge loop sequence BS:00209 beta_bulge_loop_five A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ beta bulge loop five sequence BS:00210 beta_bulge_loop_six A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ beta bulge loop six sequence BS:00211 beta_strand Range. A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:curation_manual http://purl.org/obo/owl/UniProt#UniProt_curation_manual strand uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type sequence BS:00042 URL:http://en.wikipedia.org/wiki/Beta_sheet http://en.wikipedia.org/wiki/Beta_sheet antiparallel_beta_strand Range. A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:curation_manual http://purl.org/obo/owl/UniProt#UniProt_curation_manual antiparallel beta strand sequence BS:0000341 parallel_beta_strand Range. A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:curation_manual http://purl.org/obo/owl/UniProt#UniProt_curation_manual parallel beta strand sequence BS:00151 peptide_helix Range. A helix is a secondary_structure conformation where the peptide backbone forms a coil. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR helix sequence BS:00152 left_handed_peptide_helix A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR helix-l left handed helix sequence BS:00222 right_handed_peptide_helix A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR helix right handed helix sequence BS:0000339 alpha_helix Range. The helix has 3.6 residues per turn which corersponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR a-helix helix uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type sequence BS:00040 URL:http://en.wikipedia.org/wiki/Alpha_helix http://en.wikipedia.org/wiki/Alpha_helix pi_helix Range. The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR pi helix sequence BS:00153 URL:http://en.wikipedia.org/wiki/Pi_helix http://en.wikipedia.org/wiki/Pi_helix three_ten_helix Range. The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR 3(10) helix 3-10 helix 310 helix three ten helix sequence BS:0000340 URL:http://en.wikipedia.org/wiki/310_helix http://en.wikipedia.org/wiki/310_helix polypeptide_nest_motif A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ nest nest_motif polypeptide nest motif sequence BS:00223 polypeptide_nest_left_right_motif A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ nest_left_right nest_lr polypeptide nest left right motif sequence BS:00224 polypeptide_nest_right_left_motif A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ nest_right_left nest_rl polypeptide nest right left motif sequence BS:00225 schellmann_loop A motif of six or seven consecutive residues that contains two H-bonds. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ paperclip paperclip loop schellmann loop sequence BS:00226 schellmann_loop_seven Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5). EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ schellmann loop seven seven-residue schellmann loop sequence BS:00228 schellmann_loop_six Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4). EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ schellmann loop six six-residue schellmann loop sequence BS:00227 serine_threonine_motif A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4). EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ serine/threonine motif st motif st_motif sequence BS:00229 serine_threonine_staple_motif A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ serine threonine staple motif st_staple sequence BS:00230 polypeptide_turn_motif Range. A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type turn sequence BS:00148 asx_turn_left_handed_type_one Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ asx turn left handed type one asx_turn_il sequence BS:00206 asx_turn_left_handed_type_two Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ asx turn left handed type two asx_turn_iil sequence BS:00204 asx_turn_right_handed_type_two Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ asx turn right handed type two asx_turn_iir sequence BS:00205 asx_turn_right_handed_type_one Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ asx turn type right handed type one asx_turn_ir sequence BS:00207 beta_turn A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ beta turn sequence BS:00212 beta_turn_left_handed_type_one Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ beta turn left handed type one beta_turn_il type I' beta turn type I' turn sequence BS:00215 beta_turn_left_handed_type_two Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ beta turn left handed type two beta_turn_iil type II' beta turn type II' turn sequence BS:00213 beta_turn_right_handed_type_one Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ beta turn right handed type one beta_turn_ir type I beta turn type I turn sequence BS:00216 beta_turn_right_handed_type_two Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ beta turn right handed type two beta_turn_iir type II beta turn type II turn sequence BS:00214 gamma_turn Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ gamma turn sequence BS:00219 gamma_turn_classic Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ classic gamma turn gamma turn classic sequence BS:00220 gamma_turn_inverse Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ gamma turn inverse sequence BS:00221 serine_threonine_turn A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2). EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ serine/threonine turn st_turn sequence BS:00231 st_turn_left_handed_type_one The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ st turn left handed type one st_turn_il sequence BS:00234 st_turn_left_handed_type_two The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ st turn left handed type two st_turn_iil sequence BS:00232 st_turn_right_handed_type_one The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ st turn right handed type one st_turn_ir sequence BS:00235 st_turn_right_handed_type_two The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ st turn right handed type two st_turn_iir sequence BS:00233 polypeptide_variation_site For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations. A site of sequence variation (alteration). Alternative sequence due to naturally occuring events such as polymorphisms and altermatve splicing or experimental methods such as site directed mutagenesis. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR SO:ke http://purl.org/obo/owl/SO#SO_ke sequence_variations sequence BS:00336 natural_variant_site Discrete. Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:curation_manual http://purl.org/obo/owl/UniProt#UniProt_curation_manual natural_variant sequence variation variant uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type sequence BS:00071 mutated_variant_site Discrete. Site which has been experimentally altered. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:curation_manual http://purl.org/obo/owl/UniProt#UniProt_curation_manual mutagen uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type mutagenesis mutated_site sequence BS:00036 alternate_sequence_site Discrete. Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR UniProt:curation_manual http://purl.org/obo/owl/UniProt#UniProt_curation_manual alternative_sequence isoform sequence variation var_seq uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type varsplic sequence BS:00073 SO:0001065 beta_turn_type_six A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline. SO:cb http://purl.org/obo/owl/SO#SO_cb beta turn type six cis-proline loop type VI beta turn type VI turn sequence beta_turn_type_six_a A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees. PMID:2371257 http://purl.org/obo/owl/PMID#PMID_2371257 SO:cb http://purl.org/obo/owl/SO#SO_cb beta turn type six a type VIa beta turn type VIa turn sequence beta_turn_type_six_a_one beta turn type six a one type VIa1 beta turn type VIa1 turn sequence beta_turn_type_six_a_two beta turn type six a two type VIa2 beta turn type VIa2 turn sequence beta_turn_type_six_b A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees. PMID:2371257 http://purl.org/obo/owl/PMID#PMID_2371257 SO:cb http://purl.org/obo/owl/SO#SO_cb beta turn type six b type VIb beta turn type VIb turn sequence beta_turn_type_eight A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees. PMID:2371257 http://purl.org/obo/owl/PMID#PMID_2371257 SO:cb http://purl.org/obo/owl/SO#SO_cb beta turn type eight type VIII beta turn type VIII turn sequence DRE_motif This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183. Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10. A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW. PMID:12537576 http://purl.org/obo/owl/PMID#PMID_12537576 DRE motif NDM4 WATCGATW_motif sequence DMv4_motif A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014). PMID:16827941:12537576 http://purl.org/obo/owl/PMID#PMID_16827941:12537576 directional motif v4 DMv4 DMv4 motif motif 1 element promoter motif 1 YGGTCACATR sequence E_box_motif A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015). PMID:12537576:16827941 http://purl.org/obo/owl/PMID#PMID_12537576:16827941 AWCAGCTGWT E box motif generic E box motif NDM5 sequence DMv5_motif A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162). PMID:12537576:16827941 http://purl.org/obo/owl/PMID#PMID_12537576:16827941 directional motif v5 DMv5 DMv5 motif KTYRGTATWTTT promoter motif 6 sequence DMv3_motif A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162). PMID:12537576:16827941 http://purl.org/obo/owl/PMID#PMID_12537576:16827941 directional motif v3 DMv3 DMv3 motif KNNCAKCNCTRNY promoter motif 7 sequence DMv2_motif A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162). PMID:12537576:16827941 http://purl.org/obo/owl/PMID#PMID_12537576:16827941 directional motif v2 DMv2 DMv2 motif MKSYGGCARCGSYSS promoter motif 8 sequence MTE A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159). PMID:12537576:15231738 http://purl.org/obo/owl/PMID#PMID_12537576:15231738 PMID:16858867 http://purl.org/obo/owl/PMID#PMID_16858867 CSARCSSAACGS motif ten element motif_ten_element sequence INR1_motif A promoter motif with consensus sequence TCATTCG. PMID:16827941 http://purl.org/obo/owl/PMID#PMID_16827941 directional motif p3 directional promoter motif 3 DMp3 INR1 motif sequence DPE1_motif A promoter motif with consensus sequence CGGACGT. PMID:16827941 http://purl.org/obo/owl/PMID#PMID_16827941 directional motif 5 directional promoter motif 5 DMp5 DPE1 motif sequence DMv1_motif A promoter motif with consensus sequence CARCCCT. PMID:16827941 http://purl.org/obo/owl/PMID#PMID_16827941 directional promoter motif v1 DMv1 DMv1 motif sequence GAGA_motif A non directional promoter motif with consensus sequence GAGAGCG. PMID:16827941 http://purl.org/obo/owl/PMID#PMID_16827941 GAGA GAGA motif NDM1 sequence NDM2_motif A non directional promoter motif with consensus CGMYGYCR. PMID:16827941 http://purl.org/obo/owl/PMID#PMID_16827941 NDM2 NDM2 motif non directional promoter motif 2 sequence NDM3_motif A non directional promoter motif with consensus sequence GAAAGCT. PMID:16827941 http://purl.org/obo/owl/PMID#PMID_16827941 NDM3 NDM3 motif non directional motif 3 sequence ds_RNA_viral_sequence A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke double stranded RNA virus sequence ds RNA viral sequence sequence polinton A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements. PMID:16537396 http://purl.org/obo/owl/PMID#PMID_16537396 maverick element sequence rRNA_21S A component of the large ribosomal subunit in mitochondrial rRNA. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb 21S LSU rRNA 21S ribosomal RNA 21S rRNA rRNA 21S sequence tRNA_region A region of a tRNA. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb tRNA region sequence anticodon_loop A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3. ISBN:0716719207 http://purl.org/obo/owl/ISBN#ISBN_0716719207 anti-codon loop anticodon loop sequence anticodon A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb anti-codon sequence URL:http://en.wikipedia.org/wiki/Anticodon http://en.wikipedia.org/wiki/Anticodon CCA_tail Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid. ISBN:0716719207 http://purl.org/obo/owl/ISBN#ISBN_0716719207 CCA sequence CCA tail sequence DHU_loop Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues. ISBN:071671920 http://purl.org/obo/owl/ISBN#ISBN_071671920 D loop DHU loop sequence T_loop Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C. ISBN:0716719207 http://purl.org/obo/owl/ISBN#ISBN_0716719207 T loop TpsiC loop sequence pyrrolysine_tRNA_primary_transcript A primary transcript encoding pyrrolysyl tRNA (SO:0000766). RSC:cb http://purl.org/obo/owl/RSC#RSC_cb pyrrolysine tRNA primary transcript sequence U3_snoRNA The definition is most of the old definition for snoRNA (SO:0000275). U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012 small nucleolar RNA U3 snoRNA U3 U3 small nucleolar RNA U3 snoRNA sequence URL:http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3 http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3 AU_rich_element A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable. PMID:7892223 http://purl.org/obo/owl/PMID#PMID_7892223 ARE AU rich element AU-rich element sequence URL:http://en.wikipedia.org/wiki/AU-rich_element http://en.wikipedia.org/wiki/AU-rich_element Bruno_response_element Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B. A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs. PMID:10893231 http://purl.org/obo/owl/PMID#PMID_10893231 BRE Bruno response element sequence iron_responsive_element A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins. PMID:3198610 http://purl.org/obo/owl/PMID#PMID_3198610 PMID:8710843 http://purl.org/obo/owl/PMID#PMID_8710843 IRE iron responsive element sequence URL:http://en.wikipedia.org/wiki/Iron_responsive_element http://en.wikipedia.org/wiki/Iron_responsive_element morpholino_backbone Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead. An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb sequence URL:http://en.wikipedia.org/wiki/Morpholino http://en.wikipedia.org/wiki/Morpholino PNA Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead. An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb peptide nucleic acid sequence enzymatic Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead. An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb sequence ribozymic Do not use this for feature annotation. Use ribozyme (SO:0000374) instead. An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb sequence pseudouridylation_guide_snoRNA Has RNA pseudouridylation guide activity (GO:0030558). A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue. GOC:mah http://purl.org/obo/owl/GOC#GOC_mah PMID:12457565 http://purl.org/obo/owl/PMID#PMID_12457565 pseudouridylation guide snoRNA sequence LNA Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead. An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link. CHEBI:48010 http://purl.org/obo/owl/CHEBI#CHEBI_48010 sequence LNA_oligo An oligo composed of LNA residues. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb LNA oligo locked nucleic acid sequence URL:http://en.wikipedia.org/wiki/Locked_nucleic_acid http://en.wikipedia.org/wiki/Locked_nucleic_acid TNA Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead. An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone. CHEBI:48019 http://purl.org/obo/owl/CHEBI#CHEBI_48019 sequence TNA_oligo An oligo composed of TNA residues. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb threose nucleic acid TNA oligo sequence URL:http://en.wikipedia.org/wiki/Threose_nucleic_acid http://en.wikipedia.org/wiki/Threose_nucleic_acid GNA Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead. An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA. CHEBI:48015 http://purl.org/obo/owl/CHEBI#CHEBI_48015 sequence GNA_oligo An oligo composed of GNA residues. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb glycerol nucleic acid glycol nucleic acid GNA oligo sequence URL:http://en.wikipedia.org/wiki/Glycerol_nucleic_acid http://en.wikipedia.org/wiki/Glycerol_nucleic_acid R_GNA Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead. An attribute describing a GNA sequence in the (R)-GNA enantiomer. CHEBI:48016 http://purl.org/obo/owl/CHEBI#CHEBI_48016 R GNA sequence R_GNA_oligo An oligo composed of (R)-GNA residues. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb (R)-glycerol nucleic acid (R)-glycol nucleic acid R GNA oligo sequence S_GNA Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead. An attribute describing a GNA sequence in the (S)-GNA enantiomer. CHEBI:48017 http://purl.org/obo/owl/CHEBI#CHEBI_48017 S GNA sequence S_GNA_oligo An oligo composed of (S)-GNA residues. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb (S)-glycerol nucleic acid (S)-glycol nucleic acid S GNA oligo sequence ds_DNA_viral_sequence A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA. SO:ke http://purl.org/obo/owl/SO#SO_ke double stranded DNA virus ds DNA viral sequence sequence ss_RNA_viral_sequence A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke single strand RNA virus ss RNA viral sequence sequence negative_sense_ssRNA_viral_sequence A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation. SO:ke http://purl.org/obo/owl/SO#SO_ke negative sense single stranded RNA virus negative sense ssRNA viral sequence sequence positive_sense_ssRNA_viral_sequence A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host. SO:ke http://purl.org/obo/owl/SO#SO_ke positive sense single stranded RNA virus positive sense ssRNA viral sequence sequence ambisense_ssRNA_viral_sequence A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity. SO:ke http://purl.org/obo/owl/SO#SO_ke ambisense single stranded RNA virus ambisense ssRNA viral sequence sequence RNA_polymerase_promoter A region (DNA) to which RNA polymerase binds, to begin transcription. xenbase:jb http://purl.org/obo/owl/xenbase#xenbase_jb RNA polymerase promoter sequence Phage_RNA_Polymerase_Promoter A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription. xenbase:jb http://purl.org/obo/owl/xenbase#xenbase_jb Phage RNA Polymerase Promoter sequence SP6_RNA_Polymerase_Promoter A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription. xenbase:jb http://purl.org/obo/owl/xenbase#xenbase_jb SP6 RNA Polymerase Promoter sequence T3_RNA_Polymerase_Promoter A DNA sequence to which the T3 RNA polymerase binds, to begin transcription. xenbase:jb http://purl.org/obo/owl/xenbase#xenbase_jb T3 RNA Polymerase Promoter sequence T7_RNA_Polymerase_Promoter A region (DNA) to which the T7 RNA polymerase binds, to begin transcription. xenbase:jb http://purl.org/obo/owl/xenbase#xenbase_jb T7 RNA Polymerase Promoter sequence five_prime_EST An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family. URL:http://www.ncbi.nlm.nih.gov/About/primer/est.html http://www.ncbi.nlm.nih.gov/About/primer/est.html 5' EST five prime EST sequence three_prime_EST An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs). URL:http://www.ncbi.nlm.nih.gov/About/primer/est.html http://www.ncbi.nlm.nih.gov/About/primer/est.html 3' EST three prime EST sequence translational_frameshift The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. SO:ke http://purl.org/obo/owl/SO#SO_ke ribosomal frameshift translational frameshift sequence URL:http://en.wikipedia.org/wiki/Translational_frameshift http://en.wikipedia.org/wiki/Translational_frameshift plus_1_translational_frameshift The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. SO:ke http://purl.org/obo/owl/SO#SO_ke plus 1 ribosomal frameshift plus 1 translational frameshift sequence plus_2_translational_frameshift The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. SO:ke http://purl.org/obo/owl/SO#SO_ke plus 2 ribosomal frameshift plus 2 translational frameshift sequence group_III_intron GO:0000374. Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile. PMID:11377794 http://purl.org/obo/owl/PMID#PMID_11377794 group III intron sequence URL:http://en.wikipedia.org/wiki/Group_III_intron http://en.wikipedia.org/wiki/Group_III_intron noncoding_region_of_exon 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. The maximal intersection of exon and UTR. SO:ke http://purl.org/obo/owl/SO#SO_ke noncoding region of exon sequence coding_region_of_exon An exon containing either a start or stop codon will be partially coding and partially non coding. The region of an exon that encodes for protein sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke coding region of exon sequence endonuclease_spliced_intron An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification. SO:ke http://purl.org/obo/owl/SO#SO_ke endonuclease spliced intron sequence protein_coding_gene protein coding gene sequence transgenic_insertion An insertion that derives from another organism, via the use of recombinant DNA technology. SO:bm http://purl.org/obo/owl/SO#SO_bm transgenic insertion sequence retrogene sequence silenced_by_RNA_interference RNA interference is GO:0016246. An attribute describing an epigenetic process where a gene is inactivated by RNA interference. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb silenced by RNA interference sequence silenced_by_histone_modification Histone modification is GO:0016570. An attribute describing an epigenetic process where a gene is inactivated by histone modification. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb silenced by histone modification sequence silenced_by_histone_methylation Histone methylation is GO:0016571. An attribute describing an epigenetic process where a gene is inactivated by histone methylation. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb silenced by histone methylation sequence silenced_by_histone_deacetylation Histone deacetylation is GO:0016573. An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb silenced by histone deacetylation sequence gene_silenced_by_RNA_interference A gene that is silenced by RNA interference. SO:xp http://purl.org/obo/owl/SO#SO_xp gene silenced by RNA interference RNA interference silenced gene RNAi silenced gene sequence gene_silenced_by_histone_modification A gene that is silenced by histone modification. SO:xp http://purl.org/obo/owl/SO#SO_xp gene silenced by histone modification sequence gene_silenced_by_histone_methylation A gene that is silenced by histone methylation. SO:xp http://purl.org/obo/owl/SO#SO_xp gene silenced by histone methylation sequence gene_silenced_by_histone_deacetylation A gene that is silenced by histone deacetylation. SO:xp http://purl.org/obo/owl/SO#SO_xp gene silenced by histone deacetylation sequence dihydrouridine A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb D sequence URL:http://en.wikipedia.org/wiki/Dihydrouridine http://en.wikipedia.org/wiki/Dihydrouridine RNAMOD:051 http://purl.org/obo/owl/RNAMOD#RNAMOD_051 pseudouridine The free molecule is CHEBI:17802. A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb Y sequence URL:http://en.wikipedia.org/wiki/Pseudouridine http://en.wikipedia.org/wiki/Pseudouridine RNAMOD:050 http://purl.org/obo/owl/RNAMOD#RNAMOD_050 inosine The free molecule is CHEBI:17596. A modified RNA base in which hypoxanthine is bound to the ribose ring. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ RSC:cb http://purl.org/obo/owl/RSC#RSC_cb I RNAMOD:017 sequence URL:http://en.wikipedia.org/wiki/Inosine http://en.wikipedia.org/wiki/Inosine seven_methylguanine The free molecule is CHEBI:2274. A modified RNA base in which guanine is methylated at the 7- position. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb 7-methylguanine seven methylguanine sequence ribothymidine The free molecule is CHEBI:30832. A modified RNA base in which thymine is bound to the ribose ring. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb sequence methylinosine A modified RNA base in which methylhypoxanthine is bound to the ribose ring. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb sequence mobile An attribute describing a feature that has either intra-genome or intracellular mobility. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb sequence URL:http://en.wikipedia.org/wiki/Mobile http://en.wikipedia.org/wiki/Mobile replicon A region containing at least one unique origin of replication and a unique termination site. ISBN:0716719207 http://purl.org/obo/owl/ISBN#ISBN_0716719207 sequence URL:http://en.wikipedia.org/wiki/Replicon_(genetics) http://en.wikipedia.org/wiki/Replicon_(genetics) base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Nucleobase http://en.wikipedia.org/wiki/Nucleobase amino_acid Probably in the future this will cross reference to Chebi. A sequence feature that corresponds to a single amino acid residue in a polypeptide. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb amino acid sequence URL:http://en.wikipedia.org/wiki/Amino_acid http://en.wikipedia.org/wiki/Amino_acid major_TSS major transcription start site major TSS sequence minor_TSS minor TSS sequence TSS_region The region of a gene from the 5' most TSS to the 3' TSS. BBOP:nw http://purl.org/obo/owl/BBOP#BBOP_nw TSS region sequence encodes_alternate_transcription_start_sites encodes alternate transcription start sites sequence miRNA_primary_transcript_region A part of an miRNA primary_transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke miRNA primary transcript region sequence pre_miRNA The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin sructure. SO:ke http://purl.org/obo/owl/SO#SO_ke pre-miRNA sequence miRNA_stem The stem of the hairpin loop formed by folding of the pre-miRNA. SO:ke http://purl.org/obo/owl/SO#SO_ke miRNA stem sequence miRNA_loop The loop of the hairpin loop formed by folding of the pre-miRNA. SO:ke http://purl.org/obo/owl/SO#SO_ke miRNA loop sequence synthetic_oligo An oligo composed of synthetic nucleotides. SO:ke http://purl.org/obo/owl/SO#SO_ke synthetic oligo sequence assembly A region of the genome of known length that is composed by ordering and aligning two or more different regions. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly fragment_assembly A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths. SO:ke http://purl.org/obo/owl/SO#SO_ke fragment assembly physical map sequence fingerprint_map A fingerprint_map is a physical map composed of restriction fragments. SO:ke http://purl.org/obo/owl/SO#SO_ke BACmap fingerprint map FPC FPCmap restriction map sequence STS_map An STS map is a physical map organized by the unique STS landmarks. SO:ke http://purl.org/obo/owl/SO#SO_ke STS map sequence RH_map A radiation hybrid map is a physical map. SO:ke http://purl.org/obo/owl/SO#SO_ke radiation hybrid map RH map sequence sonicate_fragment A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments. SO:ke http://purl.org/obo/owl/SO#SO_ke sonicate fragment sequence polyploid A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Polyploid http://en.wikipedia.org/wiki/Polyploid autopolyploid A polyploid where the multiple chromosome set was derived from the same organism. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Autopolyploid http://en.wikipedia.org/wiki/Autopolyploid allopolyploid A polyploid where the multiple chromosome set was derived from a different organism. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Allopolyploid http://en.wikipedia.org/wiki/Allopolyploid homing_endonuclease_binding_site The binding site (recognition site) of a homing endonuclease. The binding site is typically large. SO:ke http://purl.org/obo/owl/SO#SO_ke homing endonuclease binding site sequence octamer_motif Nature. 1986 Oct 16-22;323(6089):640-3. A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors. GOC:dh http://purl.org/obo/owl/GOC#GOC_dh PMID:3095662 http://purl.org/obo/owl/PMID#PMID_3095662 octamer motif sequence apicoplast_chromosome A chromosome originating in an apicoplast. SO:xp http://purl.org/obo/owl/SO#SO_xp apicoplast chromosome sequence sequence_collection A collection of discontinuous sequences. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence collection sequence overlapping_feature_set This feature was requested by Nicole, tracker id 1911479. It is required to gather evidence together for annotation. An example would be overlapping ESTs that support an mRNA. A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature. SO:ke http://purl.org/obo/owl/SO#SO_ke overlapping feature set sequence overlapping_EST_set A continous experimental result region extending the length of multiple overlapping EST's. SO:ke http://purl.org/obo/owl/SO#SO_ke overlapping EST set sequence ncRNA_gene ncRNA gen ncRNA gene non-coding RNA gene sequence gRNA_gene gRNA gene sequence miRNA_gene miRNA gene sequence scRNA_gene scRNA gene sequence snoRNA_gene snoRNA gene sequence snRNA_gene snRNA gene sequence SRP_RNA_gene SRP RNA gene sequence stRNA_gene stRNA gene sequence tmRNA_gene tmRNA gene sequence tRNA_gene tRNA gene sequence modified_adenosine A modified adenine is an adenine base feature that has been altered. SO:ke http://purl.org/obo/owl/SO#SO_ke modified adenosine sequence modified_inosine A modified inosine is an inosine base feature that has been altered. SO:ke http://purl.org/obo/owl/SO#SO_ke modified inosine sequence modified_cytidine A modified cytidine is a cytidine base feature which has been altered. SO:ke http://purl.org/obo/owl/SO#SO_ke modified cytidine sequence modified_guanosine modified guanosine sequence modified_uridine modified uridine sequence one_methylinosine 1-methylinosine is a modified insosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 1-methylinosine m1I one methylinosine sequence RNAMOD:018 http://purl.org/obo/owl/RNAMOD#RNAMOD_018 one_two_prime_O_dimethylinosine 1,2'-O-dimethylinosine is a modified inosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 1,2'-O-dimethylinosine m'Im one two prime O dimethylinosine sequence RNAMOD:019 http://purl.org/obo/owl/RNAMOD#RNAMOD_019 two_prime_O_methylinosine 2'-O-methylinosine is a modified inosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 2'-O-methylinosine Im two prime O methylinosine sequence RNAMOD:081 http://purl.org/obo/owl/RNAMOD#RNAMOD_081 three_methylcytidine 3-methylcytidine is a modified cytidine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 3-methylcytidine m3C three methylcytidine sequence RNAMOD:020 http://purl.org/obo/owl/RNAMOD#RNAMOD_020 five_methylcytidine 5-methylcytidine is a modified cytidine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-methylcytidine five methylcytidine m5C sequence RNAMOD:021 http://purl.org/obo/owl/RNAMOD#RNAMOD_021 two_prime_O_methylcytidine 2'-O-methylcytidine is a modified cytidine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 2'-O-methylcytidine Cm two prime O methylcytidine sequence RNAMOD:022 http://purl.org/obo/owl/RNAMOD#RNAMOD_022 two_thiocytidine 2-thiocytidine is a modified cytidine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 2-thiocytidine s2C two thiocytidine sequence RNAMOD:023 http://purl.org/obo/owl/RNAMOD#RNAMOD_023 N4_acetylcytidine N4-acetylcytidine is a modified cytidine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ ac4C N4 acetylcytidine N4-acetylcytidine sequence RNAMOD:024 http://purl.org/obo/owl/RNAMOD#RNAMOD_024 five_formylcytidine 5-formylcytidine is a modified cytidine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-formylcytidine f5C five formylcytidine sequence RNAMOD:025 http://purl.org/obo/owl/RNAMOD#RNAMOD_025 five_two_prime_O_dimethylcytidine 5,2'-O-dimethylcytidine is a modified cytidine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5,2'-O-dimethylcytidine five two prime O dimethylcytidine m5Cm sequence RNAMOD:026 http://purl.org/obo/owl/RNAMOD#RNAMOD_026 N4_acetyl_2_prime_O_methylcytidine N4-acetyl-2'-O-methylcytidine is a modified cytidine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ ac4Cm N4 acetyl 2 prime O methylcytidine N4-acetyl-2'-O-methylcytidine sequence RNAMOD:027 http://purl.org/obo/owl/RNAMOD#RNAMOD_027 lysidine Lysidine is a modified cytidine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ k2C sequence URL:http://en.wikipedia.org/wiki/Lysidine http://en.wikipedia.org/wiki/Lysidine RNAMOD:028 http://purl.org/obo/owl/RNAMOD#RNAMOD_028 N4_methylcytidine N4-methylcytidine is a modified cytidine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ m4C N4 methylcytidine N4-methylcytidine sequence RNAMOD:082 http://purl.org/obo/owl/RNAMOD#RNAMOD_082 N4_2_prime_O_dimethylcytidine N4,2'-O-dimethylcytidine is a modified cytidine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ m4Cm N4 2 prime O dimethylcytidine N4,2'-O-dimethylcytidine sequence RNAMOD:083 http://purl.org/obo/owl/RNAMOD#RNAMOD_083 five_hydroxymethylcytidine 5-hydroxymethylcytidine is a modified cytidine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-hydroxymethylcytidine five hydroxymethylcytidine hm5C sequence RNAMOD:084 http://purl.org/obo/owl/RNAMOD#RNAMOD_084 five_formyl_two_prime_O_methylcytidine 5-formyl-2'-O-methylcytidine is a modified cytidine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-formyl-2'-O-methylcytidine f5Cm five formyl two prime O methylcytidine sequence RNAMOD:095 http://purl.org/obo/owl/RNAMOD#RNAMOD_095 N4_N4_2_prime_O_trimethylcytidine N4_N4_2_prime_O_trimethylcytidine is a modified cytidine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ m42Cm N4,N4,2'-O-trimethylcytidine sequence RNAMOD:107 http://purl.org/obo/owl/RNAMOD#RNAMOD_107 one_methyladenosine 1_methyladenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 1-methyladenosine m1A one methyladenosine sequence RNAMOD:001 http://purl.org/obo/owl/RNAMOD#RNAMOD_001 two_methyladenosine 2_methyladenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 2-methyladenosine m2A two methyladenosine sequence RNAMOD:002 http://purl.org/obo/owl/RNAMOD#RNAMOD_002 N6_methyladenosine N6_methyladenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ m6A N6 methyladenosine N6-methyladenosine sequence RNAMOD:003 http://purl.org/obo/owl/RNAMOD#RNAMOD_003 two_prime_O_methyladenosine 2prime_O_methyladenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 2'-O-methyladenosine Am two prime O methyladenosine sequence RNAMOD:004 http://purl.org/obo/owl/RNAMOD#RNAMOD_004 two_methylthio_N6_methyladenosine 2_methylthio_N6_methyladenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 2-methylthio-N6-methyladenosine ms2m6A two methylthio N6 methyladenosine sequence RNAMOD:005 http://purl.org/obo/owl/RNAMOD#RNAMOD_005 N6_isopentenyladenosine N6_isopentenyladenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ i6A N6 isopentenyladenosine N6-isopentenyladenosine sequence RNAMOD:006 http://purl.org/obo/owl/RNAMOD#RNAMOD_006 two_methylthio_N6_isopentenyladenosine 2_methylthio_N6_isopentenyladenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 2-methylthio-N6-isopentenyladenosine ms2i6A two methylthio N6 isopentenyladenosine sequence RNAMOD:007 http://purl.org/obo/owl/RNAMOD#RNAMOD_007 N6_cis_hydroxyisopentenyl_adenosine N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ io6A N6 cis hydroxyisopentenyl adenosine N6-(cis-hydroxyisopentenyl)adenosine sequence RNAMOD:008 http://purl.org/obo/owl/RNAMOD#RNAMOD_008 two_methylthio_N6_cis_hydroxyisopentenyl_adenosine 2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine ms2io6A two methylthio N6 cis hydroxyisopentenyl adenosine sequence RNAMOD:009 http://purl.org/obo/owl/RNAMOD#RNAMOD_009 N6_glycinylcarbamoyladenosine N6_glycinylcarbamoyladenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ g6A N6 glycinylcarbamoyladenosine N6-glycinylcarbamoyladenosine sequence RNAMOD:010 http://purl.org/obo/owl/RNAMOD#RNAMOD_010 N6_threonylcarbamoyladenosine N6_threonylcarbamoyladenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ N6 threonylcarbamoyladenosine N6-threonylcarbamoyladenosine t6A sequence RNAMOD:011 http://purl.org/obo/owl/RNAMOD#RNAMOD_011 two_methylthio_N6_threonyl_carbamoyladenosine 2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 2-methylthio-N6-threonyl carbamoyladenosine ms2t6A two methylthio N6 threonyl carbamoyladenosine sequence RNAMOD:012 http://purl.org/obo/owl/RNAMOD#RNAMOD_012 N6_methyl_N6_threonylcarbamoyladenosine N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ m6t6A N6 methyl N6 threonylcarbamoyladenosine N6-methyl-N6-threonylcarbamoyladenosine sequence RNAMOD:013 http://purl.org/obo/owl/RNAMOD#RNAMOD_013 N6_hydroxynorvalylcarbamoyladenosine N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ hn6A N6 hydroxynorvalylcarbamoyladenosine N6-hydroxynorvalylcarbamoyladenosine sequence RNAMOD:014 http://purl.org/obo/owl/RNAMOD#RNAMOD_014 two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine 2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 2-methylthio-N6-hydroxynorvalyl carbamoyladenosine ms2hn6A two methylthio N6 hydroxynorvalyl carbamoyladenosine sequence RNAMOD:015 http://purl.org/obo/owl/RNAMOD#RNAMOD_015 two_prime_O_ribosyladenosine_phosphate 2prime_O_ribosyladenosine_phosphate is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 2'-O-ribosyladenosine (phosphate) Ar(p) two prime O ribosyladenosine phosphate sequence RNAMOD:016 http://purl.org/obo/owl/RNAMOD#RNAMOD_016 N6_N6_dimethyladenosine N6_N6_dimethyladenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ m62A N6,N6-dimethyladenosine sequence RNAMOD:080 http://purl.org/obo/owl/RNAMOD#RNAMOD_080 N6_2_prime_O_dimethyladenosine N6_2prime_O_dimethyladenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ m6Am N6 2 prime O dimethyladenosine N6,2'-O-dimethyladenosine sequence RNAMOD:088 http://purl.org/obo/owl/RNAMOD#RNAMOD_088 N6_N6_2_prime_O_trimethyladenosine N6_N6_2prime_O_trimethyladenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ m62Am N6,N6,2'-O-trimethyladenosine sequence RNAMOD:089 http://purl.org/obo/owl/RNAMOD#RNAMOD_089 one_two_prime_O_dimethyladenosine 1,2'-O-dimethyladenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 1,2'-O-dimethyladenosine m1Am one two prime O dimethyladenosine sequence RNAMOD:097 http://purl.org/obo/owl/RNAMOD#RNAMOD_097 N6_acetyladenosine N6_acetyladenosine is a modified adenosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ ac6A N6 acetyladenosine N6-acetyladenosine sequence RNAMOD:102 http://purl.org/obo/owl/RNAMOD#RNAMOD_102 seven_deazaguanosine 7-deazaguanosine is a moddified guanosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 7-deazaguanosine seven deazaguanosine sequence queuosine Queuosine is a modified 7-deazoguanosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ Q sequence URL:http://en.wikipedia.org/wiki/Queuosine http://en.wikipedia.org/wiki/Queuosine RNAMOD:043 http://purl.org/obo/owl/RNAMOD#RNAMOD_043 epoxyqueuosine Epoxyqueuosine is a modified 7-deazoguanosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ eQ sequence RNAMOD:044 http://purl.org/obo/owl/RNAMOD#RNAMOD_044 galactosyl_queuosine Galactosyl_queuosine is a modified 7-deazoguanosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ galactosyl queuosine galactosyl-queuosine galQ sequence RNAMOD:045 http://purl.org/obo/owl/RNAMOD#RNAMOD_045 mannosyl_queuosine Mannosyl_queuosine is a modified 7-deazoguanosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ mannosyl queuosine mannosyl-queuosine manQ sequence RNAMOD:046 http://purl.org/obo/owl/RNAMOD#RNAMOD_046 seven_cyano_seven_deazaguanosine 7_cyano_7_deazaguanosine is a modified 7-deazoguanosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 7-cyano-7-deazaguanosine preQ0 seven cyano seven deazaguanosine sequence RNAMOD:047 http://purl.org/obo/owl/RNAMOD#RNAMOD_047 seven_aminomethyl_seven_deazaguanosine 7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 7-aminomethyl-7-deazaguanosine preQ1 seven aminomethyl seven deazaguanosine sequence RNAMOD:048 http://purl.org/obo/owl/RNAMOD#RNAMOD_048 archaeosine Archaeosine is a modified 7-deazoguanosine. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ G+ sequence RNAMOD:049 http://purl.org/obo/owl/RNAMOD#RNAMOD_049 one_methylguanosine 1_methylguanosine is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 1-methylguanosine m1G one methylguanosine sequence RNAMOD:029 http://purl.org/obo/owl/RNAMOD#RNAMOD_029 N2_methylguanosine N2_methylguanosine is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ m2G N2 methylguanosine N2-methylguanosine sequence RNAMOD:030 http://purl.org/obo/owl/RNAMOD#RNAMOD_030 seven_methylguanosine 7_methylguanosine is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 7-methylguanosine m7G seven methylguanosine sequence RNAMOD:031 http://purl.org/obo/owl/RNAMOD#RNAMOD_031 two_prime_O_methylguanosine 2prime_O_methylguanosine is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 2'-O-methylguanosine Gm two prime O methylguanosine sequence RNAMOD:032 http://purl.org/obo/owl/RNAMOD#RNAMOD_032 N2_N2_dimethylguanosine N2_N2_dimethylguanosine is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ m22G N2,N2-dimethylguanosine sequence RNAMOD:033 http://purl.org/obo/owl/RNAMOD#RNAMOD_033 N2_2_prime_O_dimethylguanosine N2_2prime_O_dimethylguanosine is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ m2Gm N2 2 prime O dimethylguanosine N2,2'-O-dimethylguanosine sequence RNAMOD:034 http://purl.org/obo/owl/RNAMOD#RNAMOD_034 N2_N2_2_prime_O_trimethylguanosine N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ m22Gmv N2,N2,2'-O-trimethylguanosine sequence RNAMOD:035 http://purl.org/obo/owl/RNAMOD#RNAMOD_035 two_prime_O_ribosylguanosine_phosphate 2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 2'-O-ribosylguanosine (phosphate) Gr(p) two prime O ribosylguanosine phosphate sequence RNAMOD:036 http://purl.org/obo/owl/RNAMOD#RNAMOD_036 wybutosine Wybutosine is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ yW sequence RNAMOD:037 http://purl.org/obo/owl/RNAMOD#RNAMOD_037 peroxywybutosine Peroxywybutosine is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ o2yW sequence RNAMOD:038 http://purl.org/obo/owl/RNAMOD#RNAMOD_038 hydroxywybutosine Hydroxywybutosine is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ OHyW sequence RNAMOD:039 http://purl.org/obo/owl/RNAMOD#RNAMOD_039 undermodified_hydroxywybutosine Undermodified_hydroxywybutosine is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ OHyW* undermodified hydroxywybutosine sequence RNAMOD:040 http://purl.org/obo/owl/RNAMOD#RNAMOD_040 wyosine Wyosine is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ IMG sequence RNAMOD:041 http://purl.org/obo/owl/RNAMOD#RNAMOD_041 methylwyosine Methylwyosine is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ mimG sequence RNAMOD:042 http://purl.org/obo/owl/RNAMOD#RNAMOD_042 N2_7_dimethylguanosine N2_7_dimethylguanosine is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ m2,7G N2 7 dimethylguanosine N2,7-dimethylguanosine sequence RNAMOD:090 http://purl.org/obo/owl/RNAMOD#RNAMOD_090 N2_N2_7_trimethylguanosine N2_N2_7_trimethylguanosine is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ m2,2,7G N2,N2,7-trimethylguanosine sequence RNAMOD:091 http://purl.org/obo/owl/RNAMOD#RNAMOD_091 one_two_prime_O_dimethylguanosine 1_2prime_O_dimethylguanosine is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 1,2'-O-dimethylguanosine m1Gm one two prime O dimethylguanosine sequence RNAMOD:096 http://purl.org/obo/owl/RNAMOD#RNAMOD_096 four_demethylwyosine 4_demethylwyosine is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 4-demethylwyosine four demethylwyosine imG-14 sequence RNAMOD:100 http://purl.org/obo/owl/RNAMOD#RNAMOD_100 isowyosine Isowyosine is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ imG2 sequence RNAMOD:101 http://purl.org/obo/owl/RNAMOD#RNAMOD_101 N2_7_2prirme_O_trimethylguanosine N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ m2,7Gm N2 7 2prirme O trimethylguanosine N2,7,2'-O-trimethylguanosine sequence RNAMOD:106 http://purl.org/obo/owl/RNAMOD#RNAMOD_106 five_methyluridine 5_methyluridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-methyluridine five methyluridine m5U sequence URL:http://en.wikipedia.org/wiki/5-methyluridine http://en.wikipedia.org/wiki/5-methyluridine RNAMOD:052 http://purl.org/obo/owl/RNAMOD#RNAMOD_052 two_prime_O_methyluridine 2prime_O_methyluridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 2'-O-methyluridine two prime O methyluridine Um sequence RNAMOD:053 http://purl.org/obo/owl/RNAMOD#RNAMOD_053 five_two_prime_O_dimethyluridine 5_2_prime_O_dimethyluridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5,2'-O-dimethyluridine five two prime O dimethyluridine m5Um sequence RNAMOD:054 http://purl.org/obo/owl/RNAMOD#RNAMOD_054 one_methylpseudouridine 1_methylpseudouridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 1-methylpseudouridine m1Y one methylpseudouridine sequence RNAMOD:055 http://purl.org/obo/owl/RNAMOD#RNAMOD_055 two_prime_O_methylpseudouridine 2prime_O_methylpseudouridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 2'-O-methylpseudouridine two prime O methylpseudouridine Ym sequence RNAMOD:056 http://purl.org/obo/owl/RNAMOD#RNAMOD_056 two_thiouridine 2_thiouridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 2-thiouridine s2U two thiouridine sequence RNAMOD:057 http://purl.org/obo/owl/RNAMOD#RNAMOD_057 four_thiouridine 4_thiouridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 4-thiouridine four thiouridine s4U sequence RNAMOD:058 http://purl.org/obo/owl/RNAMOD#RNAMOD_058 five_methyl_2_thiouridine 5_methyl_2_thiouridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-methyl-2-thiouridine five methyl 2 thiouridine m5s2U sequence RNAMOD:059 http://purl.org/obo/owl/RNAMOD#RNAMOD_059 two_thio_two_prime_O_methyluridine 2_thio_2prime_O_methyluridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 2-thio-2'-O-methyluridine s2Um two thio two prime O methyluridine sequence RNAMOD:060 http://purl.org/obo/owl/RNAMOD#RNAMOD_060 three_three_amino_three_carboxypropyl_uridine 3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 3-(3-amino-3-carboxypropyl)uridine acp3U sequence RNAMOD:061 http://purl.org/obo/owl/RNAMOD#RNAMOD_061 five_hydroxyuridine 5_hydroxyuridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-hydroxyuridine five hydroxyuridine ho5U sequence RNAMOD:060 http://purl.org/obo/owl/RNAMOD#RNAMOD_060 five_methoxyuridine 5_methoxyuridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-methoxyuridine five methoxyuridine mo5U sequence RNAMOD:063 http://purl.org/obo/owl/RNAMOD#RNAMOD_063 uridine_five_oxyacetic_acid Uridine_5_oxyacetic_acid is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ cmo5U uridine 5-oxyacetic acid uridine five oxyacetic acid sequence RNAMOD:064 http://purl.org/obo/owl/RNAMOD#RNAMOD_064 uridine_five_oxyacetic_acid_methyl_ester Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ mcmo5U uridine 5-oxyacetic acid methyl ester uridine five oxyacetic acid methyl ester sequence RNAMOD:065 http://purl.org/obo/owl/RNAMOD#RNAMOD_065 five_carboxyhydroxymethyl_uridine 5_carboxyhydroxymethyl_uridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-(carboxyhydroxymethyl)uridine chm5U five carboxyhydroxymethyl uridine sequence RNAMOD:066 http://purl.org/obo/owl/RNAMOD#RNAMOD_066 five_carboxyhydroxymethyl_uridine_methyl_ester 5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-(carboxyhydroxymethyl)uridine methyl ester five carboxyhydroxymethyl uridine methyl ester mchm5U sequence RNAMOD:067 http://purl.org/obo/owl/RNAMOD#RNAMOD_067 five_methoxycarbonylmethyluridine Five_methoxycarbonylmethyluridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-methoxycarbonylmethyluridine five methoxycarbonylmethyluridine mcm5U sequence RNAMOD:068 http://purl.org/obo/owl/RNAMOD#RNAMOD_068 five_methoxycarbonylmethyl_two_prime_O_methyluridine Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-methoxycarbonylmethyl-2'-O-methyluridine five methoxycarbonylmethyl two prime O methyluridine mcm5Um sequence RNAMOD:069 http://purl.org/obo/owl/RNAMOD#RNAMOD_069 five_methoxycarbonylmethyl_two_thiouridine 5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-methoxycarbonylmethyl-2-thiouridine five methoxycarbonylmethyl two thiouridine mcm5s2U sequence RNAMOD:070 http://purl.org/obo/owl/RNAMOD#RNAMOD_070 five_aminomethyl_two_thiouridine 5_aminomethyl_2_thiouridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-aminomethyl-2-thiouridine five aminomethyl two thiouridine nm5s2U sequence RNAMOD:071 http://purl.org/obo/owl/RNAMOD#RNAMOD_071 five_methylaminomethyluridine 5_methylaminomethyluridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-methylaminomethyluridine five methylaminomethyluridine mnm5U sequence RNAMOD:072 http://purl.org/obo/owl/RNAMOD#RNAMOD_072 five_methylaminomethyl_two_thiouridine 5_methylaminomethyl_2_thiouridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-methylaminomethyl-2-thiouridine five methylaminomethyl two thiouridine mnm5s2U sequence RNAMOD:073 http://purl.org/obo/owl/RNAMOD#RNAMOD_073 five_methylaminomethyl_two_selenouridine 5_methylaminomethyl_2_selenouridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-methylaminomethyl-2-selenouridine five methylaminomethyl two selenouridine mnm5se2U sequence RNAMOD:074 http://purl.org/obo/owl/RNAMOD#RNAMOD_074 five_carbamoylmethyluridine 5_carbamoylmethyluridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-carbamoylmethyluridine five carbamoylmethyluridine ncm5U sequence RNAMOD:075 http://purl.org/obo/owl/RNAMOD#RNAMOD_075 five_carbamoylmethyl_two_prime_O_methyluridine 5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-carbamoylmethyl-2'-O-methyluridine five carbamoylmethyl two prime O methyluridine ncm5Um sequence RNAMOD:076 http://purl.org/obo/owl/RNAMOD#RNAMOD_076 five_carboxymethylaminomethyluridine 5_carboxymethylaminomethyluridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-carboxymethylaminomethyluridine cmnm5U five carboxymethylaminomethyluridine sequence RNAMOD:077 http://purl.org/obo/owl/RNAMOD#RNAMOD_077 five_carboxymethylaminomethyl_two_prime_O_methyluridine 5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-carboxymethylaminomethyl- 2'-O-methyluridine cmnm5Um five carboxymethylaminomethyl two prime O methyluridine sequence RNAMOD:078 http://purl.org/obo/owl/RNAMOD#RNAMOD_078 five_carboxymethylaminomethyl_two_thiouridine 5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-carboxymethylaminomethyl-2-thiouridine cmnm5s2U five carboxymethylaminomethyl two thiouridine sequence RNAMOD:079 http://purl.org/obo/owl/RNAMOD#RNAMOD_079 three_methyluridine 3_methyluridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 3-methyluridine m3U three methyluridine sequence RNAMOD:085 http://purl.org/obo/owl/RNAMOD#RNAMOD_085 one_methyl_three_three_amino_three_carboxypropyl_pseudouridine 1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 1-methyl-3-(3-amino-3-carboxypropyl) pseudouridine m1acp3Y sequence RNAMOD:086 http://purl.org/obo/owl/RNAMOD#RNAMOD_086 five_carboxymethyluridine 5_carboxymethyluridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-carboxymethyluridine cm5U five carboxymethyluridine sequence RNAMOD:087 http://purl.org/obo/owl/RNAMOD#RNAMOD_087 three_two_prime_O_dimethyluridine 3_2prime_O_dimethyluridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 3,2'-O-dimethyluridine m3Um three two prime O dimethyluridine sequence RNAMOD:092 http://purl.org/obo/owl/RNAMOD#RNAMOD_092 five_methyldihydrouridine 5_methyldihydrouridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-methyldihydrouridine five methyldihydrouridine m5D sequence RNAMOD:093 http://purl.org/obo/owl/RNAMOD#RNAMOD_093 three_methylpseudouridine 3_methylpseudouridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 3-methylpseudouridine m3Y three methylpseudouridine sequence RNAMOD:094 http://purl.org/obo/owl/RNAMOD#RNAMOD_094 five_taurinomethyluridine 5_taurinomethyluridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-taurinomethyluridine five taurinomethyluridine tm5U sequence RNAMOD:098 http://purl.org/obo/owl/RNAMOD#RNAMOD_098 five_taurinomethyl_two_thiouridine 5_taurinomethyl_2_thiouridineis a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-taurinomethyl-2-thiouridine five taurinomethyl two thiouridine tm5s2U sequence RNAMOD:099 http://purl.org/obo/owl/RNAMOD#RNAMOD_099 five_isopentenylaminomethyl_uridine 5_isopentenylaminomethyl_uridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-(isopentenylaminomethyl)uridine five isopentenylaminomethyl uridine inm5U sequence RNAMOD:103 http://purl.org/obo/owl/RNAMOD#RNAMOD_103 five_isopentenylaminomethyl_two_thiouridine 5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-(isopentenylaminomethyl)- 2-thiouridine five isopentenylaminomethyl two thiouridine inm5s2U sequence RNAMOD:104 http://purl.org/obo/owl/RNAMOD#RNAMOD_104 five_isopentenylaminomethyl_two_prime_O_methyluridine 5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature. URL:http://library.med.utah.edu/RNAmods/ http://library.med.utah.edu/RNAmods/ 5-(isopentenylaminomethyl)- 2'-O-methyluridine five isopentenylaminomethyl two prime O methyluridine inm5Um sequence RNAMOD:105 http://purl.org/obo/owl/RNAMOD#RNAMOD_105 histone_binding_site A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone. SO:ke http://purl.org/obo/owl/SO#SO_ke histone binding site sequence CDS_fragment CDS fragment incomplete CDS sequence modified_amino_acid_feature A post translationally modified amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke modified amino acid feature sequence modified_glycine A post translationally modified glycine amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke ModGly modified glycine sequence MOD:00908 http://purl.org/obo/owl/MOD#MOD_00908 modified_L_alanine A post translationally modified alanine amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke ModAla modified L alanine modified L-alanine sequence MOD:00901 http://purl.org/obo/owl/MOD#MOD_00901 modified_L_asparagine A post translationally modified asparagine amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke ModAsn modified L asparagine modified L-asparagine sequence MOD:00903 http://purl.org/obo/owl/MOD#MOD_00903 modified_L_aspartic_acid A post translationally modified aspartic acid amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke ModAsp modified L aspartic acid modified L-aspartic acid sequence MOD:00904 http://purl.org/obo/owl/MOD#MOD_00904 modified_L_cysteine A post translationally modified cysteine amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke ModCys modified L cysteine modified L-cysteine sequence MOD:00905 http://purl.org/obo/owl/MOD#MOD_00905 modified_L_glutamic_acid ModGlu modified L glutamic acid modified L-glutamic acid sequence MOD:00906 http://purl.org/obo/owl/MOD#MOD_00906 modified_L_threonine A post translationally modified threonine amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke modified L threonine modified L-threonine ModThr sequence MOD:00917 http://purl.org/obo/owl/MOD#MOD_00917 modified_L_tryptophan A post translationally modified tryptophan amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke modified L tryptophan modified L-tryptophan ModTrp sequence MOD:00918 http://purl.org/obo/owl/MOD#MOD_00918 modified_L_glutamine A post translationally modified glutamine amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke ModGln modified L glutamine modified L-glutamine sequence MOD:00907 http://purl.org/obo/owl/MOD#MOD_00907 modified_L_methionine A post translationally modified methionine amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke modified L methionine modified L-methionine ModMet sequence MOD:00913 http://purl.org/obo/owl/MOD#MOD_00913 modified_L_isoleucine A post translationally modified isoleucine amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke modified L isoleucine modified L-isoleucine ModIle sequence MOD:00910 http://purl.org/obo/owl/MOD#MOD_00910 modified_L_phenylalanine A post translationally modified phenylalanine amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke modified L phenylalanine modified L-phenylalanine ModPhe sequence MOD:00914 http://purl.org/obo/owl/MOD#MOD_00914 modified_L_histidine A post translationally modified histidie amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke ModHis modified L histidine modified L-histidine sequence MOD:00909 http://purl.org/obo/owl/MOD#MOD_00909 modified_L_serine A post translationally modified serine amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke modified L serine modified L-serine MosSer sequence MOD:00916 http://purl.org/obo/owl/MOD#MOD_00916 modified_L_lysine A post translationally modified lysine amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke modified L lysine modified L-lysine ModLys sequence MOD:00912 http://purl.org/obo/owl/MOD#MOD_00912 modified_L_leucine A post translationally modified leucine amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke modified L leucine modified L-leucine ModLeu sequence MOD:00911 http://purl.org/obo/owl/MOD#MOD_00911 modified_L_selenocysteine A post translationally modified selenocysteine amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke modified L selenocysteine modified L-selenocysteine sequence MOD:01158 http://purl.org/obo/owl/MOD#MOD_01158 modified_L_valine A post translationally modified valine amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke modified L valine modified L-valine ModVal sequence MOD:00920 http://purl.org/obo/owl/MOD#MOD_00920 modified_L_proline A post translationally modified proline amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke modified L proline modified L-proline ModPro sequence MOD:00915 http://purl.org/obo/owl/MOD#MOD_00915 modified_L_tyrosine A post translationally modified tyrosine amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke modified L tyrosine modified L-tyrosine ModTry sequence MOD:00919 http://purl.org/obo/owl/MOD#MOD_00919 modified_L_arginine A post translationally modified arginine amino acid feature. SO:ke http://purl.org/obo/owl/SO#SO_ke ModArg modified L arginine modified L-arginine sequence MOD:00902 http://purl.org/obo/owl/MOD#MOD_00902 peptidyl An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence cleaved_for_gpi_anchor_region The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor. EBI:rh http://purl.org/obo/owl/EBI#EBI_rh cleaved for gpi anchor region sequence biomaterial_region A region which is intended for use in an experiment. SO:cb http://purl.org/obo/owl/SO#SO_cb biomaterial region sequence experimental_feature 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 http://purl.org/obo/owl/SO#SO_cb analysis feature experimental output artefact experimental_output_artefact sequence biological_region A region defined by its disposition to be involved in a biological process. SO:cb http://purl.org/obo/owl/SO#SO_cb biological region sequence topologically_defined_region A region that is defined according to its relations with other regions within the same sequence. SO:cb http://purl.org/obo/owl/SO#SO_cb topologically defined region sequence translocation_breakpoint The point within a chromosome where a translocation begins or ends. SO:cb http://purl.org/obo/owl/SO#SO_cb translocation breakpoint sequence insertion_breakpoint The point within a chromosome where a insertion begins or ends. SO:cb http://purl.org/obo/owl/SO#SO_cb insertion breakpoint sequence deletion_breakpoint The point within a chromosome where a deletion begins or ends. SO:cb http://purl.org/obo/owl/SO#SO_cb deletion breakpoint sequence five_prime_flanking_region A flanking region located five prime of a specific region. SO:chado http://purl.org/obo/owl/SO#SO_chado 5' flanking region five prime flanking region sequence three_prime_flanking_region A flanking region located three prime of a specific region. SO:chado http://purl.org/obo/owl/SO#SO_chado 3' flanking region three prime flanking region sequence transcribed_fragment Term requested by the MODencode group. An experimental region, defined by a tiling array experiment to be transcribed at some level. SO:ke http://purl.org/obo/owl/SO#SO_ke transcribed fragment transfrag sequence cis_splice_site Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron. SO:cjm http://purl.org/obo/owl/SO#SO_cjm SO:ke http://purl.org/obo/owl/SO#SO_ke cis splice site sequence trans_splice_site Primary transcript region bordering trans-splice junction. SO:ke http://purl.org/obo/owl/SO#SO_ke trans splice site sequence splice_junction The boundary between an intron and an exon. SO:ke http://purl.org/obo/owl/SO#SO_ke splice boundary splice junction sequence conformational_switch MM Young, K Kirshenbaum, KA Dill & S Highsmith. Predicting conformational switches in proteins. Protein Science, 1999, 8, 1752-64. K. Kirshenbaum, M.M. Young and S. Highsmith. Predicting Allosteric Switches in Myosins. Protein Science 8(9):1806-1815. 1999. A region of a polypeptide, involved in the transition from one conformational state to another. SO:ke http://purl.org/obo/owl/SO#SO_ke polypeptide conformational switch sequence dye_terminator_read A read produced by the dye terminator method of sequencing. SO:ke http://purl.org/obo/owl/SO#SO_ke dye terminator read sequence pyrosequenced_read An example is a read produced by Roche 454 technology. A read produced by pyrosequencing technology. SO:ke http://purl.org/obo/owl/SO#SO_ke pyorsequenced read sequence ligation_based_read An example of this kind of read is one produced by ABI SOLiD. A read produced by ligation based sequencing technologies. SO:ke http://purl.org/obo/owl/SO#SO_ke ligation based read sequence polymerase_synthesis_read An example is a read produced by Illumina technology. A read produced by the polymerase based sequence by synthesis method. SO:ke http://purl.org/obo/owl/SO#SO_ke polymerase synthesis read sequence cis_regulatory_frameshift_element A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence. RFAM:jd http://purl.org/obo/owl/RFAM#RFAM_jd cis regulatory frameshift element sequence expressed_sequence_assembly From tracker [ 2372385 ] expressed_sequence_assembly. A sequence assembly derived from expressed sequences. SO:ke http://purl.org/obo/owl/SO#SO_ke expressed sequence assembly sequence DNA_binding_site A binding site that, in the molecule, interacts selectively and non-covalently with DNA. SO:ke http://purl.org/obo/owl/SO#SO_ke DNA binding site sequence cryptic_gene A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning. SO:ke http://purl.org/obo/owl/SO#SO_ke cryptic gene sequence sequence_variant_affecting_polyadenylation OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation affecting polyadenylation sequence variant affecting polyadenylation sequence three_prime_RACE_clone A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host. modENCODE:nlw http://purl.org/obo/owl/modENCODE#modENCODE_nlw 3' RACE clone sequence cassette_pseudogene Requested by the Trypanosome community. A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy. SO:ke http://purl.org/obo/owl/SO#SO_ke cassette pseudogene cassette type psedogene sequence alanine A place holder for a cross product with chebi. A Ala sequence valine A place holder for a cross product with chebi. V Val sequence leucine A place holder for a cross product with chebi. L Leu sequence isoleucine A place holder for a cross product with chebi. I Ile sequence proline A place holder for a cross product with chebi. P Pro sequence tryptophan A place holder for a cross product with chebi. Trp W sequence phenylalanine A place holder for a cross product with chebi. F Phe sequence methionine A place holder for a cross product with chebi. M Met sequence glycine A place holder for a cross product with chebi. G Gly sequence serine A place holder for a cross product with chebi. S Ser sequence threonine A place holder for a cross product with chebi. T Thr sequence tyrosine A place holder for a cross product with chebi. Tyr Y sequence cysteine A place holder for a cross product with chebi. C Cys sequence glutamine A place holder for a cross product with chebi. Gln Q sequence asparagine A place holder for a cross product with chebi. Asn N sequence lysine A place holder for a cross product with chebi. K Lys sequence arginine A place holder for a cross product with chebi. Arg R sequence histidine A place holder for a cross product with chebi. H His sequence aspartic_acid A place holder for a cross product with chebi. Asp aspartic acid D sequence glutamic_acid A place holder for a cross product with chebi. E Glu glutamic acid sequence selenocysteine A place holder for a cross product with chebi. Sec U sequence pyrrolysine A place holder for a cross product with chebi. O Pyl sequence transcribed_cluster This term was requested by Jeff Bowes, using the tracker, ID = 2594157. A region defined by a set of transcribed sequences from the same gene or expressed pseudogene. SO:ke http://purl.org/obo/owl/SO#SO_ke transcribed cluster unigene cluster sequence unigene_cluster This term was requested by Jeff Bowes, using the tracker, ID = 2594157. A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene. SO:ke http://purl.org/obo/owl/SO#SO_ke unigene cluster sequence CRISPR Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences. RFAM:jd http://purl.org/obo/owl/RFAM#RFAM_jd Clustered_Regularly_Interspaced_Short_Palindromic_Repeat CRISPR element sequence http:en.wikipedia.org/wiki/CRISPR http://purl.org/obo/owl/http#http_en.wikipedia.org/wiki/CRISPR insulator_binding_site See tracker ID 2060908. A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. SO:ke http://purl.org/obo/owl/SO#SO_ke insulator binding site sequence enhancer_binding_site A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. SO:ke http://purl.org/obo/owl/SO#SO_ke enhancer binding site sequence contig_collection See tracker ID: 2138359. A collection of contigs. SO:ke http://purl.org/obo/owl/SO#SO_ke contig collection sequence lincRNA A multiexonic non-coding RNA transcribed by RNA polymerase II. PMID:19182780 http://purl.org/obo/owl/PMID#PMID_19182780 SO:ke http://purl.org/obo/owl/SO#SO_ke large intervening non-coding RNA sequence UST An EST spanning part or all of the untranslated regions of a protein-coding transcript. SO:nlw http://purl.org/obo/owl/SO#SO_nlw UTR sequence tag sequence three_prime_UST A UST located in the 3'UTR of a protein-coding transcript. SO:nlw http://purl.org/obo/owl/SO#SO_nlw 3' UST sequence five_prime_UST An UST located in the 5'UTR of a protein-coding transcript. SO:nlw http://purl.org/obo/owl/SO#SO_nlw 5' UST sequence RST A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long. SO:nlw http://purl.org/obo/owl/SO#SO_nlw RACE sequence tag sequence three_prime_RST A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long. SO:nlw http://purl.org/obo/owl/SO#SO_nlw 3' RST sequence five_prime_RST A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long. SO:nlw http://purl.org/obo/owl/SO#SO_nlw 5' RST sequence UST_match A match against an UST sequence. SO:nlw http://purl.org/obo/owl/SO#SO_nlw UST match sequence RST_match A match against an RST sequence. SO:nlw http://purl.org/obo/owl/SO#SO_nlw RST match sequence primer_match A nucleotide match to a primer sequence. SO:nlw http://purl.org/obo/owl/SO#SO_nlw primer match sequence miRNA_antiguide A region of the pri miRNA that basepairs with the guide to form the hairpin. SO:ke http://purl.org/obo/owl/SO#SO_ke miRNA antiguide miRNA passenger strand miRNA star sequence trans_splice_junction The boundary between the spliced leader and the first exon of the mRNA. SO:ke http://purl.org/obo/owl/SO#SO_ke trans-splice junction sequence outron A region of a primary transcript, that is removed via trans splicing. PMID:16401417 http://purl.org/obo/owl/PMID#PMID_16401417 SO:ke http://purl.org/obo/owl/SO#SO_ke sequence natural_plasmid A plasmid that occurs naturally. SO:xp http://purl.org/obo/owl/SO#SO_xp natural plasmid sequence gene_trap_construct A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker. ZFIN:dh http://purl.org/obo/owl/ZFIN#ZFIN_dh gene trap construct sequence promoter_trap_construct A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic. ZFIN:dh http://purl.org/obo/owl/ZFIN#ZFIN_dh promoter trap construct sequence enhancer_trap_construct An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic. ZFIN:dh http://purl.org/obo/owl/ZFIN#ZFIN_dh enhancer trap construct sequence PAC_end A region of sequence from the end of a PAC clone that may provide a highly specific marker. ZFIN:mh http://purl.org/obo/owl/ZFIN#ZFIN_mh PAC end sequence RAPD RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers. ZFIN:mh http://purl.org/obo/owl/ZFIN#ZFIN_mh Random Amplification Polymorphic DNA sequence shadow_enhancer shadow enhancer sequence SNV SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist. SO:bm http://purl.org/obo/owl/SO#SO_bm single nucleotide variant sequence X_element_combinatorial_repeat X element combinatorial repeats contain Tbf1p binding sites,nand possible functions include a role in telomerase-independent telomerenmaintenance via recombination or as a barrier against transcriptionalnsilencing. These are usually present as a combination of one or more ofnseveral types of smaller elements (designated A, B, C, or D). This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element. URL:http://www.yeastgenome.org/help/glossary.html http://www.yeastgenome.org/help/glossary.html X element combinatorial repeat sequence Y_prime_element This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies. http:http://www.yeastgenome.org/help/glossary.html http://purl.org/obo/owl/http#http_http://www.yeastgenome.org/help/glossary.html Y' element sequence standard_draft The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete. DOI:10.1126 http://purl.org/obo/owl/DOI#DOI_10.1126 standard draft sequence high_quality_draft The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome. DOI:10.1126 http://purl.org/obo/owl/DOI#DOI_10.1126 high quality draft sequence improved_high_quality_draft The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution. DOI:10.1126 http://purl.org/obo/owl/DOI#DOI_10.1126 improved high quality draft sequence annotation_directed_improved_draft The status of a whole genome sequence,where annotation, and verification of coding regions has occurred. DOI:10.1126 http://purl.org/obo/owl/DOI#DOI_10.1126 annotation directed improvement sequence noncontiguous_finished The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions. DOI:10.1126 http://purl.org/obo/owl/DOI#DOI_10.1126 non contiguous finished sequence finished_genome The status of a whole genome sequence, with less than 1 error per 100,000 base pairs. DOI:10.1126 http://purl.org/obo/owl/DOI#DOI_10.1126 finished finished genome sequence intronic_regulatory_region A regulatory region that is part of an intron. SO:ke http://purl.org/obo/owl/SO#SO_ke intronic regulatory region sequence centromere_DNA_Element_I This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699. A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p). PMID:11222754 http://purl.org/obo/owl/PMID#PMID_11222754 CDEI Centromere DNA Element I sequence centromere_DNA_Element_II This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699. A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length. PMID:11222754 http://purl.org/obo/owl/PMID#PMID_11222754 CDEII centromere DNA Element II sequence centromere_DNA_Element_III This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699. A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex. PMID:11222754 http://purl.org/obo/owl/PMID#PMID_11222754 CDEIII centromere DNA Element III sequence telomeric_repeat The repeats are maintained by telomerase and there is generally 300 (+/-) 75 bp of TG(1-3) at a given end. Telomeric repeats function in completing chromosome replication and protecting the ends from degradation and end-to-end fusions. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880739. The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n. PMID:8720065 http://purl.org/obo/owl/PMID#PMID_8720065 telomeric repeat sequence X_element Possible functions include roles in chromosomal segregation,nmaintenance of chromosome stability, recombinational sequestering, or as anbarrier to transcriptional silencing. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site. URL:http://www.yeastgenome.org/help/glossary.html#xelemcoresequence http://www.yeastgenome.org/help/glossary.html#xelemcoresequence X element sequence YAC_end A region of sequence from the end of a YAC clone that may provide a highly specific marker. SO:ke http://purl.org/obo/owl/SO#SO_ke YAC end sequence whole_genome_sequence_status This terms and children were added to SO in response to tracker request by Patrick Chain. The paper Genome Project Standards in a New Era of Sequencing. Science October 9th 2009, addresses these terms. The status of whole genome sequence. DOI:10.1126 http://purl.org/obo/owl/DOI#DOI_10.1126 whole genome sequence status sequence heritable_phenotypic_marker A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus. JAX:hdene http://purl.org/obo/owl/JAX#JAX_hdene heritable phenotypic marker phenotypic marker sequence peptide_collection Term requested via tracker ID: 2910829. A collection of peptide sequences. BBOP:nlw http://purl.org/obo/owl/BBOP#BBOP_nlw peptide collection peptide set sequence high_identity_region Requested by tracker ID: 2902685. An experimental feature with high sequence identity to another sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke high identity region sequence processed_transcript Ensembl and Vega also use this term name. Requested by Howard Deen of MGI. A transcript for which no open reading frame has been identified and for which no other function has been determined. MGI:hdeen http://purl.org/obo/owl/MGI#MGI_hdeen processed transcript sequence assortment_derived_variation A chromosome variation derived from an event during meiosis. SO:ke http://purl.org/obo/owl/SO#SO_ke assortment derived variation sequence reference_genome A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly. SO:ke http://purl.org/obo/owl/SO#SO_ke reference genome sequence variant_genome A collection of sequences (often chromosomes) of an individual. SO:ke http://purl.org/obo/owl/SO#SO_ke variant genome sequence variant_collection A collection of one or more sequences of an individual. SO:ke http://purl.org/obo/owl/SO#SO_ke variant collection sequence alteration_attribute alteration attribute sequence chromosomal_variation_attribute chromosomal variation attribute sequence intrachromosomal sequence interchromosomal sequence insertion_attribute A quality of a chromosomal insertion,. SO:ke http://purl.org/obo/owl/SO#SO_ke insertion attribute sequence tandem sequence direct A quality of an insertion where the insert is not in a cytologically inverted orientation. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence inverted A quality of an insertion where the insert is in a cytologically inverted orientation. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence free The quality of a duplication where the new region exists independently of the original. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence inversion_attribute inversion attribute sequence pericentric sequence paracentric sequence translocaton_attribute translocation attribute sequence reciprocal sequence insertional sequence duplication_attribute duplication attribute sequence chromosomally_aberrant_genome chromosomally aberrant genome sequence assembly_error_correction A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake. SO:ke http://purl.org/obo/owl/SO#SO_ke assembly error correction sequence base_call_error_correction A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake. SO:ke http://purl.org/obo/owl/SO#SO_ke base call error correction sequence peptide_localization_signal A region of peptide sequence used to target the polypeptide molecule to a specific organelle. SO:ke http://purl.org/obo/owl/SO#SO_ke localization signal peptide localization signal sequence nuclear_localization_signal A polypeptide region that targets a polypeptide to the nucleus. SO:ke http://purl.org/obo/owl/SO#SO_ke NLS sequence URL:http://en.wikipedia.org/wiki/Nuclear_localization_signal http://en.wikipedia.org/wiki/Nuclear_localization_signal endosomal_localization_signal A polypeptide region that targets a polypeptide to the endosome. SO:ke http://purl.org/obo/owl/SO#SO_ke endosomal localization signal sequence lysosomal_localization_signal A polypeptide region that targets a polypeptide to the lysosome. SO:ke http://purl.org/obo/owl/SO#SO_ke lysosomal localization signal sequence nuclear_export_signal A polypeptide region that targets a polypeptide to he cytoplasm. SO:ke http://purl.org/obo/owl/SO#SO_ke NES nuclear export signal sequence URL:http://en.wikipedia.org/wiki/Nuclear_export_signal http://en.wikipedia.org/wiki/Nuclear_export_signal recombination_signal_sequence A region recognized by a recombinase. SO:ke http://purl.org/obo/owl/SO#SO_ke recombination signal sequence sequence URL:http://en.wikipedia.org/wiki/Recombination_Signal_Sequences http://en.wikipedia.org/wiki/Recombination_Signal_Sequences cryptic_splice_site A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error. SO:ke http://purl.org/obo/owl/SO#SO_ke cryptic splice signal cryptic splice site sequence nuclear_rim_localization_signal A polypeptide region that targets a polypeptide to the nuclear rim. SO:ke http://purl.org/obo/owl/SO#SO_ke nuclear rim localization signal sequence PMID:16027110 http://purl.org/obo/owl/PMID#PMID_16027110 p_element A P_element is a DNA transposon responsible for hybrid dysgenesis. SO:ke http://purl.org/obo/owl/SO#SO_ke P element sequence functional_variant A sequence variant in which the function of a gene product is altered with respect to a reference. SO:ke http://purl.org/obo/owl/SO#SO_ke functional variant sequence structural_variant A sequence variant that changes one or more sequence features. SO:ke http://purl.org/obo/owl/SO#SO_ke structural variant sequence transcript_function_variant A sequence variant which alters the functioning of a transcript with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke transcript function variant sequence translational_product_function_variant A sequence variant that affects the functioning of a translational product with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke translational product variant sequence level_of_transcript_variant A sequence variant which alters the level of a transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke level of transcript variant sequence decreased_transcript_level_variant A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke decreased transcript level sequence increased_transcript_level_variant A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke increased transcript level variant sequence transcript_processing_variant A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke transcript processing variant sequence editing_variant A transcript processing variant whereby the process of editing is disrupted with respect to the reference. SO:ke http://purl.org/obo/owl/SO#SO_ke editing variant sequence polyadenylation_variant A sequence variant that changes polyadenylation with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke polyadenylation variant sequence transcript_stability_variant A variant that changes the stability of a transcript with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke transcript stability variant sequence decreased_transcript_stability_variant A sequence variant that decreases transcript stability with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke decrease transcript stability variant sequence increased_transcript_stability_variant A sequence variant that increases transcript stability with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke increased transcript stability variant sequence transcription_variant A variant that changes alters the transcription of a transcript with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke transcription variant sequence rate_of_transcription_variant A sequence variant that changes the rate of transcription with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke rate of transcription variant sequence increased_transcription_rate_variant A sequence variant that increases the rate of transcription with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke increased transcription rate variant sequence decreased_transcription_rate_variant A sequence variant that decreases the rate of transcription with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke decreased transcription rate variant sequence translational_product_level_variant A functional variant that changes the translational product level with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke translational product level variant sequence polypeptide_function_variant A sequence variant which changes polypeptide functioning with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke polypeptide function variant sequence decreased_translational_product_level A sequence variant which decreases the translational product level with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke decrease translational product level sequence increased_translational_product_level A sequence variant which increases the translational product level with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke increase translational product level sequence polypeptide_gain_of_function_variant A sequence variant which causes gain of polypeptide function with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke polypeptide gain of function variant sequence polypeptide_localization_variant A sequence variant which changes the localization of a polypeptide with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke polypeptide localization variant sequence polypeptide_loss_of_function_variant A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke polypeptide loss of function variant sequence inactive_ligand_binding_site A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke inactive ligand binding site sequence polypeptide_partial_loss_of_function A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke polypeptide partial loss of function sequence polypeptide_post_translational_processing_variant A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke polypeptide post translational processing variant sequence copy_number_change A sequence variant where copies of a feature (CNV) are either increased or decreased. SO:ke http://purl.org/obo/owl/SO#SO_ke copy number change sequence gene_variant A sequence variant where the structure of the gene is changed. SO:ke http://purl.org/obo/owl/SO#SO_ke gene structure variant sequence gene_fusion A sequence variant whereby a two genes have become joined. SO:ke http://purl.org/obo/owl/SO#SO_ke gene fusion sequence regulatory_region_variant EBI term: Regulatory region variations - In regulatory region annotated by Ensembl. A sequence variant located within a regulatory region. SO:ke http://purl.org/obo/owl/SO#SO_ke regulatory region variant regulatory_region_ URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html sequence stop_retained_variant A sequence variant where at least one base in the terminator codon is changed, but the terminator remains. SO:ke http://purl.org/obo/owl/SO#SO_ke stop retained variant sequence splicing_variant A sequence variant that changes the process of splicing. SO:ke http://purl.org/obo/owl/SO#SO_ke splicing variant sequence EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html cryptic_splice_site_variant A sequence variant causing a new (functional) splice site. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html cryptic splice site activation sequence EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html cryptic_splice_acceptor A sequence variant whereby a new splice site is created due to the activation of a new acceptor. SO:ke http://purl.org/obo/owl/SO#SO_ke cryptic splice acceptor sequence cryptic_splice_donor A sequence variant whereby a new splice site is created due to the activation of a new donor. SO:ke http://purl.org/obo/owl/SO#SO_ke cryptic splice donor sequence exon_loss A sequence variant whereby an exon is lost from the transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke exon loss sequence intron_gain A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html intron gain sequence EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html splice_acceptor_variant A splice variant that changes the 2 base region at the 3' end of an intron. SO:ke http://purl.org/obo/owl/SO#SO_ke splice acceptor variant sequence splice_donor_variant A splice variant that changes the2 base region at the 5' end of an intron. SO:ke http://purl.org/obo/owl/SO#SO_ke splice donor variant sequence transcript_variant A sequence variant that changes the structure of the transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke transcript variant sequence EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html complex_change_in_transcript EBI term: Complex InDel - Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border. A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border. URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html complex_indel URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html complext change in transcript sequence stop_lost EBI term: Stop lost - In coding sequence, resulting in the loss of a stop codon. A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke stop codon lost stop lost stop_lost URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html sequence transcript_sequence_variant transcript sequence variant sequence coding_sequence_variant A sequence variant that changes the coding sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke coding sequence variant sequence codon_variant A sequence variant that changes at least one base in a codon. SO:ke http://purl.org/obo/owl/SO#SO_ke coding variant codon variant sequence EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html initiator_codon_change A codon variant that changes at least one base of the first codon of a transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke initiator codon change sequence EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html non_synonymous_codon EBI term: Non-synonymous SNPs. SNPs that are located in the coding sequence and result in an amino acid change in the encoded peptide sequence. A change that causes a non_synonymous_codon can be more than 3 bases - for example 4 base substitution. A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid or stop codon. EBI:gr http://purl.org/obo/owl/EBI#EBI_gr SO:ke http://purl.org/obo/owl/SO#SO_ke non synonymous codon non_synonymous_coding URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html sequence SO:0001584 EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html conservative_missense_codon A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious. SO:ke http://purl.org/obo/owl/SO#SO_ke conservative missense codon neutral missense codon quiet missense codon sequence EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html non_conservative_missense_codon A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties. SO:ke http://purl.org/obo/owl/SO#SO_ke non conservative missense codon sequence EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html stop_gained EBI term: Stop gained - In coding sequence, resulting in the gain of a stop codon (i.e. leading to a shortened peptide sequence). A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke nonsense ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd http://purl.org/obo/owl/ftp#ftp_//ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd nonsense codon stop codon gained stop gained stop_gained URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html sequence synonymous_codon EBI term: Synonymous SNPs - In coding sequence, not resulting in an amino acid change (i.e. silent mutation).nThis term is sometimes used synonomously with the more general term 'silent mutation', although a silent mutation may occur in non coding sequence. The best practice is to annotate to the most specific term. A sequence variant whereby a base of a codon is changed, but there is no resulting change to the encoded amino acid. SO:ke http://purl.org/obo/owl/SO#SO_ke coding-synon ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd http://purl.org/obo/owl/ftp#ftp_//ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd silent mutation silent substitution silent_mutation synonymous codon synonymous_coding sequence EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html URL:http://en.wikipedia.org/wiki/Silent_mutation http://en.wikipedia.org/wiki/Silent_mutation URL:http://en.wikipedia.org/wiki/Synonymous_mutation http://en.wikipedia.org/wiki/Synonymous_mutation frameshift_variant EBI term:Frameshift variations - In coding sequence, resulting in a frameshift. A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three. SO:ke http://purl.org/obo/owl/SO#SO_ke frameshift variant frameshift_ ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd http://purl.org/obo/owl/ftp#ftp_//ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd frameshift_coding URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html sequence terminator_codon_variant A sequence variant whereby at least one of the bases in the terminator codon is changed. SO:ke http://purl.org/obo/owl/SO#SO_ke terminator codon variant sequence frame_restoring_variant A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame. SO:ke http://purl.org/obo/owl/SO#SO_ke frame restoring variant sequence minus_1_frameshift_variant A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead. URL:http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535 http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535 -1 frameshift variant minus 1 frameshift variant sequence minus_2_frameshift_variant -2 frameshift variant minus 2 frameshift variant sequence plus_1_frameshift_variant A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward. URL:http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535 http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535 +1 frameshift variant plus 1 frameshift variant sequence plus_2_frameshift variant +2 frameshift variant plus 2 frameshift variant sequence transcript_secondary_structure_variant A sequence variant within a transcript that changes the secondary structure of the RNA product. SO:ke http://purl.org/obo/owl/SO#SO_ke transcript secondary structure variant sequence compensatory_transcript_secondary_structure_variant A secondary structure variant that compensate for the change made by a previous variant. SO:ke http://purl.org/obo/owl/SO#SO_ke compensatory transcript secondary structure variant sequence translational_product_structure_variant A sequence variant within the transcript that changes the structure of the translational product. SO:ke http://purl.org/obo/owl/SO#SO_ke translational product structure variant sequence EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html 3D_polypeptide_structure_variant A sequence variant that changes the resulting polypeptide structure. SO:ke http://purl.org/obo/owl/SO#SO_ke 3D polypeptide structure variant sequence complex_3D_structural_variant A sequence variant that changes the resulting polypeptide structure. SO:ke http://purl.org/obo/owl/SO#SO_ke complex 3D structural variant sequence conformational_change_variant A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke conformational change variant sequence complex_change_of_translational_product_variant complex change of translational product variant sequence polypeptide_sequence_variant A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke polypeptide sequence variant sequence amino_acid_deletion A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide. SO:ke http://purl.org/obo/owl/SO#SO_ke amino acid deletion sequence EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html amino_acid_insertion A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide. SO:ke http://purl.org/obo/owl/SO#SO_ke amino acid insertion sequence EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html amino_acid_substitution A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide. SO:ke http://purl.org/obo/owl/SO#SO_ke amino acid substitution sequence EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html conservative_amino_acid_substitution A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide. SO:ke http://purl.org/obo/owl/SO#SO_ke conservative amino acid substitution sequence non_conservative_amino_acid_substitution A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide. SO:ke http://purl.org/obo/owl/SO#SO_ke non conservative amino acid substitution sequence elongated_polypeptide A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke elongated polypeptide sequence EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html elongated_polypeptide_C_terminal A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus. SO:ke http://purl.org/obo/owl/SO#SO_ke elongated polypeptide C terminal sequence elongated_polypeptide_N_terminal A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus. SO:ke http://purl.org/obo/owl/SO#SO_ke elongated polypeptide N terminal sequence elongated_in_frame_polypeptide_C_terminal A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus. SO:ke http://purl.org/obo/owl/SO#SO_ke elongated in frame polypeptide C terminal sequence elongated_out_of_frame_polypeptide_C_terminal A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus. SO:ke http://purl.org/obo/owl/SO#SO_ke elongated polypeptide out of frame C terminal sequence elongated_in_frame_polypeptide_N_terminal_elongation A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus. SO:ke http://purl.org/obo/owl/SO#SO_ke elongated in frame polypeptide N terminal sequence elongated_out_of_frame_polypeptide_N_terminal A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus. SO:ke http://purl.org/obo/owl/SO#SO_ke elongated out of frame N terminal sequence polypeptide_fusion A sequence variant that causes a fusion of two polypeptide sequences. SO:ke http://purl.org/obo/owl/SO#SO_ke polypeptide fusion sequence polypeptide_truncation A sequence variant of the CD that causes a truncation of the resulting polypeptide. SO:ke http://purl.org/obo/owl/SO#SO_ke polypeptide truncation sequence EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html inactive_catalytic_site A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke inactive catalytic site sequence nc_transcript_variant Within non-coding gene - Located within a gene that does not code for a protein. A transcript variant of a non coding RNA gene. SO:ke http://purl.org/obo/owl/SO#SO_ke nc transcript variant non coding transcript variant within_non_coding_gene URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html sequence mature_miRNA_variant EBI term: Within mature miRNA - Located within a microRNA. A transcript variant located with the sequence of the mature miRNA. SO:ke http://purl.org/obo/owl/SO#SO_ke mature miRNA variant within_mature_miRNA URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html sequence NMD_transcript_variant A variant in a transcript that is the target of NMD. SO:ke http://purl.org/obo/owl/SO#SO_ke NMD transcript variant NMD_transcript URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html sequence UTR_variant A transcript variant that is located within the UTR. SO:ke http://purl.org/obo/owl/SO#SO_ke UTR variant UTR_ URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html sequence 5_prime_UTR_variant EBI term: 5prime UTR variations - In 5prime UTR (untranslated region). A UTR variant of the 5' UTR. SO:ke http://purl.org/obo/owl/SO#SO_ke 5'UTR variant 5PRIME_UTR URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html five prime UTR variant untranslated-5 ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd http://purl.org/obo/owl/ftp#ftp_//ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd sequence 3_prime_UTR_variant EBI term 3prime UTR variations - In 3prime UTR. A UTR variant of the 3' UTR. SO:ke http://purl.org/obo/owl/SO#SO_ke 3'UTR variant 3PRIME_UTR URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html three prime UTR variant untranslated-3 ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd http://purl.org/obo/owl/ftp#ftp_//ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd sequence terminal_codon_variant The terminal codon may be the terminator, or in an incomplete transcript the last available codon. A codon variant that changes at least one base of the last codon of the transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke terminal codon variant sequence incomplete_terminal_codon_variant EBI term: Partial codon - Located within the final, incomplete codon of a transcript with a shortened coding sequence where the end is unknown. A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed. SO:ke http://purl.org/obo/owl/SO#SO_ke incomplete terminal codon variant partial_codon URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html sequence intron_variant EBI term: Intronic variations - In intron. A transcript variant occurring within an intron. SO:ke http://purl.org/obo/owl/SO#SO_ke intron variant intron_ ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd http://purl.org/obo/owl/ftp#ftp_//ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd intronic URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html sequence intergenic_variant EBI term Intergenic variations - More than 5 kb either upstream or downstream of a transcript. A sequence variant located in the intergenic region, between genes. SO:ke http://purl.org/obo/owl/SO#SO_ke intergenic URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html intergenic variant sequence splice_site_variant EBI term - essential splice site - In the first 2 or the last 2 base pairs of an intron. The 5th base is on the donor (5') side of the intron. Updated to b in line with Cancer Genome Project at the Sanger. A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript. URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html essential_splice_site URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html splice site variant sequence splice_region_variant EBI term: splice site - 1-3 bps into an exon or 3-8 bps into an intron. A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron. URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html splice region variant splice_region_variant URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html sequence upstream_gene_variant Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references. A sequence variant located 5' of a gene. SO:ke http://purl.org/obo/owl/SO#SO_ke upstream gene variant sequence downstream_gene_variant Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references. A sequence variant located 3' of a gene. SO:ke http://purl.org/obo/owl/SO#SO_ke downstream gene variant sequence 5KB_downstream_variant EBI term Downstream variations - Within 5 kb downstream of the 3prime end of a transcript. A sequence variant located within 5 KB of the end of a gene. SO:ke http://purl.org/obo/owl/SO#SO_ke 5KB downstream variant downstream URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html within 5KB downstream sequence 500B_downstream_variant A sequence variant located within a half KB of the end of a gene. SO:ke http://purl.org/obo/owl/SO#SO_ke 500B downstream variant near-gene-3 ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd http://purl.org/obo/owl/ftp#ftp_//ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd sequence 5KB_upstream_variant EBI term Upstream variations - Within 5 kb upstream of the 5prime end of a transcript. A sequence variant located within 5KB 5' of a gene. SO:ke http://purl.org/obo/owl/SO#SO_ke 5kb upstream variant upstream URL:http://uswest.ensembl.org/info/docs/variation/index.html http://uswest.ensembl.org/info/docs/variation/index.html sequence 2KB_upstream_variant A sequence variant located within 2KB 5' of a gene. SO:ke http://purl.org/obo/owl/SO#SO_ke 2KB upstream variant near-gene-5 ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd http://purl.org/obo/owl/ftp#ftp_//ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd sequence rRNA_gene A gene that encodes for ribosomal RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke rRNA gene sequence piRNA_gene A gene that encodes for an piwi associated RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke piRNA gene sequence RNase_P_RNA_gene A gene that encodes an RNase P RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke RNase P RNA gene sequence RNase_MRP_RNA_gene A gene that encodes a RNase_MRP_RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke RNase MRP RNA gene sequence lincRNA_gene A gene that encodes large intervening non-coding RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke lincRNA gene sequence mathematically_defined_repeat Mathematically defined repeat regions are determined without regard to the biological origin of the repetitive region. The repeat units of a MDR are the overlapping oligomers of size k that were used to for the query. Tools that can annotate mathematically defined repeats include Tallymer (Kurtz et al 2008, BMC Genomics: 517) and RePS (Wang et al, Genome Res 12(5): 824-831.). A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness. SO:jestill http://purl.org/obo/owl/SO#SO_jestill mathematically defined repeat sequence telomerase_RNA_gene A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase. SO:ke http://purl.org/obo/owl/SO#SO_ke Telomerase RNA component telomerase RNA gene TERC sequence http:http://en.wikipedia.org/wiki/Telomerase_RNA_component http://purl.org/obo/owl/http#http_http://en.wikipedia.org/wiki/Telomerase_RNA_component targeting_vector An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications. MGD:tm http://purl.org/obo/owl/MGD#MGD_tm PMID:10354467 http://purl.org/obo/owl/PMID#PMID_10354467 targeting vector sequence genetic_marker A measurable sequence feature that varies within a population. SO:db http://purl.org/obo/owl/SO#SO_db genetic marker sequence DArT_marker A genetic marker, discovered using Diversity Arrays Technology (DArT) technology. SO:ke http://purl.org/obo/owl/SO#SO_ke DArT marker sequence kozak_sequence A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke kozak consensus kozak consensus sequence kozak sequence sequence URL:http://en.wikipedia.org/wiki/Kozak_consensus_sequence http://en.wikipedia.org/wiki/Kozak_consensus_sequence nested_transposon A transposon that is disrupted by the insertion of another element. SO:ke http://purl.org/obo/owl/SO#SO_ke nested transposon sequence nested_repeat A repeat that is disrupted by the insertion of another element. SO:ke http://purl.org/obo/owl/SO#SO_ke nested repeat sequence inframe_variant A sequence variant which does not cause a disruption of the translational reading frame. SO:ke http://purl.org/obo/owl/SO#SO_ke cds-indel inframe variant sequence inframe_codon_gain A sequence variant which gains a codon, and does not cause a disruption of the translational reading frame. SO:ke http://purl.org/obo/owl/SO#SO_ke inframe codon gain sequence inframe_codon_loss A sequence variant which loses a codon, and does not cause a disruption of the translational reading frame. SO:ke http://purl.org/obo/owl/SO#SO_ke inframe codon loss sequence retinoic_acid_responsive_element A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind. PMID:11327309 http://purl.org/obo/owl/PMID#PMID_11327309 PMID:19917671 http://purl.org/obo/owl/PMID#PMID_19917671 RARE retinoic acid responsive element sequence nucleotide_to_protein_binding_site A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. SO:ke http://purl.org/obo/owl/SO#SO_ke nucleotide to protein binding site sequence nucleotide_binding_site See GO:0000166 : nucleotide binding. A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues. SO:cb http://purl.org/obo/owl/SO#SO_cb nucleotide binding site sequence metal_binding_site See GO:0046872 : metal ion binding. A binding site that, in the molecule, interacts selectively and non-covalently with metal ions. SO:cb http://purl.org/obo/owl/SO#SO_cb metal binding site sequence ligand_binding_site A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone. SO:ke http://purl.org/obo/owl/SO#SO_ke ligand binding site sequence nested_tandem_repeat Tracker ID: 3052459. An NTR is a nested repeat of two distinct tandem motifs interspersed with each other. SO:AF http://purl.org/obo/owl/SO#SO_AF nested tandem repeat NTR sequence promoter_element promoter element sequence core_promoter_element core promoter element general transcription factor binding site sequence RNA_polymerase_II_TATA_box A TATA box core promoter of a gene transcribed by RNA polymerase II. PMID:16858867 http://purl.org/obo/owl/PMID#PMID_16858867 RNA polymerase II TATA box sequence RNA_polymerase_III_TATA_box A TATA box core promoter of a gene transcribed by RNA polymerase III. SO:ke http://purl.org/obo/owl/SO#SO_ke RNA polymerase III TATA box sequence BREd_motif A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G). PMID:16858867 http://purl.org/obo/owl/PMID#PMID_16858867 BREd BREd motif sequence DCE A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII. PMID:16858867 http://purl.org/obo/owl/PMID#PMID_16858867 downstream core element sequence DCE_SI A sub element of the DCE core promoter element, with consensus sequence CTTC. PMID:16858867 http://purl.org/obo/owl/PMID#PMID_16858867 SO:ke http://purl.org/obo/owl/SO#SO_ke DCE SI sequence DCE_SII A sub element of the DCE core promoter element with consensus sequence CTGT. PMID:16858867 http://purl.org/obo/owl/PMID#PMID_16858867 SO:ke http://purl.org/obo/owl/SO#SO_ke DCE SII sequence DCE_SIII A sub element of the DCE core promoter element with consensus sequence AGC. PMID:16858867 http://purl.org/obo/owl/PMID#PMID_16858867 SO:ke http://purl.org/obo/owl/SO#SO_ke DCE SIII sequence proximal_promoter_element proximal promoter element specific transcription factor binding site sequence RNApol_II_core_promoter The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes. PMID:16858867 http://purl.org/obo/owl/PMID#PMID_16858867 RNApol II core promoter sequence distal_promoter_element distal promoter element sequence bacterial_RNApol_promoter_sigma_70 bacterial RNA polymerase promoter sigma 70 sequence bacterial_RNApol_promoter_sigma54 bacterial RNA polymerase promoter sigma54 sequence minus_12_signal A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54. PMID:18331472 http://purl.org/obo/owl/PMID#PMID_18331472 minus 12 signal sequence minus_24_signal A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54. PMID:18331472 http://purl.org/obo/owl/PMID#PMID_18331472 minus 24 signal sequence A_box_type_1 The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true. An A box within an RNA polymerase III type 1 promoter. SO:ke http://purl.org/obo/owl/SO#SO_ke A box type 1 sequence A_box_type_2 The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true. An A box within an RNA polymerase III type 2 promoter. SO:ke http://purl.org/obo/owl/SO#SO_ke A box type 2 sequence intermediate_element A core promoter region of RNA polymerase III type 1 promoters. PMID:12381659 http://purl.org/obo/owl/PMID#PMID_12381659 IE intermediate element sequence regulatory_promoter_element A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region. PMID:12381659 http://purl.org/obo/owl/PMID#PMID_12381659 regulatory promoter element sequence transcription_regulatory_region A regulatory region that is involved in the control of the process of transcription. SO:ke http://purl.org/obo/owl/SO#SO_ke transcription regulatory region sequence translation_regulatory_region A regulatory region that is involved in the control of the process of translation. SO:ke http://purl.org/obo/owl/SO#SO_ke translation regulatory region sequence recombination_regulatory_region A regulatory region that is involved in the control of the process of recombination. SO:ke http://purl.org/obo/owl/SO#SO_ke recombination regulatory region sequence replication_regulatory_region A regulatory region that is involved in the control of the process of nucleotide replication. SO:ke http://purl.org/obo/owl/SO#SO_ke replication regulatory region sequence sequence_motif A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance. URL:http://en.wikipedia.org/wiki/Sequence_motif http://en.wikipedia.org/wiki/Sequence_motif sequence motif sequence URL:http://en.wikipedia.org/wiki/Sequence_motif http://en.wikipedia.org/wiki/Sequence_motif experimental_feature_attribute An attribute of an experimentally derived feature. SO:ke http://purl.org/obo/owl/SO#SO_ke experimental feature attribute sequence score The score of an experimentally derived feature such as a p-value. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence quality_value An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score. SO:ke http://purl.org/obo/owl/SO#SO_ke quality value sequence restriction_enzyme_recognition_site The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site. SO:ke http://purl.org/obo/owl/SO#SO_ke restriction endonuclease recognition site restriction enzyme recognition site sequence restriction_enzyme_cleavage_junction The boundary at which a restriction enzyme breaks the nucleotide sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke restriction enzyme cleavage junction sequence five_prime_restriction_enzyme_junction The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke 5' restriction enzyme junction sequence three_prime_restriction_enzyme_junction 3' restriction enzyme junction sequence blunt_end_restriction_enzyme_cleavage_site blunt end restriction enzyme cleavage site sequence sticky_end_restriction_enzyme_cleavage_site sticky end restriction enzyme cleavage site sequence blunt_end_restriction_enzyme_cleavage_junction A restriction enzyme cleavage site where both strands are cut at the same position. SO:ke http://purl.org/obo/owl/SO#SO_ke blunt end restriction enzyme cleavage site sequence single_strand_restriction_enzyme_cleavage_site A restriction enzyme cleavage site whereby only one strand is cut. SO:ke http://purl.org/obo/owl/SO#SO_ke single strand restriction enzyme cleavage site sequence restriction_enzyme_single_strand_overhang A terminal region of DNA sequence where the end of the region is not blunt ended. SO:ke http://purl.org/obo/owl/SO#SO_ke single strand overhang sticky end sequence experimentally_defined_binding_region A region that has been implicated in binding although the exact coordinates of binding may be unknown. SO:ke http://purl.org/obo/owl/SO#SO_ke experimentally defined binding region sequence ChIP_seq_region A region of sequence identified by CHiP seq technology to contain a protein binding site. SO:ke http://purl.org/obo/owl/SO#SO_ke ChIP seq region sequence ASPE_primer "A primer containing an SNV at the 3' end for accurate genotyping. URL:http://www.ncbi.nlm.nih.gov/pubmed/11252801 http://www.ncbi.nlm.nih.gov/pubmed/11252801 allele specific primer extension primer ASPE primer sequence dCAPS_primer A primer with one or more mis-matches to the DNA template corresponding to a position within a restriction enzyme recognition site. URL:http://www.ncbi.nlm.nih.gov/pubmed/9628033 http://www.ncbi.nlm.nih.gov/pubmed/9628033 dCAPS primer derived cleaved amplified polymorphic primer sequence histone_modification Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation. http:en.wikipedia.org/wiki/Histone http://purl.org/obo/owl/http#http_en.wikipedia.org/wiki/Histone histone modification histone modification site sequence histone_methylation_site A histone modification site where the modification is the methylation of the residue. SO:ke http://purl.org/obo/owl/SO#SO_ke histone methylation histone methylation site sequence histone_acetylation_site A histone modification where the modification is the acylation of the residue. SO:ke http://purl.org/obo/owl/SO#SO_ke histone acetylation histone acetylatoin site sequence H3K9_acetylation_site A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated. URL:http://en.wikipedia.org/wiki/Histone http://en.wikipedia.org/wiki/Histone H3K9 acetylation site H3K9Ac sequence H3K14_acetylation_site A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated. URL:http://en.wikipedia.org/wiki/Histone http://en.wikipedia.org/wiki/Histone H3K14 acetylation site H3K14Ac sequence H3K4_monomethylation_site A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated. URL:http://en.wikipedia.org/wiki/Histone http://en.wikipedia.org/wiki/Histone H3K4 mono-methylation site H3K4me1 sequence H3K4_trimethylation A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated. URL:http://en.wikipedia.org/wiki/Histone http://en.wikipedia.org/wiki/Histone H3K4 tri-methylation H3K4me3 sequence H3K9_trimethylation_site A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated. URL:http://en.wikipedia.org/wiki/Histone http://en.wikipedia.org/wiki/Histone H3K9 tri-methylation site H3K9Me3 sequence H3K27_monomethylation_site A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated. URL:http://en.wikipedia.org/wiki/Histone http://en.wikipedia.org/wiki/Histone H2K27 mono-methylation site H2K27Me1 sequence H3K27_trimethylation_site A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated. URL:http://en.wikipedia.org/wiki/Histone http://en.wikipedia.org/wiki/Histone H3K27 tri-methylation site H3K27Me3 sequence H3K79_monomethylation_site A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated. URL:http://en.wikipedia.org/wiki/Histone http://en.wikipedia.org/wiki/Histone H3K79 mono-methylation site H3K79me1 sequence H3K79_dimethylation_site A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated. URL:http://en.wikipedia.org/wiki/Histone http://en.wikipedia.org/wiki/Histone H3K79 di-methylation site H3K79Me2 sequence H3K79_trimethylation_site A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated. URL:http://en.wikipedia.org/wiki/Histone http://en.wikipedia.org/wiki/Histone H3K79 tri-methylation site H3K79Me3 sequence H4K20_monomethylation_site A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H34histone protein is mono-methylated. URL:http://en.wikipedia.org/wiki/Histone http://en.wikipedia.org/wiki/Histone H4K20 mono-methylation site H4K20Me1 sequence H2BK5_monomethylation_site A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated. URL:http://en.wikipedia.org/wiki/Histone http://en.wikipedia.org/wiki/Histone H2BK5 mono-methylation site sequence ISRE Term requested via tracker (2981725) by Alan Ruttenberg, April 2010. It has been described as both an enhancer and a promoter, so the parent is the more general term. An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding. URL:http://genesdev.cshlp.org/content/2/4/383.abstrac http://genesdev.cshlp.org/content/2/4/383.abstrac interferon stimulated response element sequence histone_ubiqitination_site A histone modification site where ubiquitin may be added. SO:ke http://purl.org/obo/owl/SO#SO_ke histone ubiquitination site sequence H2B_ubiquitination_site A histone modification site on H2B where ubiquitin may be added. SO:ke http://purl.org/obo/owl/SO#SO_ke H2BUbiq sequence H3K18_acetylation_site A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated. SO:ke http://purl.org/obo/owl/SO#SO_ke H3K18 acetylation site H3K18Ac sequence H3K23_acylation site A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated. SO:ke http://purl.org/obo/owl/SO#SO_ke H3K23 acylation site H3K23Ac sequence epigenetically_modified_region A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence. URL:http://en.wikipedia.org/wiki/Epigenetics http://en.wikipedia.org/wiki/Epigenetics SO:ke http://purl.org/obo/owl/SO#SO_ke epigenetically modified region sequence H3K27_acylation_site A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated. SO:ke http://purl.org/obo/owl/SO#SO_ke H3K27 acylation site H3K27Ac sequence H3K36_monomethylation_site A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated. SO:ke http://purl.org/obo/owl/SO#SO_ke H3K36 mono-methylation site H3K36<Me1 sequence H3K36_dimethylation_site A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated. SO:ke http://purl.org/obo/owl/SO#SO_ke H3K36 di-methylation site H3K36Me2 sequence H3K36_trimethylation_site A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated. SO:ke http://purl.org/obo/owl/SO#SO_ke H3K36 tri-methylation site H3K36Me3 sequence H3K4_dimethylation_site A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated. SO:ke http://purl.org/obo/owl/SO#SO_ke H3K4 di-methylation site H3K4Me2 sequence H3K27_dimethylation_site A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated. SO:ke http://purl.org/obo/owl/SO#SO_ke H3K27 di-methylation site H3K27Me2 sequence H3K9_monomethylation_site A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated. SO:ke http://purl.org/obo/owl/SO#SO_ke H3K9 mono-methylation site H3K9Me1 sequence H3K9_dimethylation_site A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated. SO:ke http://purl.org/obo/owl/SO#SO_ke H3K9 di-methylation site H3K9Me2 sequence H4K16_acylation_site A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated. SO:ke http://purl.org/obo/owl/SO#SO_ke H4K16 acylation_site H4K16Ac sequence H4K5_acylation_site A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated. SO:ke http://purl.org/obo/owl/SO#SO_ke H4K5 acylation site H4K5Ac sequence H4K8_acylation site A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated. SO:KE http://purl.org/obo/owl/SO#SO_KE H4K8 acylation site H4K8Ac sequence H3K27_methylation_site A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated. SO:ke http://purl.org/obo/owl/SO#SO_ke H3K27 methylation site sequence H3K36_methylation_site A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated. SO:ke http://purl.org/obo/owl/SO#SO_ke H3K36 methylation site sequence H3K4_methylation_site A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated. SO:ke http://purl.org/obo/owl/SO#SO_ke H3K4 methylation site sequence H3K79_methylation_site A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated. SO:ke http://purl.org/obo/owl/SO#SO_ke H3K79 methylation site sequence H3K9_methylation_site A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated. SO:ke http://purl.org/obo/owl/SO#SO_ke H3K9 methylation site sequence histone_acylation_region A histone modification, whereby the histone protein is acylated at multiple sites in a region. SO:ke http://purl.org/obo/owl/SO#SO_ke histone acylation region sequence H4K_acylation_region A region of the H4 histone whereby multiple lysines are acylated. SO:ke http://purl.org/obo/owl/SO#SO_ke H4K acylation region H4KAc sequence gene_with_non_canonical_start_codon Requested by flybase, Dec 2010. A gene with a start codon other than AUG. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence gene_with_start_codon_CUG Requested by flybase, Dec 2010. A gene with a translational start codon of CUG. SO:mc http://purl.org/obo/owl/SO#SO_mc sequence pseudogenic_gene_segment A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product. SO:hd http://purl.org/obo/owl/SO#SO_hd sequence copy_number_gain A sequence alteration whereby the copy number of a given regions is greater than the reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke copy number gain gain URL:http://www.ncbi.nlm.nih.gov/dbvar/ http://www.ncbi.nlm.nih.gov/dbvar/ sequence copy_number_loss A sequence alteration whereby the copy number of a given region is less than the reference sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke copy number loss loss URL:http://www.ncbi.nlm.nih.gov/dbvar/ http://www.ncbi.nlm.nih.gov/dbvar/ sequence UPD Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent. SO:BM http://purl.org/obo/owl/SO#SO_BM uniparental disomy UPD URL:http://www.ncbi.nlm.nih.gov/dbvar/ http://www.ncbi.nlm.nih.gov/dbvar/ sequence http:http://en.wikipedia.org/wiki/Uniparental_disomy http://purl.org/obo/owl/http#http_http://en.wikipedia.org/wiki/Uniparental_disomy maternal_uniparental_disomy Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father. SO:bm http://purl.org/obo/owl/SO#SO_bm maternal uniparental disomy sequence paternal_uniparental_disomy Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother. SO:bm http://purl.org/obo/owl/SO#SO_bm paternal uniparental disomy sequence open_chromatin_region Requested by John Calley 3125900. A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA. SO:cb http://purl.org/obo/owl/SO#SO_cb sequence SL3_acceptor_site A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:nlw http://purl.org/obo/owl/SO#SO_nlw sequence SL4_acceptor_site A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:nlw http://purl.org/obo/owl/SO#SO_nlw sequence SL5_acceptor_site A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:nlw http://purl.org/obo/owl/SO#SO_nlw sequence SL6_acceptor_site A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:nlw http://purl.org/obo/owl/SO#SO_nlw sequence SL7_acceptor_site A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:nlw http://purl.org/obo/owl/SO#SO_nlw sequence SL8_acceptor_site A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:nlw http://purl.org/obo/owl/SO#SO_nlw sequence SL9_acceptor_site A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:nlw http://purl.org/obo/owl/SO#SO_nlw sequence SL10_accceptor_site A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:nlw http://purl.org/obo/owl/SO#SO_nlw sequence SL11_acceptor_site A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:nlw http://purl.org/obo/owl/SO#SO_nlw sequence SL12_acceptor_site A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:nlw http://purl.org/obo/owl/SO#SO_nlw sequence duplicated_pseudogene A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence. URL:http://en.wikipedia.org/wiki/Pseudogene http://en.wikipedia.org/wiki/Pseudogene duplicated pseudogene sequence unitary_pseudogene This is different from a non processed pseudogene because the gene was not duplicated. An example is the L-gulono-lactone oxidase pseudogene in primates. A pseudogene, deactivated from original state by mutation, fixed in a population. URL:http://en.wikipedia.org/wiki/Pseudogene http://en.wikipedia.org/wiki/Pseudogene SO:ke http://purl.org/obo/owl/SO#SO_ke disabled gene unitary pseudogene sequence non_processed_pseudogene A pseudogene that arose from a means other than retrotransposition. SO:ke http://purl.org/obo/owl/SO#SO_ke non processed pseudogene sequence variant_quality A dependent entity that inheres in a bearer, a sequence variant. PMID:17597783 http://purl.org/obo/owl/PMID#PMID_17597783 SO:ke http://purl.org/obo/owl/SO#SO_ke variant quality sequence variant_origin A quality inhering in a variant by virtue of its origin. PMID:17597783 http://purl.org/obo/owl/PMID#PMID_17597783 SO:ke http://purl.org/obo/owl/SO#SO_ke variant origin sequence variant_frequency A physical quality which inheres to the variant by virtue of the number instances of the variant within a population. PMID:17597783 http://purl.org/obo/owl/PMID#PMID_17597783 SO:ke http://purl.org/obo/owl/SO#SO_ke variant frequency sequence unique_variant A physical quality which inheres to the variant by virtue of the number instances of the variant within a population. SO:ke http://purl.org/obo/owl/SO#SO_ke unique variant sequence rare_variant rare variant sequence polymorphic_variant polymorphic variant sequence common_variant common variant sequence fixed_variant fixed variant sequence variant_phenotype A quality inhering in a variant by virtue of its phenotype. PMID:17597783 http://purl.org/obo/owl/PMID#PMID_17597783 SO:ke http://purl.org/obo/owl/SO#SO_ke variant phenotype sequence benign_variant benign variant sequence disease_associated_variant disease associated variant sequence disease_causing_variant disease causing variant sequence lethal_variant lethal variant sequence quantitative_variant quantitative variant sequence maternal_variant maternal variant sequence paternal_variant paternal variant sequence somatic_variant somatic variant sequence germline_variant germline variant sequence pedigree_specific_variant pedigree specific variant sequence population_specific_variant population specific variant sequence de_novo_variant de novo variant sequence TF_binding_site_variant A sequence variant located within a transcription factor binding site. EBI:fc http://purl.org/obo/owl/EBI#EBI_fc sequence missense_codon A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different amino acid. SO:ke http://purl.org/obo/owl/SO#SO_ke missense ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd http://purl.org/obo/owl/ftp#ftp_//ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd missense codon sequence URL:http://en.wikipedia.org/wiki/Missense_mutation http://en.wikipedia.org/wiki/Missense_mutation complex_structural_alteration A structural sequence alteration where there are multiple equally plausible explanations for the change. SO:ke http://purl.org/obo/owl/SO#SO_ke complex URL:http://www.ncbi.nlm.nih.gov/dbvar/ http://www.ncbi.nlm.nih.gov/dbvar/ sequence structural_alteration sequence loss_of_heterozygosity LOH loss of heterozygosity sequence splice_donor_5th_base_variant A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript. EBI:gr http://purl.org/obo/owl/EBI#EBI_gr splice donor 5th base variant sequence U_box An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription. PMID:10556309 http://purl.org/obo/owl/PMID#PMID_10556309 PMID:11577982 http://purl.org/obo/owl/PMID#PMID_11577982 PMID:9649446 http://purl.org/obo/owl/PMID#PMID_9649446 sequence mating_type_region A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Mating-type_region http://en.wikipedia.org/wiki/Mating-type_region paired_end_fragment An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence exon_variant A sequence variant that changes exon sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence non_coding_exon_variant A sequence variant that changes non-coding exon sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence clone_end A read from an end of the clone sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke clone end sequence point_centromere A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae. PMID:7502067 http://purl.org/obo/owl/PMID#PMID_7502067 SO:vw http://purl.org/obo/owl/SO#SO_vw point centromere sequence regional_centromere A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions. PMID:7502067 http://purl.org/obo/owl/PMID#PMID_7502067 SO:vw http://purl.org/obo/owl/SO#SO_vw regional centromere sequence regional_centromere_central_core A conserved region within the central region of a modular centromere, where the kinetochore is formed. SO:vw http://purl.org/obo/owl/SO#SO_vw regional centromere central core sequence centromeric_repeat A repeat region found within the modular centromere. SO:ke http://purl.org/obo/owl/SO#SO_ke centromeric repeat sequence regional_centromere_inner_repeat_region The inner repeat region of a modular centromere. This region is adjacent to the central core, on each chromosome arm. SO:vw http://purl.org/obo/owl/SO#SO_vw regional centromere inner repeat region sequence regional_centromere_outer_repeat_region The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms. SO:vw http://purl.org/obo/owl/SO#SO_vw regional centromere outer repeat region sequence tasiRNA The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene. PMID:16145017 http://purl.org/obo/owl/PMID#PMID_16145017 trans acting small interfering RNA sequence tasiRNA_primary_transcript A primary transcript encoding a tasiRNA. PMID:16145017 http://purl.org/obo/owl/PMID#PMID_16145017 sequence increased_polyadenylation_variant Term requested by M. Dumontier, June 1 2011. A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference. SO:ke http://purl.org/obo/owl/SO#SO_ke increased polyadenylation variant sequence decreased_polyadenylation_variant Term requested by M. Dumontier, June 1 2011. A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference. SO:ke http://purl.org/obo/owl/SO#SO_ke decreased polyadenylation variant sequence DDB_box Note: PMID:18794354 describes the DDB box, and has lots of alignments, but doesn't actually come out with a consensus sequence. A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases. PMID:18794354 http://purl.org/obo/owl/PMID#PMID_18794354 PMID:19818632 http://purl.org/obo/owl/PMID#PMID_19818632 DDB box DDB-box sequence destruction_box A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN. PMID:12208841 http://purl.org/obo/owl/PMID#PMID_12208841 PMID:1842691 http://purl.org/obo/owl/PMID#PMID_1842691 D-box destruction box sequence ER_retention_signal A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL. doi:10.1093/jxb/50.331.157 http://purl.org/obo/owl/doi#doi_10.1093/jxb/50.331.157 PMID:2077689 http://purl.org/obo/owl/PMID#PMID_2077689 endoplasmic reticulum retention signal ER retention signal sequence KEN_box A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN. PMID:10733526 http://purl.org/obo/owl/PMID#PMID_10733526 PMID:1220884 http://purl.org/obo/owl/PMID#PMID_1220884 PMID:18426916 http://purl.org/obo/owl/PMID#PMID_18426916 KEN box sequence mitochondrial_targeting_signal A polypeptide region that targets a polypeptide to the mitochondrion. PomBase:mah http://purl.org/obo/owl/PomBase#PomBase_mah mitochondrial signal sequence mitochondrial targeting signal MTS sequence signal_anchor A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane. URL:http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php signal anchor uncleaved signal peptide sequence PIP_box A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains. PMID:9631646 http://purl.org/obo/owl/PMID#PMID_9631646 PIP box sequence phosphorylation_site A post-translationally modified region in which residues of the protein are modified by phosphorylation. PomBase:mah http://purl.org/obo/owl/PomBase#PomBase_mah phosphorylation site sequence transmembrane_helix A region that traverses the lipid bilayer and adopts a helical secondary structure. PomBase:mah http://purl.org/obo/owl/PomBase#PomBase_mah transmembrane helix sequence vacuolar_sorting_signal A polypeptide region that targets a polypeptide to the vacuole. PomBase:mah http://purl.org/obo/owl/PomBase#PomBase_mah vacuolar sorting signal sequence coding_variant_quality sequence synonymous sequence non_synonymous sequence inframe An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence non_synonymous_variant A sequence_variant which is predicted to change the protein encoded in the coding sequence. EBI:gr http://purl.org/obo/owl/EBI#EBI_gr sequence synonymous_variant sequence inframe_change_in_CDS_length inframe change in CDS length sequence inframe_increase_in_CDS_length An inframe_non_synonymous_variant that inserts bases into in the coding sequence. EBI:gr http://purl.org/obo/owl/EBI#EBI_gr inframe increase in CDS length sequence inframe_decrease_in_CDS_length An inframe_non_synonymous_variant that deletes bases from the coding sequence. EBI:gr http://purl.org/obo/owl/EBI#EBI_gr inframe decrease in CDS length sequence conservative_increase_in_CDS_length An inframe_increase_in_cds_length that inserts one or more codons into the coding sequence between existing codons. EBI:gr http://purl.org/obo/owl/EBI#EBI_gr conservative increase in CDS length sequence disruptive_increase_in_CDS_length An inframe_increase_in_cds_length that inserts one or more codons into the coding sequence within an existing codon. EBI:gr http://purl.org/obo/owl/EBI#EBI_gr disruptive increase in CDS length sequence conservative_decrease_in_CDS_length An inframe_decrease_in_cds_length that deletes one or more entire codons from the coding sequence but does not change any remaining codons. EBI:gr http://purl.org/obo/owl/EBI#EBI_gr conservative decrease in CDS length sequence disruptive_decrease_in_CDS_length An inframe_decrease_in_cds_length that deletes bases from the coding sequence starting within an existing codon. EBI:gr http://purl.org/obo/owl/EBI#EBI_gr disruptive decrease in CDS length sequence mRNA_read Requested by Bayer Cropscience June, 2011. A sequencer read of an mRNA substrate. SO:ke http://purl.org/obo/owl/SO#SO_ke mRNA read sequence genomic_DNA_read A sequencer read of a genomic DNA substrate. SO:ke http://purl.org/obo/owl/SO#SO_ke genomic DNA read sequence mRNA_contig Requested by Bayer Cropscience June, 2011. A contig composed of mRNA_reads. SO:ke http://purl.org/obo/owl/SO#SO_ke mRNA contig sequence AFLP_fragment Requested by Bayer Cropscience June, 2011. A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments. GMOD:ea http://purl.org/obo/owl/GMOD#GMOD_ea AFLP AFLP fragment AFLP-PCR amplified fragment length polymorphism amplified fragment length polymorphism PCR sequence URL:http://en.wikipedia.org/wiki/Amplified_fragment_length_polymorphism http://en.wikipedia.org/wiki/Amplified_fragment_length_polymorphism protein_hmm_match A match to a protein HMM such as pfam. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence immunoglobulin_region A region of immunoglobulin sequence, either constant or variable. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence V_region The variable region of an immunoglobulin polypeptide sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence C_region The constant region of an immunoglobulin polypeptide sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence N_region Extra nucleotides inserted between rearranged immunoglobulin segments. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence S_region The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence mobile_element_insertion Requested by the ebi. A kind of insertion where the inserted sequence is a mobile element. EBI:dvga http://purl.org/obo/owl/EBI#EBI_dvga mobile element insertion sequence novel_sequence_insertion Requested by the NCBI. An insertion the sequence of which cannot be mapped to the reference genome. NCBI:th http://purl.org/obo/owl/NCBI#NCBI_th novel sequence insertion sequence CSL_response_element A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors. PMID:19101542 http://purl.org/obo/owl/PMID#PMID_19101542 CSL response element sequence GATA_box A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G). PMID:8321208 http://purl.org/obo/owl/PMID#PMID_8321208 GATA box GATA element sequence polymorphic_pseudogene This terms is used by ensembl and vega. Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated. JAX:hd http://purl.org/obo/owl/JAX#JAX_hd polymorphic psuedogene sequence AP_1_binding_site A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors. PMID:1899230 http://purl.org/obo/owl/PMID#PMID_1899230 PMID:3034432 http://purl.org/obo/owl/PMID#PMID_3034432 PMID:3125983 http://purl.org/obo/owl/PMID#PMID_3125983 AP-1 binding site sequence CRE A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors. PMID:11483355 http://purl.org/obo/owl/PMID#PMID_11483355 PMID:11483993 http://purl.org/obo/owl/PMID#PMID_11483993 ATF/CRE site PMID:11483993 http://purl.org/obo/owl/PMID#PMID_11483993 cyclic AMP response element sequence CuRE A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast). PMID:10593913 http://purl.org/obo/owl/PMID#PMID_10593913 PMID:9188496 http://purl.org/obo/owl/PMID#PMID_9188496 PMID:9211922 http://purl.org/obo/owl/PMID#PMID_9211922 copper-response element sequence DRE A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis. PMID:11073995 http://purl.org/obo/owl/PMID#PMID_11073995 PMID:8668127 http://purl.org/obo/owl/PMID#PMID_8668127 DNA damage response element sequence FLEX_element A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain. PMID:10747048 http://purl.org/obo/owl/PMID#PMID_10747048 PMID:14871934 http://purl.org/obo/owl/PMID#PMID_14871934 FLEX element sequence forkhead_motif A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain. PMID:15195092 http://purl.org/obo/owl/PMID#PMID_15195092 forkhead motif sequence homol_D_box A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence. PMID:7501449 http://purl.org/obo/owl/PMID#PMID_7501449 PMID:8458332 http://purl.org/obo/owl/PMID#PMID_8458332 homol D box sequence homol_E_box A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence. PMID:7501449 http://purl.org/obo/owl/PMID#PMID_7501449 homol E box sequence HSE A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF. PMID:17347150 http://purl.org/obo/owl/PMID#PMID_17347150 PMID:8689565 http://purl.org/obo/owl/PMID#PMID_8689565 heat shock element sequence iron_repressed_GATA_element The synonym IDP (GATA) is found in an annotation but un-traced as far as literature goes. A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron. PMID:11956219 http://purl.org/obo/owl/PMID#PMID_11956219 PMID:17211681 http://purl.org/obo/owl/PMID#PMID_17211681 IDP (GATA) iron repressed GATA element sequence mating_type_M_box Note that this should not be confused with the M-box that has consensus sequence CATGTG and is bound by bHLH transcription factors such as MITF. A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc. PMID:9233811 http://purl.org/obo/owl/PMID#PMID_9233811 mating type M-box sequence androgen_response_element A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen. PMID:21796522 http://purl.org/obo/owl/PMID#PMID_21796522 androgen response element ARE sequence smFISH_probe A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment. PMID:18806792 http://purl.org/obo/owl/PMID#PMID_18806792 single molecule fish probe smFISH probe sequence MCB A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle. PMID:16285853 http://purl.org/obo/owl/PMID#PMID_16285853 MluI cell cycle box sequence CCAAT_motif A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels. PMID:16963626 http://purl.org/obo/owl/PMID#PMID_16963626 CCAAT motif sequence Ace2_UAS A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2. PMID:16678171 http://purl.org/obo/owl/PMID#PMID_16678171 Ace2 upstream activating sequence sequence TR_box A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis. PMID:1657709 http://purl.org/obo/owl/PMID#PMID_1657709 TR box sequence STREP_motif A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2. PMID:11739717 http://purl.org/obo/owl/PMID#PMID_11739717 STREP motif stress-starvation response element of Schizosaccharomyces pombe sequence rDNA_intergenic_spacer_element A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1). PMID:9016645 http://purl.org/obo/owl/PMID#PMID_9016645 rDIS sequence sterol_regulatory_element A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs. GO:mah http://purl.org/obo/owl/GO#GO_mah PMID:11111080 http://purl.org/obo/owl/PMID#PMID_11111080 PMID:16537923 http://purl.org/obo/owl/PMID#PMID_16537923 SRE GO:mah http://purl.org/obo/owl/GO#GO_mah sequence GT_dinucleotide_repeat paper:PMID:16043634. A dinucleotide repeat region composed of GT repeating elements. SO:ke http://purl.org/obo/owl/SO#SO_ke d(GT)n sequence GTT_trinucleotide_repeat A trinucleotide repeat region composed of GTT repeating elements. SO:ke http://purl.org/obo/owl/SO#SO_ke d(GTT) sequence Sap1_recognition_motif A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats. PMID:16166653 http://purl.org/obo/owl/PMID#PMID_16166653 PMID:7651412 http://purl.org/obo/owl/PMID#PMID_7651412 Sap1 recognitions site sequence CDRE_motif An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA. PMID:16928959 http://purl.org/obo/owl/PMID#PMID_16928959 calcineurin-dependent response element PMID:16928959 http://purl.org/obo/owl/PMID#PMID_16928959 CDRE motif sequence BAC_read_contig Requested by Bayer Cropscience December, 2011. A contig of BAC reads. GMOD:ea http://purl.org/obo/owl/GMOD#GMOD_ea BAC read contig sequence candidate_gene Requested by Bayer Cropscience December, 2011. A gene suspected of being involved in the expression of a trait. GMOD:ea http://purl.org/obo/owl/GMOD#GMOD_ea candidate gene target gene sequence positional_candidate_gene equested by Bayer Cropscience December, 2011. A candidate gene whose association with a trait is based on the gene's location on a chromosome. GMOD:ea http://purl.org/obo/owl/GMOD#GMOD_ea positional candidate gene positional target gene sequence functional_candidate_gene A candidate gene whose function has something in commonnbiologically with the trait under investigation. A candidate gene whose function has something in common biologically with the trait under investigation. GMOD:ea http://purl.org/obo/owl/GMOD#GMOD_ea functional candidate gene functional target gene sequence enhancerRNA A short ncRNA that is transcribed from an enhancer. May have a regulatory function. doi:10.1038/465173a http://purl.org/obo/owl/doi#doi_10.1038/465173a SO:cjm http://purl.org/obo/owl/SO#SO_cjm eRNA sequence PCB A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle. GO:mah http://purl.org/obo/owl/GO#GO_mah PMID:12411492 http://purl.org/obo/owl/PMID#PMID_12411492 sequence regulatory_region A region of sequence that is involved in the control of a biological process. SO:ke http://purl.org/obo/owl/SO#SO_ke regulatory region sequence URL:http://en.wikipedia.org/wiki/Regulatory_region http://en.wikipedia.org/wiki/Regulatory_region U14_snoRNA_primary_transcript The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA. PMID:2251119 http://purl.org/obo/owl/PMID#PMID_2251119 4.5S snRNA primary transcript U14 snoRNA primary transcript sequence methylation_guide_snoRNA Has RNA 2'-O-ribose methylation guide activity (GO:0030561). A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue. GOC:mah http://purl.org/obo/owl/GOC#GOC_mah PMID:12457565 http://purl.org/obo/owl/PMID#PMID_12457565 methylation guide snoRNA sequence rRNA_cleavage_RNA An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules. GOC:kgc http://purl.org/obo/owl/GOC#GOC_kgc rRNA cleavage RNA sequence exon_of_single_exon_gene An exon that is the only exon in a gene. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb exon of single exon gene single_exon singleton exon sequence cassette_array_member cassette array member sequence gene_cassette_member gene cassette member sequence gene_subarray_member gene subarray member sequence primer_binding_site Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html primer binding site sequence URL:http://en.wikipedia.org/wiki/Primer_binding_site http://en.wikipedia.org/wiki/Primer_binding_site gene_array This would include, for example, a cluster of genes each encoding the major ribosomal RNAs and a cluster of histone gene subarrays. An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so. SO:ma http://purl.org/obo/owl/SO#SO_ma gene array sequence gene_subarray This would include, for example, a cluster of genes encoding different histones. A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function. SO:ma http://purl.org/obo/owl/SO#SO_ma gene subarray sequence gene_cassette This would include, for example, the mating type gene cassettes of S. cerevisiae. Gene cassettes usually exist as linear sequences as part of a larger DNA molecule, such as a chromosome or plasmid. A gene that can be substituted for a related gene at a different site in the genome. SGD:se http://purl.org/obo/owl/SGD#SGD_se gene cassette sequence URL:http://en.wikipedia.org/wiki/Gene_cassette http://en.wikipedia.org/wiki/Gene_cassette gene_cassette_array This would include, for example, the arrays of non-functional VSG genes of Trypanosomes. An array of non-functional genes whose members, when captured by recombination form functional genes. SO:ma http://purl.org/obo/owl/SO#SO_ma gene cassette array sequence gene_group A collection of related genes. SO:ma http://purl.org/obo/owl/SO#SO_ma gene group sequence selenocysteine_tRNA_primary_transcript A primary transcript encoding seryl tRNA (SO:000269). SO:ke http://purl.org/obo/owl/SO#SO_ke selenocysteine tRNA primary transcript sequence selenocysteinyl_tRNA A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke selenocysteinyl tRNA selenocysteinyl-transfer ribonucleic acid selenocysteinyl-transfer RNA sequence syntenic_region A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species. URL:http://www.informatics.jax.org/silverbook/glossary.shtml http://www.informatics.jax.org/silverbook/glossary.shtml syntenic region sequence biochemical_region_of_peptide Range. A region of a peptide that is involved in a biochemical function. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR biochemical motif biochemical region of peptide biochemical_region sequence molecular_contact_region Range. A region that is involved a contact with another molecule. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR molecular contact region sequence intrinsically_unstructured_polypeptide_region A region of polypeptide chain with high conformational flexibility. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR disordered region intrinsically unstructured polypeptide region sequence catmat_left_handed_three A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ catmat-3l sequence catmat_left_handed_four A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ catmat-4l sequence catmat_right_handed_three A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ catmat-3r sequence catmat_right_handed_four A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ catmat-4r sequence alpha_beta_motif A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/msd-srv/msdmotif/ http://www.ebi.ac.uk/msd-srv/msdmotif/ alpha beta motif sequence lipoprotein_signal_peptide A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR lipoprotein signal peptide prokaryotic membrane lipoprotein lipid attachment site sequence no_output An experimental region wherean analysis has been run and not produced any annotation. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR no output sequence cleaved_peptide_region Range. The cleaved_peptide_regon is the a region of peptide sequence that is cleaved during maturation. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR cleaved peptide region sequence peptide_coil Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds). EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR coil peptide coil random coil sequence hydrophobic_region_of_peptide Range. Hydrophobic regions are regions with a low affinity for water. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR hydropathic hydrophobic region of peptide hydrophobic_region hydrophobicity sequence n_terminal_region The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa). EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR N-region sequence c_terminal_region The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa). EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR C-region sequence central_hydrophobic_region_of_signal_peptide The central, hydrophobic region of the signal peptide (approx 7-15 aa). EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR central hydrophobic region of signal peptide central_hydrophobic_region H-region sequence polypeptide_conserved_motif A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR motif sequence polypeptide_binding_motif A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR binding uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type polypeptide binding motif sequence polypeptide_catalytic_motif A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR catalytic_motif polypeptide catalytic motif sequence polypeptide_DNA_contact A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR SO:ke http://purl.org/obo/owl/SO#SO_ke polypeptide DNA contact sequence polypeptide_conserved_region A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR polypeptide conserved region sequence substitution A sequence alteration where the length of the change in the variant is the same as that of the reference. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence complex_substitution 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 http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html complex substitution sequence point_mutation A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. SO:immuno_workshop http://purl.org/obo/owl/SO#SO_immuno_workshop point mutation sequence URL:http://en.wikipedia.org/wiki/Point_mutation http://en.wikipedia.org/wiki/Point_mutation transition Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html sequence pyrimidine_transition A substitution of a pyrimidine, C or T, for another pyrimidine. SO:ke http://purl.org/obo/owl/SO#SO_ke pyrimidine transition sequence C_to_T_transition A transition of a cytidine to a thymine. SO:ke http://purl.org/obo/owl/SO#SO_ke C to T transition sequence C_to_T_transition_at_pCpG_site The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html C to T transition at pCpG site sequence T_to_C_transition T to C transition sequence purine_transition A substitution of a purine, A or G, for another purine. SO:ke http://purl.org/obo/owl/SO#SO_ke purine transition sequence A_to_G_transition A transition of an adenine to a guanine. SO:ke http://purl.org/obo/owl/SO#SO_ke A to G transition sequence G_to_A_transition A transition of a guanine to an adenine. SO:ke http://purl.org/obo/owl/SO#SO_ke G to A transition sequence transversion Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html sequence URL:http://en.wikipedia.org/wiki/Transversion http://en.wikipedia.org/wiki/Transversion pyrimidine_to_purine_transversion Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G. SO:ke http://purl.org/obo/owl/SO#SO_ke pyrimidine to purine transversion sequence C_to_A_transversion A transversion from cytidine to adenine. SO:ke http://purl.org/obo/owl/SO#SO_ke C to A transversion sequence C_to_G_transversion C to G transversion sequence T_to_A_transversion A transversion from T to A. SO:ke http://purl.org/obo/owl/SO#SO_ke T to A transversion sequence T_to_G_transversion A transversion from T to G. SO:ke http://purl.org/obo/owl/SO#SO_ke T to G transversion sequence purine_to_pyrimidine_transversion Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T. SO:ke http://purl.org/obo/owl/SO#SO_ke purine to pyrimidine transversion sequence A_to_C_transversion A transversion from adenine to cytidine. SO:ke http://purl.org/obo/owl/SO#SO_ke A to C transversion sequence A_to_T_transversion A transversion from adenine to thymine. SO:ke http://purl.org/obo/owl/SO#SO_ke A to T transversion sequence G_to_C_transversion A transversion from guanine to cytidine. SO:ke http://purl.org/obo/owl/SO#SO_ke G to C transversion sequence G_to_T_transversion A transversion from guanine to thymine. SO:ke http://purl.org/obo/owl/SO#SO_ke G to T transversion sequence intrachromosomal_mutation A chromosomal structure variation within a single chromosome. SO:ke http://purl.org/obo/owl/SO#SO_ke intrachromosomal mutation sequence chromosomal_deletion An incomplete chromosome. SO:ke http://purl.org/obo/owl/SO#SO_ke (bacteria)&ampDgr; (Drosophila)Df (fungi)D chromosomal deletion deficiency sequence URL:http://en.wikipedia.org/wiki/Chromosomal_deletion http://en.wikipedia.org/wiki/Chromosomal_deletion chromosomal_inversion An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type. SO:ke http://purl.org/obo/owl/SO#SO_ke (bacteria)IN (Drosophila)In (fungi)In chromosomal inversion sequence URL:http://en.wikipedia.org/wiki/Chromosomal_inversion http://en.wikipedia.org/wiki/Chromosomal_inversion interchromosomal_mutation A chromosomal structure variation whereby more than one chromosome is involved. SO:ke http://purl.org/obo/owl/SO#SO_ke interchromosomal mutation sequence indel Indels can have a different number of bases than the corresponding reference sequence. A sequence alteration which included an insertion and a deletion, affecting 2 or more bases. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html http:http://www.hgvs.org/mutnomen/recs-DNA.html#indel http://purl.org/obo/owl/http#http_http://www.hgvs.org/mutnomen/recs-DNA.html#indel sequence URL:http://en.wikipedia.org/wiki/Indel http://en.wikipedia.org/wiki/Indel duplication One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html nucleotide duplication nucleotide_duplication sequence inversion A continuous nucleotide sequence is inverted in the same position. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html inversion URL:http://www.ncbi.nlm.nih.gov/dbvar/ http://www.ncbi.nlm.nih.gov/dbvar/ sequence chromosomal_duplication An extra chromosome. SO:ke http://purl.org/obo/owl/SO#SO_ke (Drosophila)Dp (fungi)Dp chromosomal duplication sequence URL:http://en.wikipedia.org/wiki/Chromosomal_duplication http://en.wikipedia.org/wiki/Chromosomal_duplication intrachromosomal_duplication A duplication that occurred within a chromosome. SO:ke http://purl.org/obo/owl/SO#SO_ke intrachromosomal duplication sequence direct_tandem_duplication A tandem duplication where the individual regions are in the same orientation. SO:ke http://purl.org/obo/owl/SO#SO_ke direct tandem duplication sequence inverted_tandem_duplication A tandem duplication where the individual regions are not in the same orientation. SO:ke http://purl.org/obo/owl/SO#SO_ke inverted tandem duplication mirror duplication sequence intrachromosomal_transposition A chromosome structure variation whereby a transposition occurred within a chromosome. SO:ke http://purl.org/obo/owl/SO#SO_ke (Drosophila)Tp intrachromosomal transposition sequence compound_chromosome A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms. SO:ke http://purl.org/obo/owl/SO#SO_ke compound chromosome sequence Robertsonian_fusion A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere. URL:http://en.wikipedia.org/wiki/Robertsonian_translocation http://en.wikipedia.org/wiki/Robertsonian_translocation centric-fusion translocations Robertsonian fusion whole-arm translocations sequence URL:http://en.wikipedia.org/wiki/Robertsonian_fusion http://en.wikipedia.org/wiki/Robertsonian_fusion chromosomal_translocation An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual (Drosophila)T (fungi)T chromosomal translocation sequence URL:http://en.wikipedia.org/wiki/Chromosomal_translocation http://en.wikipedia.org/wiki/Chromosomal_translocation ring_chromosome A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome. URL:http://en.wikipedia.org/wiki/Ring_chromosome http://en.wikipedia.org/wiki/Ring_chromosome (Drosophila)R (fungi)C ring chromosome sequence URL:http://en.wikipedia.org/wiki/Ring_chromosome http://en.wikipedia.org/wiki/Ring_chromosome pericentric_inversion A chromosomal inversion that includes the centromere. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual pericentric inversion sequence paracentric_inversion A chromosomal inversion that does not include the centromere. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual paracentric inversion sequence reciprocal_chromosomal_translocation A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual reciprocal chromosomal translocation sequence sequence_variation_affecting_transcript OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation affecting transcript mutation causing partially characterised change in transcript mutation causing uncharacterised change in transcript sequence variant causing partially characterised change in transcript sequence variant causing uncharacterised change in transcript sequence variation affecting transcript sequence_variant_causing_partially_characterised_change_in_transcript sequence_variant_causing_uncharacterised_change_in_transcript sequence SO:1000177 SO:1000179 sequence_variant_causing_no_change_in_transcript OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is not change, it is not a good ontological term. No effect on the state of the RNA. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation causing no change in transcript sequence variant causing no change in transcript sequence sequence_variation_affecting_coding_sequence OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Any of the amino acid coding triplets of a gene are affected by the DNA mutation. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation affecting coding sequence sequence variation affecting coding sequence sequence sequence_variant_causing_initiator_codon_change_in_transcript OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation causing initiator codon change in transcript sequence variant causing initiator codon change in transcript sequence sequence_variant_causing_amino_acid_coding_codon_change_in_transcript OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutaton causing amino acid coding codon change in transcript sequence variant causing amino acid coding codon change in transcript sequence sequence_variant_causing_synonymous_codon_change_in_transcript OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. The changed codon has the same translation product as the original codon. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation causing synonymous codon change in transcript sequence variant causing synonymous codon change in transcript sequence sequence_variant_causing_non_synonymous_codon_change_in_transcript OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A DNA point mutation that causes a substitution of an amino acid by an other. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation causing non synonymous codon change in transcript non-synonymous codon change in transcript sequence variant causing non synonymous codon change in transcript sequence sequence_variant_causing_missense_codon_change_in_transcript OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. The nucleotide change in the codon leads to a new codon coding for a new amino acid. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation causing missense codon change in transcript sequence variant causing missense codon change in transcript sequence sequence_variant_causing_conservative_missense_codon_change_in_transcript The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix. The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation causing conservative missense codon change in transcript sequence variant causing conservative missense codon change in transcript sequence sequence_variant_causing_nonconservative_missense_codon_change_in_transcript The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix. The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation causing nonconservative missense codon change in transcript sequence variant causing nonconservative missense codon change in transcript sequence sequence_variant_causing_nonsense_codon_change_in_transcript OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. The nucleotide change in the codon triplet creates a terminator codon. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation causing nonsense codon change in transcript sequence variant causing nonsense codon change in transcript sequence sequence_variant_causing_terminator_codon_change_in_transcript OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke mutation causing terminator codon change in transcript sequence variant causing terminator codon change in transcript sequence sequence_variation_affecting_reading_frame OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. An umbrella term for terms describing an effect of a sequence variation on the frame of translation. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation affecting reading frame sequence variation affecting reading frame sequence frameshift_sequence_variation A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three. SO:ke http://purl.org/obo/owl/SO#SO_ke frameshift mutation frameshift sequence variation out of frame mutation sequence URL:http://en.wikipedia.org/wiki/Frameshift_mutation http://en.wikipedia.org/wiki/Frameshift_mutation sequence_variant_causing_plus_1_frameshift_mutation OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide. SO:ke http://purl.org/obo/owl/SO#SO_ke plus 1 frameshift mutation sequence variant causing plus 1 frameshift mutation sequence sequence_variant_causing_minus_1_frameshift OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide. SO:ke http://purl.org/obo/owl/SO#SO_ke minus 1 frameshift mutation sequence variant causing minus 1 frameshift sequence sequence_variant_causing_plus_2_frameshift OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides. SO:ke http://purl.org/obo/owl/SO#SO_ke plus 2 frameshift mutation sequence variant causing plus 2 frameshift sequence sequence_variant_causing_minus_2_frameshift OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides. SO:ke http://purl.org/obo/owl/SO#SO_ke minus 2 frameshift mutation sequence variant causing minus 2 frameshift sequence sequence_variant_affecting_transcript_processing OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation affecting transcript processing sequence variant affecting transcript processing sequence sequence_variant_affecting_splicing OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation affecting splicing sequence variant affecting splicing sequence sequence_variant_affecting_splice_donor OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A sequence_variant_effect that changes the splice donor sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke mutation affecting splice donor sequence variant affecting splice donor splice donor mutation sequence sequence_variant_affecting_splice_acceptor OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A sequence_variant_effect that changes the splice acceptor sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke mutation affecting splicing sequence variant affecting splice acceptor splice acceptor mutation sequence sequence_variant_causing_cryptic_splice_activation A cryptic splice site is only used when the natural splice site has been disrupted by a sequence alteration. A sequence variant causing a new (functional) splice site. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html cryptic splice activator sequence variant mutation causing cryptic splice activator sequence variant causing cryptic splice activator sequence sequence_variant_affecting_editing OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Sequence variant affects the editing of the transcript. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation affecting editing sequence variant affecting editing sequence sequence_variant_affecting_transcription OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Mutation affects the process of transcription, its initiation, progression or termination. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation affecting transcription sequence variant affecting transcription sequence sequence_variant_decreasing_rate_of_transcription OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A sequence variation that decreases the rate a which transcription of the sequence occurs. SO:ke http://purl.org/obo/owl/SO#SO_ke mutation decreasing rate of transcription sequence variation decreasing rate of transcription sequence sequence_variation_affecting_transcript_sequence OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation affecting transcript sequence sequence variation affecting transcript sequence sequence sequence_variant_increasing_rate_of_transcription OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation increasing rate of transcription sequence variation increasing rate of transcription sequence sequence_variant_affecting_rate_of_transcription OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A mutation that alters the rate a which transcription of the sequence occurs. SO:ke http://purl.org/obo/owl/SO#SO_ke mutation affecting rate of transcription sequence variant affecting rate of transcription sequence sequence variant_affecting_transcript_stability OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Sequence variant affects the stability of the transcript. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation affecting transcript stability sequence variant affecting transcript stability sequence sequence_variant_increasing_transcript_stability OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Sequence variant increases the stability (half-life) of the transcript. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation increasing transcript stability sequence variant increasing transcript stability sequence sequence_variant_decreasing_transcript_stability OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Sequence variant decreases the stability (half-life) of the transcript. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation decreasing transcript stability sequence variant decreasing transcript stability sequence sequence_variation_affecting_level_of_transcript OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke mutation affecting level of transcript sequence variation affecting level of transcript sequence sequence_variation_decreasing_level_of_transcript OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A sequence variation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke mutation decreasing level of transcript sequence variation decreasing level of transcript sequence sequence_variation_increasing_level_of_transcript OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A sequence_variation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke mutation increasing level of transcript sequence variation increasing level of transcript sequence sequence_variant_affecting_translational_product OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A sequence variant causing a change in primary translation product of a transcript. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation affecting translational product mutation causing partially characterised change of translational product mutation causing uncharacterised change of translational product sequence variant affecting translational product sequence variant causing partially characterised change of translational product sequence variant causing uncharacterised change of translational product sequence_variant_causing_partially_characterised_change_of_translational_product sequence_variant_causing_uncharacterised_change_of_translational_product sequence SO:1000090 SO:1000091 sequence_variant_causing_no_change_of_translational_product OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also, as there is no change, this is not a good ontological term. The sequence variant at RNA level does not lead to any change in polypeptide. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation causing no change of translational product sequence variant causing no change of translational product sequence sequence_variant_causing_complex_change_of_translational_product OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Any sequence variant effect that is known at nucleotide level but cannot be explained by using other key terms. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation causing complex change of translational product sequence variant causing complex change of translational product sequence sequence_variant_causing_amino_acid_substitution OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. The replacement of a single amino acid by another. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation causing amino acid substitution sequence variant causing amino acid substitution sequence sequence_variant_causing_conservative_amino_acid_substitution OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation causing conservative amino acid substitution sequence variant causing conservative amino acid substitution sequence sequence_variant_causing_nonconservative_amino_acid_substitution OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation causing nonconservative amino acid substitution sequence variant causing nonconservative amino acid substitution sequence sequence_variant_causing_amino_acid_insertion OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation causing amino acid insertion sequence variant causing amino acid insertion sequence sequence_variant_causing_amino_acid_deletion OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation causing amino acid deletion sequence variant causing amino acid deletion sequence sequence_variant_causing_polypeptide_truncation OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062). EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation causing polypeptide truncation sequence variant causing polypeptide truncation sequence sequence_variant_causing_polypeptide_elongation OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. The extension of the translational product at either (or both) the N-terminus and/or the C-terminus. EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation causing polypeptide elongation sequence variant causing polypeptide elongation sequence mutation_causing_polypeptide_N_terminal_elongation OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. . EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation causing polypeptide N terminal elongation polypeptide N-terminal elongation sequence mutation_causing_polypeptide_C_terminal_elongation OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. . EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation causing polypeptide C terminal elongation polypeptide C-terminal elongation sequence sequence_variant_affecting_level_of_translational_product OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation affecting level of translational product sequence variant affecting level of translational product sequence sequence_variant_decreasing_level_of_translation_product OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutationdecreasing level of translation product sequence variant decreasing level of translation product sequence sequence_variant_increasing_level_of_translation_product OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutationt increasing level of translation product sequence variant increasing level of translation product sequence sequence_variant_affecting_polypeptide_amino_acid_sequence OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation affecting polypeptide amino acid sequence sequence variant affecting polypeptide amino acid sequence sequence mutation_causing_inframe_polypeptide_N_terminal_elongation OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. inframe polypeptide N-terminal elongation mutation causing inframe polypeptide N terminal elongation sequence mutation_causing_out_of_frame_polypeptide_N_terminal_elongation OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation causing out of frame polypeptide N terminal elongation out of frame polypeptide N-terminal elongation sequence mutaton_causing_inframe_polypeptide_C_terminal_elongation inframe_polypeptide C-terminal elongation mutaton causing inframe polypeptide C terminal elongation sequence mutation_causing_out_of_frame_polypeptide_C_terminal_elongation OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation causing out of frame polypeptide C terminal elongation out of frame polypeptide C-terminal elongation sequence frame_restoring_sequence_variant A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame. SO:ke http://purl.org/obo/owl/SO#SO_ke frame restoring mutation frame restoring sequence variant sequence sequence_variant_affecting_3D_structure_of_polypeptide OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule. SO:ke http://purl.org/obo/owl/SO#SO_ke mutation affecting 3D structure of polypeptide mutation causing partially characterised 3D structural change mutation causing uncharacterised 3D structural change sequence variant affecting 3D structure of polypeptide sequence variant affecting 3D-structure of polypeptide sequence variant causing partially characterised 3D structural change sequence variant causing uncharacterised 3D structural change sequence_variant_causing_partially_characterised_3D_structural_change sequence_variant_causing_uncharacterised_3D_structural_change sequence SO:1000113 SO:1000114 sequence_variant_causing_no_3D_structural_change OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is no effect, it is not a good term. mutation causing no 3D structural change sequence variant causing no 3D structural change sequence sequence_variant_causing_complex_3D_structural_change OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation causing complex 3D structural change sequence variant causing complex 3D structural change sequence sequence_variant_causing_conformational_change OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation causing conformational change sequence variant causing conformational change sequence sequence_variant_affecting_polypeptide_function OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation affecting polypeptide function sequence variant affecting polypeptide function sequence sequence_variant_causing_loss_of_function_of_polypeptide OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. loss of function of polypeptide mutation causing loss of function of polypeptide sequence variant causing loss of function of polypeptide sequence sequence_variant_causing_inactive_ligand_binding_site OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation causing inactive ligand binding site sequence variant causing inactive ligand binding site sequence sequence_variant_causing_inactive_catalytic_site OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation causing inactive catalytic site sequence variant causing inactive catalytic site sequence sequence_variant_causing_polypeptide_localization_change OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation causing polypeptide localization change sequence variant causing polypeptide localization change sequence sequence_variant_causing_polypeptide_post_translational_processing_change OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation causing polypeptide post translational processing change polypeptide post-translational processing affected sequence variant causing polypeptide post translational processing change sequence polypeptide_post_translational_processing_affected polypeptide_post-translational_processing_affected sequence sequence_variant_causing_partial_loss_of_function_of_polypeptide OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation causing partial loss of function of polypeptide partial loss of function of polypeptide sequence variant causing partial loss of function of polypeptide sequence sequence_variant_causing_gain_of_function_of_polypeptide OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. gain of function of polypeptide mutation causing gain of function of polypeptide sequence variant causing gain of function of polypeptide sequence sequence_variant_affecting_transcript_secondary_structure OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule. SO:ke http://purl.org/obo/owl/SO#SO_ke mutation affecting transcript secondary structure sequence variant affecting transcript secondary structure sequence sequence_variant_causing_compensatory_transcript_secondary_structure_mutation OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation causing compensatory transcript secondary structure mutation sequence variant causing compensatory transcript secondary structure mutation sequence sequence_variant_effect OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.nUpdated after discussion with Peter Taschner - Feb 09. The effect of a change in nucleotide sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence variant effect sequence sequence_variant_causing_polypeptide_fusion OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. mutation causing polypeptide fusion sequence variant causing polypeptide fusion sequence autosynaptic_chromosome An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome. PMID:6804304 http://purl.org/obo/owl/PMID#PMID_6804304 (Drosophila)A autosynaptic chromosome sequence homo_compound_chromosome A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved. SO:ke http://purl.org/obo/owl/SO#SO_ke homo compound chromosome homo-compound chromosome sequence hetero_compound_chromosome A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual SO:ke http://purl.org/obo/owl/SO#SO_ke hetero compound chromosome hetero-compound chromosome sequence chromosome_fission A chromosome that occurred by the division of a larger chromosome. SO:ke http://purl.org/obo/owl/SO#SO_ke chromosome fission sequence dexstrosynaptic_chromosome An autosynaptic chromosome carrying the two right (D = dextro) telomeres. FB:manual http://purl.org/obo/owl/FB#FB_manual dexstrosynaptic chromosome sequence laevosynaptic_chromosome LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres. FB:manual http://purl.org/obo/owl/FB#FB_manual laevosynaptic chromosome sequence free_duplication A chromosome structure variation whereby the duplicated sequences are carried as a free centric element. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual free duplication sequence free_ring_duplication A ring chromosome which is a copy of another chromosome. SO:ke http://purl.org/obo/owl/SO#SO_ke (Drosophila)R free ring duplication sequence complex_chromosomal_mutation A chromosome structure variant with 4 or more breakpoints. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual SO:ke http://purl.org/obo/owl/SO#SO_ke complex chromosomal mutation sequence deficient_translocation A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual (Drosophila)Df (Drosophila)DfT deficient translocation sequence inversion_cum_translocation A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual (Drosophila)InT (Drosophila)T inversion cum translocation sequence bipartite_duplication An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual (Drosophila)bDp bipartite duplication sequence cyclic_translocation A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual cyclic translocation sequence bipartite_inversion A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed). FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual (Drosophila)bIn bipartite inversion sequence uninverted_insertional_duplication An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual (Drosophila)eDp uninverted insertional duplication sequence inverted_insertional_duplication An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual (Drosophila)iDp inverted insertional duplication sequence insertional_duplication A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication). SO:ke http://purl.org/obo/owl/SO#SO_ke (Drosophila)Dpp insertional duplication sequence interchromosomal_transposition A chromosome structure variation whereby a transposition occurred between chromosomes. SO:ke http://purl.org/obo/owl/SO#SO_ke (Drosophila)Tp interchromosomal transposition sequence inverted_interchromosomal_transposition An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual (Drosophila)iTp inverted interchromosomal transposition sequence uninverted_interchromosomal_transposition An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual (Drosophila)eTp uninverted interchromosomal transposition sequence inverted_intrachromosomal_transposition An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual (Drosophila)iTp inverted intrachromosomal transposition sequence uninverted_intrachromosomal_transposition An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual (Drosophila)eTp uninverted intrachromosomal transposition sequence unoriented_insertional_duplication Flag - unknown in the definition. An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual (Drosophila)uDp unoriented insertional duplication sequence unoriented_interchromosomal_transposition FLAG - term describes an unknown. An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual (Drosophila)uTp unorientated interchromosomal transposition sequence unoriented_intrachromosomal_transposition FLAG - definition describes an unknown. An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual (Drosophila)uTp unorientated intrachromosomal transposition sequence uncharacterised_chromosomal_mutation uncharacterised chromosomal mutation sequence deficient_inversion A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual SO:ke http://purl.org/obo/owl/SO#SO_ke (Drosophila)Df (Drosophila)DfIn deficient inversion sequence tandem_duplication A duplication consisting of 2 identical adjacent regions. SO:ke http://purl.org/obo/owl/SO#SO_ke erverted URL:http://www.ncbi.nlm.nih.gov/dbvar/ http://www.ncbi.nlm.nih.gov/dbvar/ tandem duplication sequence partially_characterised_chromosomal_mutation partially characterised chromosomal mutation sequence sequence_variant_affecting_gene_structure OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A sequence_variant_effect that changes the gene structure. SO:ke http://purl.org/obo/owl/SO#SO_ke mutation affecting gene structure sequence variant affecting gene structure sequence sequence_variant_causing_gene_fusion OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A sequence_variant_effect that changes the gene structure by causing a fusion to another gene. SO:ke http://purl.org/obo/owl/SO#SO_ke mutation causing gene fusion sequence variant causing gene fusion sequence chromosome_number_variation A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. SO:ke http://purl.org/obo/owl/SO#SO_ke chromosome number variation sequence chromosome_structure_variation chromosome structure variation sequence sequence_variant_causes_exon_loss OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A sequence variant affecting splicing and causes an exon loss. SO:ke http://purl.org/obo/owl/SO#SO_ke mutation causes exon loss sequence variant causes exon loss sequence sequence_variant_causes_intron_gain OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A sequence variant effect, causing an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072). EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html mutation causes intron gain sequence variant causes intron gain sequence sequence_variant_causing_cryptic_splice_donor_activation OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. sequence variant causing cryptic splice donor activation sequence sequence_variant_causing_cryptic_splice_acceptor_activation OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. sequence variant causing cryptic splice acceptor activation sequence alternatively_spliced_transcript A transcript that is alternatively spliced. SO:xp http://purl.org/obo/owl/SO#SO_xp alternatively spliced transcript sequence encodes_1_polypeptide A gene that is alternately spliced, but encodes only one polypeptide. SO:ke http://purl.org/obo/owl/SO#SO_ke encodes 1 polypeptide sequence encodes_greater_than_1_polypeptide A gene that is alternately spliced, and encodes more than one polypeptide. SO:ke http://purl.org/obo/owl/SO#SO_ke encodes greater than 1 polypeptide sequence encodes_different_polypeptides_different_stop A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons. SO:ke http://purl.org/obo/owl/SO#SO_ke encodes different polypeptides different stop sequence encodes_overlapping_peptides_different_start A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons. SO:ke http://purl.org/obo/owl/SO#SO_ke encodes overlapping peptides different start sequence encodes_disjoint_polypeptides A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences. SO:ke http://purl.org/obo/owl/SO#SO_ke encodes disjoint polypeptides sequence encodes_overlapping_polypeptides_different_start_and_stop A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons. SO:ke http://purl.org/obo/owl/SO#SO_ke encodes overlapping polypeptides different start and stop sequence alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping sequence encodes_overlapping_peptides A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences. SO:ke http://purl.org/obo/owl/SO#SO_ke encodes overlapping peptides sequence cryptogene A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence dicistronic_primary_transcript A primary transcript that has the quality dicistronic. SO:xp http://purl.org/obo/owl/SO#SO_xp dicistronic primary transcript sequence member_of_regulon member of regulon sequence alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non-overlapping sequence CDS_independently_known A CDS with the evidence status of being independently known. SO:xp http://purl.org/obo/owl/SO#SO_xp CDS independently known sequence orphan_CDS A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence. SO:ma http://purl.org/obo/owl/SO#SO_ma orphan CDS sequence CDS_supported_by_domain_match_data A CDS that is supported by domain similarity. SO:xp http://purl.org/obo/owl/SO#SO_xp CDS supported by domain match data sequence CDS_supported_by_sequence_similarity_data A CDS that is supported by sequence similarity data. SO:xp http://purl.org/obo/owl/SO#SO_xp CDS supported by sequence similarity data sequence CDS_predicted A CDS that is predicted. SO:ke http://purl.org/obo/owl/SO#SO_ke CDS predicted sequence status_of_coding_sequence sequence CDS_supported_by_EST_or_cDNA_data A CDS that is supported by similarity to EST or cDNA data. SO:xp http://purl.org/obo/owl/SO#SO_xp CDS supported by EST or cDNA data sequence internal_Shine_Dalgarno_sequence A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria. PMID:12519954 http://purl.org/obo/owl/PMID#PMID_12519954 SO:ke http://purl.org/obo/owl/SO#SO_ke internal Shine Dalgarno sequence internal Shine-Dalgarno sequence sequence recoded_mRNA The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals. URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=8811194&amp;dopt=Abstract http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=8811194&amp;dopt=Abstract recoded mRNA sequence minus_1_translationally_frameshifted An attribute describing a translational frameshift of -1. SO:ke http://purl.org/obo/owl/SO#SO_ke minus 1 translationally frameshifted sequence plus_1_translationally_frameshifted An attribute describing a translational frameshift of +1. SO:ke http://purl.org/obo/owl/SO#SO_ke plus 1 translationally frameshifted sequence mRNA_recoded_by_translational_bypass A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon. URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=8811194&amp;dopt=Abstract http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=8811194&amp;dopt=Abstract mRNA recoded by translational bypass sequence mRNA_recoded_by_codon_redefinition A recoded_mRNA that was modified by an alteration of codon meaning. SO:ma http://purl.org/obo/owl/SO#SO_ma mRNA recoded by codon redefinition sequence stop_codon_redefinition_as_selenocysteine sequence stop_codon_readthrough sequence recoding_stimulatory_region A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA. URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=12519954&amp;dopt=Abstract http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=12519954&amp;dopt=Abstract recoding stimulatory region recoding stimulatory signal sequence four_bp_start_codon A non-canonical start codon with 4 base pairs. SO:ke http://purl.org/obo/owl/SO#SO_ke 4bp start codon four bp start codon sequence stop_codon_redefinition_as_pyrrolysine sequence archaeal_intron Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism. An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease. PMID:9301331 http://purl.org/obo/owl/PMID#PMID_9301331 SO:ma http://purl.org/obo/owl/SO#SO_ma archaeal intron sequence tRNA_intron Could be a cross product with Gene ontology, GO:0006388. An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification. SO:ke http://purl.org/obo/owl/SO#SO_ke pre-tRNA intron tRNA intron sequence CTG_start_codon A non-canonical start codon of sequence CTG. SO:ke http://purl.org/obo/owl/SO#SO_ke CTG start codon sequence SECIS_element The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031 SECIS element sequence URL:http://en.wikipedia.org/wiki/SECIS_element http://en.wikipedia.org/wiki/SECIS_element retron Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence three_prime_recoding_site The recoding stimulatory signal located downstream of the recoding site. SO:ke http://purl.org/obo/owl/SO#SO_ke three prime recoding site sequence three_prime_stem_loop_structure A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region. PMID:12519954 http://purl.org/obo/owl/PMID#PMID_12519954 SO:ke http://purl.org/obo/owl/SO#SO_ke three prime stem loop structure sequence five_prime_recoding_site The recoding stimulatory signal located upstream of the recoding site. SO:ke http://purl.org/obo/owl/SO#SO_ke five prime recoding site sequence flanking_three_prime_quadruplet_recoding_signal Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons. PMID:12519954 http://purl.org/obo/owl/PMID#PMID_12519954 SO:ke http://purl.org/obo/owl/SO#SO_ke flanking three prime quadruplet recoding signal sequence UAG_stop_codon_signal A stop codon signal for a UAG stop codon redefinition. SO:ke http://purl.org/obo/owl/SO#SO_ke UAG stop codon signal sequence UAA_stop_codon_signal A stop codon signal for a UAA stop codon redefinition. SO:ke http://purl.org/obo/owl/SO#SO_ke UAA stop codon signal sequence regulon A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal. ISBN:0198506732 http://purl.org/obo/owl/ISBN#ISBN_0198506732 sequence URL:http://en.wikipedia.org/wiki/Regulon http://en.wikipedia.org/wiki/Regulon UGA_stop_codon_signal A stop codon signal for a UGA stop codon redefinition. SO:ke http://purl.org/obo/owl/SO#SO_ke UGA stop codon signal sequence three_prime_repeat_recoding_signal A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements. PMID:12519954 http://purl.org/obo/owl/PMID#PMID_12519954 SO:ke http://purl.org/obo/owl/SO#SO_ke three prime repeat recoding signal sequence distant_three_prime_recoding_signal A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon. URL:http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=8709208&amp;dopt=Abstract http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=8709208&amp;dopt=Abstract distant three prime recoding signal sequence stop_codon_signal This term does not include the stop codons that are redefined. An example would be a stop codon that partially overlapped a frame shifting site would be an example stimulatory signal. A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding. PMID:12519954 http://purl.org/obo/owl/PMID#PMID_12519954 SO:ke http://purl.org/obo/owl/SO#SO_ke stop codon signal sequence databank_entry The sequence referred to by an entry in a databank such as Genbank or SwissProt. SO:ke http://purl.org/obo/owl/SO#SO_ke accession databank entry sequence gene_segment Requested by tracker 2021594, July 2008, by Alex. A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination. GOC:add http://purl.org/obo/owl/GOC#GOC_add gene segment sequence adjacent_to 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 http://purl.org/obo/owl/PMID#PMID_20226267 SO:ke http://purl.org/obo/owl/SO#SO_ke sequence associated_with This relationship is vague and up for discussion. sequence complete_evidence_for_feature 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. 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 http://purl.org/obo/owl/SO#SO_ke sequence connects_on Example: A splice_junction connects_on exon, exon, mature_transcript. 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 http://purl.org/obo/owl/PMID#PMID_20226267 sequence contained_by The inverse is contains. Example: intein contained_by immature_peptide_region. X contained_by Y iff X starts after start of Y and X ends before end of Y. PMID:20226267 http://purl.org/obo/owl/PMID#PMID_20226267 sequence contains Example: pre_miRNA contains miRNA_loop. The inverse of contained_by. PMID:20226267 http://purl.org/obo/owl/PMID#PMID_20226267 sequence derives_from sequence disconnected_from Example: intron disconnected from exon {on primary_transcript}. X is disconnected_from Y iff it is not the case that X overlaps Y. PMID:20226267 http://purl.org/obo/owl/PMID#PMID_20226267 sequence edited_from sequence edited_to sequence evidence_for_feature 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. B is evidence_for_feature A, if an instance of B supports the existence of A. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence exemplar_of Tracker id: 2594157. X is exemplar of Y if X is the best evidence for Y. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence finished_by Example CDS finished_by stop_codon. Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary. PMID:20226267 http://purl.org/obo/owl/PMID#PMID_20226267 sequence finishes Example: stop_codon finishes CDS. X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary. PMID:20226267 http://purl.org/obo/owl/PMID#PMID_20226267 sequence gained 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. X gained Y if X is a variant_of X' and Y part of X but not X'. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence genome_of sequence guided_by sequence guides sequence has_integral_part Example: mRNA has_integral_part CDS. X has_integral_part Y if and only if: X has_part Y and Y part_of X. URL:http://precedings.nature.com/documents/3495/version/1 http://precedings.nature.com/documents/3495/version/1 sequence has_origin sequence has_part Example: operon has_part gene. Inverse of part_of. URL:http://precedings.nature.com/documents/3495/version/1 http://precedings.nature.com/documents/3495/version/1 sequence has_quality The relationship between a feature and an attribute. sequence homologous_to sequence integral_part_of Example: exon integral_part_of transcript. X integral_part_of Y if and only if: X part_of Y and Y has_part X. URL:http://precedings.nature.com/documents/3495/version/1 http://precedings.nature.com/documents/3495/version/1 sequence is_consecutive_sequence_of Example: region is consecutive_sequence of base. 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 http://purl.org/obo/owl/PMID#PMID_20226267 sequence lost 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. X lost Y if X is a variant_of X' and Y part of X' but not X. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence maximally_overlaps Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR. A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y. PMID:20226267 http://purl.org/obo/owl/PMID#PMID_20226267 sequence member_of 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. sequence non_functional_homolog_of A relationship between a pseudogenic feature and its functional ancestor. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence orthologous_to sequence overlaps Example: coding_exon overlaps CDS. X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y. PMID:20226267 http://purl.org/obo/owl/PMID#PMID_20226267 sequence paralogous_to sequence part_of Example: amino_acid part_of polypeptide. X part_of Y if X is a subregion of Y. URL:http://precedings.nature.com/documents/3495/version/1 http://precedings.nature.com/documents/3495/version/1 sequence partial_evidence_for_feature B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence position_of sequence processed_from Example: miRNA processed_from miRNA_primary_transcript. Inverse of processed_into. URL:http://precedings.nature.com/documents/3495/version/1 http://precedings.nature.com/documents/3495/version/1 sequence processed_into Example: miRNA_primary_transcript processed into miRNA. X is processed_into Y if a region X is modified to create Y. URL:http://precedings.nature.com/documents/3495/version/1 http://precedings.nature.com/documents/3495/version/1 sequence recombined_from sequence recombined_to sequence sequence_of sequence similar_to sequence started_by Example: CDS started_by start_codon. X is strted_by Y if Y is part_of X and X and Y share a 5' boundary. PMID:20226267 http://purl.org/obo/owl/PMID#PMID_20226267 sequence starts Example: start_codon starts CDS. X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary. PMID:20226267 http://purl.org/obo/owl/PMID#PMID_20226267 sequence trans_spliced_from sequence trans_spliced_to sequence transcribed_from Example: primary_transcript transcribed_from gene. X is transcribed_from Y if X is synthesized from template Y. URL:http://precedings.nature.com/documents/3495/version/1 http://precedings.nature.com/documents/3495/version/1 sequence transcribed_to Example: gene transcribed_to primary_transcript. Inverse of transcribed_from. URL:http://precedings.nature.com/documents/3495/version/1 http://precedings.nature.com/documents/3495/version/1 sequence translates_to Example: codon translates_to amino_acid. Inverse of translation _of. URL:http://precedings.nature.com/documents/3495/version/1 http://precedings.nature.com/documents/3495/version/1 sequence translation_of Example: Polypeptide translation_of CDS. X is translation of Y if X is translated by ribosome to create Y. URL:http://precedings.nature.com/documents/3495/version/1 http://precedings.nature.com/documents/3495/version/1 sequence variant_of Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith. 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 http://purl.org/obo/owl/SO#SO_immuno_workshop sequence