{"id":84,"date":"2022-06-20T15:59:33","date_gmt":"2022-06-20T14:59:33","guid":{"rendered":"https:\/\/insdc.org\/?page_id=84"},"modified":"2022-07-21T14:52:46","modified_gmt":"2022-07-21T13:52:46","slug":"controlled-vocabulary-regulatoryclass","status":"publish","type":"page","link":"https:\/\/www.insdc.org\/submitting-standards\/controlled-vocabulary-regulatoryclass\/","title":{"rendered":"Controlled vocabulary for \/regulatory_class"},"content":{"rendered":"<p>A new qualifier was introduced in version 10.4 (November 2014) of the Feature table definitions to be supported from 15-DEC-2014: \/regulatory_class<\/p>\n<p>This page was last updated in December 2017.<\/p>\n<p>The text below outlines the format and the present list of allowed controlled vocabulary. Please note that mappings to <a href=\"http:\/\/www.sequenceontology.org\/miso\">Sequence Ontology (SO)<\/a> are given in brackets () but should not be used as part of the value format. Please see below for examples.<\/p>\n<p><strong>Qualifier:<\/strong> \/regulatory_class<\/p>\n<p><strong>Definition:<\/strong> a structured description of the classification of transcriptional, translational, replicational and chromatin structure related regulatory elements in a sequence <br \/>\n<strong>Value format:<\/strong> “TYPE”<br \/>\nwhere TYPE is one of the following: attenuator, CAAT_signal, enhancer, enhancer_blocking_element, GC_signal, imprinting_control_region, insulator, locus_control_region, minus_35_signal, minus_10_signal, polyA_signal_sequence, promoter, response_element, ribosome_binding_site, riboswitch, silencer, TATA_box, terminator, other<br \/>\n<strong>Examples:<\/strong><br \/>\n\/regulatory_class=”promoter”<br \/>\n\/regulatory_class=”enhancer”<br \/>\n\/regulatory_class=”ribosome_binding_site”<\/p>\n<p><strong>Comment: <\/strong>TYPE is a term taken from the INSDC controlled vocabulary for regulatory classes:<\/p>\n<p><strong>attenuator<\/strong> (SO:0000140)<strong>: <\/strong>1) region of DNA at which regulation of termination of transcription occurs, which controls the expression of some bacterial operons;<br \/>\n2) sequence segment located between the promoter and the first structural gene that causes partial termination of transcription.<\/p>\n<p><strong>CAAT_signal<\/strong> (SO:0000172)<strong>: <\/strong>CAAT box; 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 or T)CAATCT [1,2].<\/p>\n<p>References: [1] Efstratiadis, A. et al. Cell 21, 653-668 (1980); [2] Nevins, J.R. “The pathway of eukaryotic mRNA formation” Ann Rev Biochem 52, 441-466 (1983)<\/p>\n<p><strong>DNase_I_hypersensitive_site <\/strong>(SO:0000685): DNA region representing open chromatin structure that is hypersensitive to digestion by DNase I.<\/p>\n<p><strong>enhancer<\/strong> (SO:0000165)<strong>:<\/strong> 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.<\/p>\n<p><strong>enhancer_blocking_element: <\/strong>a transcriptional cis regulatory region that when located between an enhancer and a gene’s promoter prevents the enhancer from modulating the expression of the gene. Sometimes referred to as an insulator but may not include the barrier function of an insulator.<\/p>\n<p><strong>GC_signal <\/strong>(SO:0000173)<strong>: <\/strong>GC box; a conserved GC-rich region located upstream of the start point of eukaryotic transcription units and which may occur in multiple copies or in either orientation; consensus=GGGCGG<\/p>\n<p><strong>imprinting_control_region: <\/strong>a regulatory region that controls epigenetic imprinting and affects the expression of target genes in an allele- or parent-of-origin-specific manner. Associated regulatory elements may include differentially methylated regions and non-coding RNAs.<\/p>\n<p><strong>insulator <\/strong>(SO:0000627)<strong>: <\/strong>a chromatin boundary element or barrier that can block the encroachment of condensed chromatin from an adjacent region. May also include enhancer-blocking activity.<\/p>\n<p><strong>locus_control_region <\/strong>(SO:0000037)<strong>: <\/strong>a DNA region that includes DNase hypersensitive sites located 5′ to a gene or gene cluster, and which confers high-level, position-independent, and copy number-dependent expression on that gene or gene cluster.<\/p>\n<p><strong>matrix_attachment_region <\/strong>(SO:0000036)<strong>:<\/strong> DNA region that is required for the binding of chromatin to the nuclear matrix.<\/p>\n<p><strong>minus_35_signal <\/strong>(SO:0000176)<strong>: <\/strong>a conserved hexamer about 35 bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA<\/p>\n<p><strong>minus_10_signal <\/strong>(SO:0000175)<strong>: <\/strong>Pribnow box; 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 [1,2,3,4]<\/p>\n<p>References: [1] Schaller, H., Gray, C., and Hermann, K. Proc Natl Acad Sci USA 72, 737-741 (1974); [2] Pribnow, D. Proc Natl Acad Sci USA 72, 784-788 (1974); [3] Hawley, D.K. and McClure, W.R. “Compilation and analysis of Escherichia coli promoter DNA sequences” Nucl Acid Res 11, 2237-2255 (1983); [4] Rosenberg, M. and Court, D. “Regulatory sequences involved in the promotion and termination of RNA transcription” Ann Rev Genet 13, 319-353 (1979)<\/p>\n<p><strong>polyA_signal_sequence <\/strong>(SO:0000551)<strong>: <\/strong>the recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA or ATTAAA.<\/p>\n<p><strong>promoter <\/strong>(SO:0000167)<strong>: <\/strong>region on a DNA molecule involved in RNA polymerase binding to initiate transcription.<\/p>\n<p><strong>recoding_stimulatory_region <\/strong>(SO:1001268)<strong>:<\/strong> site in an mRNA sequence that stimulates the recoding of a region in the same mRNA; for annotating a region of an mRNA that controls a recoding event, e.g., regulates stop codon translational readthrough, selenocysteine incorporation or ribosomal slippage.<\/p>\n<p><strong>recombination_enhancer <\/strong>(<span>SO:0002059<\/span>): a<span> regulatory region that promotes or induces the process of recombination.<\/span><\/p>\n<p><strong>replication_regulatory_region <\/strong>(SO:0001682)<strong>:<\/strong> region that is involved in the control of the process of nucleotide replication but is not the origin of replication.<\/p>\n<p><strong>response_element: <\/strong>a regulatory element that acts in response to a stimulus, usually via transcription factor binding.<\/p>\n<p><strong>ribosome_binding_site <\/strong>(SO:0000552)<strong>: <\/strong>ribosome binding site<\/p>\n<p><strong>riboswitch <\/strong>(SO:0000035)<strong>:<\/strong> 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.<\/p>\n<p><strong>silencer <\/strong>(SO:0000625)<strong>: <\/strong>a regulatory region which upon binding of transcription factors suppresses the transcription of the gene(s) it controls.<\/p>\n<p><strong>TATA_box <\/strong>(SO:0000174)<strong>: <\/strong>Goldberg-Hogness box; a conserved AT-rich septamer found about 25 bp before the start point of some eukaryotic RNA polymerase II transcript unit which may be involved in positioning the enzyme for correct initiation; consensus=TATA(A or T)A(A or T) [1,2];<\/p>\n<p>References: [1] Efstratiadis, A. et al. Cell 21, 653-668 (1980); [2] Corden, J., et al. “Promoter sequences of eukaryotic protein-encoding genes” Science 209, 1406-1414 (1980)<\/p>\n<p><strong>terminator <\/strong>(SO:0000141)<strong>: <\/strong>sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.<\/p>\n<p><strong>transcriptional_cis_regulatory_region <\/strong>(SO:0001055)<strong>:<\/strong> modulates the transcription of a gene or genes.<\/p>\n<p><strong>uORF<\/strong> (<span>SO:0002027): a<span> short open reading frame that is found in the 5′ untranslated region of an mRNA and plays a role in translational regulation.<\/span><\/span><strong> <\/strong><\/p>\n<p><strong>other: <\/strong>\/regulatory_class not included in any other term.<\/p>\n<p>regulatory classes not yet in the INSDC \/regulatory_class controlled vocabulary can be annotated by entering \/regulatory_class=”other” with \/note=”[brief explanation of novel regulatory_class]”;<\/p>\n<p> <\/p>\n","protected":false},"excerpt":{"rendered":"<p>A new qualifier was introduced in version 10.4 (November 2014) of the Feature table definitions to be supported from 15-DEC-2014: \/regulatory_class This page was last updated in December 2017. The text below outlines the format and the present list of allowed controlled vocabulary. Please note that…<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":233,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"acf":[],"_links":{"self":[{"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages\/84"}],"collection":[{"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/comments?post=84"}],"version-history":[{"count":1,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages\/84\/revisions"}],"predecessor-version":[{"id":85,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages\/84\/revisions\/85"}],"up":[{"embeddable":true,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages\/233"}],"wp:attachment":[{"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/media?parent=84"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}