Controlled vocabulary for /regulatory_class

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 on 12-OCT-2016.

The text below outlines the format and the present list of allowed controlled vocabulary.

Qualifier: /regulatory_class
Definition: a structured description of the classification of transcriptional and translational regulatory elements in a sequence          
Value format: "TYPE"
where 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
Examples:
/regulatory_class="promoter"
/regulatory_class="enhancer"
/regulatory_class="ribosome_binding_site"

Comment: TYPE is a term taken from the INSDC controlled vocabulary for regulatory classes:

attenuator: 1) region of DNA at which regulation of termination of transcription occurs, which controls the expression of some bacterial operons;
2) sequence segment located between the promoter and the first structural gene that causes partial termination of transcription.

CAAT_signal: 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].

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)

DNase_I_hypersensitive_site: DNA region representing open chromatin structure that is hypersensitive to digestion by DNase I.

enhancer: 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.

enhancer_blocking_element: 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.

GC_signal: 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

imprinting_control_region: 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.

insulator: a chromatin boundary element or barrier that can block the encroachment of condensed chromatin from an adjacent region. May also include enhancer-blocking activity.

locus_control_region: 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.

matrix_attachment_region: DNA region that is required for the binding of chromatin to the nuclear matrix.

minus_35_signal: a conserved hexamer about 35 bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA

minus_10_signal: 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]

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)

polyA_signal_sequence: the recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA or ATTAAA.

promoter: region on a DNA molecule involved in RNA polymerase binding to initiate transcription.

recoding_stimulatory_region: 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.

replication_regulatory_region: region that is involved in the control of the process of nucleotide replication but is not the origin of replication.

response_element: a regulatory element that acts in response to a stimulus, usually via transcription factor binding.

ribosome_binding_site: ribosome binding site

riboswitch: 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.

silencer: a regulatory region which upon binding of transcription factors suppresses the transcription of the gene(s) it controls.

TATA_box: 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];

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)

terminator: sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.

transcriptional_cis_regulatory_region: modulates the transcription of a gene or genes.

Other: /regulatory_class not included in any other term.

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]";