Regulatory Regions

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Working group

MeiYee Law

Aims of term development

The aim of this working group is to further develop the Sequence Ontology terms to better define regulatory regions.


name: G_box

name: L-box

name: I-box

name: TSS

  • current child of “primary transcript region”
  • propose to add child of “initiator”
  • ref: smale & baltimore (1989)

name: transcriptional_cis_regulatory_region

  • SO accession: SO:0001055
  • synonym: cis_acting_DNA_regulatory_element, cis acting DNA regulatory element (proposed), cis acting sequence (proposed), cis-acting DNA sequence (Butler & Kadonaga 2001)(proposed)
  • ref: Priest et al 2009, Kadanoga (2002)
  • parent: regulatory_promoter element

name: cis-regulatory module

  • SO accession: SO:0000727
  • def: A regulatory region where transcription factor binding sites clustered to regulate spatial and temporal gene expression. "CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome...". A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network.
  • synonyms: CRM, TF module, transcription factor module
  • children: silencer, locus control region, enhancer, promoters, insulators
  • ref:

name: insulator element

name: proximal promoter element

  • Accession: 0001668
  • def: -250 → -40. upstream of core promoter element.
  • parent: transcriptional cis regulatory region (proposed) (current: regulatory_promoter_element)

name: poly-pyrimidine sequence

  • organism: c. elegans, drosophila (present but motif locations variable from species to species)
  • def: binding sites for DNA replication-related element factor (Dref) and Nf1
  • ref: Sleumer et al (2012)
  • parent: RPG promoter

name: enhancer

name: TCT motif

  • def: cis-regulatory element, conserved sequence "YYC+1TTTYY”, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator.
  • synonym: TCT element, polypyrimidine initiator
  • parent: core promoter element, RNApol II core promoter
  • ref:


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