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The-Sequence-Ontology / SO-Ontologies

Collect of SO Ontologies
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RARE Definition and parent term revisions #458

Closed RLovering closed 5 years ago

RLovering commented 5 years ago

Hi please can the parent and the definition for this term be revised:

SO:0001653 | retinoic_acid_responsive_element revise the definition so that the location of the RARE is less specific NEW Definition: A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the proximal promoter and enhancer regions of retinoic acid-responsive genes, to which retinoic acid receptors bind.

REMOVE the parent 'promoter' because the RARE is not bound by basal transcription machinery. (see GitHub ticket #457)

ADD new parent TF_binding_site because it is a binding site for RAR.

I have asked experts to comment on whether additional other parents are required eg: CRM, or transcriptional_cis_regulatory_region. Can we assume it always acts in 'cis'. I think it is located in both enhancers and promoter flanking regions so the parent term transcriptional_cis_regulatory_region could probably be added.

Thanks

Ruth

davidwsant commented 5 years ago

Hi Ruth,

As suggested, the RARE term has been moved and can now be found under TF_binding_site.