TF Info Page for RORA (Nuclear receptor)

Conclusion

Assessment Binding Mode Motif Status Notes Comments
Known motif 1 Monomer or homomultimer High-throughput in vitro

Description

Description: RAR related orphan receptor A [Source:HGNC Symbol;Acc:HGNC:10258]
Entrez Summary The protein encoded by this gene is a member of the NR1 subfamily of nuclear hormone receptors. It can bind as a monomer or as a homodimer to hormone response elements upstream of several genes to enhance the expression of those genes. The encoded protein has been shown to interact with NM23-2, a nucleoside diphosphate kinase involved in organogenesis and differentiation, as well as with NM23-1, the product of a tumor metastasis suppressor candidate gene. Also, it has been shown to aid in the transcriptional regulation of some genes involved in circadian rhythm. Four transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Feb 2014]
Ensembl ID: ENSG00000069667
External Link: CisBP
Interpro IPR000536; IPR001628; IPR001723; IPR003079; IPR008946; ;
Protein Domain: ENSP00000261523
Protein Domain: ENSP00000309753
Protein Domain: ENSP00000335087
Protein Domain: ENSP00000402971
Protein Domain: ENSP00000484955
Domain:
Protein: ENSP00000261523DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000309753DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000335087DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000402971DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000484955DBD: Nuclear Hormone ReceptorOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_DNA Binding_
PMIDS:7926749 7926749 15941850 15821743 7926749 12467577
Vaquerizas 2009 TF classification
"a" Has direct evidence of TF function;
"b" Has evidence for an orthologous TF;
"c" contains likely DBDs, but has no functional evidence;
"x" is an unlikely TF such as predicted gene, genes with likely non-specific DBDs or that have function outside transcription;
"other" category contains proteins without clear DBDs they curated from external sources.
a
CisBP considers it as a TF? Yes
TFclass considers it as a TF? Yes
Has GO:0003700 "transcription factor activity, sequence-specific DNA binding" Yes
GO-Info GO:0003700
sequence-specific DNA binding transcription factor activity
IDA - PMID:11053433, PMID:17545671, PMID:18658046,
GO:0004879
ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity
IEA - GO_REF:0000002
GO:0098531
transcription factor activity, direct ligand regulated sequence-specific DNA binding
IDA - PMID:19965867
Initial Assessment
1a1 Protein has a high confidence PWM (HT-SELEX, PBM or B1H model) or there is a crystal structure that supports sequence specific DNA binding;
1a2 There is high confidence data for a close ortholog (as defined in CisBP);
2a1 There is lower confidence direct evidence, such as a Jaspar, Hocomoco or Transfac model;
2a2 There is lower confidence evidence for an close ortholog;
3a There is decent circumstantial evidence for its role as a TF or not;
4a Two or more datasets predict it as a TF;
5a One of the source datasets predicts is as a TF
1a1, Direct HQ evidence
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source Annotation Motif Evidence
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
SELEXJASPARDirect
SELEXJASPARDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
MiscHocoMocoDirect
PBMDREAM_contestInferred - Rora (100% AA Identity, Mus musculus)
SMiLE-seqIsakova2017Inferred - RORB (92% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RORB (92% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RORB (92% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RORB (92% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RORB (92% AA Identity, Homo sapiens)
PBMDREAM_contestInferred - Rorb (92% AA Identity, Mus musculus)
PBMZoo_01Inferred - rorb (92% AA Identity, Tetraodon nigroviridis)
TransfacTransfacLicense requiredInferred - RORB (92% AA Identity, Homo sapiens)
SMiLE-seqIsakova2017Inferred - RORC (90% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RORC (90% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RORC (90% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RORC (90% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RORC (90% AA Identity, Homo sapiens)
MiscHocoMocoInferred - RORC (90% AA Identity, Homo sapiens)
MiscHOMERInferred - Rorc (90% AA Identity, Mus musculus)
PBMZoo_01Inferred - rorc (84% AA Identity, Tetraodon nigroviridis)
PBMZoo_01Inferred - AAEL009588 (77% AA Identity, Aedes aegypti)
HT-SELEXNitta2015Inferred - Hr46 (77% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - Hr46 (77% AA Identity, Drosophila melanogaster)

Structure

Structure PDB Not_Covered

Experimental History

Method Constructs
Tried in PBM?
(Whether the protein was tried in PBM or not)
Tried in HT-SELEX
(Whether the protein was tried in HT-SELEX or not, and if so, then what kind of clones were tested)
Other Information?
(Tried with another method and failed?)

External Contribution