TF Info Page for RARA (Nuclear receptor)

Conclusion

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

Description

Description: retinoic acid receptor alpha [Source:HGNC Symbol;Acc:HGNC:9864]
Entrez Summary This gene represents a nuclear retinoic acid receptor. The encoded protein, retinoic acid receptor alpha, regulates transcription in a ligand-dependent manner. This gene has been implicated in regulation of development, differentiation, apoptosis, granulopoeisis, and transcription of clock genes. Translocations between this locus and several other loci have been associated with acute promyelocytic leukemia. Alternatively spliced transcript variants have been found for this locus.[provided by RefSeq, Sep 2010]
Ensembl ID: ENSG00000131759
External Link: CisBP
Interpro IPR000536; IPR001628; IPR001723; IPR003078; IPR008946; ;
Protein Domain: ENSP00000254066
Protein Domain: ENSP00000377643
Protein Domain: ENSP00000389993
Protein Domain: ENSP00000377648
Protein Domain: ENSP00000377649
Domain:
Protein: ENSP00000254066DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000377643DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000389993DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000377648DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000377649DBD: Nuclear Hormone ReceptorOther: Hormone_recep

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_DNA Binding_
PMIDS:1312934
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:18922886, PMID:20413580
GO:0003708
retinoic acid receptor activity
IDA - PMID:2825025
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
SMiLE-seqIsakova2017Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXYin2017Direct
HT-SELEXYin2017Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
TransfacTransfacLicense requiredDirect
MiscHocoMocoDirect
MiscHocoMocoDirect
PBMBadis09Inferred - Rara (98% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - RARB (97% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RARB (97% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RARB (97% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RARB (97% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RARB (97% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RARB (97% AA Identity, Homo sapiens)
PBMZoo_01Inferred - Rarb (97% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - RARG (97% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RARG (97% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RARG (97% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RARG (97% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RARG (97% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RARG (97% AA Identity, Homo sapiens)
PBMZoo_01Inferred - RARG (97% AA Identity, Homo sapiens)
PBMDREAM_contestInferred - Rarg (97% AA Identity, Mus musculus)
SMiLE-seqIsakova2017Inferred - Rarg (97% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - RARB (97% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - RARG (97% AA Identity, Homo sapiens)
MiscHocoMocoInferred - RARB (97% AA Identity, Homo sapiens)
MiscHocoMocoInferred - RARG (97% AA Identity, Homo sapiens)
MiscHocoMocoInferred - RARG (97% AA Identity, Homo sapiens)
MiscHOMERInferred - Rarg (97% AA Identity, Mus musculus)

Structure

Structure PDB 1DSZ

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