TF Info Page for RARG (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 gamma [Source:HGNC Symbol;Acc:HGNC:9866]
Entrez Summary This gene encodes a retinoic acid receptor that belongs to the nuclear hormone receptor family. Retinoic acid receptors (RARs) act as ligand-dependent transcriptional regulators. When bound to ligands, RARs activate transcription by binding as heterodimers to the retinoic acid response elements (RARE) found in the promoter regions of the target genes. In their unbound form, RARs repress transcription of their target genes. RARs are involved in various biological processes, including limb bud development, skeletal growth, and matrix homeostasis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
Ensembl ID: ENSG00000172819
External Link: CisBP
Interpro IPR000536; IPR001628; IPR001723; IPR003078; IPR008946; ;
Protein Domain: ENSP00000343698
Protein Domain: ENSP00000377947
Protein Domain: ENSP00000388510
Protein Domain: ENSP00000444335
Protein Domain: ENSP00000454385
Protein Domain: ENSP00000454604
Domain:
Protein: ENSP00000343698DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000377947DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000388510DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000444335DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000454385DBD: Nuclear Hormone ReceptorOther:
Protein: ENSP00000454604DBD: Nuclear Hormone ReceptorOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_DNA Binding
Transactivation_
PMIDS:2544807 15327771
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
ISS - GO_REF:0000024
GO:0003708
retinoic acid receptor activity
IEA - GO_REF:0000019
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
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXYin2017Direct
HT-SELEXYin2017Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
PBMZoo_01Direct
TransfacTransfacLicense requiredDirect
MiscHocoMocoDirect
MiscHocoMocoDirect
PBMDREAM_contestInferred - Rarg (100% AA Identity, Mus musculus)
SMiLE-seqIsakova2017Inferred - Rarg (100% AA Identity, Mus musculus)
MiscHOMERInferred - Rarg (100% AA Identity, Mus musculus)
SMiLE-seqIsakova2017Inferred - RARA (97% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RARA (97% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RARA (97% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RARA (97% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RARA (97% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RARA (97% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RARA (97% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - RARA (97% AA Identity, Homo sapiens)
MiscHocoMocoInferred - RARA (97% AA Identity, Homo sapiens)
MiscHocoMocoInferred - RARA (97% AA Identity, Homo sapiens)
PBMBadis09Inferred - Rara (95% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - RARB (94% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RARB (94% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RARB (94% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RARB (94% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RARB (94% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RARB (94% AA Identity, Homo sapiens)
PBMZoo_01Inferred - Rarb (94% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - RARB (94% AA Identity, Homo sapiens)
MiscHocoMocoInferred - RARB (94% AA Identity, Homo sapiens)

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