TF Info Page for RFX4 (RFX)

Conclusion

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

Description

Description: regulatory factor X4 [Source:HGNC Symbol;Acc:HGNC:9985]
Entrez Summary This gene is a member of the regulatory factor X gene family, which encodes transcription factors that contain a highly-conserved winged helix DNA binding domain. The protein encoded by this gene is structurally related to regulatory factors X1, X2, X3, and X5. It has been shown to interact with itself as well as with regulatory factors X2 and X3, but it does not interact with regulatory factor X1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2011]
Ensembl ID: ENSG00000111783
External Link: CisBP
Interpro IPR003150; ;
Protein Domain: ENSP00000229387
Protein Domain: ENSP00000350552
Protein Domain: ENSP00000376585
Protein Domain: ENSP00000447735
Domain:
Protein: ENSP00000229387DBD: RFXOther:
Protein: ENSP00000350552DBD: RFXOther:
Protein: ENSP00000376585DBD: RFXOther:
Protein: ENSP00000447735DBD: RFXOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene Candidate_DNA-Binding
sequence-specific_Co-activation
DNA Binding_
PMIDS:11682486
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.
b
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:0001077
RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a
IDA - PMID:16893423
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-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
PBMBadis09Inferred - Rfx4 (100% AA Identity, Mus musculus)
PBMZoo_01Inferred - RFX4 (98% AA Identity, Cavia porcellus)
PBMZoo_01Inferred - GB41876 (65% AA Identity, Apis mellifera)
PBMZoo_01Inferred - XP_002157607.1 (64% AA Identity, Hydra magnipapillata)
HT-SELEXJolma2010Inferred - RFX3 (61% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RFX3 (61% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - RFX3 (61% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RFX3 (61% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RFX3 (61% AA Identity, Homo sapiens)
MiscHocoMocoInferred - RFX3 (61% AA Identity, Homo sapiens)
MiscHOMERInferred - RFX3 (61% AA Identity, Homo sapiens)
HT-SELEXNitta2015Inferred - Rfx (60% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Rfx (60% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Rfx (60% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Rfx (60% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Rfx (60% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - RFX2 (60% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RFX2 (60% AA Identity, Homo sapiens)
SMiLE-seqIsakova2017Inferred - RFX2 (60% AA Identity, Mus musculus)
SELEXJASPARInferred - RFX2 (60% AA Identity, Homo sapiens)
MiscHocoMocoInferred - RFX2 (60% AA Identity, Homo sapiens)
MiscHOMERInferred - RFX2 (60% AA Identity, Homo sapiens)
PBMZoo_01Inferred - PHUM046580 (58% AA Identity, Pediculus humanus)
PBMZoo_01Inferred - RFX1 (58% AA Identity, Anolis carolinensis)
HT-SELEXYin2017Inferred - RFX1 (58% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RFX1 (58% AA Identity, Homo sapiens)
PBMZoo_01Inferred - rfx1a (58% AA Identity, Tetraodon nigroviridis)
TransfacTransfacLicense requiredInferred - RFX1 (58% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - RFX1 (58% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - RFX1 (58% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - RFX1 (58% AA Identity, Homo sapiens)
ChIP-seqJASPARInferred - Rfx1 (58% AA Identity, Mus musculus)
MiscHocoMocoInferred - RFX1 (58% AA Identity, Homo sapiens)
PBMBadis09Inferred - Rfx3 (57% AA Identity, Mus musculus)
PBMCEPDInferred - daf-19 (56% AA Identity, Caenorhabditis elegans)
PBMZoo_01Inferred - G4VLF2_SCHMA (56% AA Identity, Schistosoma mansoni)
PBMZoo_01Inferred - RFX2 (56% AA Identity, Homo sapiens)
PBMZoo_01Inferred - RFX2 (56% AA Identity, Ornithorhynchus anatinus)
PBMZoo_01Inferred - Sjc_0102030 (55% AA Identity, Schistosoma japonicum)

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