TF Info Page for RFX5 (RFX)

Conclusion

Assessment Binding Mode Motif Status Notes Comments
Known motif 1 Monomer or homomultimer High-throughput in vitro Has a putative AT-hook

Description

Description: regulatory factor X5 [Source:HGNC Symbol;Acc:HGNC:9986]
Entrez Summary A lack of MHC-II expression results in a severe immunodeficiency syndrome called MHC-II deficiency, or the bare lymphocyte syndrome (BLS; MIM 209920). At least 4 complementation groups have been identified in B-cell lines established from patients with BLS. The molecular defects in complementation groups B, C, and D all lead to a deficiency in RFX, a nuclear protein complex that binds to the X box of MHC-II promoters. The lack of RFX binding activity in complementation group C results from mutations in the RFX5 gene encoding the 75-kD subunit of RFX (Steimle et al., 1995). RFX5 is the fifth member of the growing family of DNA-binding proteins sharing a novel and highly characteristic DNA-binding domain called the RFX motif. Multiple alternatively spliced transcript variants have been found but the full-length natures of only two have been determined. [provided by RefSeq, Jul 2008]
Ensembl ID: ENSG00000143390
External Link: CisBP
Interpro IPR003150; IPR029298;
Protein Domain: ENSP00000290524
Protein Domain: ENSP00000389130
Protein Domain: ENSP00000396810
Protein Domain: ENSP00000390769
Protein Domain: ENSP00000398666
Protein Domain: ENSP00000409187
Domain:
Protein: ENSP00000290524DBD: RFXOther: RFX5_DNA_bdg
Protein: ENSP00000389130DBD: RFXOther: RFX5_DNA_bdg
Protein: ENSP00000396810DBD: RFXOther:
Protein: ENSP00000390769DBD: RFXOther:
Protein: ENSP00000398666DBD: RFXOther:
Protein: ENSP00000409187DBD: RFXOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene Candidate_Transcription Factor Binding
tf co-factor binding
DNA-Binding
sequence-specific_Co-activation_
PMIDS:9806546
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
IBA - GO_REF:0000033
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-SELEXYin2017Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
ChIP-seqENCODEDirect
ChIP-seqENCODEDirect
ChIP-seqENCODEDirect
ChIP-seqENCODEDirect
SELEXJASPARDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
MiscHOMERDirect
HT-SELEXYin2017Inferred - RFX7 (58% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RFX7 (58% AA Identity, Homo sapiens)
PBMBadis09Inferred - Rfx7 (58% AA Identity, Mus musculus)
PBMDREAM_contestInferred - Rfx7 (58% AA Identity, Mus musculus)

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