TF Info Page for SOX4 (HMG/Sox)

Conclusion

Assessment Binding Mode Motif Status Notes Comments
Known motif 1 Monomer or homomultimer High-throughput in vitro Also binds ssDNA loops.

Description

Description: SRY-box 4 [Source:HGNC Symbol;Acc:HGNC:11200]
Entrez Summary This intronless gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins, such as syndecan binding protein (syntenin). The protein may function in the apoptosis pathway leading to cell death as well as to tumorigenesis and may mediate downstream effects of parathyroid hormone (PTH) and PTH-related protein (PTHrP) in bone development. The solution structure has been resolved for the HMG-box of a similar mouse protein. [provided by RefSeq, Jul 2008]
Ensembl ID: ENSG00000124766
External Link: CisBP
Interpro IPR009071; ;
Protein Domain: ENSP00000244745
Domain:
Protein: ENSP00000244745DBD: HMGOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene Candidate_DNA-Binding
sequence-specific_DNA Binding
Transactivation_
PMIDS:7706298
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:0001077
RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a
IDA - PMID:19147588
GO:0003700
sequence-specific DNA binding transcription factor activity
IDA - PMID:16631117, PMID:7706298
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
PBMScharer09Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
MiscHocoMocoDirect
PBMBadis09Inferred - Sox4 (98% AA Identity, Mus musculus)
MiscHOMERInferred - Sox4 (98% AA Identity, Mus musculus)
PBMBadis09Inferred - Sox11 (95% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - SOX11 (95% AA Identity, Homo sapiens)

Structure

Structure PDB 3U2B

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