TF Info Page for SOX9 (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 9 [Source:HGNC Symbol;Acc:HGNC:11204]
Entrez Summary The protein encoded by this gene recognizes the sequence CCTTGAG along with other members of the HMG-box class DNA-binding proteins. It acts during chondrocyte differentiation and, with steroidogenic factor 1, regulates transcription of the anti-Muellerian hormone (AMH) gene. Deficiencies lead to the skeletal malformation syndrome campomelic dysplasia, frequently with sex reversal. [provided by RefSeq, Jul 2008]
Ensembl ID: ENSG00000125398
External Link: CisBP
Interpro IPR009071; IPR022151;
Protein Domain: ENSP00000245479
Domain:
Protein: ENSP00000245479DBD: HMGOther: Sox_N

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_DNA Binding_
PMIDS:15590666
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:20484372, PMID:20530484, PMID:21367821
GO:0003700
sequence-specific DNA binding transcription factor activity
IDA - PMID:10805756 | IMP - PMID:8640233
GO:0003705
RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity
IDA - PMID:20484372, PMID:21412441
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-SELEXJolma2013Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
SELEXJASPARDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
MiscHocoMocoDirect
HT-SELEXYin2017Inferred - SOX8 (98% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - SOX8 (98% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - SOX8 (98% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - SOX8 (98% AA Identity, Homo sapiens)
PBMBadis09Inferred - Sox8 (98% AA Identity, Mus musculus)
SMiLE-seqIsakova2017Inferred - SOX10 (95% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - SOX10 (95% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - SOX10 (95% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - SOX10 (95% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - SOX10 (95% AA Identity, Homo sapiens)
PBMDREAM_contestInferred - Sox10 (95% AA Identity, Mus musculus)
COMPILEDJASPARInferred - SOX10 (95% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - SOX10 (95% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - SOX10 (95% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - SOX10 (95% AA Identity, Homo sapiens)
MiscHocoMocoInferred - SOX10 (95% AA Identity, Homo sapiens)

Structure

Structure PDB 4EUW

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