TF Info Page for SOX2 (HMG/Sox)

Conclusion

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

Description

Description: SRY-box 2 [Source:HGNC Symbol;Acc:HGNC:11195]
Entrez Summary This intronless gene encodes a member of the SRY-related HMG-box (SOX) family of transcription factors involved in the regulation of embryonic development and in the determination of cell fate. The product of this gene is required for stem-cell maintenance in the central nervous system, and also regulates gene expression in the stomach. Mutations in this gene have been associated with optic nerve hypoplasia and with syndromic microphthalmia, a severe form of structural eye malformation. This gene lies within an intron of another gene called SOX2 overlapping transcript (SOX2OT). [provided by RefSeq, Jul 2008]
Ensembl ID: ENSG00000181449
External Link: CisBP
Interpro IPR009071; IPR022097;
Protein Domain: ENSP00000323588
Domain:
Protein: ENSP00000323588DBD: HMGOther: SOXp

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_DNA Binding
Transactivation_
PMIDS:15860457
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
IEA - GO_REF:0000019
GO:0003700
sequence-specific DNA binding transcription factor activity
IDA - PMID:16153702, PMID:18027866 | NAS - PMID:78
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
SMiLE-seqIsakova2017Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
MiscHocoMocoDirect
ChIP-seqhmCHIPInferred - Sox2 (100% AA Identity, Mus musculus)
ChIP-seqhmCHIPInferred - Sox2 (100% AA Identity, Mus musculus)
ChIP-seqJASPARInferred - Sox2 (100% AA Identity, Mus musculus)
PBMBadis09Inferred - Sox1 (95% AA Identity, Mus musculus)
PBMBadis09Inferred - Sox21 (95% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - SOX14 (94% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - SOX14 (94% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - SOX14 (94% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - SOX14 (94% AA Identity, Homo sapiens)
PBMBadis09Inferred - Sox14 (94% AA Identity, Mus musculus)
PBMDREAM_contestInferred - Sox14 (94% AA Identity, Mus musculus)
HT-SELEXNitta2015Inferred - Sox21a (92% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Sox21a (92% AA Identity, Drosophila melanogaster)

Structure

Structure PDB 1GT0

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