The Human Transcription Factors

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	TBA
Ensembl ID:	ENSG00000125398
External Link:	T144092_1.02
Interpro	IPR009071; IPR022151;
Protein Domain:
Protein: ENSP00000245479	DBD: HMG	Other: 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-SELEX	Jolma2013		Direct
HT-SELEX	Jolma2013		Direct
HT-SELEX	Jolma2013		Direct
HT-SELEX	Jolma2013		Direct
HT-SELEX	Jolma2013		Direct
HT-SELEX	Jolma2013		Direct
HT-SELEX	Jolma2013		Direct
HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
SELEX	JASPAR		Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct
HT-SELEX	Yin2017		Inferred - SOX8 (98% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - SOX8 (98% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - SOX8 (98% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - SOX8 (98% AA Identity, Homo sapiens)
PBM	Badis09		Inferred - Sox8 (98% AA Identity, Mus musculus)
SMiLE-seq	Isakova2017		Inferred - SOX10 (95% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - SOX10 (95% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - SOX10 (95% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - SOX10 (95% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - SOX10 (95% AA Identity, Homo sapiens)
PBM	DREAM_contest		Inferred - Sox10 (95% AA Identity, Mus musculus)
COMPILED	JASPAR		Inferred - SOX10 (95% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - SOX10 (95% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - SOX10 (95% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - SOX10 (95% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - 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

Name
Email
Comment
Reference

{"regions": [{"startStyle": "curved", "end": 173, "endStyle": "curved", "aliStart": 105, "text": "HMG", "colour": "#228B22", "aliEnd": 173, "start": 105, "href": "http://pfam.xfam.org/family/PF00505.17", "type": "pfama", "display": "true", "metadata": {"end": 173, "description": "High mobility group (HMG) box domains are involved in binding DNA, and may be involved in protein-protein interactions as well. The structure of the HMG-box domain consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin. Many of these proteins are regulators of gene expression. HMG-box proteins are found in a variety of eukaryotic organisms, and can be broadly divided into two groups, based on sequence-dependent and sequence-independent DNA recognition; the former usually contain one HMG-box motif, while the latter can contain multiple HMG-box motifs.", "database": "PfamA", "aliStart": 105, "scoreName": "E-value", "accession": "PF00505.17", "start": 105, "score": 1.9000000000000001e-25, "identifier": "HMG (high mobility group) box", "type": "DBD", "aliEnd": 173}}, {"startStyle": "straight", "end": 94, "endStyle": "straight", "aliStart": 23, "text": "Sox_N", "colour": "#9999ff", "aliEnd": 94, "start": 22, "href": "http://pfam.xfam.org/family/PF12444.6", "type": "pfama", "display": "true", "metadata": {"end": 94, "description": "This domain family is found in eukaryotes, and is typically between 69 and 88 amino acids in length. The family is found in association with Pfam:PF00505. There are two conserved sequence motifs: YDW and PVR. This family contains Sox8, Sox9 and Sox10 proteins which have structural similarity. Sox proteins are involved in developmental processes.", "database": "PfamA", "aliStart": 23, "scoreName": "E-value", "accession": "PF12444.6", "start": 22, "score": 9.300000000000001e-26, "identifier": "Sox developmental protein N terminal ", "type": "DBD", "aliEnd": 94}}], "length": 510}

TF Info Page for SOX9 (HMG/Sox)