The Human Transcription Factors

Conclusion

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

Description

Description:	SRY-box 6 [Source:HGNC Symbol;Acc:HGNC:16421]
Entrez Summary	TBA
Ensembl ID:	ENSG00000110693
External Link:	T144085_1.02
Interpro	IPR009071; ;
Protein Domain:
Protein: ENSP00000379644	DBD: HMG	Other:
Protein: ENSP00000434455	DBD: HMG	Other:
Protein: ENSP00000433233	DBD: HMG	Other:
Protein: ENSP00000432134	DBD: HMG	Other:
Protein: ENSP00000434892	DBD: HMG	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding_ PMIDS:7567444 11504872
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 NAS - PMID:1614875
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-seq	Isakova2017		Direct
Transfac	Transfac	License required	Direct
PBM	DREAM_contest		Inferred - Sox6 (100% AA Identity, Mus musculus)
ChIP-seq	JASPAR		Inferred - Sox6 (100% AA Identity, Mus musculus)
Misc	HOMER		Inferred - Sox6 (100% AA Identity, Mus musculus)
PBM	Badis09		Inferred - Sox13 (92% AA Identity, Mus musculus)
SMiLE-seq	Isakova2017		Inferred - SOX5 (92% AA Identity, Homo sapiens)
PBM	Badis09		Inferred - Sox5 (92% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - SOX5 (92% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - SOX5 (92% AA Identity, Homo sapiens)
SELEX	JASPAR		Inferred - Sox5 (92% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - SOX13 (92% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - SOX5 (92% AA Identity, Homo sapiens)

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

Name
Email
Comment
Reference

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{"regions": [{"startStyle": "curved", "end": 665, "endStyle": "curved", "aliStart": 597, "text": "HMG", "colour": "#228B22", "aliEnd": 665, "start": 597, "href": "http://pfam.xfam.org/family/PF00505.17", "type": "pfama", "display": "true", "metadata": {"end": 665, "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": 597, "scoreName": "E-value", "accession": "PF00505.17", "start": 597, "score": 1.5e-22, "identifier": "HMG (high mobility group) box", "type": "DBD", "aliEnd": 665}}], "length": 805}

{"regions": [{"startStyle": "curved", "end": 689, "endStyle": "curved", "aliStart": 621, "text": "HMG", "colour": "#228B22", "aliEnd": 689, "start": 621, "href": "http://pfam.xfam.org/family/PF00505.17", "type": "pfama", "display": "true", "metadata": {"end": 689, "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": 621, "scoreName": "E-value", "accession": "PF00505.17", "start": 621, "score": 1.7e-22, "identifier": "HMG (high mobility group) box", "type": "DBD", "aliEnd": 689}}], "length": 829}

{"regions": [{"startStyle": "curved", "end": 662, "endStyle": "curved", "aliStart": 594, "text": "HMG", "colour": "#228B22", "aliEnd": 662, "start": 594, "href": "http://pfam.xfam.org/family/PF00505.17", "type": "pfama", "display": "true", "metadata": {"end": 662, "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": 594, "scoreName": "E-value", "accession": "PF00505.17", "start": 594, "score": 1.5e-22, "identifier": "HMG (high mobility group) box", "type": "DBD", "aliEnd": 662}}], "length": 802}

TF Info Page for SOX6 (HMG/Sox)