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 21 [Source:HGNC Symbol;Acc:HGNC:11197]

Entrez Summary

SRY-related HMG-box (SOX) genes encode a family of DNA-binding proteins containing a 79-amino acid HMG (high mobility group) domain that shares at least 50% sequence identity with the DNA-binding HMG box of the SRY protein (MIM 480000). SOX proteins are divided into 6 subgroups based on sequence similarity within and outside of the HMG domain. For additional background information on SOX genes, see SOX1 (MIM 602148).[supplied by OMIM, Apr 2004]

Ensembl ID:

ENSG00000125285

External Link:

CisBP

Interpro

IPR009071; IPR022097;

Protein Domain:

ENSP00000366144

Domain:

Protein: ENSP00000366144	DBD: HMG	Other: SOXp

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding_ PMIDS:12446692
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:0000981 sequence-specific DNA binding RNA polymerase II transcription factor activity NAS - PMID:10441749 GO:0003700 sequence-specific DNA binding transcription factor activity ISS - GO_REF:0000024
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
PBM	Badis09		Inferred - Sox21 (98% AA Identity, Mus musculus)
SMiLE-seq	Isakova2017		Inferred - SOX2 (94% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - SOX2 (94% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - SOX2 (94% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - SOX2 (94% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - SOX2 (94% AA Identity, Homo sapiens)
ChIP-seq	hmCHIP		Inferred - Sox2 (94% AA Identity, Mus musculus)
ChIP-seq	hmCHIP		Inferred - Sox2 (94% AA Identity, Mus musculus)
ChIP-seq	JASPAR		Inferred - Sox2 (94% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - SOX2 (94% AA Identity, Homo sapiens)
HT-SELEX	Nitta2015		Inferred - Sox21b (92% AA Identity, Drosophila melanogaster)

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

{"regions": [{"startStyle": "curved", "end": 76, "endStyle": "curved", "aliStart": 8, "text": "HMG", "colour": "#228B22", "aliEnd": 76, "start": 8, "href": "http://pfam.xfam.org/family/PF00505.17", "type": "pfama", "display": "true", "metadata": {"end": 76, "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": 8, "scoreName": "E-value", "accession": "PF00505.17", "start": 8, "score": 4e-28, "identifier": "HMG (high mobility group) box", "type": "DBD", "aliEnd": 76}}, {"startStyle": "straight", "end": 146, "endStyle": "jagged", "aliStart": 77, "text": "SOXp", "colour": "#9999ff", "aliEnd": 97, "start": 77, "href": "http://pfam.xfam.org/family/PF12336.6", "type": "pfama", "display": "true", "metadata": {"end": 146, "description": "This domain family is found in eukaryotes, and is approximately 80 amino acids in length. The family is found in association with Pfam:PF00505. There are two conserved sequence motifs: KKDK and LPG. This family is made up of SOX transcription factors. These are involved in upregulation of nestin, a neural promoter.", "database": "PfamA", "aliStart": 77, "scoreName": "E-value", "accession": "PF12336.6", "start": 77, "score": 4.5e-07, "identifier": "SOX transcription factor", "type": "DBD", "aliEnd": 97}}], "length": 277}

TF Info Page for SOX21 (HMG/Sox)