SOX6 SRY-box transcription factor 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SOX6provided by HGNC
Official Full Name: SRY-box transcription factor 6provided by HGNC
Primary source: HGNC:HGNC:16421
See related: Ensembl:ENSG00000110693 MIM:607257; AllianceGenome:HGNC:16421
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SOXD; HSSOX6; TOLCAS
Summary: This gene encodes a member of the D subfamily of sex determining region y-related transcription factors that are characterized by a conserved DNA-binding domain termed the high mobility group box and by their ability to bind the minor groove of DNA. The encoded protein is a transcriptional activator that is required for normal development of the central nervous system, chondrogenesis and maintenance of cardiac and skeletal muscle cells. The encoded protein interacts with other family members to cooperatively activate gene expression. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Mar 2009]
Expression: Broad expression in brain (RPKM 4.6), kidney (RPKM 4.5) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11p15.2

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (15966449..16738477, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (16064414..16835856, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (15987995..16760024, complement)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Clinical implications and genetical insights of SOX6 expression in acute myeloid leukemia.
Title: Clinical implications and genetical insights of SOX6 expression in acute myeloid leukemia.
MiR-19b-3p Inhibits Hypoxia-Ischemia Encephalopathy by Inhibiting SOX6 Expression via Activating Wnt/beta-catenin Pathway.
Title: MiR-19b-3p Inhibits Hypoxia-Ischemia Encephalopathy by Inhibiting SOX6 Expression via Activating Wnt/β-catenin Pathway.
Circ_0001498 contributes to lipopolysaccharide-induced lung cell apoptosis and inflammation in sepsis-related acute lung injury via upregulating SOX6 by interacting with miR-574-5p.
Title: Circ_0001498 contributes to lipopolysaccharide-induced lung cell apoptosis and inflammation in sepsis-related acute lung injury via upregulating SOX6 by interacting with miR-574-5p.
Circ_0123996 promotes the proliferation, inflammation, and fibrosis of mesangial cells by sponging miR-203a-3p to upregulate SOX6 in diabetic nephropathy.
Title: Circ_0123996 promotes the proliferation, inflammation, and fibrosis of mesangial cells by sponging miR-203a-3p to upregulate SOX6 in diabetic nephropathy.
An Osteoporosis Susceptibility Allele at 11p15 Regulates SOX6 Expression by Modulating TCF4 Chromatin Binding.
Title: An Osteoporosis Susceptibility Allele at 11p15 Regulates SOX6 Expression by Modulating TCF4 Chromatin Binding.
Identification of a novel circ_0001946/miR-1290/SOX6 ceRNA network in esophageal squamous cell cancer.
Title: Identification of a novel circ_0001946/miR-1290/SOX6 ceRNA network in esophageal squamous cell cancer.
Identification of SOX6 and SOX12 as Prognostic Biomarkers for Clear Cell Renal Cell Carcinoma: A Retrospective Study Based on TCGA Database.
Title: Identification of SOX6 and SOX12 as Prognostic Biomarkers for Clear Cell Renal Cell Carcinoma: A Retrospective Study Based on TCGA Database.
SOX6 Expression Is Sensitive for Peritoneal Epithelioid Malignant Mesothelioma, But Not Specific in the Differential Diagnosis With Tubo-ovarian Serous Neoplasia.
Title: SOX6 Expression Is Sensitive for Peritoneal Epithelioid Malignant Mesothelioma, But Not Specific in the Differential Diagnosis With Tubo-ovarian Serous Neoplasia.
Sox6 expression distinguishes dorsally and ventrally biased dopamine neurons in the substantia nigra with distinctive properties and embryonic origins.
Title: Sox6 expression distinguishes dorsally and ventrally biased dopamine neurons in the substantia nigra with distinctive properties and embryonic origins.
Targeting protein lysine methyltransferase G9A impairs self-renewal of chronic myelogenous leukemia stem cells via upregulation of SOX6.
Title: Targeting protein lysine methyltransferase G9A impairs self-renewal of chronic myelogenous leukemia stem cells via upregulation of SOX6.

Submit: New GeneRIF Correction See all GeneRIFs (65)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Tolchin-Le Caignec syndrome MedGen: C5436509 OMIM: 618971 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
A genome-wide association analysis implicates SOX6 as a candidate gene for wrist bone mass. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis of blood-pressure traits in African-ancestry individuals reveals common associated genes in African and non-African populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study in Chinese identifies novel loci for blood pressure and hypertension. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. EBI GWAS Catalog EBI GWAS CatalogPubMed
GWAS of Longevity in CHARGE Consortium Confirms APOE and FOXO3 Candidacy. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of novel germline polymorphisms governing capecitabine sensitivity. EBI GWAS Catalog EBI GWAS CatalogPubMed
Multistage genome-wide association meta-analyses identified two new loci for bone mineral density. EBI GWAS Catalog EBI GWAS CatalogPubMed
Powerful bivariate genome-wide association analyses suggest the SOX6 gene influencing both obesity and osteoporosis phenotypes in males. EBI GWAS Catalog EBI GWAS CatalogPubMed
The Contribution of Common Genetic Variation to Nicotine and Cotinine Glucuronidation in Multiple Ethnic/Racial Populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SOX6_844 (e-PCR)
- UniSTS:277764

SHGC-37207 (e-PCR)
- UniSTS:5127

D11S4042 (e-PCR)
- UniSTS:153869

WI-17892 (e-PCR)
- UniSTS:80926

SHGC-82799 (e-PCR)
- UniSTS:102432

SHGC-104674 (e-PCR)
- UniSTS:168993

G63381 (e-PCR)
- UniSTS:140345

RH94315 (e-PCR)
- UniSTS:85843

SHGC-35069 (e-PCR)
- UniSTS:37738

UniSTS:144491 (e-PCR)
- UniSTS:144491

Sox6 (e-PCR), detects polymorphism
- UniSTS:144491

RH65285 (e-PCR)
- UniSTS:46963

Sox6 (e-PCR), detects polymorphism
- UniSTS:536442

G33060 (e-PCR)
- UniSTS:117636

RH45425 (e-PCR)
- UniSTS:76699

SHGC-153595 (e-PCR)
- UniSTS:177834

WI-16902 (e-PCR)
- UniSTS:19635

D11S1397 (e-PCR)
- UniSTS:15546

RH68714 (e-PCR)
- UniSTS:28347

D11S2336 (e-PCR)
- UniSTS:59835

WI-17844 (e-PCR)
- UniSTS:52420

STS-H69535 (e-PCR)
- UniSTS:62663

SHGC-83953 (e-PCR)
- UniSTS:103624

SHGC-83873 (e-PCR)
- UniSTS:101843

SHGC-83438 (e-PCR)
- UniSTS:182495

D11S2872 (e-PCR)
- UniSTS:152050

G30608 (e-PCR)
- UniSTS:37621

RH120774 (e-PCR)
- UniSTS:132854

A010A46 (e-PCR)
- UniSTS:9978

D11S4044 (e-PCR)
- UniSTS:51451

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	NAS Non-traceable Author Statement more info	PubMed
enables DNA-binding transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA-binding transcription factor activity	NAS Non-traceable Author Statement more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables DNA-binding transcription repressor activity	ISS Inferred from Sequence or Structural Similarity more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in brain development	IDA Inferred from Direct Assay more info	PubMed
involved_in cartilage condensation	ISS Inferred from Sequence or Structural Similarity more info
involved_in cartilage development	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell fate commitment	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to transforming growth factor beta stimulus	IDA Inferred from Direct Assay more info	PubMed
involved_in central nervous system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in chondrocyte differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in muscle organ development	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cardiac muscle cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cartilage development	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of chondrocyte differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of chondrocyte differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of mesenchymal stem cell differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-templated transcription	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in spinal cord oligodendrocyte cell differentiation	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of chromatin	ISA Inferred from Sequence Alignment more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info
located_in nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: transcription factor SOX-6

Names: SRY (sex determining region Y)-box 6; SRY-box 6; SRY-box containing gene 6

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_012881.2 RefSeqGene

Range

386931..777028

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001145811.2 → NP_001139283.1 transcription factor SOX-6 isoform b

See identical proteins and their annotated locations for NP_001139283.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) has multiple differences in the coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1. Variants 1 and 3 both encode the same isoform (b).

Source sequence(s)

AC009869, AC013595, AC027016, AC068405, AC103794

Consensus CDS

CCDS53604.1

UniProtKB/Swiss-Prot

P35712

Related

ENSP00000432134.1, ENST00000528252.5

Conserved Domains (1) summary

cd01388
Location:593 → 664

SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
NM_001145819.2 → NP_001139291.2 transcription factor SOX-6 isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (a) has a distinct N-terminus and is longer than isoform b. Variants 4 and 6 both encode the same isoform (a).

Source sequence(s)

AC009869, AC013595, AC027016, AC068405, AC103794

Consensus CDS

CCDS91447.1

UniProtKB/Swiss-Prot

P35712, Q86VX7, Q9BXQ3, Q9BXQ4, Q9BXQ5, Q9H0I8

Related

ENSP00000433233.1, ENST00000528429.5
NM_001367872.1 → NP_001354801.1 transcription factor SOX-6 isoform d

Status: REVIEWED

Source sequence(s)

AC009869, AC013595, AC026639, AC027016, AC068405, AC100865, AC103794
NM_001367873.1 → NP_001354802.1 transcription factor SOX-6 isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (6) encodes the longest isoform (a). Variants 4 and 6 both encode the same isoform (a).

Source sequence(s)

AC009869, AC013595, AC027016, AC068405, AC103794

Consensus CDS

CCDS91447.1

UniProtKB/Swiss-Prot

P35712, Q86VX7, Q9BXQ3, Q9BXQ4, Q9BXQ5, Q9H0I8

Related

ENSP00000507545.1, ENST00000683767.1
NM_017508.3 → NP_059978.2 transcription factor SOX-6 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform b. Variants 1 and 3 both encode the same isoform (b).

Source sequence(s)

AC009869, AC013595, AC027016, AC068405, AC103794

Consensus CDS

CCDS53604.1

Related

ENSP00000434455.2, ENST00000527619.6
NM_033326.3 → NP_201583.2 transcription factor SOX-6 isoform c

See identical proteins and their annotated locations for NP_201583.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (c) has a distinct N-terminus and is longer than isoform b.

Source sequence(s)

AC009869, AC103794, AF309034, AK097455

Consensus CDS

CCDS7821.1

UniProtKB/Swiss-Prot

P35712

Related

ENSP00000379644.3, ENST00000396356.7

Conserved Domains (1) summary

cd01388
Location:600 → 671

SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...