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

Gene ID: 55553, updated on 5-Sep-2021

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
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
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Genomic context

See SOX6 in Genome Data Viewer
Location:
11p15.2
Exon count:
22
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (15966449..16738477, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (15987995..16760024, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984370 Neighboring gene long intergenic non-protein coding RNA 2682 Neighboring gene uncharacterized LOC105376572 Neighboring gene microRNA 6073 Neighboring gene VISTA enhancer hs1720 Neighboring gene VISTA enhancer hs883 Neighboring gene VISTA enhancer hs236 Neighboring gene VISTA enhancer hs717 Neighboring gene VISTA enhancer hs1301 Neighboring gene uncharacterized LOC112268084 Neighboring gene SOX6 proximal promoter region Neighboring gene aldo-keto reductase family 1 member B1 pseudogene 3 Neighboring gene uncharacterized LOC105376571 Neighboring gene RNA, 7SL, cytoplasmic 188, pseudogene Neighboring gene chromosome 11 open reading frame 58 Neighboring gene pleckstrin homology domain containing A7 Neighboring gene RN7SK pseudogene 90

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
A genome-wide association analysis implicates SOX6 as a candidate gene for wrist bone mass.
GeneReviews: Not available
Genome-wide association analysis of blood-pressure traits in African-ancestry individuals reveals common associated genes in African and non-African populations.
GeneReviews: Not available
Genome-wide association study in Chinese identifies novel loci for blood pressure and hypertension.
GeneReviews: Not available
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
GeneReviews: Not available
GWAS of Longevity in CHARGE Consortium Confirms APOE and FOXO3 Candidacy.
GeneReviews: Not available
Identification of novel germline polymorphisms governing capecitabine sensitivity.
GeneReviews: Not available
Multistage genome-wide association meta-analyses identified two new loci for bone mineral density.
GeneReviews: Not available
Powerful bivariate genome-wide association analyses suggest the SOX6 gene influencing both obesity and osteoporosis phenotypes in males.
GeneReviews: Not available
The Contribution of Common Genetic Variation to Nicotine and Cotinine Glucuronidation in Multiple Ethnic/Racial Populations.
GeneReviews: Not available
Tolchin-Le Caignec syndrome
MedGen: C5436509 OMIM: 618971 GeneReviews: Not available
not available
Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.
GeneReviews: Not available

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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
PubMed 
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
PubMed 
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 cardiac muscle cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
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
PubMed 
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 transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
involved_in spinal cord oligodendrocyte cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
located_in chromatin ISA
Inferred from Sequence Alignment
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
PubMed 
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

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)

NEW Try the new Transcript table

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

  1. NG_012881.1 RefSeqGene

    Range
    5001..514941
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001145811.2NP_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:593664
    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 ...
  2. NM_001145819.2NP_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
    Related
    ENSP00000433233.1, ENST00000528429.5
  3. NM_001367872.1NP_001354801.1  transcription factor SOX-6 isoform d

    Status: REVIEWED

    Source sequence(s)
    AC009869, AC013595, AC026639, AC027016, AC068405, AC100865, AC103794
  4. NM_001367873.1NP_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
    Related
    ENSP00000507545.1, ENST00000683767.1
  5. NM_017508.3NP_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
    CCDS53605.1
    Related
    ENSP00000434455.2, ENST00000527619.6
  6. NM_033326.3NP_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:600671
    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 ...

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    15966449..16738477 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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