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

    Gene ID: 55553, updated on 17-Jun-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SOX6 in Genome Data Viewer
    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_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902800 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:15887657-15887820 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3180 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:15969994-15970143 Neighboring gene long intergenic non-protein coding RNA 2682 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4479 Neighboring gene MPRA-validated peak1212 silencer Neighboring gene uncharacterized LOC105376572 Neighboring gene uncharacterized LOC124900593 Neighboring gene microRNA 6073 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:16086747 Neighboring gene MPRA-validated peak1213 silencer Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:16133413 Neighboring gene MPRA-validated peak1214 silencer Neighboring gene VISTA enhancer hs1720 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:16199331 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:16200444 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:16210951 Neighboring gene VISTA enhancer hs883 Neighboring gene VISTA enhancer hs236 Neighboring gene VISTA enhancer hs717 Neighboring gene VISTA enhancer hs1301 Neighboring gene SOX6 proximal promoter region Neighboring gene aldo-keto reductase family 1 member B1 pseudogene 3 Neighboring gene MPRA-validated peak1218 silencer Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr11:16628669-16629170 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr11:16629171-16629670 Neighboring gene uncharacterized LOC105376571 Neighboring gene RNA, 7SL, cytoplasmic 188, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:16691581-16692082 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:16691079-16691580 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:16699888-16700416 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:16700417-16700944 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:16730412-16730912 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:16730913-16731413 Neighboring gene MPRA-validated peak1219 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:16800297-16801020 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:16802139-16802833 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:16801021-16801743 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:16802834-16803527 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:16803848-16804825 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:16812092-16812592 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:16812593-16813093 Neighboring gene chromosome 11 open reading frame 58 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:16823697-16824896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:16836605-16837105 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
    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
    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
    Genome-wide association study in Chinese identifies novel loci for blood pressure and hypertension.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
    EBI GWAS Catalog
    GWAS of Longevity in CHARGE Consortium Confirms APOE and FOXO3 Candidacy.
    EBI GWAS Catalog
    Identification of novel germline polymorphisms governing capecitabine sensitivity.
    EBI GWAS Catalog
    Multistage genome-wide association meta-analyses identified two new loci for bone mineral density.
    EBI GWAS Catalog
    Powerful bivariate genome-wide association analyses suggest the SOX6 gene influencing both obesity and osteoporosis phenotypes in males.
    EBI GWAS Catalog
    The Contribution of Common Genetic Variation to Nicotine and Cotinine Glucuronidation in Multiple Ethnic/Racial Populations.
    EBI GWAS Catalog
    Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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
     
    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

    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_012881.2 RefSeqGene

      Range
      386931..777028
      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
      Consensus CDS
      CCDS91447.1
      UniProtKB/Swiss-Prot
      P35712, Q86VX7, Q9BXQ3, Q9BXQ4, Q9BXQ5, Q9H0I8
      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
      Consensus CDS
      CCDS91447.1
      UniProtKB/Swiss-Prot
      P35712, Q86VX7, Q9BXQ3, Q9BXQ4, Q9BXQ5, Q9H0I8
      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
      CCDS53604.1
      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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      16064414..16835856 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)