U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    SOX4 SRY-box transcription factor 4 [ Homo sapiens (human) ]

    Gene ID: 6659, updated on 27-Nov-2024

    Summary

    Official Symbol
    SOX4provided by HGNC
    Official Full Name
    SRY-box transcription factor 4provided by HGNC
    Primary source
    HGNC:HGNC:11200
    See related
    Ensembl:ENSG00000124766 MIM:184430; AllianceGenome:HGNC:11200
    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
    CSS10; EVI16
    Summary
    This intronless gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins, such as syndecan binding protein (syntenin). The protein may function in the apoptosis pathway leading to cell death as well as to tumorigenesis and may mediate downstream effects of parathyroid hormone (PTH) and PTH-related protein (PTHrP) in bone development. The solution structure has been resolved for the HMG-box of a similar mouse protein. [provided by RefSeq, Jul 2008]
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SOX4 in Genome Data Viewer
    Location:
    6p22.3
    Exon count:
    1
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (21593751..21598619)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (21466412..21471279)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (21593982..21598850)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 581 Neighboring gene MPRA-validated peak5728 silencer Neighboring gene uncharacterized LOC107986579 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:21586838-21587370 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16982 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16983 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21588011-21588668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24140 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16984 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24141 Neighboring gene bolA family member 2 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24142 Neighboring gene MPRA-validated peak5729 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:21649156-21649656 Neighboring gene uncharacterized LOC124901483 Neighboring gene Sharpr-MPRA regulatory region 7931

    Genomic regions, transcripts, and products

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Coffin-Siris syndrome 10
    MedGen: C4760583 OMIM: 618506 GeneReviews: Coffin-Siris Syndrome
    not available

    EBI GWAS Catalog

    Description
    Genome-wide association study using extreme truncate selection identifies novel genes affecting bone mineral density and fracture risk.
    EBI GWAS Catalog
    Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
    EBI GWAS Catalog
    Hypertrophy-associated polymorphisms ascertained in a founder cohort applied to heart failure risk and mortality.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    NOT enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables miRNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription cis-regulatory region binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    involved_in T cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in ascending aorta morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in atrial septum primum morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in camera-type eye morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cardiac right ventricle morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cellular response to glucose stimulus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in endocrine pancreas development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in glial cell development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in glial cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in glucose homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in heart development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in hematopoietic stem cell homeostasis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in kidney morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mesenchyme development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mitral valve morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of myoblast differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of protein ubiquitination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in nervous system development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in neuroepithelial cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in noradrenergic neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of N-terminal peptidyl-lysine acetylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of canonical Wnt signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of gamma-delta T cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of insulin secretion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of myoblast differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of translation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in pro-B cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein stabilization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of DNA damage response, signal transduction by p53 class mediator IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of protein stability IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to hypoxia IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in somatic stem cell population maintenance IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in spinal cord development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in sympathetic nervous system development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in ventricular septum morphogenesis 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 cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    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
    PubMed 
    part_of transcription regulator complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    transcription factor SOX-4
    Names
    SRY (sex determining region Y)-box 4
    SRY-box 4
    SRY-related HMG-box gene 4
    ecotropic viral integration site 16

    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_029166.1 RefSeqGene

      Range
      5011..9879
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_003107.3NP_003098.1  transcription factor SOX-4

      See identical proteins and their annotated locations for NP_003098.1

      Status: REVIEWED

      Source sequence(s)
      AJ420500, AL136179, BM817788, CF147018, CN419098, CX873598, HY065060, X70683
      Consensus CDS
      CCDS4547.1
      UniProtKB/Swiss-Prot
      Q06945
      Related
      ENSP00000244745.1, ENST00000244745.4
      Conserved Domains (1) summary
      cd01388
      Location:58129
      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 vertebrates, and ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      21593751..21598619
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      21466412..21471279
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)