Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    SOX9 SRY-box 9 [ Homo sapiens (human) ]

    Gene ID: 6662, updated on 14-Oct-2018

    Summary

    Official Symbol
    SOX9provided by HGNC
    Official Full Name
    SRY-box 9provided by HGNC
    Primary source
    HGNC:HGNC:11204
    See related
    Ensembl:ENSG00000125398 MIM:608160; Vega:OTTHUMG00000166300
    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
    CMD1; SRA1; CMPD1; SRXX2; SRXY10
    Summary
    The protein encoded by this gene recognizes the sequence CCTTGAG along with other members of the HMG-box class DNA-binding proteins. It acts during chondrocyte differentiation and, with steroidogenic factor 1, regulates transcription of the anti-Muellerian hormone (AMH) gene. Deficiencies lead to the skeletal malformation syndrome campomelic dysplasia, frequently with sex reversal. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in testis (RPKM 26.5), brain (RPKM 25.2) and 17 other tissues See more
    Orthologs

    Genomic context

    See SOX9 in Genome Data Viewer
    Location:
    17q24.3
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 17 NC_000017.11 (72121020..72126420)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (70117161..70122561)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene SOX9 antisense RNA 1 Neighboring gene TES enhancer upstream of SOX9 Neighboring gene uncharacterized LOC107987249 Neighboring gene SOX9 promoter region Neighboring gene SOX9 enhancer E7 Neighboring gene long intergenic non-protein coding RNA 2003

    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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    46,XY sex reversal 10
    MedGen: C4225331 OMIM: 616425 GeneReviews: Not available
    not available
    Camptomelic dysplasia
    MedGen: C1861922 OMIM: 114290 GeneReviews: Campomelic Dysplasia
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2012-07-26)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2012-07-26)

    ClinGen Genome Curation PagePubMed

    NHGRI GWAS Catalog

    Description
    A meta-analysis of thyroid-related traits reveals novel loci and gender-specific differences in the regulation of thyroid function.
    NHGRI GWA Catalog
    Genetic variation in prostate-specific antigen-detected prostate cancer and the effect of control selection on genetic association studies.
    NHGRI GWA Catalog
    Genetics of coronary artery calcification among African Americans, a meta-analysis.
    NHGRI GWA Catalog
    Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.
    NHGRI GWA Catalog
    Genome-wide association study of lung function decline in adults with and without asthma.
    NHGRI GWA Catalog
    Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
    NHGRI GWA Catalog
    Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
    NHGRI GWA Catalog
    Identification of a susceptibility locus for severe adolescent idiopathic scoliosis on chromosome 17q24.3.
    NHGRI GWA Catalog

    Pathways from BioSystems

    • Deactivation of the beta-catenin transactivating complex, organism-specific biosystem (from REACTOME)
      Deactivation of the beta-catenin transactivating complex, organism-specific biosystemThe mechanisms involved in downregulation of TCF-dependent transcription are not yet very well understood. beta-catenin is known to recruit a number of transcriptional repressors, including Reptin, S...
    • Endochondral Ossification, organism-specific biosystem (from WikiPathways)
      Endochondral Ossification, organism-specific biosystemEndochondral ossification is the process by which the embryonic cartilaginous model of most bones contributes to longitudinal growth and is gradually replaced by bone. During endochondral ossificatio...
    • Neural Crest Differentiation, organism-specific biosystem (from WikiPathways)
      Neural Crest Differentiation, organism-specific biosystemGene regulatory network model of cranial neural crest cell (CNCC) development, adaped from PMID: 19575671. Most interactions in the model are proposed to regulate transcription of core factors involv...
    • Signal Transduction, organism-specific biosystem (from REACTOME)
      Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
    • Signaling by Wnt, organism-specific biosystem (from REACTOME)
      Signaling by Wnt, organism-specific biosystemWNT signaling pathways control a wide range of developmental and adult process in metozoans including cell proliferation, cell fate decisions, cell polarity and stem cell maintenance (reviewed in Sai...
    • Spinal Cord Injury, organism-specific biosystem (from WikiPathways)
      Spinal Cord Injury, organism-specific biosystemThis pathway provides an overview of cell types, therapeutic targets, drugs, new proposed targets and pathways implicated in spinal cord injury. Spinal cord injury is a complex multistep process that...
    • TCF dependent signaling in response to WNT, organism-specific biosystem (from REACTOME)
      TCF dependent signaling in response to WNT, organism-specific biosystem19 WNT ligands and 10 FZD receptors have been identified in human cells; interactions amongst these ligands and receptors vary in a developmental and tissue-specific manner and lead to activation of ...
    • cAMP signaling pathway, organism-specific biosystem (from KEGG)
      cAMP signaling pathway, organism-specific biosystemcAMP is one of the most common and universal second messengers, and its formation is promoted by adenylyl cyclase (AC) activation after ligation of G protein-coupled receptors (GPCRs) by ligands incl...
    • cAMP signaling pathway, conserved biosystem (from KEGG)
      cAMP signaling pathway, conserved biosystemcAMP is one of the most common and universal second messengers, and its formation is promoted by adenylyl cyclase (AC) activation after ligation of G protein-coupled receptors (GPCRs) by ligands incl...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA-binding transcription activator activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    DNA-binding transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
     
    DNA-binding transcription factor activity, RNA polymerase II-specific ISM
    Inferred from Sequence Model
    more info
    PubMed 
    DNA-binding transcription factor activity, RNA polymerase II-specific NAS
    Non-traceable Author Statement
    more info
    PubMed 
    RNA polymerase II proximal promoter sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    bHLH transcription factor binding IEA
    Inferred from Electronic Annotation
    more info
     
    beta-catenin binding IEA
    Inferred from Electronic Annotation
    more info
     
    chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enhancer binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enhancer sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    pre-mRNA intronic binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein heterodimerization activity IEA
    Inferred from Electronic Annotation
    more info
     
    protein kinase A catalytic subunit binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein kinase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    ERK1 and ERK2 cascade ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    Harderian gland development IEA
    Inferred from Electronic Annotation
    more info
     
    Notch signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    Sertoli cell development IEA
    Inferred from Electronic Annotation
    more info
     
    Sertoli cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    anterior head development IEA
    Inferred from Electronic Annotation
    more info
     
    astrocyte fate commitment IEA
    Inferred from Electronic Annotation
    more info
     
    branching involved in ureteric bud morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    bronchus cartilage development IEA
    Inferred from Electronic Annotation
    more info
     
    cAMP-mediated signaling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cartilage condensation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cartilage development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cell fate specification ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cell-cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to BMP stimulus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cellular response to epidermal growth factor stimulus ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    cellular response to heparin ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    cellular response to interleukin-1 IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    cellular response to mechanical stimulus ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    cellular response to retinoic acid IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    cellular response to transforming growth factor beta stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    central nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    chondrocyte differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    chondrocyte differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    chondrocyte differentiation involved in endochondral bone morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    chondrocyte hypertrophy ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    chromatin remodeling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cochlea morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cytoskeleton organization IEA
    Inferred from Electronic Annotation
    more info
     
    endocardial cushion morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    endocrine pancreas development IEA
    Inferred from Electronic Annotation
    more info
     
    epidermal growth factor receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    epithelial cell proliferation involved in prostatic bud elongation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    epithelial to mesenchymal transition ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    epithelial tube branching involved in lung morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    extracellular matrix organization IEA
    Inferred from Electronic Annotation
    more info
     
    hair follicle development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    heart development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    heart valve development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    heart valve formation IEA
    Inferred from Electronic Annotation
    more info
     
    heart valve morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    intestinal epithelial structure maintenance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    intrahepatic bile duct development IEA
    Inferred from Electronic Annotation
    more info
     
    lacrimal gland development IEA
    Inferred from Electronic Annotation
    more info
     
    limb bud formation IEA
    Inferred from Electronic Annotation
    more info
     
    lung epithelial cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    lung smooth muscle development IEA
    Inferred from Electronic Annotation
    more info
     
    male germ-line sex determination ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    male gonad development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    male gonad development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    mammary gland development IEA
    Inferred from Electronic Annotation
    more info
     
    metanephric nephron tubule formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    morphogenesis of a branching epithelium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    morphogenesis of an epithelium IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    negative regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of biomineral tissue development IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of biomineral tissue development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of bone mineralization IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of canonical Wnt signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of chondrocyte differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of epithelial cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of epithelial cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of immune system process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of mesenchymal cell apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of myoblast differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of ossification ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of photoreceptor cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of pri-miRNA transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of transcription, DNA-templated IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    neural crest cell development IEA
    Inferred from Electronic Annotation
    more info
     
    neural crest cell fate specification ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    notochord development IEA
    Inferred from Electronic Annotation
    more info
     
    nucleosome assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    oligodendrocyte differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    ossification IEA
    Inferred from Electronic Annotation
    more info
     
    otic vesicle formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of branching involved in ureteric bud morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of cartilage development IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of cell proliferation involved in heart morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of chondrocyte differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    positive regulation of chondrocyte differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of chondrocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of epithelial cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of epithelial cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of epithelial cell proliferation IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    positive regulation of epithelial cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of extracellular matrix assembly IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of kidney development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of male gonad development IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of mesenchymal cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of mesenchymal stem cell differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of phosphatidylinositol 3-kinase signaling ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of protein phosphorylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription, DNA-templated IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    prostate gland development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    protein kinase B signaling IEA
    Inferred from Electronic Annotation
    more info
     
    protein localization to nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    protein-containing complex assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of branching involved in lung morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of cell cycle process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of cell proliferation involved in tissue homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of epithelial cell proliferation involved in lung morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    renal vesicle induction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    retina development in camera-type eye ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    retinal rod cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    signal transduction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    skeletal system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    somatic stem cell population maintenance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    spermatogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    tissue homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    trachea cartilage development IEA
    Inferred from Electronic Annotation
    more info
     
    transcription initiation from RNA polymerase II promoter TAS
    Traceable Author Statement
    more info
     
    ureter morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    ureter smooth muscle cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    ureter urothelium development IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    nuclear transcription factor complex IEA
    Inferred from Electronic Annotation
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    transcription factor SOX-9
    Names
    SRY (sex determining region Y)-box9
    SRY (sex-determining region Y)-box 9 protein
    SRY-related HMG-box, gene 9

    NCBI Reference Sequences (RefSeq)

    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_012490.1 RefSeqGene

      Range
      5001..10401
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000346.3NP_000337.1  transcription factor SOX-9

      See identical proteins and their annotated locations for NP_000337.1

      Status: REVIEWED

      Source sequence(s)
      AC007461, BC007951, BC018276, Z46629
      Consensus CDS
      CCDS11689.1
      UniProtKB/Swiss-Prot
      P48436
      Related
      ENSP00000245479.2, OTTHUMP00000232537, ENST00000245479.2, OTTHUMT00000389032
      Conserved Domains (2) summary
      cd01388
      Location:104174
      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 ...
      pfam12444
      Location:2294
      Sox_N; Sox developmental protein N terminal

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p12 Primary Assembly

      Range
      72121020..72126420
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Support Center