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    Sox9 SRY (sex determining region Y)-box 9 [ Mus musculus (house mouse) ]

    Gene ID: 20682, updated on 14-Jan-2025

    Summary

    Official Symbol
    Sox9provided by MGI
    Official Full Name
    SRY (sex determining region Y)-box 9provided by MGI
    Primary source
    MGI:MGI:98371
    See related
    Ensembl:ENSMUSG00000000567 AllianceGenome:MGI:98371
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    mSox9; mKIAA4243; 2010306G03Rik
    Summary
    Enables DNA-binding transcription activator activity, RNA polymerase II-specific; beta-catenin binding activity; and nucleic acid binding activity. Involved in several processes, including ERK1 and ERK2 cascade; kidney epithelium development; and positive regulation of morphogenesis of an epithelium. Acts upstream of or within several processes, including negative regulation of cell differentiation; regulation of macromolecule metabolic process; and skeletal system development. Located in nucleus. Part of transcription regulator complex. Is expressed in several structures, including alimentary system; central nervous system; embryo mesenchyme; genitourinary system; and sensory organ. Used to study campomelic dysplasia. Human ortholog(s) of this gene implicated in campomelic dysplasia; lung cancer; and lung carcinoma. Orthologous to human SOX9 (SRY-box transcription factor 9). [provided by Alliance of Genome Resources, Jan 2025]
    Expression
    Broad expression in limb E14.5 (RPKM 30.6), colon adult (RPKM 27.7) and 16 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Sox9 in Genome Data Viewer
    Location:
    11 E2; 11 77.27 cM
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (112673036..112678583)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (112782210..112787757)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_31060 Neighboring gene STARR-seq mESC enhancer starr_31061 Neighboring gene predicted gene, 39461 Neighboring gene STARR-seq mESC enhancer starr_31062 Neighboring gene VISTA enhancer mm634 Neighboring gene STARR-seq mESC enhancer starr_31063 Neighboring gene Sox9 enhancer E250 Neighboring gene Sox9 enhancer E195 Neighboring gene Sox9 enhancer E84 Neighboring gene cDNA sequence BC006965 Neighboring gene Sox9 enhancer SOM Neighboring gene Sox9 testis enhancer TES Neighboring gene Sox9 promoter region Neighboring gene predicted gene 11681 Neighboring gene predicted gene, 30562

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

    Interactions

    General gene information

    Clone Names

    • KIAA4243

    Gene Ontology Provided by MGI

    Items 1 - 25 of 30
    Function Evidence Code Pubs
    enables DNA binding PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific  
    enables DNA-binding transcription activator activity, RNA polymerase II-specific  
    enables DNA-binding transcription factor activity PubMed 
    enables DNA-binding transcription factor activity PubMed 
    enables DNA-binding transcription factor activity  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables bHLH transcription factor binding  
    enables bHLH transcription factor binding  
    enables beta-catenin binding PubMed 
    enables beta-catenin binding PubMed 
    enables chromatin binding  
    enables chromatin binding  
    enables cis-regulatory region sequence-specific DNA binding PubMed 
    enables cis-regulatory region sequence-specific DNA binding  
    enables pre-mRNA intronic binding PubMed 
    enables protein binding PubMed 
    enables protein kinase A catalytic subunit binding  
    enables protein kinase A catalytic subunit binding  
    enables sequence-specific DNA binding PubMed 
    enables sequence-specific DNA binding  
    enables sequence-specific double-stranded DNA binding  
    enables transcription cis-regulatory region binding PubMed 
    Items 1 - 25 of 30
    Items 1 - 25 of 211
    Process Evidence Code Pubs
    involved_in ERK1 and ERK2 cascade PubMed 
    acts_upstream_of_or_within Harderian gland development PubMed 
    acts_upstream_of_or_within Notch signaling pathway PubMed 
    acts_upstream_of_or_within Sertoli cell development PubMed 
    acts_upstream_of_or_within Sertoli cell differentiation PubMed 
    acts_upstream_of_or_within anterior head development PubMed 
    involved_in aortic valve morphogenesis  
    involved_in aortic valve morphogenesis  
    acts_upstream_of apoptotic process PubMed 
    acts_upstream_of_or_within astrocyte fate commitment PubMed 
    acts_upstream_of bone mineralization PubMed 
    involved_in branching involved in ureteric bud morphogenesis PubMed 
    acts_upstream_of_or_within bronchus cartilage development PubMed 
    involved_in cAMP-mediated signaling  
    acts_upstream_of canonical Wnt signaling pathway PubMed 
    acts_upstream_of_or_within cartilage condensation PubMed 
    involved_in cartilage condensation  
    acts_upstream_of cartilage development PubMed 
    involved_in cartilage development PubMed 
    acts_upstream_of_or_within cartilage development PubMed 
    involved_in cartilage development PubMed 
    acts_upstream_of_or_within cell fate commitment PubMed 
    acts_upstream_of cell population proliferation PubMed 
    acts_upstream_of cell proliferation involved in heart morphogenesis PubMed 
    acts_upstream_of_or_within cell-cell adhesion PubMed 
    involved_in cellular response to BMP stimulus  
    involved_in cellular response to epidermal growth factor stimulus PubMed 
    involved_in cellular response to heparin PubMed 
    involved_in cellular response to interleukin-1  
    involved_in cellular response to mechanical stimulus PubMed 
    acts_upstream_of_or_within cellular response to retinoic acid PubMed 
    involved_in cellular response to transforming growth factor beta stimulus PubMed 
    involved_in cellular response to transforming growth factor beta stimulus  
    involved_in central nervous system development PubMed 
    acts_upstream_of_or_within chondrocyte development PubMed 
    involved_in chondrocyte differentiation  
    involved_in chondrocyte differentiation PubMed 
    involved_in chondrocyte differentiation PubMed 
    acts_upstream_of chondrocyte differentiation PubMed 
    acts_upstream_of_or_within chondrocyte differentiation PubMed 
    involved_in chondrocyte differentiation PubMed 
    involved_in chondrocyte differentiation  
    involved_in chondrocyte differentiation involved in endochondral bone morphogenesis  
    involved_in chondrocyte differentiation involved in endochondral bone morphogenesis  
    involved_in chondrocyte hypertrophy PubMed 
    involved_in chromatin remodeling  
    involved_in chromatin remodeling  
    acts_upstream_of_or_within cochlea morphogenesis PubMed 
    acts_upstream_of_or_within cytoskeleton organization PubMed 
    acts_upstream_of_or_within endocardial cushion morphogenesis PubMed 
    acts_upstream_of_or_within endochondral bone morphogenesis PubMed 
    acts_upstream_of_or_within endocrine pancreas development PubMed 
    involved_in epidermal growth factor receptor signaling pathway PubMed 
    acts_upstream_of epithelial cell proliferation PubMed 
    acts_upstream_of_or_within epithelial cell proliferation involved in prostatic bud elongation PubMed 
    acts_upstream_of_or_within epithelial to mesenchymal transition PubMed 
    acts_upstream_of_or_within epithelial tube branching involved in lung morphogenesis PubMed 
    acts_upstream_of_or_within epithelial tube branching involved in lung morphogenesis PubMed 
    acts_upstream_of extracellular matrix assembly PubMed 
    acts_upstream_of_or_within extracellular matrix organization PubMed 
    involved_in gene expression PubMed 
    acts_upstream_of glandular epithelial cell differentiation PubMed 
    acts_upstream_of_or_within glial cell fate specification PubMed 
    involved_in growth plate cartilage chondrocyte growth PubMed 
    acts_upstream_of_or_within hair follicle development PubMed 
    involved_in heart development  
    acts_upstream_of_or_within heart development PubMed 
    involved_in heart valve development PubMed 
    acts_upstream_of_or_within heart valve formation PubMed 
    acts_upstream_of_or_within heart valve morphogenesis PubMed 
    acts_upstream_of_or_within homeostasis of number of cells within a tissue PubMed 
    acts_upstream_of intestinal epithelial cell differentiation PubMed 
    acts_upstream_of_or_within intestinal epithelial structure maintenance PubMed 
    acts_upstream_of_or_within intrahepatic bile duct development PubMed 
    acts_upstream_of_or_within lacrimal gland development PubMed 
    involved_in limb bud formation PubMed 
    acts_upstream_of_or_within lung epithelial cell differentiation PubMed 
    acts_upstream_of_or_within lung smooth muscle development PubMed 
    acts_upstream_of_or_within male germ-line sex determination PubMed 
    involved_in male gonad development PubMed 
    acts_upstream_of_or_within male gonad development PubMed 
    acts_upstream_of_or_within male gonad development PubMed 
    involved_in male gonad development  
    acts_upstream_of_or_within male sex determination PubMed 
    involved_in mammary gland development PubMed 
    acts_upstream_of mesenchymal cell apoptotic process PubMed 
    acts_upstream_of mesenchymal cell proliferation PubMed 
    acts_upstream_of_or_within metanephric nephron tubule formation PubMed 
    involved_in metanephric tubule development PubMed 
    acts_upstream_of_or_within morphogenesis of a branching epithelium PubMed 
    acts_upstream_of_or_within morphogenesis of a branching epithelium PubMed 
    involved_in morphogenesis of an epithelium  
    acts_upstream_of_or_within negative regulation of DNA-templated transcription PubMed 
    involved_in negative regulation of DNA-templated transcription PubMed 
    involved_in negative regulation of DNA-templated transcription  
    acts_upstream_of_or_within negative regulation of apoptotic process PubMed 
    involved_in negative regulation of beta-catenin-TCF complex assembly PubMed 
    involved_in negative regulation of biomineral tissue development PubMed 
    involved_in negative regulation of biomineral tissue development  
    acts_upstream_of_or_within negative regulation of bone mineralization PubMed 
    acts_upstream_of_or_within negative regulation of canonical Wnt signaling pathway PubMed 
    involved_in negative regulation of canonical Wnt signaling pathway PubMed 
    involved_in negative regulation of canonical Wnt signaling pathway PubMed 
    acts_upstream_of_or_within negative regulation of chondrocyte differentiation PubMed 
    acts_upstream_of_or_within negative regulation of epithelial cell differentiation PubMed 
    acts_upstream_of_or_within negative regulation of epithelial cell proliferation PubMed 
    involved_in negative regulation of fatty acid oxidation PubMed 
    acts_upstream_of_or_within negative regulation of gene expression PubMed 
    involved_in negative regulation of immune system process PubMed 
    acts_upstream_of_or_within negative regulation of mesenchymal cell apoptotic process PubMed 
    involved_in negative regulation of miRNA transcription  
    involved_in negative regulation of miRNA transcription  
    acts_upstream_of_or_within negative regulation of myoblast differentiation PubMed 
    involved_in negative regulation of ossification PubMed 
    involved_in negative regulation of ossification  
    involved_in negative regulation of osteoblast differentiation PubMed 
    involved_in negative regulation of osteoblast differentiation PubMed 
    acts_upstream_of_or_within negative regulation of photoreceptor cell differentiation PubMed 
    involved_in negative regulation of transcription by RNA polymerase II  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II PubMed 
    involved_in negative regulation of transcription by RNA polymerase II  
    acts_upstream_of_or_within neural crest cell development PubMed 
    involved_in neural crest cell fate specification  
    acts_upstream_of_or_within neuron fate specification PubMed 
    involved_in notochord development PubMed 
    involved_in nucleosome assembly  
    involved_in nucleosome assembly  
    involved_in oligodendrocyte differentiation  
    acts_upstream_of_or_within oligodendrocyte differentiation PubMed 
    involved_in ossification PubMed 
    involved_in otic vesicle development PubMed 
    acts_upstream_of_or_within otic vesicle formation PubMed 
    acts_upstream_of_or_within positive regulation of DNA-templated transcription PubMed 
    involved_in positive regulation of DNA-templated transcription PubMed 
    acts_upstream_of_or_within positive regulation of DNA-templated transcription PubMed 
    involved_in positive regulation of DNA-templated transcription  
    involved_in positive regulation of branching involved in ureteric bud morphogenesis PubMed 
    acts_upstream_of_or_within positive regulation of cartilage development PubMed 
    involved_in positive regulation of cartilage development  
    acts_upstream_of_or_within positive regulation of cell population proliferation PubMed 
    involved_in positive regulation of cell population proliferation  
    acts_upstream_of_or_within positive regulation of cell proliferation involved in heart morphogenesis PubMed 
    involved_in positive regulation of chondrocyte differentiation  
    involved_in positive regulation of chondrocyte differentiation PubMed 
    involved_in positive regulation of chondrocyte differentiation PubMed 
    involved_in positive regulation of chondrocyte differentiation  
    involved_in positive regulation of chondrocyte proliferation  
    involved_in positive regulation of chondrocyte proliferation  
    acts_upstream_of_or_within positive regulation of epithelial cell differentiation PubMed 
    acts_upstream_of_or_within positive regulation of epithelial cell migration PubMed 
    involved_in positive regulation of epithelial cell migration  
    involved_in positive regulation of epithelial cell migration PubMed 
    acts_upstream_of_or_within positive regulation of epithelial cell proliferation PubMed 
    involved_in positive regulation of epithelial cell proliferation PubMed 
    acts_upstream_of_or_within positive regulation of extracellular matrix assembly PubMed 
    acts_upstream_of_or_within positive regulation of gene expression PubMed 
    involved_in positive regulation of gene expression  
    involved_in positive regulation of kidney development PubMed 
    involved_in positive regulation of male gonad development  
    involved_in positive regulation of male gonad development  
    acts_upstream_of_or_within positive regulation of mesenchymal cell proliferation PubMed 
    involved_in positive regulation of mesenchymal stem cell differentiation  
    involved_in positive regulation of mesenchymal stem cell differentiation  
    acts_upstream_of_or_within positive regulation of protein catabolic process PubMed 
    acts_upstream_of_or_within positive regulation of protein phosphorylation PubMed 
    acts_upstream_of_or_within positive regulation of stem cell proliferation PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II PubMed 
    involved_in positive regulation of transcription by RNA polymerase II PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II PubMed 
    involved_in positive regulation of transcription by RNA polymerase II PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II PubMed 
    involved_in positive regulation of transcription by RNA polymerase II PubMed 
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in prostate gland development PubMed 
    acts_upstream_of_or_within prostate gland morphogenesis PubMed 
    acts_upstream_of_or_within protein localization to nucleus PubMed 
    acts_upstream_of protein phosphorylation PubMed 
    involved_in protein-containing complex assembly  
    involved_in protein-containing complex assembly  
    acts_upstream_of_or_within regulation of DNA-templated transcription PubMed 
    acts_upstream_of_or_within regulation of branching involved in lung morphogenesis PubMed 
    acts_upstream_of_or_within regulation of cell adhesion PubMed 
    involved_in regulation of cell cycle process  
    involved_in regulation of cell cycle process  
    acts_upstream_of_or_within regulation of cell differentiation PubMed 
    acts_upstream_of_or_within regulation of cell population proliferation PubMed 
    acts_upstream_of_or_within regulation of cell proliferation involved in tissue homeostasis PubMed 
    acts_upstream_of_or_within regulation of epithelial cell proliferation involved in lung morphogenesis PubMed 
    acts_upstream_of_or_within regulation of gene expression PubMed 
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II PubMed 
    involved_in renal vesicle induction PubMed 
    involved_in response to fatty acid PubMed 
    involved_in response to organic cyclic compound  
    acts_upstream_of_or_within retina development in camera-type eye PubMed 
    acts_upstream_of retinal rod cell differentiation PubMed 
    acts_upstream_of_or_within retinal rod cell differentiation PubMed 
    involved_in signal transduction PubMed 
    involved_in skeletal system development  
    involved_in skeletal system development  
    acts_upstream_of_or_within somatic stem cell population maintenance PubMed 
    acts_upstream_of_or_within spermatogenesis PubMed 
    acts_upstream_of stem cell proliferation PubMed 
    involved_in tissue homeostasis PubMed 
    acts_upstream_of_or_within trachea cartilage development PubMed 
    acts_upstream_of transcription by RNA polymerase II PubMed 
    acts_upstream_of transcription by RNA polymerase II PubMed 
    acts_upstream_of type I pneumocyte differentiation PubMed 
    acts_upstream_of_or_within ureter development PubMed 
    acts_upstream_of_or_within ureter morphogenesis PubMed 
    acts_upstream_of_or_within ureter smooth muscle cell differentiation PubMed 
    involved_in ureter urothelium development PubMed 
    Items 1 - 25 of 211
    Component Evidence Code Pubs
    located_in nucleoplasm  
    located_in nucleoplasm  
    is_active_in nucleus  
    located_in nucleus PubMed 
    located_in nucleus  
    part_of protein-containing complex  
    part_of protein-containing complex  
    part_of transcription regulator complex PubMed 
    part_of transcription regulator complex PubMed 
    part_of transcription regulator complex  

    General protein information

    Preferred Names
    transcription factor SOX-9
    Names
    SRY-box containing gene 9

    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.

    mRNA and Protein(s)

    1. NM_011448.4NP_035578.3  transcription factor SOX-9

      See identical proteins and their annotated locations for NP_035578.3

      Status: VALIDATED

      Source sequence(s)
      AK030187, AL683879
      Consensus CDS
      CCDS25595.1
      UniProtKB/Swiss-Prot
      Q04887, Q8C7L2, Q91ZK2, Q99KQ0
      UniProtKB/TrEMBL
      Q571J2
      Related
      ENSMUSP00000000579.3, ENSMUST00000000579.3
      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: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000077.7 Reference GRCm39 C57BL/6J

      Range
      112673036..112678583
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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