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    Sox2 SRY (sex determining region Y)-box 2 [ Mus musculus (house mouse) ]

    Gene ID: 20674, updated on 9-Dec-2024

    Summary

    Official Symbol
    Sox2provided by MGI
    Official Full Name
    SRY (sex determining region Y)-box 2provided by MGI
    Primary source
    MGI:MGI:98364
    See related
    Ensembl:ENSMUSG00000074637 AllianceGenome:MGI:98364
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    lcc; ysb; Sox-2
    Summary
    This intronless gene encodes a member of the SRY-related HMG-box (SOX) family of transcription factors involved in the regulation of embryonic development and in the determination of cell fate. The product of this gene is required for stem-cell maintenance in the central nervous system, and also regulates gene expression in the stomach. Mutations in a similar gene in human have been associated with optic nerve hypoplasia and with syndromic microphthalmia, a severe form of structural eye malformation. This gene lies within an intron of another gene called SOX2 overlapping transcript (Sox2ot). [provided by RefSeq, Sep 2015]
    Orthologs
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    Genomic context

    See Sox2 in Genome Data Viewer
    Location:
    3 A3; 3 16.93 cM
    Exon count:
    1
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (34704144..34706610)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (34649995..34652461)

    Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene predicted gene 20515 Neighboring gene predicted gene, 34599 Neighboring gene STARR-seq mESC enhancer starr_07369 Neighboring gene SOX2 overlapping transcript (non-protein coding) Neighboring gene Sox2 5' regulatory region Neighboring gene microRNA 1897 Neighboring gene Sox2 SRR2 enhancer Neighboring gene SRR18 enhancer downstream of Sox2 Neighboring gene N-4 enhancer downstream of Sox2 Neighboring gene STARR-seq mESC enhancer starr_07376 Neighboring gene STARR-seq mESC enhancer starr_07377 Neighboring gene predicted gene, 34941 Neighboring gene STARR-seq mESC enhancer starr_07378 Neighboring gene predicted gene 3143

    Genomic regions, transcripts, and products

    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

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    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 IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    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 RNA polymerase II cis-regulatory region sequence-specific DNA binding IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    enables RNA polymerase II-specific DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables chromatin DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables miRNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables miRNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    enables transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription cis-regulatory region binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables transcription cis-regulatory region binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of Notch signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of Wnt signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in adenohypophysis development IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within adenohypophysis development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within anatomical structure formation involved in morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within cell fate commitment IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within cell fate specification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cellular response to cadmium ion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within cerebral cortex development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within detection of mechanical stimulus involved in equilibrioception IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within detection of mechanical stimulus involved in sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within diencephalon morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within embryonic organ development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in endodermal cell fate specification IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within endodermal cell fate specification ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    acts_upstream_of_or_within epithelial tube branching involved in lung morphogenesis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in eye development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in forebrain development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within forebrain neuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in inner ear development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in inner ear development IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within inner ear morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within lens induction in camera-type eye IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within lung alveolus development IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within male genitalia development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of Wnt signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in negative regulation of canonical Wnt signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of canonical Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of canonical Wnt signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of cell cycle G1/S phase transition IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of cell cycle G1/S phase transition ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of epithelial cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of epithelial cell proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of neuron differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of osteoblast differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of neuroblast proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of neuron differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of neuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neuron fate commitment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neuronal stem cell population maintenance IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within olfactory placode formation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of osteoblast differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in osteoblast differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in osteoblast differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within pigment biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of MAPK cascade IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of MAPK cascade ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of Notch signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of cell differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of cell-cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of cell-cell adhesion ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of epithelial cell differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of neuroblast proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of neuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within 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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of cysteine-type endopeptidase activity ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of myofibroblast cell apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of myofibroblast cell apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within regulation of neurogenesis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to growth factor IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to growth factor ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in response to oxygen-glucose deprivation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to oxygen-glucose deprivation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within response to retinoic acid IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to wounding IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within retina morphogenesis in camera-type eye IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in somatic stem cell population maintenance IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within somatic stem cell population maintenance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in somatic stem cell population maintenance ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within stem cell differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in stem cell population maintenance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in tissue regeneration IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within tongue development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of trophectodermal cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    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 IC
    Inferred by Curator
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    part_of transcription regulator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    transcription factor SOX-2
    Names
    SRY-box containing gene 2

    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_011443.4NP_035573.3  transcription factor SOX-2

      See identical proteins and their annotated locations for NP_035573.3

      Status: REVIEWED

      Source sequence(s)
      AL606746, AW494059, BM938133, BY713734, CD354017, CF164429, CX205480
      Consensus CDS
      CCDS38413.1
      UniProtKB/Swiss-Prot
      P48432
      UniProtKB/TrEMBL
      Q60I23
      Related
      ENSMUSP00000096755.3, ENSMUST00000099151.6
      Conserved Domains (2) summary
      cd01388
      Location:42113
      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 ...
      pfam12336
      Location:112202
      SOXp; SOX transcription factor

    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_000069.7 Reference GRCm39 C57BL/6J

      Range
      34704144..34706610
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)