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    Sox13 SRY (sex determining region Y)-box 13 [ Mus musculus (house mouse) ]

    Gene ID: 20668, updated on 3-Dec-2024

    Summary

    Official Symbol
    Sox13provided by MGI
    Official Full Name
    SRY (sex determining region Y)-box 13provided by MGI
    Primary source
    MGI:MGI:98361
    See related
    Ensembl:ENSMUSG00000070643 AllianceGenome:MGI:98361
    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
    Sox-13
    Summary
    Enables DNA-binding transcription repressor activity and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in several processes, including gamma-delta T cell differentiation; positive regulation of cell differentiation; and spinal cord oligodendrocyte cell differentiation. Acts upstream of or within regulation of gamma-delta T cell differentiation. Located in cytoplasm and nucleus. Is expressed in several structures, including alimentary system; central nervous system; early conceptus; genitourinary system; and hair follicle. Orthologous to human SOX13 (SRY-box transcription factor 13). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in lung adult (RPKM 49.3), small intestine adult (RPKM 36.4) and 24 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Sox13 in Genome Data Viewer
    Location:
    1 E4; 1 57.91 cM
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (133310038..133352159, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (133382300..133424459, complement)

    Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene Ren1 promoter and enhancer region Neighboring gene STARR-positive B cell enhancer ABC_E11089 Neighboring gene renin 1 structural Neighboring gene ethanolamine kinase 2 Neighboring gene STARR-seq mESC enhancer starr_02283 Neighboring gene STARR-seq mESC enhancer starr_02289 Neighboring gene VISTA enhancer mm573 Neighboring gene STARR-seq mESC enhancer starr_02292 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:135446523-135446815 Neighboring gene ribosomal protein L7A pseudogene Neighboring gene predicted gene, 23939

    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)
    • Endonuclease-mediated (1) 
    • Targeted (5)  1 citation

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    involved_in cell fate commitment IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in gamma-delta T cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of canonical Wnt signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of canonical Wnt signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of brown fat cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of gamma-delta T cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regulation of gamma-delta T cell differentiation IDA
    Inferred from Direct Assay
    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 IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm 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
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    transcription factor SOX-13
    Names
    SRY-box containing gene 13

    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_001420920.1NP_001407849.1  transcription factor SOX-13 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC068906
      UniProtKB/TrEMBL
      D3Z7I3
    2. NM_001420922.1NP_001407851.1  transcription factor SOX-13 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC068906
      UniProtKB/Swiss-Prot
      Q04891, Q922L3
      UniProtKB/TrEMBL
      D3Z7I3
      Related
      ENSMUSP00000092130.5, ENSMUST00000094551.5
    3. NM_001420923.1NP_001407852.1  transcription factor SOX-13 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC068906
      UniProtKB/Swiss-Prot
      Q04891, Q922L3
      UniProtKB/TrEMBL
      D3Z7I3
    4. NM_001420924.1NP_001407853.1  transcription factor SOX-13 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC068906
      UniProtKB/TrEMBL
      D3Z7I3
    5. NM_001420925.1NP_001407854.1  transcription factor SOX-13 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC068906
      UniProtKB/TrEMBL
      D3Z7I3
      Related
      ENSMUSP00000122980.2, ENSMUST00000144386.8
    6. NM_011439.3NP_035569.2  transcription factor SOX-13 isoform 2

      See identical proteins and their annotated locations for NP_035569.2

      Status: VALIDATED

      Source sequence(s)
      AC068906
      Consensus CDS
      CCDS48363.1
      UniProtKB/Swiss-Prot
      Q04891, Q922L3
      UniProtKB/TrEMBL
      D3Z7I3
      Related
      ENSMUSP00000119729.3, ENSMUST00000153799.8
      Conserved Domains (1) summary
      cd01388
      Location:415486
      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_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_000067.7 Reference GRCm39 C57BL/6J

      Range
      133310038..133352159 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006529276.5XP_006529339.1  transcription factor SOX-13 isoform X3

      See identical proteins and their annotated locations for XP_006529339.1

      UniProtKB/TrEMBL
      D3Z7I3
      Conserved Domains (2) summary
      cd01388
      Location:417488
      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 ...
      pfam03154
      Location:225334
      Atrophin-1; Atrophin-1 family
    2. XM_036162973.1XP_036018866.1  transcription factor SOX-13 isoform X2

      UniProtKB/TrEMBL
      D3Z7I3
      Conserved Domains (1) summary
      cd01388
      Location:422493
      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 ...
    3. XM_011247945.4XP_011246247.1  transcription factor SOX-13 isoform X1

      See identical proteins and their annotated locations for XP_011246247.1

      UniProtKB/TrEMBL
      D3Z7I3
      Conserved Domains (2) summary
      cd01388
      Location:423494
      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 ...
      pfam03154
      Location:231340
      Atrophin-1; Atrophin-1 family