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    Sox13 SRY-box transcription factor 13 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 289026, updated on 3-Apr-2024

    Summary

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    Official Symbol
    Sox13provided by RGD
    Official Full Name
    SRY-box transcription factor 13provided by RGD
    Primary source
    RGD:1309674
    See related
    Ensembl:ENSRNOG00000028353 AllianceGenome:RGD:1309674
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and identical protein binding activity. Predicted to be involved in several processes, including gamma-delta T cell differentiation; positive regulation of cell differentiation; and spinal cord oligodendrocyte cell differentiation. Predicted to act upstream of or within regulation of gamma-delta T cell differentiation. Predicted to be located in cytoplasm and nucleoplasm. Predicted to be active in nucleus. Orthologous to human SOX13 (SRY-box transcription factor 13). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Lung (RPKM 149.9), Kidney (RPKM 113.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    13q13
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (47383145..47427572, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (44831097..44875522, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (50434702..50479118)

    Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102550525 Neighboring gene renin Neighboring gene ethanolamine kinase 2 Neighboring gene uncharacterized LOC103692077 Neighboring gene uncharacterized LOC134481497 Neighboring gene small nuclear ribonucleoprotein polypeptide E

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. SOX13 exhibits a distinct spatial and temporal expression pattern during chondrogenesis, neurogenesis, and limb development. Wang Y, et al. J Histochem Cytochem, 2006 Dec. PMID 16835393, Free PMC Article
    2. Sex-determining region Y-related protein SOX13 is a diabetes autoantigen expressed in pancreatic islets. Kasimiotis H, et al. Diabetes, 2000 Apr. PMID 10871192
    3. Cloning and characterization of mouse mSox13 cDNA. Kido S, et al. Gene, 1998 Feb 27. PMID 9524265
    4. High expression of the HMG box factor sox-13 in arterial walls during embryonic development. Roose J, et al. Nucleic Acids Res, 1998 Jan 15. PMID 9421502, Free PMC Article
    5. Regulation of gammadelta versus alphabeta T lymphocyte differentiation by the transcription factor SOX13. Melichar HJ, et al. Science, 2007 Jan 12. PMID 17218525

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription repressor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    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 transcription regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription cis-regulatory region binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of brown fat cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of gamma-delta T cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of gamma-delta T cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    transcription factor SOX-13
    Names
    SRY (sex determining region Y)-box 13
    SRY box 13
    SRY-box containing gene 13

    NCBI Reference Sequences (RefSeq)

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    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_001105952.1 → NP_001099422.1  transcription factor SOX-13

      See identical proteins and their annotated locations for NP_001099422.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473958
      UniProtKB/TrEMBL
      A6IC79, A6IC80
      Related
      ENSRNOP00000068223.2, ENSRNOT00000076857.2
      Conserved Domains (2) summary
      PHA03195
      Location:250 → 418
      PHA03195; tegument protein VP11/12; Provisional
      cd01388
      Location:414 → 485
      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_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086031.1 Reference GRCr8

      Range
      47383145..47427572 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006249762.5 → XP_006249824.1  transcription factor SOX-13 isoform X3

      UniProtKB/TrEMBL
      A6IC80, D4A8S0
      Related
      ENSRNOP00000030216.6
      Conserved Domains (2) summary
      cd01388
      Location:415 → 486
      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 ...
      cl28045
      Location:251 → 419
      Herpes_UL46; Herpesvirus UL46 protein

    2. XM_039090434.2 → XP_038946362.1  transcription factor SOX-13 isoform X3

      UniProtKB/TrEMBL
      A6IC80, D4A8S0
      Conserved Domains (2) summary
      cd01388
      Location:415 → 486
      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 ...
      cl28045
      Location:251 → 419
      Herpes_UL46; Herpesvirus UL46 protein

    3. XM_063272079.1 → XP_063128149.1  transcription factor SOX-13 isoform X4

      UniProtKB/TrEMBL
      A6IC79

    4. XM_063272078.1 → XP_063128148.1  transcription factor SOX-13 isoform X2

    5. XM_063272077.1 → XP_063128147.1  transcription factor SOX-13 isoform X1

    Nucleotide Protein Strain
    Heading Accession and Version

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