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    Sox2 SRY-box transcription factor 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 499593, updated on 9-Dec-2024

    Summary

    Official Symbol
    Sox2provided by RGD
    Official Full Name
    SRY-box transcription factor 2provided by RGD
    Primary source
    RGD:1565646
    See related
    EnsemblRapid:ENSRNOG00000090426 AllianceGenome:RGD:1565646
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1565646
    Summary
    Enables DNA-binding transcription activator activity, RNA polymerase II-specific and transcription cis-regulatory region binding activity. Involved in several processes, including adenohypophysis development; regulation of myofibroblast cell apoptotic process; and response to oxygen-glucose deprivation. Located in nucleus. Used to study congestive heart failure. Biomarker of alcohol use disorder. Human ortholog(s) of this gene implicated in breast cancer; nasal cavity cancer; and syndromic microphthalmia 3. Orthologous to human SOX2 (SRY-box transcription factor 2). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 93.0) and Lung (RPKM 9.9) See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Sox2 in Genome Data Viewer
    Location:
    2q24
    Exon count:
    1
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (119465131..119467542)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (117536929..117539340)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (121165137..121167545)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC103691527 Neighboring gene uncharacterized LOC120100802 Neighboring gene heterogeneous nuclear ribonucleoprotein A3 like 1 Neighboring gene uncharacterized LOC108350241 Neighboring gene uncharacterized LOC120100803 Neighboring gene keratin-associated protein 10-4-like

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by RGD

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

    General protein information

    Preferred Names
    transcription factor SOX-2
    Names
    SRY (sex determining region Y)-box 2
    SRY box 2
    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_001109181.2NP_001102651.1  transcription factor SOX-2

      See identical proteins and their annotated locations for NP_001102651.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000002
      UniProtKB/TrEMBL
      A6IHU9, D4A543
      Related
      ENSRNOP00000103840.1, ENSRNOT00000129472.1
      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_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086020.1 Reference GRCr8

      Range
      119465131..119467542
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)