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

Gene ID: 20674, updated on 17-May-2022

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
109 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)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 3 NC_000069.5 (34548927..34551383)

Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene predicted gene 20515 Neighboring gene predicted gene, 34599 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

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

Homology

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 ISO
Inferred from Sequence Orthology
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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 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 ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
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 anatomical structure morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cell fate commitment IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 
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 forebrain development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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 multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
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 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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
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
PubMed 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
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 
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 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 ISO
Inferred from Sequence Orthology
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
PubMed 
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 
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
 
involved_in positive regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of cysteine-type endopeptidase activity involved in apoptotic process ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of gene expression 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 regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
involved_in response to growth factor ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within response to organic substance IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within response to retinoic acid IDA
Inferred from Direct Assay
more info
PubMed 
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 ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within stem cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within stem cell population maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in stem cell population maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within tongue development 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 ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
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)

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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_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: Mus musculus Annotation Release 109 details...Open this link in a new tab

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)