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

Gene ID: 20674, updated on 17-May-2016
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 Vega:OTTMUSG00000021249
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; 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
Location:
3 16.93 cM; 3 A2-B
Exon count:
1
Annotation release Status Assembly Chr Location
105 current GRCm38.p3 (GCF_000001635.23) 3 NC_000069.6 (34650005..34652461)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 3 NC_000069.5 (34548927..34551383)

Chromosome 3 - NC_000069.6Genomic Context describing neighboring genes Neighboring gene SOX2 overlapping transcript (non-protein coding) Neighboring gene predicted gene, 42205 Neighboring gene microRNA 1897 Neighboring gene predicted gene, 34941 Neighboring gene predicted gene 3143

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA binding IGI
Inferred from Genetic Interaction
more info
PubMed 
DNA binding ISO
Inferred from Sequence Orthology
more info
 
RNA polymerase II transcription factor activity, sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
chromatin DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
miRNA binding ISO
Inferred from Sequence Orthology
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
PubMed 
transcription factor activity, sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor activity, sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription regulatory region DNA binding ISO
Inferred from Sequence Orthology
more info
 
transcription regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
contributes_to transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
adenohypophysis development IMP
Inferred from Mutant Phenotype
more info
PubMed 
anatomical structure formation involved in morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell cycle arrest ISO
Inferred from Sequence Orthology
more info
 
cell fate commitment IDA
Inferred from Direct Assay
more info
PubMed 
cell fate specification IMP
Inferred from Mutant Phenotype
more info
PubMed 
cerebral cortex development IMP
Inferred from Mutant Phenotype
more info
PubMed 
detection of mechanical stimulus involved in equilibrioception IMP
Inferred from Mutant Phenotype
more info
PubMed 
detection of mechanical stimulus involved in sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
PubMed 
diencephalon morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
embryonic organ development IMP
Inferred from Mutant Phenotype
more info
PubMed 
endodermal cell fate specification ISO
Inferred from Sequence Orthology
more info
PubMed 
epithelial tube branching involved in lung morphogenesis IDA
Inferred from Direct Assay
more info
PubMed 
forebrain neuron differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
inner ear morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
lens induction in camera-type eye IGI
Inferred from Genetic Interaction
more info
PubMed 
lung alveolus development IDA
Inferred from Direct Assay
more info
PubMed 
male genitalia development IMP
Inferred from Mutant Phenotype
more info
PubMed 
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of Wnt signaling pathway IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of canonical Wnt signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of canonical Wnt signaling pathway ISO
Inferred from Sequence Orthology
more info
 
negative regulation of cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of epithelial cell proliferation ISO
Inferred from Sequence Orthology
more info
 
negative regulation of neuron differentiation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of osteoblast differentiation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription from RNA polymerase II promoter IGI
Inferred from Genetic Interaction
more info
PubMed 
neuron fate commitment IMP
Inferred from Mutant Phenotype
more info
PubMed 
neuronal stem cell population maintenance IGI
Inferred from Genetic Interaction
more info
PubMed 
olfactory placode formation IGI
Inferred from Genetic Interaction
more info
PubMed 
osteoblast differentiation ISO
Inferred from Sequence Orthology
more info
 
pigment biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of MAPK cascade ISO
Inferred from Sequence Orthology
more info
 
positive regulation of Notch signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell differentiation ISO
Inferred from Sequence Orthology
more info
 
positive regulation of cell-cell adhesion ISO
Inferred from Sequence Orthology
more info
 
positive regulation of epithelial cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of neuroblast proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of neuron differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription from RNA polymerase II promoter IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of transcription from RNA polymerase II promoter IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription from RNA polymerase II promoter ISO
Inferred from Sequence Orthology
more info
PubMed 
positive regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
regulation of cysteine-type endopeptidase activity involved in apoptotic process ISO
Inferred from Sequence Orthology
more info
 
regulation of gene expression ISO
Inferred from Sequence Orthology
more info
 
regulation of neurogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
regulation of transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
response to growth factor ISO
Inferred from Sequence Orthology
more info
 
response to organic substance IDA
Inferred from Direct Assay
more info
PubMed 
response to retinoic acid IDA
Inferred from Direct Assay
more info
PubMed 
retina morphogenesis in camera-type eye IMP
Inferred from Mutant Phenotype
more info
PubMed 
sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
PubMed 
somatic stem cell population maintenance ISO
Inferred from Sequence Orthology
more info
 
stem cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
stem cell population maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
tongue development IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcription from RNA polymerase II promoter ISO
Inferred from Sequence Orthology
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm ISO
Inferred from Sequence Orthology
more info
 
cytosol ISO
Inferred from Sequence Orthology
more info
 
nuclear transcription factor complex IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
nucleus IC
Inferred by Curator
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus ISO
Inferred from Sequence Orthology
more info
 
transcription factor complex IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
transcription factor SOX-2
Names
SRY-box containing gene 2

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, OTTMUSP00000023485, ENSMUST00000099151, OTTMUST00000050334
    Conserved Domains (2) summary
    pfam12336
    Location:112202
    SOXp; SOX transcription factor
    cd01388
    Location:42113
    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: Mus musculus Annotation Release 105 details...

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

Reference GRCm38.p3 C57BL/6J

Genomic

  1. NC_000069.6 Reference GRCm38.p3 C57BL/6J

    Range
    34650005..34652461
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate Mm_Celera

Genomic

  1. AC_000025.1 Alternate Mm_Celera

    Range
    34551711..34554169
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)