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    SOX2 SRY (sex determining region Y)-box 2 [ Homo sapiens (human) ]

    Gene ID: 6657, updated on 16-Jun-2013
    Official Symbol
    SOX2provided by HGNC
    Official Full Name
    SRY (sex determining region Y)-box 2provided by HGNC
    Primary source
    HGNC:11195
    See related
    Ensembl:ENSG00000181449; HPRD:08921; MIM:184429; Vega:OTTHUMG00000158222
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ANOP3; MCOPS3
    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 this gene 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, Jul 2008]
    Location :
    3q26.3-q27
    Sequence :
    Chromosome: 3; NC_000003.11 (181429712..181432224)
    See SOX2 in Epigenomics, MapViewer

    Chromosome 3 - NC_000003.11Genomic Context describing neighboring genes Neighboring gene FBR-MuSV-associated ubiquitously expressed (fox derived) pseudogene 2 Neighboring gene ribosomal protein L7a pseudogene 25 Neighboring gene SOX2 overlapping transcript (non-protein coding) Neighboring gene uncharacterized LOC100996490 Neighboring gene eukaryotic translation initiation factor 4E pseudogene Neighboring gene uncharacterized LOC401103

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    Microphthalmia syndromic 3

    Summary from GeneReviews: SOX2-Related Eye Disorders Go to GeneReviews

    Disease Characteristics
    SOX2-related eye disorders are characterized by anophthalmia and/or microphthalmia, which are usually bilateral, severe, and apparent at birth or by prenatal ultrasound examination. Other common findings include brain malformations, esophageal atresia, and cryptorchidism and/or micropenis in males. Postnatal growth failure, delayed motor development, and learning disability are common.
    Diagnosis Testing
    The diagnosis of SOX2-related eye disorders is established by clinical findings, cytogenetic or molecular analysis to detect deletions of 3q27 (which includes SOX2), and molecular genetic testing. SOX2 is the only gene associated with SOX2-related eye disorders. Molecular genetic testing to detect sequence variants identifies mutations in about 10%-15% of individuals with bilateral anophthalmia/microphthalmia.
    Genetic Counseling
    SOX2-related eye disorders are inherited in an autosomal dominant manner, most often resulting from a de novo mutation. The risk to the sibs of a proband is usually small; however, if a parent of a proband has germline mosaicism, the risk to the sibs may be as high as 50%. Prenatal diagnosis for pregnancies at increased risk is possible if the disease-causing mutation in the family is known. Fetal ultrasound examination reveals marked reduction in the size of the globes.
    References

    Summary from GeneReviews: Anophthalmia / Microphthalmia Overview Go to GeneReviews

    Disease Characteristics
    Anophthalmia refers to complete absence of the globe in the presence of ocular adnexa (eyelids, conjunctiva, and lacrimal apparatus). Microphthalmia is defined as a globe with a total axial length (TAL) that is at least two standard deviations below the mean for age. Classification of microphthalmia is according to the anatomic appearance of the globe and severity of axial length reduction. Severe microphthalmia refers to a globe with a corneal diameter less than 4 mm and a TAL less than 10 mm at birth or less than 12 mm after age one year. Simple microphthalmia refers to an eye that is anatomically intact except for its short TAL. Complex microphthalmia refers to an eye with anterior segment dysgenesis and/or posterior segment dysgenesis. Anophthalmia/microphthalmia (A/M) can be unilateral or bilateral. A/M is a heterogenous condition with various etiologies. It can be isolated or can occur with other anomalies or as part of a well-defined syndrome. One-third of individuals with A/M have associated malformations. Heritable causes of A/M include chromosome abnormalities and syndromic or nonsyndromic single gene disorders.
    Diagnosis Testing
    The diagnosis of anophthalmia/microphthalmia (A/M) is based on clinical examination and imaging studies including: A-scan ultrasonography to measure total axial length; B-scan ultrasonography to evaluate the internal structures of the globe; and CT scan or MRI of the brain and orbits to evaluate the size and internal structures of the globe, the optic nerve and extraocular muscles, and brain anatomy. Evaluation for other malformations, assessment of hearing, chromosome analysis, family history, and parental eye examinations may help establish the underlying cause. Mutations in the following genes are associated with A/M: SIX3, HESX1, BCOR, SHH, PAX6, RAX, CHD7 (CHARGE syndrome), IKBKG (incontinentia pigmenti), NDP (Norrie disease), SOX2 (SOX2-related eye disorders), POMT1 (Walker-Warburg syndrome), and SIX6.
    Genetic Counseling
    If a proband has an inherited or de novo chromosome abnormality or a specific syndrome associated with A/M, genetic counseling, and possibly genetic testing, for that condition is indicated. Rarely, isolated anophthalmia may be inherited in an autosomal dominant, autosomal recessive, or X-linked manner. Assuming that one-half of cases are sporadic and one-half inherited, the empiric risk for sibs without a clear etiology or family history is 10%-15%. Prenatal diagnosis for pregnancies at increased risk for chromosome abnormalities and some syndromic forms of A/M is possible. Transvaginal ultrasound examination may detect the eyes from 12 weeks' gestation onward; in most reports, eye malformations are detected only after 22 weeks' gestation. The sensitivity of transvaginal ultrasound examination in detecting A/M is not known. Three-dimensional and four-dimensional ultrasound examination may be used in some centers to detect complex malformations of the face, including A/M. MRI may be a useful adjunct to ultrasound examination in detection of anophthalmia.
    References
    Products Interactant Other Gene Complex Source Pubs Description
    P48431 Q13285 NR5A1    HPRD  PubMed  
    P48431 P14859 POU2F1    HPRD  PubMed  
    P48431 Q01860 POU5F1    HPRD  PubMed  
    BioGRID:112540 BioGRID:106601 ACTL6A    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:121938 ALX4    BioGRID  PubMed Two-hybrid 
    BioGRID:112540 BioGRID:113894 ARID1A    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:107533 CHD4    BioGRID  PubMed Affinity Capture-MS; Affinity Capture-Western 
    BioGRID:112540 BioGRID:120775 CHD7    BioGRID  PubMed Affinity Capture-MS; Affinity Capture-Western 
    BioGRID:112540 BioGRID:107869 CTBP1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:107870 CTBP2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:107903 CUX1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:107988 DBC1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:115582 DNAJA2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:124527 DOCK7    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:120172 GATAD2A    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:121529 GATAD2B    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:109315 HDAC1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:109316 HDAC2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:114368 HDAC3    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:109442 HOXA5    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:119788 MBD3    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:110368 MECP2    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:112540 BioGRID:114562 MTA1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:114652 MTA2    BioGRID  PubMed Affinity Capture-MS; Affinity Capture-Western 
    BioGRID:112540 BioGRID:119124 MYEF2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:114973 NCOR1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:114974 NCOR2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:110853 NFIB    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:111114 PAX6    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:112540 BioGRID:111456 POU5F1    BioGRID  PubMed Reconstituted Complex 
    BioGRID:112540 BioGRID:111824 RAD23B    BioGRID  PubMed Affinity Capture-Western; Co-localization 
    BioGRID:112540 BioGRID:111863 RBBP4    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:111866 RBBP7    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:111923 RFX3    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:114166 RUVBL1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:116067 RUVBL2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:112206 SALL1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:112204 SALL2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:118043 SALL3    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:117439 SIN3A    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:114045 SMARCA5    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:112482 SMARCB1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:112483 SMARCC1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:112485 SMARCC2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:112486 SMARCD1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:112540 SOX2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:112543 SOX5    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:119036 SOX8    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:116367 SUPT16H    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:122834 TBL1XR1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:112791 TCF3    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:112862 TEAD1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:113142 TWIST1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:113348 XPO1    BioGRID  PubMed Reconstituted Complex 
    BioGRID:112540 BioGRID:122138 XPO4    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:112796 ZEB1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:113403 ZNF24    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112540 BioGRID:117074 ZNF281    BioGRID  PubMed Affinity Capture-Western 
    • Cardiac Progenitor Differentiation, organism-specific biosystem (from WikiPathways)
      Cardiac Progenitor Differentiation, organism-specific biosystemFactors involved in the induction of cardiac differentiation in vitro and in vivo. This model was based on the below two review articles.
    • Hippo signaling pathway, organism-specific biosystem (from KEGG)
      Hippo signaling pathway, organism-specific biosystemHippo signaling is an evolutionarily conserved signaling pathway that controls organ size from flies to humans. In humans and mice, the pathway consists of the MST1 and MST2 kinases, their cofactor S...
    • Hippo signaling pathway, conserved biosystem (from KEGG)
      Hippo signaling pathway, conserved biosystemHippo signaling is an evolutionarily conserved signaling pathway that controls organ size from flies to humans. In humans and mice, the pathway consists of the MST1 and MST2 kinases, their cofactor S...
    • SIDS Susceptibility Pathways, organism-specific biosystem (from WikiPathways)
      SIDS Susceptibility Pathways, organism-specific biosystemIn this model, we provide an integrated view of Sudden Infant Death Syndrome (SIDS) at the level of implicated tissues, signaling networks and genetics. The purpose of this model is to serve as an ov...
    • Wnt Signaling Pathway and Pluripotency, organism-specific biosystem (from WikiPathways)
      Wnt Signaling Pathway and Pluripotency, organism-specific biosystemThis pathway was adapted from several resources and is designed to provide a theoretical frame-work for examining Wnt signaling and interacting components in the context of embryonic stem-cell plurip...

    Markers

    Homology

    Clone Names

    • MGC2413

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    adenohypophysis development IEA
    Inferred from Electronic Annotation
    more info
     
    cell cycle arrest IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cerebral cortex development IEA
    Inferred from Electronic Annotation
    more info
     
    chromatin organization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    detection of mechanical stimulus involved in equilibrioception IEA
    Inferred from Electronic Annotation
    more info
     
    detection of mechanical stimulus involved in sensory perception of sound IEA
    Inferred from Electronic Annotation
    more info
     
    diencephalon morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    endodermal cell fate specification IDA
    Inferred from Direct Assay
    more info
     
    epithelial tube branching involved in lung morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    eye development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    forebrain development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    forebrain neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    glial cell fate commitment NAS
    Non-traceable Author Statement
    more info
    PubMed 
    inner ear development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    inner ear morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    lens induction in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
     
    lung alveolus development IEA
    Inferred from Electronic Annotation
    more info
     
    male genitalia development IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of canonical Wnt receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of epithelial cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of osteoblast differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of transcription from RNA polymerase II promoter ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    neuron fate commitment IEA
    Inferred from Electronic Annotation
    more info
     
    neuronal stem cell maintenance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    olfactory placode formation IEA
    Inferred from Electronic Annotation
    more info
     
    osteoblast differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    pigment biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    pituitary gland development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    positive regulation of MAPK cascade IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of Notch signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of epithelial cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of neuroblast proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of transcription from RNA polymerase II promoter IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription, DNA-dependent IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of cysteine-type endopeptidase activity involved in apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of transcription, DNA-dependent IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of transcription, DNA-dependent NAS
    Non-traceable Author Statement
    more info
    PubMed 
    response to growth factor stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    response to retinoic acid IEA
    Inferred from Electronic Annotation
    more info
     
    response to wounding IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    retina morphogenesis in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
     
    somatic stem cell maintenance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    somatic stem cell maintenance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    tongue development IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus IC
    Inferred by Curator
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus NAS
    Non-traceable Author Statement
    more info
    PubMed 
    transcription factor complex TAS
    Traceable Author Statement
    more info
    PubMed 
    Preferred Names
    transcription factor SOX-2
    Names
    transcription factor SOX-2
    transcription factor SOX2
    SRY-related HMG-box 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.

    Genomic

    1. NG_009080.1 RefSeqGene

      Range
      4991..7503
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_003106.3NP_003097.1  transcription factor SOX-2

      Status: REVIEWED

      Source sequence(s)
      AC117415, BC013923, BF305585, CN430685, DA388996
      Consensus CDS
      CCDS3239.1
      UniProtKB/Swiss-Prot
      P48431
      Related
      ENSP00000323588, OTTHUMP00000212684, ENST00000325404, OTTHUMT00000350419
      Conserved Domains (2) summary
      cd01388
      Location:40111
      Blast Score: 280
      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 ...
      pfam12336
      Location:110200
      Blast Score: 196
      SOXp; SOX transcription factor

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

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

    Reference GRCh37.p10 Primary Assembly

    Genomic

    1. NC_000003.11 Reference GRCh37.p10 Primary Assembly

      Range
      181429712..181432224
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000135.1 Alternate HuRef

      Range
      178834536..178837048
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.0

    Genomic

    1. NC_018914.1 Alternate CHM1_1.0

      Range
      181292447..181294959
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

      Supplemental Content

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