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    SOX2 SRY-box transcription factor 2 [ Homo sapiens (human) ]

    Gene ID: 6657, updated on 24-Sep-2024

    Summary

    Official Symbol
    SOX2provided by HGNC
    Official Full Name
    SRY-box transcription factor 2provided by HGNC
    Primary source
    HGNC:HGNC:11195
    See related
    Ensembl:ENSG00000181449 MIM:184429; AllianceGenome:HGNC:11195
    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]
    Orthologs
    NEW
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    Genomic context

    See SOX2 in Genome Data Viewer
    Location:
    3q26.33
    Exon count:
    1
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (181711925..181714436)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (184516501..184519012)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (181429713..181432224)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene SOX2 overlapping transcript Neighboring gene uncharacterized LOC102724604 Neighboring gene NANOG hESC enhancer GRCh37_chr3:181172287-181172788 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:181252985-181254184 Neighboring gene ribosomal protein L7a pseudogene 25 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:181422577-181423078 Neighboring gene SOX2 5' regulatory region Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:181430703-181431554 Neighboring gene SRR2 enhancer downstream of SOX2 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:181445376-181446114 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:181473577-181474268 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:181474397-181475049 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:181499765-181500277 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:181503691-181504191 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:181538013-181538512 Neighboring gene RNA, 7SL, cytoplasmic 703, pseudogene Neighboring gene RNA, 5S ribosomal pseudogene 150

    Genomic regions, transcripts, and products

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Anophthalmia/microphthalmia-esophageal atresia syndrome
    MedGen: C1859773 OMIM: 206900 GeneReviews: SOX2 Disorder
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2012-07-06)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2012-07-06)

    ClinGen Genome Curation PagePubMed

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC2413

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in adenohypophysis development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in chromatin organization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    acts_upstream_of_or_within endodermal cell fate specification IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in eye development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in forebrain development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in forebrain development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in glial cell fate commitment NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in inner ear development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in inner ear development IEP
    Inferred from Expression Pattern
    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 cell cycle G1/S phase transition IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of epithelial cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in neuronal stem cell population maintenance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in osteoblast differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in pituitary gland development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of MAPK cascade IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of cell-cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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 
    involved_in regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in regulation of cysteine-type endopeptidase activity involved in apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of myofibroblast cell apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to growth factor IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to oxygen-glucose deprivation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to wounding IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in somatic stem cell population maintenance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in somatic stem cell population maintenance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in tissue regeneration IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    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 NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of transcription regulator complex TAS
    Traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    transcription factor SOX-2
    Names
    SRY (sex determining region Y)-box 2
    SRY-box 2
    SRY-related HMG-box gene 2
    sex determining region Y-box 2
    transcription factor SOX2

    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.

    Genomic

    1. NG_009080.1 RefSeqGene

      Range
      4991..7503
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_719

    mRNA and Protein(s)

    1. NM_003106.4NP_003097.1  transcription factor SOX-2

      See identical proteins and their annotated locations for NP_003097.1

      Status: REVIEWED

      Source sequence(s)
      AC117415, BC013923, BF305585, CN430685, DA388996
      Consensus CDS
      CCDS3239.1
      UniProtKB/Swiss-Prot
      P48431, Q14537
      UniProtKB/TrEMBL
      A0A0U3FYV6, B2R6J0
      Related
      ENSP00000323588.1, ENST00000325404.3
      Conserved Domains (2) summary
      cd01388
      Location:40111
      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:110200
      SOXp; SOX transcription factor

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      181711925..181714436
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      184516501..184519012
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)