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Aliases for SOX2 Gene

Aliases for SOX2 Gene

  • SRY-Box 2 2 3 5
  • SRY (Sex Determining Region Y)-Box 2 2 3
  • Sex Determining Region Y-Box 2 3
  • SRY-Related HMG-Box Gene 2 3
  • Transcription Factor SOX-2 3
  • Transcription Factor SOX2 3
  • SRY Box 2 2
  • MCOPS3 3
  • ANOP3 3

External Ids for SOX2 Gene

Previous GeneCards Identifiers for SOX2 Gene

  • GC03P178128
  • GC03P182273
  • GC03P182831
  • GC03P182750
  • GC03P182912
  • GC03P181429
  • GC03P178834

Summaries for SOX2 Gene

Entrez Gene Summary for SOX2 Gene

  • 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]

GeneCards Summary for SOX2 Gene

SOX2 (SRY-Box 2) is a Protein Coding gene. Diseases associated with SOX2 include Microphthalmia, Syndromic 3 and Sox2-Related Eye Disorders. Among its related pathways are Mesodermal Commitment Pathway and Signaling by Wnt. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and protein heterodimerization activity. An important paralog of this gene is SOX1.

UniProtKB/Swiss-Prot for SOX2 Gene

  • Transcription factor that forms a trimeric complex with OCT4 on DNA and controls the expression of a number of genes involved in embryonic development such as YES1, FGF4, UTF1 and ZFP206 (By similarity). Critical for early embryogenesis and for embryonic stem cell pluripotency. May function as a switch in neuronal development. Downstream SRRT target that mediates the promotion of neural stem cell self-renewal (By similarity). Keeps neural cells undifferentiated by counteracting the activity of proneural proteins and suppresses neuronal differentiation (By similarity).

Gene Wiki entry for SOX2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SOX2 Gene

Genomics for SOX2 Gene

Regulatory Elements for SOX2 Gene

Enhancers for SOX2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03G181689 1.6 dbSUPER 12.4 -20.4 -20389 4.7 ZNF146 POLR2A SMARCA4 MAFK NFE2L2 EZH2 SOX2 ENSG00000276690 ENSG00000276074
GH03G181755 1.3 FANTOM5 ENCODE dbSUPER 14.4 +44.6 44623 1.5 ZNF140 FEZF1 CHD7 POLR2A ZSCAN5C ZBTB20 MAZ HLF ATF2 PRDM6 SOX2 ENSG00000278026 RN7SL703P
GH03G181700 1.4 FANTOM5 ENCODE dbSUPER 7.3 -11.2 -11239 0.7 CTCF MXI1 CBX3 RBBP5 RAD21 ZNF143 SMC3 SCRT1 ZNF654 MAZ SOX2 ENSG00000239381
GH03G181694 1.6 FANTOM5 Ensembl ENCODE dbSUPER 6.3 -16.2 -16171 1.8 CTCF L3MBTL2 SUZ12 NRF1 ZBTB11 CBX2 RBBP5 ELF1 ZBTB7A HDAC2 SOX2 ENSG00000276690 ENSG00000276074
GH03G181757 0.7 ENCODE dbSUPER 11 +46.0 45955 0.5 OSR2 CHD7 PRDM1 SOX2 ENSG00000278026 RN7SL703P
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SOX2 on UCSC Golden Path with GeneCards custom track

Promoters for SOX2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000162670 176 1001 PKNOX1 FEZF1 BMI1 ZNF2 ZEB1 ETS1 GLIS2 EGR1 ZNF366 SCRT2

Genomic Location for SOX2 Gene

Chromosome:
3
Start:
181,711,924 bp from pter
End:
181,714,436 bp from pter
Size:
2,513 bases
Orientation:
Plus strand

Genomic View for SOX2 Gene

Genes around SOX2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SOX2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SOX2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SOX2 Gene

Proteins for SOX2 Gene

  • Protein details for SOX2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P48431-SOX2_HUMAN
    Recommended name:
    Transcription factor SOX-2
    Protein Accession:
    P48431
    Secondary Accessions:
    • Q14537

    Protein attributes for SOX2 Gene

    Size:
    317 amino acids
    Molecular mass:
    34310 Da
    Quaternary structure:
    • Interacts with ZSCAN10. Interacts with SOX3 and FGFR1.
    SequenceCaution:
    • Sequence=AAA35997.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=CAA83435.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SOX2 Gene

neXtProt entry for SOX2 Gene

Post-translational modifications for SOX2 Gene

  • Sumoylation inhibits binding on DNA and negatively regulates the FGF4 transactivation.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SOX2 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for SOX2 (SOX2)

No data available for DME Specific Peptides for SOX2 Gene

Domains & Families for SOX2 Gene

Gene Families for SOX2 Gene

Protein Domains for SOX2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SOX2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SOX2: view

No data available for UniProtKB/Swiss-Prot for SOX2 Gene

Function for SOX2 Gene

Molecular function for SOX2 Gene

GENATLAS Biochemistry:
SRY related HMG box gene 2,expressed in inner cell mass,primitive ectoderm,developing CNS,lens,induced by chordin,repressed by BMP4,activating FGF4,repressing osteopontin,inducing beta and delta crystallin expression,modulator of LINE retroposons promoter activity
UniProtKB/Swiss-Prot Function:
Transcription factor that forms a trimeric complex with OCT4 on DNA and controls the expression of a number of genes involved in embryonic development such as YES1, FGF4, UTF1 and ZFP206 (By similarity). Critical for early embryogenesis and for embryonic stem cell pluripotency. May function as a switch in neuronal development. Downstream SRRT target that mediates the promotion of neural stem cell self-renewal (By similarity). Keeps neural cells undifferentiated by counteracting the activity of proneural proteins and suppresses neuronal differentiation (By similarity).

LifeMap Function Summary for SOX2 Gene

SOX2 as growth factor is involved in stem cell differentiation protocols towards the derivation of the following cells:

Gene Ontology (GO) - Molecular Function for SOX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000976 transcription regulatory region sequence-specific DNA binding IEA --
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding IEA --
GO:0003677 DNA binding NAS 7849401
GO:0003700 transcription factor activity, sequence-specific DNA binding NAS 7849401
GO:0005515 protein binding IPI 18456656
genes like me logo Genes that share ontologies with SOX2: view
genes like me logo Genes that share phenotypes with SOX2: view

Human Phenotype Ontology for SOX2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SOX2 Gene

MGI Knock Outs for SOX2:

Animal Model Products

Targeted motifs for SOX2 Gene
HOMER Transcription Factor Regulatory Elements motif SOX2
  • Consensus sequence: CCCATTGTTC Submotif: canonical Cell Type: mES GEO ID: GSE11431

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SOX2

No data available for Enzyme Numbers (IUBMB) and Transcription Factor Targets for SOX2 Gene

Localization for SOX2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SOX2 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SOX2 gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 2
cytoskeleton 2
plasma membrane 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for SOX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus NAS,IC 7849401
GO:0005654 nucleoplasm TAS --
GO:0005667 transcription factor complex TAS 19736317
GO:0005737 cytoplasm IDA 18027866
GO:0005829 cytosol IDA 18000303
genes like me logo Genes that share ontologies with SOX2: view

Pathways & Interactions for SOX2 Gene

genes like me logo Genes that share pathways with SOX2: view

SIGNOR curated interactions for SOX2 Gene

Activates:
Is activated by:

Gene Ontology (GO) - Biological Process for SOX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter ISS --
GO:0001649 osteoblast differentiation IDA 18187129
GO:0001654 eye development IEP 18285410
GO:0001714 endodermal cell fate specification IDA 21245162
GO:0006325 chromatin organization NAS 7849401
genes like me logo Genes that share ontologies with SOX2: view

Drugs & Compounds for SOX2 Gene

(1) Drugs for SOX2 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for SOX2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SOX2: view

Transcripts for SOX2 Gene

mRNA/cDNA for SOX2 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(138) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SOX2 Gene

SRY (sex determining region Y)-box 2:
Representative Sequences:

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SOX2

Alternative Splicing Database (ASD) splice patterns (SP) for SOX2 Gene

No ASD Table

Relevant External Links for SOX2 Gene

GeneLoc Exon Structure for
SOX2
ECgene alternative splicing isoforms for
SOX2

Expression for SOX2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SOX2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SOX2 Gene

This gene is overexpressed in Brain - Amygdala (x5.1), Brain - Nucleus accumbens (basal ganglia) (x5.0), Brain - Caudate (basal ganglia) (x5.0), Brain - Putamen (basal ganglia) (x4.2), and Brain - Hippocampus (x4.0).

Protein differential expression in normal tissues from HIPED for SOX2 Gene

This gene is overexpressed in Fetal Brain (41.7) and Lung (27.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SOX2 Gene



Protein tissue co-expression partners for SOX2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SOX2 Gene:

SOX2

SOURCE GeneReport for Unigene cluster for SOX2 Gene:

Hs.518438

Evidence on tissue expression from TISSUES for SOX2 Gene

  • Nervous system(4.9)
  • Lung(4.6)
  • Eye(4.4)
  • Skin(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SOX2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • hypothalamus
  • mouth
  • outer ear
  • pituitary gland
  • skull
Thorax:
  • breast
  • chest wall
  • esophagus
  • heart
  • lung
  • rib
  • rib cage
  • trachea
Abdomen:
  • stomach
Pelvis:
  • ovary
  • penis
  • prostate
  • testicle
  • urethra
  • urinary bladder
  • uterus
  • vagina
  • vulva
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • toe
  • upper limb
General:
  • blood
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with SOX2: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for SOX2 Gene

Orthologs for SOX2 Gene

This gene was present in the common ancestor of animals.

Orthologs for SOX2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SOX2 34 35
  • 97.69 (n)
dog
(Canis familiaris)
Mammalia SOX2 34 35
  • 96.32 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SOX2 35
  • 95 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SOX2 34 35
  • 94.64 (n)
rat
(Rattus norvegicus)
Mammalia Sox2 34
  • 93.8 (n)
mouse
(Mus musculus)
Mammalia Sox2 34 16 35
  • 93.48 (n)
oppossum
(Monodelphis domestica)
Mammalia SOX2 35
  • 88 (a)
OneToOne
chicken
(Gallus gallus)
Aves SOX2 34 35
  • 85.93 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia sox2 34
  • 79.42 (n)
Str.6201 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.18817 34
zebrafish
(Danio rerio)
Actinopterygii sox2 34 35
  • 81.1 (n)
wufc14d07 34
fruit fly
(Drosophila melanogaster)
Insecta SoxN 35
  • 26 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea sox-2 35
  • 36 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 34 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4045 34
Species where no ortholog for SOX2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SOX2 Gene

ENSEMBL:
Gene Tree for SOX2 (if available)
TreeFam:
Gene Tree for SOX2 (if available)

Paralogs for SOX2 Gene

(8) SIMAP similar genes for SOX2 Gene using alignment to 1 proteins:

Pseudogenes.org Pseudogenes for SOX2 Gene

genes like me logo Genes that share paralogs with SOX2: view

Variants for SOX2 Gene

Sequence variations from dbSNP and Humsavar for SOX2 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs104893805 Pathogenic, Microphthalmia, syndromic, 3 (MCOPS3) [MIM:206900] 181,712,581(+) CAAGC(C/G/T)CCTGG intron-variant, reference, missense
VAR_075627 Microphthalmia, syndromic, 3 (MCOPS3) [MIM:206900]
VAR_075629 Microphthalmia, syndromic, 3 (MCOPS3) [MIM:206900]
rs104893799 Pathogenic 181,712,889(+) AGGAC(C/T)AGCTG intron-variant, reference, stop-gained
rs104893800 Pathogenic 181,712,637(+) TCGAC(G/T)AGGCT intron-variant, reference, stop-gained

Variation tolerance for SOX2 Gene

Residual Variation Intolerance Score: 54% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.34; 7.45% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SOX2 Gene

Human Gene Mutation Database (HGMD)
SOX2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SOX2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for SOX2 Gene

Disorders for SOX2 Gene

MalaCards: The human disease database

(40) MalaCards diseases for SOX2 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
microphthalmia, syndromic 3
  • optic nerve hypoplasia and abnormalities of the central nervous system
sox2-related eye disorders
embryonal carcinoma
  • primary extragonadal embryonal carcinoma
microphthalmia
  • microphthalmos
colon squamous cell carcinoma
  • colonic epidermoid carcinoma
- elite association - COSMIC cancer census association via MalaCards
Search SOX2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SOX2_HUMAN
  • Microphthalmia, syndromic, 3 (MCOPS3) [MIM:206900]: A disease characterized by the rare association of malformations including uni- or bilateral anophthalmia or microphthalmia, and esophageal atresia with trachoesophageal fistula. Microphthalmia is a disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues (anophthalmia). In many cases, microphthalmia/anophthalmia occurs in association with syndromes that include non-ocular abnormalities. {ECO:0000269 PubMed:12612584, ECO:0000269 PubMed:24033328}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SOX2

Genetic Association Database (GAD)
SOX2
Human Genome Epidemiology (HuGE) Navigator
SOX2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SOX2
genes like me logo Genes that share disorders with SOX2: view

No data available for Genatlas for SOX2 Gene

Publications for SOX2 Gene

  1. SOX2 has gender-specific genetic effects on diabetic nephropathy in samples from patients with type 1 diabetes mellitus in the GoKinD study. (PMID: 20114006) Gu H.F. … Brismar K. (Gend Med 2009) 3 22 46 64
  2. The cDNA sequence and chromosomal location of the human SOX2 gene. (PMID: 7849401) Stevanovic M. … Goodfellow P. (Mamm. Genome 1994) 2 3 4 64
  3. Recurrent copy number gain of transcription factor SOX2 and corresponding high protein expression in oral squamous cell carcinoma. (PMID: 19787784) Freier K. … Radlwimmer B. (Genes Chromosomes Cancer 2010) 3 22 64
  4. Expression of the embryonic stem cell transcription factor SOX2 in human skin: relevance to melanocyte and merkel cell biology. (PMID: 20042675) Laga A.C. … Murphy G.F. (Am. J. Pathol. 2010) 3 22 64
  5. SOX2 modulates alternative splicing in transitional cell carcinoma. (PMID: 20138825) Tung C.L. … Li C. (Biochem. Biophys. Res. Commun. 2010) 3 22 64

Products for SOX2 Gene

  • Addgene plasmids for SOX2

Sources for SOX2 Gene

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