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SOX2 Gene(Protein Coding)

SRY-Box 2

GCID:
GC03P181711
GIFtS:
57
Genes Participants
UDN Logo

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 Tracheoesophageal Fistula. Among its related pathways are Ectoderm Differentiation and Cytokine Signaling in Immune system. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity 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

Additional gene information 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

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for SOX2 Gene

Promoters and enhancers for SOX2 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH03I181709 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 550.8 +1.9 1924 8.1 PKNOX1 SIN3A FEZF1 GLI4 ZNF2 ETS1 GLIS2 ZNF213 ZNF143 PAF1 ENSG00000278026 SOX2 SOX2-OT
GH03I181755 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 14.4 +44.6 44622 1.5 MAZ ZNF189 HLF ZNF140 FEZF1 ATF2 SP1 PRDM6 POLR2A BCL6B SOX2 ENSG00000278026 RN7SL703P SOX2-OT
GH03I181700 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 7.3 -11.2 -11238 0.7 CTCF MXI1 RAD21 SMC3 ZNF143 ZNF444 SCRT1 SMARCE1 ZNF654 MAZ ENSG00000239381 ENSG00000276690 SOX2 SOX2-OT
GH03I181694 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 6.3 -16.2 -16171 1.8 CTCF L3MBTL2 NFATC3 NRF1 BACH1 ELF1 NR3C1 SNIP1 CTBP2 PRDM1 SOX2 ENSG00000239381 ENSG00000276690 ENSG00000276074 SOX2-OT
GH03I181757 Enhancer 0.6 ENCODE dbSUPER 11 +46.0 45954 0.5 OSR2 ZNF335 PRDM1 SOX2 ENSG00000278026 RN7SL703P SOX2-OT
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SOX2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SOX2 gene promoter:

Genomic Locations for SOX2 Gene

Genomic Locations for SOX2 Gene
chr3:181,711,924-181,714,436
(GRCh38/hg38)
Size:
2,513 bases
Orientation:
Plus strand
chr3:181,429,712-181,432,224
(GRCh37/hg19)

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 Structure • Gene Density

RefSeq DNA sequence for SOX2 Gene

Proteins for SOX2 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • 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

Protein Expression for SOX2 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SOX2 Gene

  • Sumoylation inhibits binding on DNA and negatively regulates the FGF4 transactivation.

Other Protein References for SOX2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SOX2 Gene

Domains & Families for SOX2 Gene

Gene Families for SOX2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

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

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

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:

Phenotypes From GWAS Catalog for SOX2 Gene

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 proximal promoter sequence-specific DNA binding IEA --
GO:0003677 DNA binding NAS 7849401
GO:0003700 DNA binding transcription factor activity 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

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

Nucleus.

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
cytoskeleton 3
plasma membrane 2
extracellular 2
mitochondrion 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
See all subcellular structures

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 by RNA polymerase II 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

Products:

  1. Drug

(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

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

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:

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

Products:

  1. Primer

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

mRNA expression in normal human tissues for SOX2 Gene
mRNA expression by GTEx for SOX2 GenemRNA expression by BioGPS 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(2.2)
  • Muscle(2)

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
Regions:
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

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 33 34
  • 97.69 (n)
dog
(Canis familiaris)
 Mammalia SOX2 33 34
  • 96.32 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia SOX2 34
  • 95 (a)
 OneToOne
cow
(Bos Taurus)
 Mammalia SOX2 33 34
  • 94.64 (n)
rat
(Rattus norvegicus)
 Mammalia Sox2 33
  • 93.8 (n)
mouse
(Mus musculus)
 Mammalia Sox2 33 16 34
  • 93.48 (n)
oppossum
(Monodelphis domestica)
 Mammalia SOX2 34
  • 88 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves SOX2 33 34
  • 85.93 (n)
tropical clawed frog
(Silurana tropicalis)
 Amphibia sox2 33
  • 79.42 (n)
Str.6201 33
African clawed frog
(Xenopus laevis)
 Amphibia Xl.18817 33
zebrafish
(Danio rerio)
 Actinopterygii sox2 33 34
  • 81.1 (n)
wufc14d07 33
fruit fly
(Drosophila melanogaster)
 Insecta SoxN 34
  • 26 (a)
 OneToMany
worm
(Caenorhabditis elegans)
 Secernentea sox-2 34
  • 36 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 34 (a)
 OneToMany
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.4045 33
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

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 Variation AA Info Type
rs104893799 pathogenic, Microphthalmia syndromic 3 181,712,889(+) C/T coding_sequence_variant, stop_gained
rs104893800 pathogenic, Microphthalmia syndromic 3 181,712,637(+) G/T coding_sequence_variant, stop_gained
rs104893801 pathogenic, Microphthalmia syndromic 3 181,712,608(+) C/A coding_sequence_variant, stop_gained
rs104893802 pathogenic, Microphthalmia syndromic 3 181,712,650(+) T/C coding_sequence_variant, missense_variant
rs104893803 pathogenic, Microphthalmia syndromic 3 181,712,823(+) C/G/T coding_sequence_variant, missense_variant, 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)

Additional Variant Information 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

(36) MalaCards diseases for SOX2 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
microphthalmia, syndromic 3
  • mcops3
tracheoesophageal fistula
  • tracheoesophageal fistula with or without esophageal atresia
microphthalmia
  • microphthalmos
esophageal atresia
  • congenital atresia of esophagus
embryonal carcinoma
  • primary extragonadal embryonal 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.

Additional Disease Information for SOX2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 HF … Brismar K (Gender medicine 2009) 3 22 44 58
  2. The cDNA sequence and chromosomal location of the human SOX2 gene. (PMID: 7849401) Stevanovic M … Goodfellow P (Mammalian genome : official journal of the International Mammalian Genome Society 1994) 2 3 4 58
  3. SOX2 modulates alternative splicing in transitional cell carcinoma. (PMID: 20138825) Tung CL … Li C (Biochemical and biophysical research communications 2010) 3 22 58
  4. Expression of the embryonic stem cell transcription factor SOX2 in human skin: relevance to melanocyte and merkel cell biology. (PMID: 20042675) Laga AC … Murphy GF (The American journal of pathology 2010) 3 22 58
  5. 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 58

Products for SOX2 Gene

  • Addgene plasmids for SOX2

Sources for SOX2 Gene

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