Human Gene SOX2 (ENST00000325404.3_4) from GENCODE V47lift37
  Description: SRY-box transcription factor 2 (from RefSeq NM_003106.4)
Gencode Transcript: ENST00000325404.3_4
Gencode Gene: ENSG00000181449.4_11
Transcript (Including UTRs)
   Position: hg19 chr3:181,429,713-181,432,224 Size: 2,512 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg19 chr3:181,430,149-181,431,102 Size: 954 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:181,429,713-181,432,224)mRNA (may differ from genome)Protein (317 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SOX2_HUMAN
DESCRIPTION: RecName: Full=Transcription factor SOX-2;
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).
SUBUNIT: Interacts with ZSCAN10 (By similarity). Interacts with SOX3 and FGFR1 (By similarity).
SUBCELLULAR LOCATION: Nucleus.
PTM: Sumoylation inhibits binding on DNA and negatively regulates the FGF4 transactivation (By similarity).
DISEASE: Defects in SOX2 are the cause of microphthalmia syndromic type 3 (MCOPS3) [MIM:206900]. Microphthalmia is a clinically heterogeneous 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. MCOPS3 is characterized by the rare association of malformations including uni- or bilateral anophthalmia or microphthalmia, and esophageal atresia with trachoesophageal fistula.
BIOTECHNOLOGY: POU5F1/OCT4, SOX2, MYC/c-Myc and KLF4 are the four Yamanaka factors. When combined, these factors are sufficient to reprogram differentiated cells to an embryonic-like state designated iPS (induced pluripotent stem) cells. iPS cells exhibit the morphology and growth properties of ES cells and express ES cell marker genes.
SIMILARITY: Contains 1 HMG box DNA-binding domain.
SEQUENCE CAUTION: Sequence=AAA35997.1; Type=Erroneous initiation; Sequence=CAA83435.1; Type=Erroneous initiation;
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SOX2";
WEB RESOURCE: Name=Wikipedia; Note=Sox2 entry; URL="http://en.wikipedia.org/wiki/Sox2";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SOX2
Diseases sorted by gene-association score: microphthalmia, syndromic 3* (1379), sox2-related eye disorders* (200), microphthalmia (24), esophageal atresia (24), embryonal carcinoma (23), colon squamous cell carcinoma (15), central nervous system teratoma (15), fryns microphthalmia syndrome (12), central nervous system germ cell tumor (10), germ cell and embryonal cancer (10), nut midline carcinoma (10), lung squamous cell carcinoma (9), optic nerve hypoplasia (9), anophthalmia/microphthalmia (8), teratoma (8), oral cavity cancer (8), lambert-eaton myasthenic syndrome (8), venous hemangioma (7), ampulla of vater adenocarcinoma (7), orbital cyst (6), ocular cancer (6), ablepharon-macrostomia syndrome (6), ovarian embryonal carcinoma (6), tracheoesophageal fistula (6), vulvar intraepithelial neoplasia (6), cervical squamous cell carcinoma (6), schizencephaly (6), non-functioning pancreatic endocrine tumor (5), cloacogenic carcinoma (5), congenital aphakia (5), atypical choroid plexus papilloma (5), pulmonary immaturity (5), cellular schwannoma (4), extragonadal seminoma (4), wolfram syndrome 2 (4), microphthalmia, isolated 1 (4), botryoid rhabdomyosarcoma (4), coloboma (3), brain cancer (2), cornelia de lange syndrome (2), cell type cancer (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 42.66 RPKM in Brain - Amygdala
Total median expression: 459.43 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -154.20436-0.354 Picture PostScript Text
3' UTR -243.701122-0.217 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR009071 - HMG_superfamily
IPR022097 - TF_SOX

Pfam Domains:
PF00505 - HMG (high mobility group) box
PF09011 - HMG-box domain
PF12336 - SOX transcription factor

SCOP Domains:
47095 - HMG-box

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1O4X - NMR MuPIT 2LE4 - NMR MuPIT


ModBase Predicted Comparative 3D Structure on P48431
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000976 transcription regulatory region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0035198 miRNA binding
GO:0043565 sequence-specific DNA binding
GO:0044212 transcription regulatory region DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001649 osteoblast differentiation
GO:0001654 eye development
GO:0001714 endodermal cell fate specification
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007050 cell cycle arrest
GO:0007275 multicellular organism development
GO:0009611 response to wounding
GO:0010468 regulation of gene expression
GO:0019221 cytokine-mediated signaling pathway
GO:0021781 glial cell fate commitment
GO:0021983 pituitary gland development
GO:0021984 adenohypophysis development
GO:0022409 positive regulation of cell-cell adhesion
GO:0030900 forebrain development
GO:0035019 somatic stem cell population maintenance
GO:0042246 tissue regeneration
GO:0043281 regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0043410 positive regulation of MAPK cascade
GO:0045597 positive regulation of cell differentiation
GO:0045665 negative regulation of neuron differentiation
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048839 inner ear development
GO:0050680 negative regulation of epithelial cell proliferation
GO:0070848 response to growth factor
GO:0090090 negative regulation of canonical Wnt signaling pathway
GO:0097150 neuronal stem cell population maintenance

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription factor complex
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK312595 - Homo sapiens cDNA, FLJ92971, highly similar to Homo sapiens SRY (sex determining region Y)-box 2 (SOX2), mRNA.
JD510157 - Sequence 491181 from Patent EP1572962.
JD330010 - Sequence 311034 from Patent EP1572962.
JD085008 - Sequence 66032 from Patent EP1572962.
JD267546 - Sequence 248570 from Patent EP1572962.
BC013923 - Homo sapiens SRY (sex determining region Y)-box 2, mRNA (cDNA clone MGC:2413 IMAGE:2823424), complete cds.
L07335 - Homo sapiens (clone 6AR33) HMG box mRNA, 3' end cds.
Z31560 - H.sapiens sox-2 mRNA (partial).
KJ892185 - Synthetic construct Homo sapiens clone ccsbBroadEn_01579 SOX2 gene, encodes complete protein.
AB464715 - Synthetic construct DNA, clone: pF1KB9652, Homo sapiens SOX2 gene for SRY (sex determining region Y)-box 2, without stop codon, in Flexi system.
EU446654 - Synthetic construct Homo sapiens clone IMAGE:100070028; IMAGE:100011863; FLH258294.01L SRY (sex determining region Y)-box 2 (SOX2) gene, encodes complete protein.
HW243466 - JP 2013512690-A/17: RNA PREPARATIONS COMPRISING PURIFIED MODIFIED RNA FOR REPROGRAMMING CELLS.
LF715488 - JP 2016171804-A/17: RNA PREPARATIONS COMPRISING PURIFIED MODIFIED RNA FOR REPROGRAMMING CELLS.
KM822781 - Homo sapiens isolate S1 sex determining region Y-box 2 (SOX2) mRNA, partial cds.
JD450941 - Sequence 431965 from Patent EP1572962.
JD042339 - Sequence 23363 from Patent EP1572962.
JD317732 - Sequence 298756 from Patent EP1572962.
JD135118 - Sequence 116142 from Patent EP1572962.
JD240433 - Sequence 221457 from Patent EP1572962.
JD339983 - Sequence 321007 from Patent EP1572962.
JA484179 - Sequence 17 from Patent EP2247750.
JD063530 - Sequence 44554 from Patent EP1572962.
JB025505 - Sequence 53 from Patent EP2505645.
JB025512 - Sequence 60 from Patent EP2505645.
LY605671 - KR 1020180081836-A/17: RNA PREPARATIONS COMPRISING PURIFIED MODIFIED RNA FOR REPROGRAMMING CELLS.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P48431 (Reactome details) participates in the following event(s):

R-HSA-480204 POU5F1 (OCT4), SOX2, NANOG, KLF4, PBX1, SMAD2 bind the NANOG promoter
R-HSA-480685 POU5F1 (OCT4), SOX2, NANOG bind the SOX2 promoter
R-HSA-1112609 POU5F1 (OCT4), SOX2, NANOG, ZSCAN10, PRDM14, SMAD2, FOXP1-ES bind the POU5F1 (OCT4) promoter
R-HSA-2972948 POU5F1 (OCT4), SOX2, NANOG bind the GSC promoter
R-HSA-2972949 POU5F1 (OCT4), SOX2, NANOG bind the EOMES promoter
R-HSA-2972956 POU5F1 (OCT4), SOX2, NANOG bind the STAT3 promoter
R-HSA-2972960 POU5F1 (OCT4), SOX2, NANOG bind the FGF2 promoter
R-HSA-2972962 POU5F1 (OCT4), SOX2, NANOG bind the TDGF1 promoter
R-HSA-2972964 POU5F1 (OCT4), SOX2, NANOG bind the FOXD3 promoter
R-HSA-2972965 POU5F1 (OCT4), SOX2, NANOG bind the TSC22D1 promoter
R-HSA-2972966 POU5F1 (OCT4), SOX2, NANOG bind the HHEX promoter
R-HSA-2972967 POU5F1 (OCT4), SOX2, NANOG bind the EPHA1 promoter
R-HSA-2972975 POU5F1 (OCT4), SOX2, NANOG Bind the SALL1 Promoter
R-HSA-2972977 POU5F1 (OCT4), SOX2, NANOG bind the DKK1 promoter
R-HSA-2972978 POU5F1 (OCT4), SOX2, NANOG bind the ZIC3 promoter
R-HSA-2972979 POU5F1 (OCT4), NANOG bind the CDX2 promoter
R-HSA-6800120 POU5F1 (OCT4), SOX2, NANOG bind DPPA4 gene
R-HSA-5626938 Beta-catenin binds SOX proteins
R-HSA-452723 Transcriptional regulation of pluripotent stem cells
R-HSA-2892245 POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation
R-HSA-2892247 POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation
R-HSA-3769402 Deactivation of the beta-catenin transactivating complex
R-HSA-6785807 Interleukin-4 and 13 signaling
R-HSA-1266738 Developmental Biology
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-449147 Signaling by Interleukins
R-HSA-195721 Signaling by WNT
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-162582 Signal Transduction
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000325404.1, ENST00000325404.2, NM_003106, P48431, Q14537, SOX2_HUMAN, uc317rwf.1, uc317rwf.2
UCSC ID: ENST00000325404.3_4
RefSeq Accession: NM_003106.4
Protein: P48431 (aka SOX2_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SOX2:
sox2 (SOX2 Disorder)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.