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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SOX2 Gene

protein-coding   GIFtS: 64
GCID: GC03P181429

SRY (sex determining region Y)-box 2
 Explore 70 diseases affiliated with
SOX2 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for SOX2    

Aliases
for SOX2 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
SRY (Sex Determining Region Y)-Box 21 2
MCOPS32 5
ANOP32
SRY-Related HMG-Box Gene 22
Transcription Factor SOX-22
Transcription Factor SOX22

External Ids:    HGNC: 111951   Entrez Gene: 66572   Ensembl: ENSG000001814497   OMIM: 1844295   UniProtKB: P484313   

Export aliases for SOX2 gene to outside databases

Previous GC identifers: GC03P178128 GC03P182273 GC03P182831 GC03P182750 GC03P182912 GC03P178834


Summaries
for SOX2 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for SOX2:
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)

UniProtKB/Swiss-Prot: SOX2_HUMAN, P48431
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)

Gene Wiki entry for SOX2


Genomic Views
for SOX2 gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000003.11  NC_018914.1  NT_005612.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SOX2 gene promoter:
         ISGF-3   RFX1   Sp1   MyoD   Egr-2   MZF-1   MEF-2A   GATA-6   aMEF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: SOX2 promoter sequence
   Search SABiosciences Chromatin IP Primers for SOX2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SOX2


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3q26.3-q27   Ensembl cytogenetic band:  3q26.33   HGNC cytogenetic band: 3q26.3-q27

SOX2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SOX2 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P181429:  view genomic region     (about GC identifiers)

Start:
 181,429,714 bp from pter      End:
 181,432,224 bp from pter
Size:
 2,511 bases      Orientation:
 plus strand

Proteins
for SOX2 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: SOX2_HUMAN, P48431 (See protein sequence)
Recommended Name: Transcription factor SOX-2  
Size: 317 amino acids; 34310 Da
Subunit: Interacts with ZSCAN10 (By similarity). Interacts with SOX3 and FGFR1 (By similarity)
Subcellular location: Nucleus
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
Sequence caution: Sequence=AAA35997.1; Type=Erroneous initiation; Sequence=CAA83435.1; Type=Erroneous initiation;
2 PDB 3D structures from and Proteopedia for SOX2:
1O4X (3D)        2LE4 (3D)    
Secondary accessions: Q14537

Explore the universe of human proteins at neXtProt for SOX2: NX_P48431

Post-translational modifications:

  • Sumoylation inhibits binding on DNA and negatively regulates the FGF4 transactivation (By similarity)1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_P48431

    • SOX2 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_003097.1  
    ENSEMBL proteins: 
     ENSP00000439111   ENSP00000323588  

    Human Recombinant Protein Products: 
    EMD Millipore Purified and/or Recombinant SOX2 Protein
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    OriGene Purified Protein: SOX2
    OriGene Protein Over-expression Lysate: SOX2
    OriGene Custom Protein Services for SOX2 
    GenScript Custom Purified and Recombinant Proteins Services for SOX2
    Novus Biologicals SOX2 Proteins
    Novus Biologicals SOX2 Lysate
    Browse Sino Biological Recombinant Proteins
    ProSpec Recombinant Protein for SOX2
    Uscn Proteins for SOX2

    Gene Ontology (GO): 5 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005625soluble fraction ----
    GO:0005634nucleus NAS7849401
    GO:0005667transcription factor complex TAS19736317
    GO:0005737cytoplasm IDA18027866
    GO:0005829cytosol IDA18000303


    SOX2 for ontologies           About GeneDecksing



    SOX2 Antibody Products: 
    EMD Millipore Mono- and Polyclonal Antibodies for the study of SOX2
    R&D Systems Antibodies for SOX2
    Cell Signaling Technology (CST) Antibodies for SOX2 
    OriGene Antibodies (see all 6): SOX2
    OriGene Custom Antibody Services for SOX2 
    GenScript Custom Superior Antibodies Services for SOX2
    Novus Biologicals SOX2 Antibodies
    Abcam antibodies for SOX2 
    Uscn Antibodies for SOX2
    ThermoFisher Antibody for SOX2

    Assay Products for SOX2: 
    EMD Millipore Kits and Assays for the Analysis of SOX2
    OriGene Custom Immunoassay Development
    Browse OriGene Fluorogenic Cell Assay Kits
    R&D Systems Multiplex/Array Assay Kits & Reagents for SOX2         (see all)
    GenScript Custom Assay Services for SOX2
    Cell Signaling Technology (CST) Sandwich ELISA Kits for SOX2
    Browse Enzo Life Sciences for kits & assays
    Uscn ELISAs and CLIAs for SOX2

    Protein Domains /
    Families
    for SOX2 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    SOX2 for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR009071 HMG_superfamily
     IPR022097 TF_SOX

    Graphical View of Domain Structure for InterPro Entry P48431

    ProtoNet protein and cluster: P48431

    UniProtKB/Swiss-Prot: SOX2_HUMAN, P48431
    Similarity: Contains 1 HMG box DNA-binding domain


    Function
    for SOX2 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         UniProtKB/Swiss-Prot: SOX2_HUMAN, P48431
    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)

         Genatlas biochemistry entry for SOX2:
    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

    miRNA
    Products:            		miRTarBase miRNAs that target SOX2:
    hsa-mir-522 (MIRT005692), hsa-mir-126 (MIRT005370), hsa-mir-145 (MIRT000307)

    OriGene 3'-UTR Clone: SOX2
    Browse MicroRNA Expression Plasmids
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SOX2
    8/31 QIAGEN miScript miRNA Assays for microRNAs that regulate SOX2 (see all 31):
    hsa-miR-607 hsa-miR-520d-5p hsa-miR-429 hsa-miR-300 hsa-miR-371-5p hsa-miR-373* hsa-miR-374c hsa-miR-548g
    SwitchGear 3'UTR luciferase reporter plasmid: SOX2 3' UTR sequence
    Inhib. RNA
    Products:            		Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for SOX2 (see all 7)
    OriGene shRNA RFP: SOX2
    OriGene siRNA: SOX2
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SOX2

    Gene Editing
    Products:    		DNA2.0 Custom Protein Engineering Service for SOX2

    Clone
    Products:             		Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
    OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for SOX2 (see all 3)
    OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for SOX2
    OriGene custom cloning services – gene synthesis, subcloning, mutagenesis, variant library, vector shuttling 
    GenScript: all cDNA clones in your preferred vector: SOX2 (NM_003106)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SOX2
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SOX2 

    Cell Line
    Products:             		GenScript Custom overexpressing Cell Line Services for SOX2
    LifeMap BioReagents: cell lines associated with SOX2: Human Embryonic Stem Cell Line ESI-017,
    Human Embryonic Stem Cell Line ESI-035, Human Embryonic Stem Cell Line ESI-049, Human Embryonic Stem Cell Line ESI-051,
    Human Embryonic Stem Cell Line ESI-053

    In Situ Assay
    Products:       
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SOX2

    Gene Ontology (GO): 5/9 molecular function terms (GO ID links to tree view) (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000976transcription regulatory region sequence-specific DNA binding IEA--
    GO:0001077RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription IEA--
    GO:0003677DNA binding NAS7849401
    GO:0003682chromatin binding IEA--
    GO:0003700sequence-specific DNA binding transcription factor activity NAS7849401


    SOX2 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for SOX2:
     Increased HPV18 LCR reporter a 

    Animal Models:
         Mouse knock-outs for SOX2: Sox2tm3Lpev Sox2tm4Lpev Sox2tm3Skn Sox2tm2.1Lpev
         15/22 MGI mutant phenotypes (inferred from 21 alleles) (MGI details for Sox2) (see all 22):
     behavior/neurological  cellular  craniofacial  digestive/alimentary  embryogenesis 
     endocrine/exocrine gland  growth/size  hearing/vestibular/ear  homeostasis/metabolism  immune system 
     integument  mortality/aging  muscle  nervous system  no phenotypic analysis 

    SOX2 for phenotypes           About GeneDecksing


    Pathways & Interactions
    for SOX2 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways - 5/10 super-pathways (see all 10) About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Wnt / Hedgehog / Notch
    		Wnt / Hedgehog / Notch1.00
    2Selected targets of Oct-3/4
    		Selected targets of Oct-3/41.00
    3Transcriptional Regulatory Network in Embryonic Stem Cell
    		Transcriptional Regulatory Network in Embryonic Stem Cell1.00
    4Oct4 in Mammalian ESC Pluripotency
    		Oct4 in Mammalian ESC Pluripotency1.00
    5Nanog in Mammalian ESC Pluripotency
    		Nanog in Mammalian ESC Pluripotency1.00

    Pathway sources
    See GeneCards unified pathways
    Show all pathways

    1 EMD Millipore Pathway for SOX2
        Selected targets of Oct-3/4

    5/6 Downloadable PowerPoint Slides of QIAGEN Pathway Central Maps for SOX2 (see all 6)
        Transcriptional Regulatory Network in Embryonic Stem Cell
    Molecular Mechanisms of Cancer
    Oct4 in Mammalian ESC Pluripotency
    Human Embryonic Stem Cell Pluripotency
    Nanog in Mammalian ESC Pluripotency

    1 Cell Signaling Technology (CST) Pathway for SOX2
        Wnt / Hedgehog / Notch

    2 BioSystems Pathways for SOX2 
        Wnt Signaling Pathway and Pluripotency
    SIDS Susceptibility Pathways



    SOX2 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for SOX2

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/71 Interacting proteins for SOX2 (P484313 ENSP000003235884) via UniProtKB, MINT, STRING, and/or I2D (see all 71)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ALX4Q9H1613, ENSP000003327444I2D: score=2 STRING: ENSP00000332744
    POU2F1P148593, ENSP000002714114I2D: score=2 STRING: ENSP00000271411
    NANOGQ9H9S03, ENSP000002293074I2D: score=1 STRING: ENSP00000229307
    NR5A1Q132853, ENSP000003626904I2D: score=1 STRING: ENSP00000362690
    XPO4Q9C0E23, ENSP000002553054I2D: score=1 STRING: ENSP00000255305
    About this table

    Gene Ontology (GO): 5/57 biological process terms (GO ID links to tree view) (see all 57):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter ISS--
    GO:0001649osteoblast differentiation IDA18187129
    GO:0001654eye development IEP18285410
    GO:0001708cell fate specification ----
    GO:0001714endodermal cell fate specification IDA--


    SOX2 for ontologies           About GeneDecksing



    Drugs & Compounds
    for SOX2 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    SOX2 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SOX2
    2 Novoseek chemical compound relationships for SOX2 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    retinoic acid 2.72 3 12841584 (2), 17525239 (1)
    zinc 0 2 8641144 (1), 9435279 (1)

    Search CenterWatch for drugs/clinical trials and news about SOX2 

    Transcripts
    for SOX2 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for SOX2 gene: 
    NM_003106.3  

    Unigene Cluster for SOX2:

    SRY (sex determining region Y)-box 2
    Hs.518438  [show with all ESTs]
    Unigene Representative Sequence: NM_003106
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000431565 ENST00000325404(uc003fkx.3)

    miRNA
    Products:             		 OriGene 3'-UTR Clone: SOX2
    Browse OriGene MicroRNA Expression Plasmids
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SOX2
    8/31 QIAGEN miScript miRNA Assays for microRNAs that regulate SOX2 (see all 31):
    hsa-miR-607 hsa-miR-520d-5p hsa-miR-429 hsa-miR-300 hsa-miR-371-5p hsa-miR-373* hsa-miR-374c hsa-miR-548g
    SwitchGear 3'UTR luciferase reporter plasmid: SOX2 3' UTR sequence
    Inhib. RNA
    Products:             		Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for SOX2 (see all 7)
    OriGene shRNA RFP: SOX2
    OriGene siRNA: SOX2
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SOX2
    Clone
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    OriGene custom cloning services – gene synthesis, subcloning, mutagenesis, variant library, vector shuttling 
    GenScript: all cDNA clones in your preferred vector: SOX2 (NM_003106)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SOX2 
    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SOX2
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SOX2

    Additional cDNA sequence: 

    AK312595.1 BC013923.2 L07335.1 Z31560.1 

    9 DOTS entries:

    DT.110032  DT.100779994  DT.91685066  DT.120898896  DT.100025773  DT.100770335  DT.100643943  DT.91704238 
    DT.100649253 

    24/138 AceView cDNA sequences (see all 138):

    AI073494 AI933292 AU117840 BE795592 BM976277 BM682840 CB850659 AI566840 
    AI598137 AI936860 BM978785 BE792833 BM718943 BQ045260 BF057693 BM668019 
    BG152545 BM700202 BU931277 BE797259 AI161208 AI364474 BI917204 AI080072 

    GeneLoc Exon Structure


    Expression
    for SOX2 gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SOX2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GAGAAAACCC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    SOX2 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    10/69 LifeMap In Vivo Development Anatomical Compartments/Cells (see all 69) 
    Tissue Anatomical Compartment CellCategory (developmental path)
    EyeNeuroblastic LayerEarly Retinal Progenitor CellsRetina
    EyeNeuroblastic LayerLate Retinal Progenitor CellsRetina
    Inner Cell MassInner Cell MassInner Cell Mass CellsEarly Embryo
    Gut TubeVentral Foregut EndodermMultipotent Lung Progenitor CellsLung
    TrophoblastTrophoblastTrophoblast CellsExtraembryonic Tissues
    AmnionAmniotic MembraneAmniotic CellsAmnion, Extraembryonic Tissues
    Early Embryo (Zygote)Morula8-Cell EmbryoEarly Embryo
    Early Embryo (Zygote)MorulaMorula CellsEarly Embryo
    Early Embryo (Zygote)Zygote2-Cell EmbryoEarly Embryo
    Early Embryo (Zygote)Zygote4-Cell EmbryoEarly Embryo
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 10/58 LifeMap Cells (see all 58) 
    NameCategory
    Induced pluripotent stem cell line 20D17 (Induced Pluripotent Stem Cell)Early Embryo, Fibroblast
    Induced pluripotent stem cell line 492B4 (Induced Pluripotent Stem Cell)Early Embryo, Fibroblast
    Induced pluripotent stem cell line 201B6 (Induced Pluripotent Stem Cell)Early Embryo, Fibroblast
    Induced pluripotent stem cell line 253G1 (Induced Pluripotent Stem Cell)Early Embryo, Fibroblast
    Induced pluripotent stem cell line A6 (Induced Pluripotent Stem Cell)Early Embryo, Fibroblast
    Induced pluripotent stem cell line Bi 1-3 (Induced Pluripotent Stem Cell)Early Embryo, Fibroblast
    Induced pluripotent stem cell line hIPS1 (Induced Pluripotent Stem Cell)Early Embryo, Fibroblast
    Induced pluripotent stem cell line hIPS2 (Induced Pluripotent Stem Cell)Early Embryo, Fibroblast
    Induced pluripotent stem cell line MRC5 (Induced Pluripotent Stem Cell)Early Embryo, Fibroblast
    Induced pluripotent stem cells (A1AT deficiency patient) (Induced Pluripotent Stem Cell)Early Embryo, Fibroblast

    See SOX2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SOX2

    SOURCE GeneReport for Unigene cluster: Hs.518438
        SABiosciences Expression via Pathway-Focused PCR Arrays including SOX2 (see all 8): 
              Neurogenesis in human mouse rat
              Cell Lineage Identification in human mouse rat
              Stem Cell Transcription Factors in human mouse rat
              WNT Signaling Targets in human mouse rat
              Mesenchymal Stem Cell in human mouse rat

    Primer
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    Browse OriGene validated miRNA SYBR primer pairs
    SABiosciences RT2 qPCR Primer Assay in human, mouse, rat SOX2
    QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SOX2
    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SOX2
    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SOX2

    Orthologs
    for SOX2 gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    This gene was present in the common ancestor of animals.

    Orthologs for SOX2 gene from 5/18 species (see all 18)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves SOX21 SRY (sex determining region Y)-box 2 85.93(n)
    93.97(a)    		   396105  NM_205188.1  NP_990519.1 
    African clawed frog
    (Xenopus laevis)    		 Amphibia Xl.188172 Xenopus laevis transcribed sequences 90.03(n)    BI446671.1 
    zebrafish
    (Danio rerio)    		 Actinopterygii wufc14d072 Danio rerio cDNA clone MGC65860 IMAGE6799998, complete more 82(n)    BC056743.1 
    honey bee
    (Apis mellifera)    		 Insecta --
    		 --
    		 19(a)
    		 1 → many
    		 Group13.3(374348-449748)
    worm
    (Caenorhabditis elegans)    		 Secernentea sox-26
    sox-46
    		 Protein SOX-4
    		 34(a)
    24(a)
    		 1 ↔ many
    possible ortholog
    		 X(7458248-7463691)
    X(3505427-3506378)


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

    Paralogs
    for SOX2 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SOX2 gene
    SOX132  SOX42  SOX12  SOX142  SOX32  SOX92  SOX122  SOX152  
    SOX182  SOX52  ENSG000002587242  SOX212  SOX172  SOX62  SOX112  SOX82  
    SRY2  SOX102  SOX72  
    8 SIMAP similar genes for SOX2 using alignment to 1 protein entry:     SOX2_HUMAN:
    soxB    SOX3    SRY    SOX1    SOX10    SOX14
    SOX15    SOX21

    SOX2 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for SOX2
    PGOHUM00000249794


    Genomic Variants
    for SOX2 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/72 NCBI SNPs in SOX2 are shown (see all 72)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 3 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1048938081,2
    		Cpathogenic204022517(+) ACGGCA/GCAGCG 2 T A mis10--------
    rs1048938031,2
    		Cpathogenic204022625(+) TGAACC/TAGCGC 2 Q * stg10--------
    rs1048938021,2
    		Cpathogenic204022798(+) GCGGCC/TGCGAG 2 P L mis10--------
    rs1048938001,2
    		Cpathogenic204022811(+) TCGACG/TAGGCT 2 E * stg10--------
    rs1048938011,2
    		Cpathogenic204022840(+) TTTGTA/CGGAGA 2 * S stg10--------
    rs1048938051,2
    		Cpathogenic204022867(+) CAAGCC/GCCTGG 2 P R mis10--------
    rs1048938041,2
    		Cpathogenic204022925(+) GCGGGC/TAGCGG 2 Q * stg10--------
    rs1048938061,2
    		Cpathogenic204022950(+) ATGAAG/TGCCTT 2 K N mis10--------
    rs98671811,2
    		H--178832541(+) AAGAAC/GTAAAA 1 -- us2k13Minor allele frequency- G:0.00EA NS 298
    rs766901911,2
    		F,--178832713(+) AGATTG/AGAGAA 1 -- us2k11Minor allele frequency- A:0.04WA 118

    HapMap Linkage Disequilibrium report for SOX2 (181429714 - 181432224 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for SOX2: --
    Human Gene Mutation Database (HGMD): SOX2

    Locus Specific Mutation Databases (LSDB): SOX2

    SABiosciences Cancer Mutation PCR Assays
    2 SABiosciences qBiomarker Copy Number PCR Arrays containing SOX2:
    Oncogenes & Tumor Suppressor Genes 384HC
    Lung Cancer
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SOX2
    DNA2.0 Custom Variant and Variant Library Synthesis for SOX2

    Disorders / Diseases
    for SOX2 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    SOX2 for disorders           About GeneDecksing

    OMIM gene information: 184429   
    OMIM disorders: 206900  
    UniProtKB/Swiss-Prot: SOX2_HUMAN, P48431
  • 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

    20/70 diseases for SOX2 (see all 70):    About MalaCards
    optic nerve hypoplasia    microphthalmia    esophageal atresia/tracheoesophageal fistula    lambert-eaton myasthenic syndrome
    optic nerve hypoplasia and abnormalities of the central nervous system    anophthalmia/microphthalmia    tracheoesophageal fistula    cornelia de lange syndrome
    microphthalmia syndromic 3    dermatofibrosarcoma protuberans    anophthalmia    ampulla of vater adenocarcinoma
    hearing loss    sensorineural hearing loss    cataract-glaucoma    squamous cell carcinoma
    type 1 diabetes mellitus    myasthenic syndrome    esophageal atresia    dermatofibrosarcoma

    6 diseases from the University of Copenhagen DISEASES database for SOX2:
    Teratoma     Microphthalmia     Embryonal carcinoma     Malignant glioma
    Coloboma     Seminoma

    10 Novoseek disease relationships for SOX2 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    anophthalmia 85.4 15 17522144 (5), 18385794 (2), 15503273 (2), 19471311 (1) (see all 7)
    microphthalmia 75.3 9 17522144 (3), 18385794 (2), 16651659 (2), 18285410 (1)
    eye abnormalities 67.2 1 18385794 (1)
    carcinoma embryonal 58.6 3 9343393 (1), 9669521 (1), 17324942 (1)
    teratoma 46.1 10 17464316 (5)
    metaplasia 37.2 9 19520737 (3), 14719100 (2), 15910596 (1), 14655050 (1) (see all 5)
    hearing loss sensorineural 23.9 1 18407919 (1)
    gastric cancer 8.95 7 18268498 (3), 15910596 (1), 17136346 (1)
    small cell lung cancer 3.93 2 16077994 (1), 10760287 (1)
    tumors 0 1 15983380 (1)

    GeneTests: SOX2
    SOX2-Related Eye Disorders
    Anophthalmia/Microphthalmia

    Human Genome Epidemiology (HuGE) Navigator: SOX2 (6 documents)

    Export disorders for SOX2 gene to outside databases

    Publications
    for SOX2 gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for SOX2 gene, integrated from 9 sources (see all 287):
    (articles sorted by number of sources associating them with SOX2)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. The cDNA sequence and chromosomal location of the human SOX2 gene. (PubMed id 7849401)1, 2, 3 Stevanovic M....Goodfellow P. (1994)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. Mutations in SOX2 cause anophthalmia. (PubMed id 12612584)1, 2 Fantes J.... FitzPatrick D.R. (2003)
    4. Expression of Sox2 in mature and immature teratomas of central nervous system. (PubMed id 17464316)1, 9 Phi J.H....Wang K.C. (2007)
    5. Helicobacter pylori induces gastric mucosal intestina l metaplasia through the inhibition of interleukin-4-mediated HMG box protein S ox2 expression. (PubMed id 19520737)1, 9 Asonuma S....Shimosegawa T. (2009)
    6. Aberrant expression of SOX2 upregulates MUC5AC gastric foveolar mucin in mucinous cancers of the colorectum and related lesions. (PubMed id 18027866)1, 9 Park E.T....Kim Y.S. (2008)
    7. SOX2 is frequently downregulated in gastric cancers and inhibits cell growth through cell-cycle arrest and apoptosis. (PubMed id 18268498)1, 9 Otsubo T....Yuasa Y. (2008)
    8. Transcription factor SOX2 up-regulates stomach-specific pepsinogen A gene expression. (PubMed id 17136346)1, 9 Tani Y....Yuasa Y. (2007)
    9. Expression of the SRY-related HMG box protein SOX2 in human gastric carcinoma. (PubMed id 14719100)1, 9 Li X.L....Yuasa Y. (2004)
    10. Identification of DPPA4 and other genes as putative Sox2:Oct-3/4 target genes using a combination of in silico analysis and transcription-based assays. (PubMed id 18366076)1, 9 Chakravarthy H....Rizzino A. (2008)

    External Searches for SOX2 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing SOX2 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 6657 HGNC: 11195 AceView: SOX2 Ensembl:ENSG00000181449 euGenes: HUgn6657
    ECgene: SOX2 H-InvDB: SOX2

    Other Databases showing SOX2 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing SOX2 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SOX2 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SOX2
    Wikipedia http://en.wikipedia.org/wiki/Sox2

    Intellectual Property
    for SOX2 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for SOX2 gene:
    Search GeneIP for patents involving SOX2

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    Products
    for SOX2 gene

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    About This Section

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     SOX2 Proteins, Antibodies, CLIAs, and ELISAs
     Cell Lines associated with SOX2: Human Embryonic Stem Cell Line ESI-017,
    Human Embryonic Stem Cell Line ESI-035, Human Embryonic Stem Cell Line ESI-049, Human Embryonic Stem Cell Line ESI-051,
    Human Embryonic Stem Cell Line ESI-053
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