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SOX6 Gene

protein-coding   GIFtS: 58
GCID: GC11M015949

SRY (Sex Determining Region Y)-Box 6

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
SRY (Sex Determining Region Y)-Box 61 2
HSSOX62
SOXD2
SRY-Box Containing Gene 62
Transcription Factor SOX-62

External Ids:    HGNC: 164211   Entrez Gene: 555532   Ensembl: ENSG000001106937   OMIM: 6072575   UniProtKB: P357123   

Export aliases for SOX6 gene to outside databases

Previous GC identifers: GC11M017086 GC11M016740 GC11M016032 GC11M015957 GC11M015673


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SOX6 Gene:
This gene encodes a member of the D subfamily of sex determining region y-related transcription factors that are
characterized by a conserved DNA-binding domain termed the high mobility group box and by their ability to bind
the minor groove of DNA. The encoded protein is a transcriptional activator that is required for normal
development of the central nervous system, chondrogenesis and maintenance of cardiac and skeletal muscle cells.
The encoded protein interacts with other family members to cooperatively activate gene expression. Alternative
splicing results in multiple transcript variants.(provided by RefSeq, Mar 2009)

GeneCards Summary for SOX6 Gene:
SOX6 (SRY (sex determining region Y)-box 6) is a protein-coding gene. Diseases associated with SOX6 include campomelic dysplasia, and craniosynostosis. GO annotations related to this gene include protein heterodimerization activity and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is SOX13.

UniProtKB/Swiss-Prot: SOX6_HUMAN, P35712
Function: Transcriptional activator. Binds specifically to the DNA sequence 5'-AACAAT-3'. Plays a key role in
several developmental processes, including neurogenesis and skeleton formation

Gene Wiki entry for SOX6 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000011.10  NC_018922.2  NT_009237.19  
Regulatory elements:
   Regulatory transcription factor binding sites in the SOX6 gene promoter:
         CREB   AREB6   Sox5   C/EBPbeta   deltaCREB   LyF-1   C/EBPalpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): SOX6 promoter sequence
   Search Chromatin IP Primers for SOX6

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SOX6


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

Entrez Gene cytogenetic band: 11p15.3   Ensembl cytogenetic band:  11p15.1   HGNC cytogenetic band: 11p15.3

SOX6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SOX6 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M015949:  view genomic region     (about GC identifiers)

Start:
15,987,995 bp from pter      End:
16,761,138 bp from pter
Size:
773,144 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: SOX6_HUMAN, P35712 (See protein sequence)
Recommended Name: Transcription factor SOX-6  
Size: 828 amino acids; 91921 Da
Subunit: Interacts with DAZAP2 (By similarity)
Sequence caution: Sequence=BC037866; Type=Frameshift; Positions=505;
Secondary accessions: Q86VX7 Q9BXQ3 Q9BXQ4 Q9BXQ5 Q9H0I8
Alternative splicing: 4 isoforms:  P35712-1   P35712-2   P35712-3   P35712-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SOX6: NX_P35712

Explore proteomics data for SOX6 at MOPED

Post-translational modifications: 

  • Sumoylation inhibits the transcriptional activity1
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SOX6 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (4 alternative transcripts): 
    NP_001139283.1  NP_001139291.1  NP_059978.1  NP_201583.2  

    ENSEMBL proteins: 
     ENSP00000324948   ENSP00000432134   ENSP00000434455   ENSP00000433233   ENSP00000436170  
     ENSP00000432577   ENSP00000434892   ENSP00000432596   ENSP00000339876   ENSP00000379644  

    SOX6 Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
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    Browse recombinant and purified proteins available from Enzo Life Sciences
    OriGene Purified Proteins for SOX6
    Browse OriGene Protein Over-expression Lysates
    OriGene MassSpec for SOX6
    OriGene Custom Protein Services for SOX6
    GenScript Custom Purified and Recombinant Proteins Services for SOX6
    Novus Biologicals SOX6 Protein
    Novus Biologicals SOX6 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for SOX6

    SOX6 Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of SOX6
    R&D Systems Antibodies for SOX6
    OriGene Antibodies for SOX6
    OriGene Custom Antibody Services for SOX6
    Novus Biologicals SOX6 Antibodies
    Abcam antibodies for SOX6
    Cloud-Clone Corp. Antibodies for SOX6
    ThermoFisher Antibodies for SOX6
    LSBio Antibodies in human, mouse, rat for SOX6

    SOX6 Assay Products:

    Browse Kits and Assays available from EMD Millipore
    OriGene Custom Assay Services for SOX6
    Browse R&D Systems for biochemical assays
    GenScript Custom Assay Services for SOX6
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for SOX6
    Cloud-Clone Corp. CLIAs for SOX6


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    SOX: SRY (sex determining region Y)-boxes

    1 InterPro protein domain:
     IPR009071 HMG_box_dom

    Graphical View of Domain Structure for InterPro Entry P35712

    ProtoNet protein and cluster: P35712

    UniProtKB/Swiss-Prot: SOX6_HUMAN, P35712
    Similarity: Contains 1 HMG box DNA-binding domain


    SOX6 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SOX6_HUMAN, P35712
    Function: Transcriptional activator. Binds specifically to the DNA sequence 5'-AACAAT-3'. Plays a key role in
    several developmental processes, including neurogenesis and skeleton formation

         Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding NAS1614875
    GO:0003700sequence-specific DNA binding transcription factor activity NAS1614875
    GO:0005515protein binding IPI--
    GO:0043565sequence-specific DNA binding IEA--
    GO:0044212transcription regulatory region DNA binding IEA--
         
    SOX6 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for SOX6:
     Increased gamma-H2AX phosphory 

         9 MGI mutant phenotypes (inferred from 3 alleles(MGI details for Sox6):
     cardiovascular system  craniofacial  growth/size/body  homeostasis/metabolism  limbs/digits/tail 
     mortality/aging  normal  respiratory system  skeleton 

    SOX6 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Sox6tm2.2Vlf for SOX6

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SOX6
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for SOX6

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SOX6
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SOX6

    Transcription Factor Targeting: 
    Targeting motifs: HOMER Transcription Factor Regulatory Elements motif viewer 
                                          Consensus sequence:  CCATTGTTNY 

    miRNA
    Products:
        
    miRTarBase miRNAs that target SOX6:
    hsa-mir-1 (MIRT003203), hsa-mir-499a-5p (MIRT004658)

    Block miRNA regulation of human, mouse, rat SOX6 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SOX6 (see all 147):
    hsa-miR-576-3p hsa-miR-100* hsa-miR-520f hsa-miR-3074-3p hsa-miR-138-2* hsa-miR-342-3p hsa-miR-208b hsa-miR-200b
    SwitchGear 3'UTR luciferase reporter plasmidSOX6 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for SOX6
    Predesigned siRNA for gene silencing in human, mouse, rat SOX6

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for SOX6

    Clone
    Products:
         
    OriGene clones in human, mouse for SOX6 (see all 24)
    OriGene ORF clones in mouse, rat for SOX6
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 4): SOX6 (NM_033326)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SOX6
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SOX6

    Cell Line
    Products:
         
    GenScript Custom overexpressing Cell Line Services for SOX6
    Browse ESI BIO Cell Lines and PureStem Progenitors for SOX6 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SOX6


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    SOX6_HUMAN, P35712: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2
    extracellular2

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus NAS1614875
    GO:0005730NOT nucleolus IDA--

    SOX6 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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    SuperPaths for SOX6 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1ERK Signaling
    Molecular Mechanisms of Cancer0.51
    2Endochondral Ossification
    Endochondral Ossification

    1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for SOX6
        Molecular Mechanisms of Cancer

    1 BioSystems Pathway for SOX6
        Endochondral Ossification


        Pathway & Disease-focused RT2 Profiler PCR Array including SOX6: 
              Stem Cell Transcription Factors in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for SOX6

    Selected Interacting proteins for SOX6 (P357121, 3) via UniProtKB, MINT, STRING, and/or I2D (see all 13)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SHOXO152661, 3EBI-3505706,EBI-3505698 I2D: score=1 
    CENPKQ9BS163I2D: score=2 
    CTBP2P565453I2D: score=2 
    CTNNB1P352223I2D: score=1 
    DAZAP2Q150383I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 26):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IEA--
    GO:0000902cell morphogenesis IEA--
    GO:0001701in utero embryonic development IEA--
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated NAS1614875

    SOX6 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SOX6

    1 Novoseek inferred chemical compound relationship for SOX6 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    retinoic acid 28.3 8 15527762 (3), 14988021 (3)



    SOX6 for compounds           About GeneDecksing



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for SOX6 gene (4 alternative transcripts): 
    NM_001145811.1  NM_001145819.1  NM_017508.2  NM_033326.3  

    Unigene Cluster for SOX6:

    SRY (sex determining region Y)-box 6
    Hs.368226  [show with all ESTs]
    Unigene Representative Sequence: NM_017508
    18 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000316399 ENST00000528252 ENST00000527619(uc009ygs.2) ENST00000528429
    ENST00000527840 ENST00000524650 ENST00000531297 ENST00000533411 ENST00000530378(uc001mmh.1)
    ENST00000533870(uc001mmi.3) ENST00000533658(uc001mmj.3) ENST00000526673
    ENST00000529469 ENST00000525835 ENST00000524520 ENST00000525259 ENST00000352083(uc001mme.3 uc001mmd.3 uc001mmf.3)
    ENST00000396356(uc001mmg.3)
    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat SOX6 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SOX6 (see all 147):
    hsa-miR-576-3p hsa-miR-100* hsa-miR-520f hsa-miR-3074-3p hsa-miR-138-2* hsa-miR-342-3p hsa-miR-208b hsa-miR-200b
    SwitchGear 3'UTR luciferase reporter plasmidSOX6 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for SOX6
    Predesigned siRNA for gene silencing in human, mouse, rat SOX6
    Clone
    Products:
         
    OriGene clones in human, mouse for SOX6 (see all 24)
    OriGene ORF clones in mouse, rat for SOX6
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 4): SOX6 (NM_033326)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SOX6
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SOX6
    Primer
    Products:
        
    OriGene qSTAR qPCR primer pairs in human, mouse for SOX6
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SOX6
      QuantiTect SYBR Green Assays in human, mouse, rat SOX6
      QuantiFast Probe-based Assays in human, mouse, rat SOX6

    Additional mRNA sequence: 

    AF309034.1 AK021785.1 AK097455.1 AK124165.1 AK310506.1 AL136780.1 AL833302.1 BC029429.1 
    BC037866.1 BC047064.1 X65663.1 

    16 DOTS entries:

    DT.100747279  DT.443096  DT.91714037  DT.312559  DT.100677728  DT.101976514  DT.95371971  DT.120686517 
    DT.429593  DT.91914269  DT.120686573  DT.97836345  DT.100751624  DT.120686626  DT.120686612  DT.95192412 

    Selected AceView cDNA sequences (see all 79):

    AA716716 BU662466 BG942566 H57501 BM754693 BU167102 BX091675 AA436263 
    AA436138 AL136780 BX113900 AA563703 AW300597 H52387 AI086297 AA694285 
    AI631074 BC047064 BU657066 BU662739 NM_033326 N38857 AF309034 BM827319 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for SOX6    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19 ^ 20a · 20b ^ 21 ^ 22a · 22b
    SP1:              -     -                 -     -     -     -                                                     -                 -                           
    SP2:                                      -     -     -     -                                                     -                                             
    SP3:                    -                 -     -     -     -                                   -                                                               
    SP4:              -     -                 -                                                                                                                     
    SP5:              -     -                                                                                                                                       


    ECgene alternative splicing isoforms for SOX6

    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SOX6 expression in normal human tissues (normalized intensities)      SOX6 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCATCTTTGG
    SOX6 Expression
    About this image


    SOX6 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 17) fully expand
     
     Cartilage (Muscoskeletal System)    fully expand to see all 23 entries
             Chondrocytes Synchondroses
             Chondrocyte-like cells
     
     Bone (Muscoskeletal System)    fully expand to see all 23 entries
             Prechondrocytes Autopod Epiphyseal End
             Bone Marrow
             Chondrocyte-like cells
     
     Brain (Nervous System)    fully expand to see all 10 entries
             Pre-myelinating Oligodendrocyte Cells Spinal Cord White Matter
             Lateral Ventricle
     
     Head Mesenchyme (Muscoskeletal System)    fully expand to see all 2 entries
             Chondrocytes Branchial Arch 2
     
     Primitive Streak (Early Embryonic Tissues)
             Notochord Cells Notochord
    SOX6 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SOX6 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.368226

    UniProtKB/Swiss-Prot: SOX6_HUMAN, P35712
    Tissue specificity: Expressed in a wide variety of tissues, most abundantly in skeletal muscle

        Pathway & Disease-focused RT2 Profiler PCR Array including SOX6: 
              Stem Cell Transcription Factors in human mouse rat

    Primer
    Products:
    OriGene qSTAR qPCR primer pairs in human, mouse for SOX6
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SOX6
    QuantiTect SYBR Green Assays in human, mouse, rat SOX6
    QuantiFast Probe-based Assays in human, mouse, rat SOX6
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SOX6

    (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)
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    This gene was present in the common ancestor of animals.

    Orthologs for SOX6 gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sox61 , 5 SRY-box containing gene 65
    SRY (sex determining region Y)-box 61
    92.46(n)1
    96.13(a)1
      7 (61.29 cM)5
    206791  NM_001277326.11  NP_001264255.11 
     1154713445 
    chicken
    (Gallus gallus)
    Aves SOX61 SRY (sex determining region Y)-box 6 87.26(n)
    93.82(a)
      423068  XM_004941397.1  XP_004941454.1 
    lizard
    (Anolis carolinensis)
    Reptilia SOX66
    SRY (sex determining region Y)-box 6
    82(a)
    1 ↔ 1
    1(65750533-66066919)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia BX750509.12   -- 82.72(n)    BX750509.1 
    zebrafish
    (Danio rerio)
    Actinopterygii sox61 SRY-box containing gene 6 76.4(n)
    80.1(a)
      567154  NM_001123009.1  NP_001116481.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Sox102F3 transcription factor 54(a)   102C3   --
    worm
    (Caenorhabditis elegans)
    Secernentea egl-133 Expression: pi lineage, gonad, head
    neurons, tail more
    71(a)   X(5703590-5708655)   --


    ENSEMBL Gene Tree for SOX6 (if available)
    TreeFam Gene Tree for SOX6 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SOX6 gene
    SOX132  SOX22  SOX42  SOX12  SOX142  SOX32  SOX92  SOX122  
    SOX152  SOX182  SOX52  ENSG000002587242  SOX212  SOX172  SOX112  SOX82  
    SRY2  SOX102  SOX72  
    10 SIMAP similar genes for SOX6 using alignment to 6 protein entries:     SOX6_HUMAN (see all proteins):
    SOX5P    SOX17    SRY    soxB    SOX25    SOX27
    SOX26    SOX28    SOX5    SOX10

    SOX6 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SOX6 (see all 8070)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1468669951,2
    --15770699(+) TACAAG/TCATTT 4 -- int10--------
    rs754822161,2
    C,F--15772818(+) GAAAGA/GCAGGA 4 -- int11Minor allele frequency- G:0.05WA 118
    rs340165461,2
    C--15824505(+) ACAAA-/C/CAAA
            
    AAACA
    4 -- int11NA 2
    rs754602551,2
    C--15848678(+) GCATCA/GCCTCA 4 -- int13Minor allele frequency- G:0.17NA 6
    rs105495671,2
    C--15865974(+) tacag-/GTgtgtg 4 -- int10--------
    rs2003091921,2
    --15903934(+) CTTCT-/TCTTTTT 4 -- int10--------
    rs110238661,2
    C,F,A--15903935(+) TTCTTT/CTTTTT 4 -- int1 trp33Minor allele frequency- C:0.40NA WA CSA 5
    rs667052291,2
    C--15903937(+) TTCTT-/C/CTT 
            
    TTTTT
    8 -- int1 cds11NA 2
    rs340234021,2
    C--15903955(+) TTTTTTT/-GAGAT 4 -- int11Minor allele frequency- -:0.50NA 2
    rs1499404031,2
    C--15905131(+) TTGTT-/TTGA  
            
    GTTGT
    4 -- int10--------

    HapMap Linkage Disequilibrium report for SOX6 (15987995 - 16237995 bp, first 250kb of SOX6)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for SOX6 (see all 26):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2631763CNV Deletion19546169
    esv2666456CNV Deletion23128226
    esv2461915CNV Deletion19546169
    esv2744137CNV Deletion23290073
    esv2744139CNV Deletion23290073
    esv2744135CNV Deletion23290073
    esv2740786CNV Deletion23290073
    esv2744134CNV Deletion23290073
    esv2051843CNV Deletion18987734
    esv2744138CNV Deletion23290073

    Human Gene Mutation Database (HGMD): SOX6
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SOX6
    DNA2.0 Custom Variant and Variant Library Synthesis for SOX6

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 607257    OMIM disorders: --

    14 diseases for SOX6:    About MalaCards
    campomelic dysplasia    craniosynostosis    osteoporosis    brain cancer
    osteoarthritis    myopathy    esophageal squamous cell carcinoma    obesity
    squamous cell carcinoma    esophagitis    cervicitis    pancreatitis
    neuronitis    endotheliitis


    SOX6 for disorders           About GeneDecksing

    1 Novoseek inferred disease relationship for SOX6 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    carcinoma 3.2 1 14988021 (1)

    Genetic Association Database (GAD): SOX6
    Human Genome Epidemiology (HuGE) Navigator: SOX6 (14 documents)

    Export disorders for SOX6 gene to outside databases

    (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)
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    PubMed articles for SOX6 gene, integrated from 10 sources (see all 63):
    (articles sorted by number of sources associating them with SOX6)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning, characterization and chromosome mapping of the human SOX6 gene. (PubMed id 11255018)1, 2, 3, 9 Cohen-Barak O.... Brilliant M.H. (Gene 2001)
    2. Powerful bivariate genome-wide association analyses suggest the SOX6 gene influencing both obesity and osteoporosis phenotypes in males. (PubMed id 19714249)1, 4, 9 Liu Y.Z....Deng H.W. (PLoS ONE 2009)
    3. A genome-wide association analysis implicates SOX6 as a candidate gene for wrist bone mass. (PubMed id 21104366)1, 4 Tan L....Deng H. (Sci China Life Sci 2010)
    4. An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility Loci for osteoporosis-related traits. (PubMed id 20548944)1, 4 Hsu Y.H....Kiel D.P. (PLoS Genet. 2010)
    5. Genomewide linkage and peakwide association analyses of carotid plaque in Caribbean Hispanics. (PubMed id 20966410)1, 4 Dong C....Sacco R.L. ( a journal of cerebral circulation 2010)
    6. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    7. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    8. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. (PubMed id 19240061)1, 4 Trynka G....Wijmenga C. (Gut 2009)
    9. Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies. (PubMed id 19801982)1, 4 Rivadeneira F....Uitterlinden A.G. (Nat. Genet. 2009)
    10. High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men. (PubMed id 19453261)1, 4 Yerges L.M....Zmuda J.M. (J. Bone Miner. Res. 2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 55553 HGNC: 16421 AceView: SOX6 Ensembl:ENSG00000110693 euGenes: HUgn55553
    ECgene: SOX6 H-InvDB: SOX6

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for SOX6 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SOX6 gene:
    Search GeneIP for patents involving SOX6

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



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