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

SIX1 Gene

protein-coding   GIFtS: 62
GCID: GC14M061111

SIX homeobox 1

(Previous names: sine oculis homeobox (Drosophila) homolog 1, sine oculis...)
(Previous symbol: DFNA23)
 Explore 23 diseases affiliated with
SIX1 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for SIX1    

Aliases
for SIX1 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
SIX Homeobox 11 2     Sine Oculis Homeobox (Drosophila) Homolog 11
DFNA231 2 5     Sine Oculis Homeobox Homolog 1 (Drosophila)1
Sine Oculis Homeobox Homolog 12 3     TIP392
BOS32 5     Homeobox Protein SIX12
Deafness, Autosomal Dominant 231     

External Ids:    HGNC: 108871   Entrez Gene: 64952   Ensembl: ENSG000001267787   OMIM: 6012055   UniProtKB: Q154753   

Export aliases for SIX1 gene to outside databases

Previous GC identifers: GC14M058438 GC14M054906 GC14M059102 GC14M060182 GC14M041274


Summaries
for SIX1 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 SIX1:
The protein encoded by this gene is a homeobox protein that is similar to the Drosophila 'sine oculis' gene product.
This gene is found in a cluster of related genes on chromosome 14 and is thought to be involved in limb development.
Defects in this gene are a cause of autosomal dominant deafness type 23 (DFNA23) and branchiootic syndrome type 3
(BOS3). (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: SIX1_HUMAN, Q15475
Function: May be involved in limb tendon and ligament development (By similarity)

Gene Wiki entry for SIX1


Genomic Views
for SIX1 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_000014.8  NC_018925.1  NT_026437.12  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SIX1 gene promoter:
         AREB6   PPAR-alpha   IRF-2   FOXJ2 (long isoform)   FOXJ2   POU3F2 (N-Oct-5b)   Nkx2-5   Evi-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: SIX1 promoter sequence
   Search SABiosciences Chromatin IP Primers for SIX1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SIX1


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

Entrez Gene cytogenetic band: 14q23.1   Ensembl cytogenetic band:  14q23.1   HGNC cytogenetic band: 14q23.1

SIX1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SIX1 gene location

GeneLoc information about chromosome 14         GeneLoc Exon Structure

GeneLoc location for GC14M061111:  view genomic region     (about GC identifiers)

Start:
 61,110,132 bp from pter      End:
 61,124,977 bp from pter
Size:
 14,846 bases      Orientation:
 minus strand

Proteins
for SIX1 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: SIX1_HUMAN, Q15475 (See protein sequence)
Recommended Name: Homeobox protein SIX1  
Size: 284 amino acids; 32210 Da
Subcellular location: Nucleus
Secondary accessions: Q53Y16 Q96H64

Explore the universe of human proteins at neXtProt for SIX1: NX_Q15475

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q15475

    • SIX1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_005973.1  
    ENSEMBL proteins: 
     ENSP00000247182   ENSP00000450952   ENSP00000450739   ENSP00000452700  

    Human Recombinant Protein Products: 
    Browse Purified and Recombinant Proteins at EMD Millipore
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    Browse OriGene full length recombinant human proteins expressed in human HEK293 cells
    OriGene Protein Over-expression Lysate: SIX1
    OriGene Custom Protein Services for SIX1 
    GenScript Custom Purified and Recombinant Proteins Services for SIX1
    Novus Biologicals SIX1 Protein
    Novus Biologicals SIX1 Lysate
    Browse Sino Biological Recombinant Proteins
    ProSpec Recombinant Protein for SIX1
    Uscn Proteins for SIX1

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005667transcription factor complex ISS--
    GO:0005730nucleolus IDA--


    SIX1 for ontologies           About GeneDecksing



    SIX1 Antibody Products: 
    EMD Millipore Mono- and Polyclonal Antibodies for the study of SIX1
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    Novus Biologicals SIX1 Antibodies
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    Uscn Antibodies for SIX1
    Search ThermoFisher Antibodies for SIX1

    Assay Products for SIX1: 
    Browse Kits and Assays available from EMD Millipore
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    Browse OriGene Fluorogenic Cell Assay Kits
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    GenScript Custom Assay Services for SIX1
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    Uscn ELISAs and CLIAs for SIX1

    Protein Domains /
    Families
    for SIX1 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    SIX1 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR017970 Homeobox_CS
     IPR001356 Homeodomain
     IPR009057 Homeodomain-like

    Graphical View of Domain Structure for InterPro Entry Q15475

    ProtoNet protein and cluster: Q15475

    1 Blocks protein family: IPB000047 Lambda and other repressor helix-turn-helix signature

    UniProtKB/Swiss-Prot: SIX1_HUMAN, Q15475
    Similarity: Belongs to the SIX/Sine oculis homeobox family
    Similarity: Contains 1 homeobox DNA-binding domain


    Function
    for SIX1 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: SIX1_HUMAN, Q15475
    Function: May be involved in limb tendon and ligament development (By similarity)

         Genatlas biochemistry entry for SIX1:
    Drosophila sine oculis homolog SIX1 homeo box encoding gene,expressed during development in limb tendons,also expressed
    in skeletal and smooth muscle

    miRNA
    Products:            		miRTarBase miRNAs that target SIX1:
    hsa-mir-185 (MIRT005550)

    OriGene 3'-UTR Clone: SIX1
    Browse MicroRNA Expression Plasmids
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SIX1
    8/37 QIAGEN miScript miRNA Assays for microRNAs that regulate SIX1 (see all 37):
    hsa-miR-429 hsa-miR-200a hsa-miR-30d hsa-miR-138-2* hsa-miR-570 hsa-miR-141 hsa-miR-30a hsa-miR-208a
    SwitchGear 3'UTR luciferase reporter plasmid: SIX1 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 SIX1 (see all 7)
    OriGene shRNA RFP: SIX1
    OriGene siRNA: SIX1
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SIX1

    Gene Editing
    Products:    		DNA2.0 Custom Protein Engineering Service for SIX1

    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 SIX1 (see all 3)
    OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for SIX1
    OriGene custom cloning services – gene synthesis, subcloning, mutagenesis, variant library, vector shuttling 
    GenScript: all cDNA clones in your preferred vector: SIX1 (NM_005982)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SIX1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SIX1 

    Cell Line
    Products:             		GenScript Custom overexpressing Cell Line Services for SIX1
    LifeMap BioReagents: cell lines associated with SIX1: PureStem E15, Meso-prx/latp Progenitor,
    PureStem SK11, NCr-fac & Meso-prx Progenitor

    In Situ Assay
    Products:       
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SIX1

    Gene Ontology (GO): 5/6 molecular function terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IDA19497856
    GO:0003682chromatin binding IEA--
    GO:0003700sequence-specific DNA binding transcription factor activity ISS--
    GO:0005515protein binding IPI16189514
    GO:0043565sequence-specific DNA binding IDA15141091


    SIX1 for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-outs for SIX1: Six1tm1Kwk Six1tm2Kwk
         15/20 MGI mutant phenotypes (inferred from 9 alleles) (MGI details for Six1) (see all 20):
     behavior/neurological  cardiovascular system  cellular  craniofacial  digestive/alimentary 
     embryogenesis  endocrine/exocrine gland  growth/size  hearing/vestibular/ear  hematopoietic system 
     immune system  limbs/digits/tail  mortality/aging  muscle  nervous system 

    SIX1 for phenotypes           About GeneDecksing


    Pathways & Interactions
    for SIX1 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



    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for SIX1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 13)

    5/19 Interacting proteins for SIX1 (Q154751, 2, 3 ENSP000002471824) via UniProtKB, MINT, STRING, and/or I2D (see all 19)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CCDC85BQ158342, 3, ENSP000003116954MINT-67082 I2D: score=5 STRING: ENSP00000311695
    MDFIQ997501, 2, 3, ENSP000002303214EBI-743675,EBI-724076 MINT-66374 I2D: score=6 STRING: ENSP00000230321
    DACH1Q9UI363, ENSP000003527124I2D: score=3 STRING: ENSP00000352712
    EYA1Q995023, ENSP000003426264I2D: score=3 STRING: ENSP00000342626
    AESQ081173, ENSP000002215614I2D: score=1 STRING: ENSP00000221561
    About this table

    Gene Ontology (GO): 5/45 biological process terms (GO ID links to tree view) (see all 45):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IEA--
    GO:0001657ureteric bud development ISS--
    GO:0001658branching involved in ureteric bud morphogenesis ISS--
    GO:0001759organ induction ISS--
    GO:0001822kidney development ISS--


    SIX1 for ontologies           About GeneDecksing



    Drugs & Compounds
    for SIX1 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
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SIX1
    Search CenterWatch for drugs/clinical trials and news about SIX1 

    Transcripts
    for SIX1 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 SIX1 gene: 
    NM_005982.3  

    Unigene Cluster for SIX1:

    SIX homeobox 1
    Hs.633506  [show with all ESTs]
    Unigene Representative Sequence: NM_005982
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000247182(uc001xfb.4) ENST00000555955 ENST00000553535 ENST00000554986
    ENST00000555627

    miRNA
    Products:             		 OriGene 3'-UTR Clone: SIX1
    Browse OriGene MicroRNA Expression Plasmids
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SIX1
    8/37 QIAGEN miScript miRNA Assays for microRNAs that regulate SIX1 (see all 37):
    hsa-miR-429 hsa-miR-200a hsa-miR-30d hsa-miR-138-2* hsa-miR-570 hsa-miR-141 hsa-miR-30a hsa-miR-208a
    SwitchGear 3'UTR luciferase reporter plasmid: SIX1 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 SIX1 (see all 7)
    OriGene shRNA RFP: SIX1
    OriGene siRNA: SIX1
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SIX1
    Clone
    Products:             		 OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for SIX1 (see all 3)
    OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for SIX1
    OriGene custom cloning services – gene synthesis, subcloning, mutagenesis, variant library, vector shuttling 
    GenScript: all cDNA clones in your preferred vector: SIX1 (NM_005982)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SIX1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SIX1 
    Primer
    Products:            		 OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for SIX1
    Browse OriGene validated miRNA SYBR primer pairs
    SABiosciences RT2 qPCR Primer Assay in human, mouse, rat SIX1
      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SIX1
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SIX1

    Additional cDNA sequence: 

    AK093780.1 BC008874.2 BT007083.1 X91868.1 

    5 DOTS entries:

    DT.110833  DT.210942  DT.92421992  DT.206169  DT.99950944 

    24/130 AceView cDNA sequences (see all 130):

    AA988491 BM975666 BQ182990 AI860806 BE671377 BF111239 BF433117 BE350547 
    AW409771 AW016919 BI495857 BE765761 AI298421 AW341127 AI701028 BU607471 
    BF436137 AI375023 AW770317 BE791327 BE670478 BE765452 BE220876 BF433105 

    GeneLoc Exon Structure


    Expression
    for SIX1 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

    SIX1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

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

    SIX1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    10/51 LifeMap In Vivo Development Anatomical Compartments/Cells (see all 51) 
    Tissue Anatomical Compartment CellCategory (developmental path)
    Head MesenchymeHypobranchial MusclesMyoblastsSkeletal Muscle
    KidneyMetanephric MesenchymeMetanephric Mesenchyme CellsKidney
    LimbForelimb Dorsal MusclesMononuclear MyocytesSkeletal Muscle
    LimbForelimb Ventral MusclesMononuclear MyocytesSkeletal Muscle
    LimbHindlimb Dorsal MuscleMononuclear MyocytesSkeletal Muscle
    LimbHindlimb Ventral MuscleMononuclear MyocytesSkeletal Muscle
    Skeletal MuscleMandibular Arch MusclesMuscle Progenitor CellsSkeletal Muscle
    Skeletal MuscleMandibular Arch MusclesMyoblastsSkeletal Muscle
    Skeletal MuscleThoracic Epaxial MyotomeMononuclear MyocytesSkeletal Muscle
    Skeletal MuscleThoracic Epaxial MyotomeMyoblastsSkeletal Muscle
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 10/11 LifeMap Cells (see all 11) 
    NameCategory
    PureStem™ mesenchymal Progenitor SK11 (Embryonic Progenitor Cell)Adipose, Bone, Cartilage
    PureStem™ mesenchymal progenitor E15 (Embryonic Progenitor Cell)Adipose, Bone, Cartilage
    PureStem™ progenitor T42 (Embryonic Progenitor Cell)
    PureStem™ mesenchymal progenitor SM30 (Embryonic Progenitor Cell)Adipose, Bone, Cartilage
    PureStem™ mesenchymal progenitor 7SMOO32 (Embryonic Progenitor Cell)Adipose, Bone, Cartilage
    PureStem™ mesenchymal progenitor 7PEND24 (Embryonic Progenitor Cell)Cartilage, Neural Crest
    PureStem™ mesenchymal progenitor 4D20.8 (Embryonic Progenitor Cell)Lateral Plate Mesoderm, Neural Crest
    PureStem™ progenitor EN7 (Embryonic Progenitor Cell)
    PureStem™ progenitor SM22 (Embryonic Progenitor Cell)
    Cell sheets (Stepwise differentia...)

    See SIX1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SIX1

    SOURCE GeneReport for Unigene cluster: Hs.633506

    UniProtKB/Swiss-Prot: SIX1_HUMAN, Q15475
    Tissue specificity: Specifically expressed in skeletal muscle

        SABiosciences Expression via Pathway-Focused PCR Arrays including SIX1: 
              WNT Signaling Targets in human mouse rat
              Homeobox (HOX) Genes in human mouse rat

    Primer
    Products:    		 OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for SIX1
    Browse OriGene validated miRNA SYBR primer pairs
    SABiosciences RT2 qPCR Primer Assay in human, mouse, rat SIX1
    QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SIX1
    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SIX1
    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SIX1

    Orthologs
    for SIX1 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 SIX1 gene from 5/21 species (see all 21)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves SIX11 SIX homeobox 1 85.11(n)
    92.55(a)    		   693262  NM_001044685.1  NP_001038150.1 
    lizard
    (Anolis carolinensis)    		 Reptilia SIX16
    SIX16
    		 --
    		 84(a)
    73(a)
    		 possible ortholog
    1 ↔ 1
    		 GL343261.1(826117-841214)
    GL343568.1(43945-55241)
    African clawed frog
    (Xenopus laevis)    		 Amphibia Six12 homeobox protein SIX1 80.11(n)    BC045122.1 
    zebrafish
    (Danio rerio)    		 Actinopterygii Dr.276812 Transcribed sequence with moderate similarity to protein more 80.5(n)    CK147432.1 
    fruit fly
    (Drosophila melanogaster)    		 Insecta so3 circadian rhythm transcription factor 87(a)
    (best of 2)    		   2 43C1   --


    ENSEMBL Gene Tree for SIX1 (if available)
    TreeFam Gene Tree for SIX1 (if available) 

    Paralogs
    for SIX1 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SIX1 gene
    SIX42  SIX52  SIX22  SIX32  SIX62  
    6 SIMAP similar genes for SIX1 using alignment to 3 protein entries:     SIX1_HUMAN (see all proteins):
    SIX6    AREC3    SIX2    SIX3    SIX4    SIX5

    SIX1 for paralogs           About GeneDecksing



    Genomic Variants
    for SIX1 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

    10/130 NCBI SNPs in SIX1 are shown (see all 130)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 14 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1048944781,2
    		Cpathogenic61115522(-) CAGCTA/GCTGCT 2 Y C mis10--------
    rs1511306371,2
    		--61110950(+) TGAGAA/GCCCCT 1 -- ds50010--------
    rs1411451331,2
    		C,--61111134(+) GGGGG-/AAAAAC 1 -- ds50010--------
    rs1508726011,2
    		C,--61111223(+) AAAAT-/AAGAAGGC 1 -- ds50010--------
    rs106896481,2
    		C--61111226(+) ATAAGAAG/-GCCTT 1 -- ds50011Minor allele frequency- -:0.00NA 2
    rs1400880051,2
    		--61111478(+) GCTAAA/GTACAG 1 -- ut310--------
    rs619938311,2
    		--61111505(+) CCCCAG/AGCAAA 1 -- ut312Minor allele frequency- A:0.04NA 122
    rs1469673311,2
    		--61111523(+) TGGAGC/GCTACA 1 -- ut310--------
    rs1379949571,2
    		--61111625(+) ACAATA/GTTTCT 1 -- ut310--------
    rs1818331901,2
    		--61111786(+) TAGAAA/GTTAAT 1 -- ut310--------

    HapMap Linkage Disequilibrium report for SIX1 (61110132 - 61124977 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for SIX1
         1 Indel: 58683
    Human Gene Mutation Database (HGMD): SIX1

    SABiosciences Cancer Mutation PCR Assays
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    Disorders / Diseases
    for SIX1 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
    SIX1 for disorders           About GeneDecksing

    OMIM gene information: 601205   
    OMIM disorders: 608389  605192  
    UniProtKB/Swiss-Prot: SIX1_HUMAN, Q15475
  • Defects in SIX1 are the cause of deafness autosomal dominant type 23 (DFNA23) [MIM:605192]. A form of
    • non-syndromic deafness characterized by prelingual, bilateral, symmetric hearing loss with a conductive component
    present in some but not all patients
  • Defects in SIX1 are the cause of branchiootic syndrome type 3 (BOS3) [MIM:608389]. BOS3 is a syndrome
    • characterized by usually bilateral branchial cleft fistulas or cysts, sensorineural and/or conductive hearing loss,
    pre-auricular pits, and structural defects of the outer, middle or inner ear. Otic defects include malformed and
    hypoplastic pinnae, a narrowed external ear canal, bulbous internal auditory canal, stapes fixation, malformed and
    hypoplastic cochlea. Branchial and otic anomalies are as those seen in individuals with the branchiootorenal syndrome.
    However, renal anomalies are absent in branchiootic syndrome patients
  • Note=Defects in SIX1 could be a cause of branchiootorenal syndrome (BOR). BOR is an autosomal dominant
    • disorder manifested by various combinations of preauricular pits, branchial fistulae or cysts, lacrimal duct stenosis,
    hearing loss, structural defects of the outer, middle, or inner ear, and renal dysplasia. Associated defects include
    asthenic habitus, long narrow facies, constricted palate, deep overbite, and myopia. Hearing loss may be due to
    mondini type cochlear defect and stapes fixation. Penetrance of BOR syndrome is high, although expressivity can be
    extremely variable

    20/23 diseases for SIX1 (see all 23):    About MalaCards
    deafness, autosomal dominant 23    branchiootic syndrome    enlarged vestibular aqueduct    malignant peripheral nerve sheath tumor
    lacrimal duct obstruction    brachiootic syndrome 3    branchiootorenal spectrum disorders    branchiootorenal syndrome
    renal agenesis    hearing loss    wilms tumor    myopia
    breast cancer    glaucoma    hepatocellular carcinoma    ovarian carcinoma
    cervical cancer    cervicitis    pharyngitis    osteosarcoma

    3 diseases from the University of Copenhagen DISEASES database for SIX1:
    Branchiootorenal syndrome     Lacrimal duct obstruction     Renal agenesis

    10 Novoseek disease relationships for SIX1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    bor syndrome 97.1 18 16491411 (3), 19389353 (2), 17637804 (2), 17238186 (2) (see all 11)
    renal anomaly 87.9 1 18177466 (1)
    urinary tract anomaly 73.2 2 20110314 (1), 16971658 (1)
    rhabdomyosarcoma 35.1 1 15805264 (1)
    metastasis 25.4 10 19726885 (3), 20074369 (2), 17409410 (1), 19331807 (1) (see all 6)
    renal failure chronic 5.46 1 16971658 (1)
    breast cancer 0 13 15805264 (4), 19726885 (4), 20074369 (2), 19726883 (1)
    tumors 0 16 15805264 (4), 17409410 (2), 19726885 (2), 19726883 (2)
    carcinoma 0 2 17409410 (2), 20074369 (1), 19726883 (1)
    cancer 0 5 19726885 (2), 17409410 (1), 20074369 (1), 18381426 (1)

    GeneTests: SIX1
    Branchiootorenal Spectrum Disorders

    Human Genome Epidemiology (HuGE) Navigator: SIX1 (2 documents)

    Export disorders for SIX1 gene to outside databases

    Publications
    for SIX1 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 SIX1 gene, integrated from 9 sources (see all 83):
    (articles sorted by number of sources associating them with SIX1)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. SIX1 mutations cause branchio-oto-renal syndrome by disruption of EYA1-SIX1-DNA complexes. (PubMed id 15141091)1, 2, 3, 9 Ruf R.G.... Hildebrandt F. (2004)
    2. Cloning of the human SIX1 gene and its assignment to chromosome 14. (PubMed id 8617500)1, 2, 3 Boucher C.A.... Johnson K.J. (1996)
    3. SIX1 mutation screening in 247 branchio-oto-renal syndrome families: a recurrent missense mutation associated with BOR. (PubMed id 18330911)1, 2, 9 Kochhar A....Smith R.J. (2008)
    4. Branchio-oto-renal syndrome: detection of EYA1 and SIX1 mutations in five out of six Danish families by combining linkage, MLPA and sequencing analyses. (PubMed id 17637804)1, 2, 9 Sanggaard K.M....Tranebjaerg L. (2007)
    5. Mutation screening of the EYA1, SIX1, and SIX5 genes in a large cohort of patients harboring branchio-oto-renal syndrome calls into question the pathogenic role of SIX5 mutations. (PubMed id 21280147)1, 2 Krug P.... Heidet L. (2011)
    6. 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)
    7. Six1 expands the mouse mammary epithelial stem/progen itor cell pool and induces mammary tumors that undergo epithelial-mesenchymal t ransition. (PubMed id 19726883)1, 9 McCoy E.L....Ford H.L. (2009)
    8. Biochemical and functional characterization of six SI X1 Branchio-oto-renal syndrome mutations. (PubMed id 19497856)1, 9 Patrick A.N....Ford H.L. (2009)
    9. Six1 overexpression in mammary cells induces genomic instability and is sufficient for malignant transformation. (PubMed id 18381426)1, 9 Coletta R.D....Ford H.L. (2008)
    10. The Six1 homeoprotein induces human mammary carcinoma cells to undergo epithelial-mesenchymal transition and metastasis in mice thro ugh increasing TGF-beta signaling. (PubMed id 19726885)1, 9 Micalizzi D.S....Ford H.L. (2009)

    External Searches for SIX1 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
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    Genome Databases showing SIX1 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 6495 HGNC: 10887 AceView: SIX1 Ensembl:ENSG00000126778 euGenes: HUgn6495
    ECgene: SIX1 H-InvDB: SIX1

    Other Databases showing SIX1 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing SIX1 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 SIX1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for SIX1 Genetics and Cytogenetics in Oncology and Haematology
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SIX1

    Intellectual Property
    for SIX1 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for SIX1 gene:
    Search GeneIP for patents involving SIX1

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



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    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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