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

SIX5 Gene

protein-coding   GIFtS: 57
GCID: GC19M046268

SIX Homeobox 5

(Previous names: sine oculis homeobox (Drosophila) homolog 5, sine oculis...)
(Previous symbol: DMAHP)
  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)
About This Section

Aliases
SIX Homeobox 51 2     Sine Oculis Homeobox (Drosophila) Homolog 51
DMAHP1 2 3 5     Sine Oculis Homeobox Homolog 5 (Drosophila)1
Sine Oculis Homeobox Homolog 52 3     Dystrophia Myotonica-Associated Homeodomain Protein2
DM Locus-Associated Homeodomain Protein2 3     Homeobox Protein SIX52
BOR22 5     

External Ids:    HGNC: 108911   Entrez Gene: 1479122   Ensembl: ENSG000001770457   OMIM: 6009635   UniProtKB: Q8N1963   

Export aliases for SIX5 gene to outside databases

Previous GC identifers: GC19U990028 GC19M050959 GC19M042696


(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 SIX5 Gene:
The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the
regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene.
Mutations in this gene are a cause of branchiootorenal syndrome type 2. (provided by RefSeq, Jul 2009)

GeneCards Summary for SIX5 Gene: 
SIX5 (SIX homeobox 5) is a protein-coding gene. Diseases associated with SIX5 include six5-related branchiootorenal spectrum disorders, and congenital myotonic dystrophy. GO annotations related to this gene include sequence-specific DNA binding and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is SIX4.

UniProtKB/Swiss-Prot: SIX5_HUMAN, Q8N196
Function: Transcription factor that is thought to be involved in regulation of organogenesis. May be involved in
determination and maintenance of retina formation. Binds a 5'-GGTGTCAG-3' motif present in the ARE regulatory
element of ATP1A1. Binds a 5'-TCA[AG][AG]TTNC-3' motif present in the MEF3 element in the myogenin promoter, and
in the IGFBP5 promoter (By similarity). Thought to be regulated by association with Dach and Eya proteins, and
seems to be coactivated by EYA1, EYA2 and EYA3 (By similarity)

Gene Wiki entry for SIX5 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000019.9  NC_018930.2  NT_011109.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SIX5 gene promoter:
         SRF   Sp1   SRF (504 AA)   CUTL1   Nkx2-5   Tal-1beta   Roaz   AREB6   ITF-2   RSRFC4   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSIX5 promoter sequence
   Search SABiosciences Chromatin IP Primers for SIX5

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SIX5


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

Entrez Gene cytogenetic band: 19q13.32   Ensembl cytogenetic band:  19q13.32   HGNC cytogenetic band: 19q13.32

SIX5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SIX5 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M046268:  view genomic region     (about GC identifiers)

Start:
46,268,043 bp from pter      End:
46,272,497 bp from pter
Size:
4,455 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SIX5_HUMAN, Q8N196 (See protein sequence)
Recommended Name: Homeobox protein SIX5  
Size: 739 amino acids; 74562 Da
Subunit: Probably binds DNA dimer. Interacts with EYA3, and probably EYA1 and EYA2 (By similarity)
Subcellular location: Cytoplasm. Nucleus
Developmental stage: At the begin of fourth week of development detected in cytoplasm of somite cells, and at the
end of fourth week is accumulated in the nucleus. Between the sixth and eighth week of development detected in
the nucleus of limb bud cells
Sequence caution: Sequence=AAH33204.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing; Sequence=AK074826;
Type=Erroneous termination; Positions=721; Note=Translated as Glu;

Explore the universe of human proteins at neXtProt for SIX5: NX_Q8N196

Explore proteomics data for SIX5 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q8N196

  • SIX5 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SIX5 Protein Expression
    REFSEQ proteins: NP_787071.2  
    ENSEMBL proteins: 
     ENSP00000316842   ENSP00000453239   ENSP00000453189  

    Human Recombinant Protein Products for SIX5: 
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    OriGene Purified Protein for SIX5
    OriGene Protein Over-expression Lysate for SIX5
    OriGene MassSpec for SIX5 
    OriGene Custom Protein Services for SIX5
    GenScript Custom Purified and Recombinant Proteins Services for SIX5
    Novus Biologicals SIX5 Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for SIX5 

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005737cytoplasm IDA--

    SIX5 for ontologies           About GeneDecksing



    SIX5 Antibody Products: 
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    Assay Products for SIX5: 
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    Cloud-Clone Corp. ELISAs for SIX5 
    Cloud-Clone Corp. CLIAs for SIX5


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    SIX: Homeoboxes / SINE class

    3 InterPro protein domains:
     IPR017970 Homeobox_CS
     IPR001356 Homeodomain
     IPR009057 Homeodomain-like

    Graphical View of Domain Structure for InterPro Entry Q8N196

    ProtoNet protein and cluster: Q8N196

    UniProtKB/Swiss-Prot: SIX5_HUMAN, Q8N196
    Similarity: Belongs to the SIX/Sine oculis homeobox family
    Similarity: Contains 1 homeobox DNA-binding domain


    SIX5 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,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SIX5_HUMAN, Q8N196
    Function: Transcription factor that is thought to be involved in regulation of organogenesis. May be involved in
    determination and maintenance of retina formation. Binds a 5'-GGTGTCAG-3' motif present in the ARE regulatory
    element of ATP1A1. Binds a 5'-TCA[AG][AG]TTNC-3' motif present in the MEF3 element in the myogenin promoter, and
    in the IGFBP5 promoter (By similarity). Thought to be regulated by association with Dach and Eya proteins, and
    seems to be coactivated by EYA1, EYA2 and EYA3 (By similarity)

         Genatlas biochemistry entry for SIX5:
    Drosophila sine oculis homolog SIX5,myotonic dystrophy (DM) locus-associated homeo box encoding gene,expressed in
    skeletal muscle,heart and brain,also expressed in eye,especially in lens epithelium,potentially involved in the
    development of adult onset cataracts frequently observed in DM,homolog to the muscle-specific transcription
    factor AREC3,inhibited in dystrophia myotonica by CTG repeat expansion in 3'-non-coding region of DMPK,abuting
    its own 5'end

         Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding ----
    GO:0003700sequence-specific DNA binding transcription factor activity IEA--
    GO:0005515protein binding IPI16713569
    GO:0043565sequence-specific DNA binding IEA--
         
    SIX5 for ontologies           About GeneDecksing


    Phenotypes:
         5 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Six5):
     endocrine/exocrine gland  homeostasis/metabolism  muscle  reproductive system  vision/eye 

    SIX5 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Six5tm1Rdd for SIX5

       inGenious Targeting Laboratory - Custom generated mouse model solutions for SIX5 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for SIX5

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SIX5 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SIX5 

    miRNA
    Products:
        
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SIX5
    8/14 QIAGEN miScript miRNA Assays for microRNAs that regulate SIX5 (see all 14):
    hsa-miR-676 hsa-miR-4255 hsa-miR-29c hsa-miR-29a hsa-miR-624* hsa-miR-133b hsa-miR-650 hsa-miR-633
    SwitchGear 3'UTR luciferase reporter plasmidSIX5 3' UTR sequence
    Inhib. RNA
    Products:
        
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for SIX5
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    Gene Editing
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    Sirion Biotech Customized adenovirus for overexpression of SIX5

    Clone
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    OriGene clones in human, mouse for SIX5 (see all 7)
    OriGene ORF clones in mouse, rat for SIX5
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: SIX5 (NM_175875)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SIX5
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SIX5
    Sirion Biotech Customized lentivirus for stable overexpression of SIX5 
                         Customized lentivirus expression plasmids for stable overexpression of SIX5 

    Cell Line
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    GenScript Custom overexpressing Cell Line Services for SIX5
    Search LifeMap BioReagents cell lines for SIX5
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SIX5


    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for SIX5

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    4 Interacting proteins for SIX5 (Q8N1961, 2, 3 ENSP000003168424) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ATXN1P542531, 2, 3, ENSP000002447694EBI-946167,EBI-930964 MINT-2878839 MINT-2878858 MINT-2855987 MINT-2878877 I2D: score=3 STRING: ENSP00000244769
    EYA3Q995043, ENSP000003629784I2D: score=3 STRING: ENSP00000362978
    HMGB1P094293, ENSP000003430404I2D: score=1 STRING: ENSP00000343040
    SRFP118313, ENSP000002653544I2D: score=2 STRING: ENSP00000265354
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0002088lens development in camera-type eye IEA--
    GO:0006351transcription, DNA-dependent IEA--
    GO:0006355regulation of transcription, DNA-dependent ----
    GO:0007286spermatid development IEA--
    GO:0008285negative regulation of cell proliferation IEA--

    SIX5 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 SIX5

    Search CenterWatch for drugs/clinical trials and news about SIX5

    (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,
    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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SIX5 gene: 
    NM_175875.4  

    Unigene Cluster for SIX5:

    SIX homeobox 5
    Hs.43314  [show with all ESTs]
    Unigene Representative Sequence: NM_175875
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000317578(uc002pdb.3) ENST00000560160 ENST00000560168
    miRNA
    Products:
         
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SIX5
    8/14 QIAGEN miScript miRNA Assays for microRNAs that regulate SIX5 (see all 14):
    hsa-miR-676 hsa-miR-4255 hsa-miR-29c hsa-miR-29a hsa-miR-624* hsa-miR-133b hsa-miR-650 hsa-miR-633
    SwitchGear 3'UTR luciferase reporter plasmidSIX5 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for SIX5
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SIX5
    Clone
    Products:
         
    OriGene clones in human, mouse for SIX5 (see all 7)
    OriGene ORF clones in mouse, rat for SIX5
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: SIX5 (NM_175875)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SIX5
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SIX5
    Sirion Biotech Customized lentivirus for stable overexpression of SIX5 
                         Customized lentivirus expression plasmids for stable overexpression of SIX5 
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for SIX5
    SABiosciences RT2 qPCR Primer Assay in human, mouse, rat SIX5
      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SIX5
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SIX5

    Additional mRNA sequence: 

    AK074826.1 BC033204.1 BC084563.1 

    4 DOTS entries:

    DT.455347  DT.100022475  DT.40229560  DT.97795215 

    24/311 AceView cDNA sequences (see all 311):

    BQ070737 BQ185710 CK299372 BU168309 BM677303 BC033204 BX419830 AI027251 
    BF873848 BM665068 M87312 NM_175875 BQ919325 BM737690 BX420052 CF136022 
    BF339767 CD676116 CD106470 BG951959 AI123378 AI659650 BI770992 U46546 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for SIX5    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b
    SP1:                              
    SP2:              -               


    ECgene alternative splicing isoforms for SIX5

    (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

    SIX5 expression in normal human tissues (normalized intensities)      SIX5 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTATGCCTCC
    SIX5 Expression
    About this image


    SIX5 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/8 selected tissues (see all 8) fully expand
     
     Brain (Nervous System)    fully expand to see all 5 entries
             Thalamus
             brain/midbrain   
     
     Neural Tube (Nervous System)    fully expand to see all 3 entries
             Metencephalon
     
     Limb (Muscoskeletal System)    fully expand to see all 2 entries
             limb/hindlimb   
     
     Eye (Sensory Organs)
             Retina
     
     Lower Urinary Tract (Urinary System)
             visceral organ   

    See SIX5 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SIX5

    SOURCE GeneReport for Unigene cluster: Hs.43314

    UniProtKB/Swiss-Prot: SIX5_HUMAN, Q8N196
    Tissue specificity: Expressed in adult but not in fetal eyes. Found in corneal epithelium and endothelium, lens
    epithelium, ciliary body epithelia, cellular layers of the retina and the sclera

        SABiosciences Custom PCR Arrays for SIX5
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SIX5
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SIX5

    (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 SIX5 gene from 4/9 species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Six51 , 5 sine oculis-related homeobox 5 homolog (Drosophila)5
    sine oculis-related homeobox 51
    85.07(n)1
    87.9(a)1
      7 (9.46 cM)5
    204751  NM_011383.11  NP_035513.11 
     190945945 
    zebrafish
    (Danio rerio)
    Actinopterygii six4.31 sine oculis homeobox homolog 4.3 48.35(n)
    42.7(a)
      65235  NM_131720.1  NP_571795.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Six46
    Six4
    31(a)
    1 → many
    3L(20781986-20785877)
    worm
    (Caenorhabditis elegans)
    Secernentea ceh-346
    unc-396
    Protein UNC-39
    36(a)
    26(a)
    possible ortholog
    possible ortholog
    V(5315513-5319577)
    V(14373389-14375887)


    ENSEMBL Gene Tree for SIX5 (if available)
    TreeFam Gene Tree for SIX5 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SIX5 gene
    SIX42  SIX22  SIX12  SIX32  SIX62  
    7 SIMAP similar genes for SIX5 using alignment to 3 protein entries:     SIX5_HUMAN (see all proteins):
    AREC3    PKNOX1    SIX1    SIX6    SIX3    SIX4
    SIX2

    SIX5 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) 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

    10/219 SNPs in SIX5 are shown (see all 219)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0329424
    Branchiootorenal syndrome 2 (BOR2)4--see VAR_0329422 A T mis40--------
    VAR_0329434
    Branchiootorenal syndrome 2 (BOR2)4--see VAR_0329432 G R mis40--------
    VAR_0329414
    Branchiootorenal syndrome 2 (BOR2)4--see VAR_0329412 A T mis40--------
    rs803564641,2,4
    C,FBranchiootorenal syndrome 2 (BOR2)4 pathogenic146459141(-) CGTGAC/TGGGTG 2 T M mis11Minor allele frequency- T:0.00NA 4338
    rs803564631,2
    Cpathogenic146459941(-) GGGGCA/GGGGGT 2 R G mis10--------
    rs803564621,2
    Cpathogenic146460148(-) TGTCCA/GCCGAG 2 T A mis10--------
    rs803564611,2
    Cpathogenic146461448(-) ACCACA/GCCTTC 2 T A mis10--------
    VAR_0329454
    ----see VAR_0329452 L V mis40--------
    rs754946881,2
    C,F--42703242(+) GCCCTA/GTATCT 1 -- us2k11Minor allele frequency- G:0.18WA 118
    rs1402645481,2
    --46457576(+) ATTGTC/TTTAAA 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for SIX5 (46268043 - 46272497 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for SIX5:    About this table     
    Variant IDTypeSubtypePubMed ID
    dgv3957n71CNV Loss21882294
    nsv912166CNV Loss21882294
    dgv3954n71CNV Loss21882294
    dgv3955n71CNV Loss21882294
    dgv3956n71CNV Loss21882294
    nsv912170CNV Loss21882294


    Human Gene Mutation Database (HGMD): SIX5
    SABiosciences Cancer Mutation PCR Assays
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    (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.)
    About This Section
    OMIM gene information: 600963   
    OMIM disorders: 610896  
    UniProtKB/Swiss-Prot: SIX5_HUMAN, Q8N196
  • Branchiootorenal syndrome 2 (BOR2) [MIM:610896]: A syndrome characterized by branchial cleft fistulas or
    cysts, sensorineural and/or conductive hearing loss, pre-auricular pits, structural defects of the outer, middle
    or inner ear, and renal malformations. Note=The disease is caused by mutations affecting the gene represented in
    this entry

  • 11 diseases for SIX5:    About MalaCards
    six5-related branchiootorenal spectrum disorders    congenital myotonic dystrophy    branchiootorenal spectrum disorders    lacrimal duct obstruction
    branchiootorenal syndrome    myotonic dystrophy type 1    myotonic dystrophy    myocardial stunning
    fragile x syndrome    myopia    cataract

    3 diseases from the University of Copenhagen DISEASES database for SIX5:
    Myotonic dystrophy     Branchiootorenal syndrome     Lacrimal duct obstruction

    SIX5 for disorders           About GeneDecksing

    6 Novoseek inferred disease relationships for SIX5 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    myotonic dystrophy 90.8 18 11526199 (2), 10332037 (1), 9241282 (1), 15201450 (1) (see all 14)
    bor syndrome 90.7 4 17637804 (1), 19215039 (1), 18177466 (1)
    testicular atrophy 61.8 2 11470409 (2)
    defect conduction 56.3 2 11726559 (1)
    conduction abnormalities 55.7 2 12397222 (1)
    cataract 39.4 4 11726559 (1), 9949207 (1)

    GeneTests: SIX5
    GeneReviews: SIX5
    Genetic Association Database (GAD): SIX5
    Human Genome Epidemiology (HuGE) Navigator: SIX5 (2 documents)

    Export disorders for SIX5 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)
    About This Section

    PubMed articles for SIX5 gene, integrated from 9 sources (see all 49):
    (articles sorted by number of sources associating them with SIX5)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A novel homeodomain-encoding gene is associated with a large CpG island interrupted by the myotonic dystrophy unstable (CTG)n repeat. (PubMed id 8595416)1, 2, 3, 9 Boucher C.A.... Johnson K.J. (1995)
    2. Characterization of the expression of DMPK and SIX5 in the human eye and implications for pathogenesis in myotonic dystrophy. (PubMed id 9949207)1, 2, 9 Winchester C.L.... Johnson K.J. (1999)
    3. Transcription factor SIX5 is mutated in patients with branchio-oto- renal syndrome. (PubMed id 17357085)1, 2, 9 Hoskins B.E.... Hildebrandt F. (2007)
    4. Six and Eya expression during human somitogenesis and MyoD gene family activation. (PubMed id 12500905)1, 2, 9 Fougerousse F....Maire P. (2002)
    5. Assessment of a polymorphism of SDK1 with hypertensio n in Japanese Individuals. (PubMed id 19851296)1, 4 Oguri M....Yamada Y. (2010)
    6. Association of genetic variants with hemorrhagic stro ke in Japanese individuals. (PubMed id 20198315)1, 4 Yoshida T....Yamada Y. (2010)
    7. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    8. 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)
    9. Functional analysis of the homeodomain protein SIX5. (PubMed id 10756185)1, 2 Harris S.E.... Johnson K.J. (2000)
    10. Expression of a homeobox gene (SIX5) in borderline ovarian tumours. (PubMed id 10823141)1, 9 Winchester C....Thomas M. (2000)

    (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)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 147912 HGNC: 10891 AceView: DMPKandSIX5andDMWD Ensembl:ENSG00000177045 euGenes: HUgn147912
    ECgene: SIX5 H-InvDB: SIX5

    (According to HUGE)
    About This Section
      --

    (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 SIX5 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SIX5 gene:
    Search GeneIP for patents involving SIX5

    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: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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