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

WDR46 Gene

protein-coding   GIFtS: 48
GCID: GC06M033246

WD repeat domain 46

(Previous name: chromosome 6 open reading frame 11 )
(Previous symbol: C6orf11)
 Explore 3 diseases affiliated with
WDR46 via our new
 Human Malady Compendium 
Biological research products
for WDR46
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
WD Repeat Domain 461 2     WD Repeat-Containing Protein BING42 3
BING41 2 3     Chromosome 6 Open Reading Frame 111
C6orf111 2 3     FP2212
UTP71 2     WD Repeat-Containing Protein 462

External Ids:    HGNC: 139231   Entrez Gene: 92772   Ensembl: ENSG000002270577   OMIM: 6114405   UniProtKB: O152133   

Export aliases for WDR46 gene to outside databases

Previous GC identifers: GC06M033355 GC06Mc33315 GC06M032988


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

Gene Wiki entry for WDR46


(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_000006.11  NC_018917.1  NT_007592.15  NT_113891.2  NT_167245.1  NT_167247.1  NT_167248.1  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the WDR46 gene promoter:
         Sp1   p53   AP-1   ATF-2   Olf-1   HNF-4alpha2   CUTL1   HNF-4alpha1   YY1   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidWDR46 promoter sequence
   Search SABiosciences Chromatin IP Primers for WDR46

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat WDR46


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

Entrez Gene cytogenetic band: 6p21.3   Ensembl cytogenetic band:  6p21.32   HGNC cytogenetic band: 6p21.3

WDR46 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
WDR46 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M033246:  view genomic region     (about GC identifiers)

Start:
33,246,880 bp from pter      End:
33,257,304 bp from pter
Size:
10,425 bases      Orientation:
minus strand

4 alternative locations:
Chr6-,ALT_REF_LOCI_3 33,224,810-33,246,271      Chr6-,ALT_REF_LOCI_2 33,168,491-33,218,102      Chr6-,ALT_REF_LOCI_5 33,332,077-33,342,471     
Chr6-,ALT_REF_LOCI_6 33,175,727-33,221,731     

(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: WDR46_HUMAN, O15213 (See protein sequence)
Recommended Name: WD repeat-containing protein 46  
Size: 610 amino acids; 68071 Da
Secondary accessions: A6NDP5 Q5HYZ0 Q5STK5 Q5STR3

Explore the universe of human proteins at neXtProt for WDR46: NX_O15213

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_O15213

  • WDR46 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001157739.1  NP_005443.3  

    ENSEMBL proteins: 
     ENSP00000363746   ENSP00000405568  

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    Uscn Proteins for WDR46

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--


    WDR46 for ontologies           About GeneDecksing



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

    WDR46 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR012952 BING4_C_dom
     IPR001680 WD40_repeat
     IPR017986 WD40_repeat_dom
     IPR015943 WD40/YVTN_repeat-like_dom

    Graphical View of Domain Structure for InterPro Entry O15213

    ProtoNet protein and cluster: O15213

    1 Blocks protein family: IPB012952 BING4

    UniProtKB/Swiss-Prot: WDR46_HUMAN, O15213
    Similarity: Contains 6 WD repeats


    (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

    miRNA
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--


    WDR46 for ontologies           About GeneDecksing


    3 GenomeRNAi human phenotypes for WDR46:
     Decreased Hepatitis C virus re  Nuclear 40S maturation defects  Nucleolar pre-40S maturation d 


    (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:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for WDR46

    STRING Interaction Network Preview (showing 5 interactants - click image to see 20)

    5/112 Interacting proteins for WDR46 (O152133 ENSP000003637464) via UniProtKB, MINT, STRING, and/or I2D (see all 112)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4AP628053I2D: score=2 
    HIST1H4BP628053I2D: score=2 
    HIST1H4CP628053I2D: score=2 
    HIST1H4DP628053I2D: score=2 
    HIST1H4EP628053I2D: score=2 
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--


    WDR46 for ontologies           About GeneDecksing



    (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 WDR46
    Search CenterWatch for drugs/clinical trials and news about WDR46 

    (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 WDR46 gene (2 alternative transcripts): 
    NM_001164267.1  NM_005452.5  

    Unigene Cluster for WDR46:

    WD repeat domain 46
    Hs.520063  [show with all ESTs]
    Unigene Representative Sequence: NM_005452
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000467874 ENST00000473611 ENST00000461951 ENST00000374617(uc011dra.2 uc003ods.3 uc010juo.1)
    ENST00000489905 ENST00000444176 ENST00000488944 ENST00000477718 ENST00000468157
    ENST00000481025

    miRNA
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    Inhib. RNA
    Products:
         
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    OriGene shRNA RFP: WDR46
    OriGene siRNA: WDR46
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    Clone
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat WDR46

    Additional cDNA sequence: 

    AF447870.1 AK292171.1 AK292616.1 AK297925.1 AK298151.1 AK308534.1 AK311388.1 AK315616.1 
    BC000388.2 

    21 DOTS entries:

    DT.214300  DT.100822238  DT.100822237  DT.100822221  DT.121364774  DT.92457212  DT.100770860  DT.95253275 
    DT.121364635  DT.100822225  DT.100841651  DT.121364785  DT.121364791  DT.100662443  DT.100822223  DT.121364685 
    DT.98083365  DT.100030751  DT.100836115  DT.100838589  DT.121364744 

    24/447 AceView cDNA sequences (see all 447):

    BM851796 CA416809 BX951566 CR597118 AL527887 AA776348 AI610795 AI421287 
    AL579741 CR615634 BX332248 BX353559 AL526244 BG250391 CB161305 BE502046 
    NM_005452 BG283791 F06119 BQ954602 BM810952 BU633065 BX283822 BC000388 

    GeneLoc Exon Structure


    (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

    WDR46 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GATGAGGAAC

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

    About this image
    See WDR46 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for WDR46

    SOURCE GeneReport for Unigene cluster: Hs.520063
        SABiosciences Custom PCR Arrays for WDR46
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for WDR46

    (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 eukaryotes.

    Orthologs for WDR46 gene from 8/30 species (see all 30)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Wdr461 , 5 WD repeat domain 461, 5 83.5(n)1
    85.53(a)1
      17 (17.98 cM)5
    573151  NM_020603.21  NP_065628.11 
     339406605 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.71662 Transcribed sequence with weak similarity to protein more 75.58(n)    BX737105.1 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc637932 hypothetical protein MGC63793 73.33(n)   393596  BC056828.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG22601 CG2260 52.52(n)
    44.93(a)
      31732  NM_132213.1  NP_572441.1 
    worm
    (Caenorhabditis elegans)
    Secernentea wdr-461 Protein WDR-46 52.05(n)
    46.27(a)
      178185  NM_069957.4  NP_502358.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes UTP7(YER082C)4
    UTP71
    Nucleolar protein, component of the small subunit (SSU) more4
    Utp7p1
    46.32(n)1
    42.86(a)1
      5(325936-324272)4
    8568151, 4  NP_011005.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT3G105301 transducin/WD40 domain-containing protein 48.22(n)
    38.99(a)
      820218  NM_111889.3  NP_187664.2 
    rice
    (Oryza sativa)
    Liliopsida Os01g01831001 hypothetical protein 49.41(n)
    43.58(a)
      4325333  NM_001048759.1  NP_001042224.1 


    ENSEMBL Gene Tree for WDR46 (if available)
    TreeFam Gene Tree for WDR46 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (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

    10/224 NCBI SNPs in WDR46 are shown (see all 224    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs24751,2
    C--33247107(+) GNCTTC/TGCCTC 4 A syn12Minor allele frequency- T:0.00MN NA 186
    rs2009618441,2
    --33247134(+) TGAAGC/GCTCTG 4 S R mis10--------
    rs1496727001,2
    C,--33247189(+) AGAGTA/GAGAAG 2 -- int10--------
    rs31851801,2
    C--33247280(-) GAGGAA/CCACAG 4 E D mis11Minor allele frequency- C:0.00NA 2
    rs1999471601,2
    --33247290(+) CATCCA/GTGACC 4 T M mis10--------
    rs1455998931,2
    C,--33247333(+) GCTGCA/GGCCCT 4 R C mis10--------
    rs1898844751,2
    C,--33247434(+) GTCAGA/GGAACT 2 -- int10--------
    rs726544971,2
    C,F,--33247595(+) ACCTCG/AGCCAG 4 /A syn13Minor allele frequency- A:0.00NS NA EU 6631
    rs1428502841,2
    C--33247606(+) GGCTCG/ATGGGT 4 /R /* stg11Minor allele frequency- A:0.00NA 4548
    rs726544981,2
    C,F,--33247685(+) GAGGGT/CAGCAC 2 -- int11Minor allele frequency- C:0.00NS 730

    HapMap Linkage Disequilibrium report for WDR46 (33246880 - 33257304 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for WDR46
         1 CNV: 64478

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

    WDR46 for disorders           About GeneDecksing

    OMIM gene information: 611440    OMIM disorders: --

    3 diseases for WDR46:    About MalaCards
    systemic lupus erythematosus    lupus erythematosus    malaria

    Human Genome Epidemiology (HuGE) Navigator: WDR46 (2 documents)

    Export disorders for WDR46 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 WDR46 gene, integrated from 9 sources (see all 18):
    (articles sorted by number of sources associating them with WDR46)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. TAPASIN, DAXX, RGL2, HKE2 and four new genes (BING 1, 3 to 5) form a dense cluster at the centromeric end of the MHC. (PubMed id 9545376)1, 2, 3 Herberg J.A.... Trowsdale J. (1998)
    2. Large-scale cDNA transfection screening for genes related to cancer development and progression. (PubMed id 15498874)1, 2 Wan D....Gu J. (2004)
    3. 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)
    4. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (2003)
    5. Genomic analysis of the Tapasin gene, located close to the TAP loci in the MHC. (PubMed id 9521053)1, 3 Herberg J.A.... Trowsdale J. (1998)
    6. WDR46 is a Genetic Risk Factor for Aspirin-Exacerbated Respiratory Disease in a Korean Population. (PubMed id 22754713)1 Pasaje C.F....Shin H.D. (2012)
    7. The proteomic analysis of endogenous FAT10 substrates identifies p62/SQSTM1 as a substrate of FAT10ylation. (PubMed id 22797925)1 Aichem A....Groettrup M. (2012)
    8. Functional proteomics establishes the interaction of S IRT7 with chromatin remodeling complexes and expands its role in regulation of R NA polymerase I transcription. (PubMed id 22586326)1 Tsai Y.C....Cristea I.M. (2012)
    9. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    10. High-density SNP screening of the major histocompatib ility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PubMed id 19851445)1 Barcellos L.F....Criswell L.A. (2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    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: 9277 HGNC: 13923 AceView: C6orf11 Ensembl:ENSG00000227057 euGenes: HUgn9277
    ECgene: WDR46 H-InvDB: WDR46

    (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 WDR46 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 WDR46 gene:
    Search GeneIP for patents involving WDR46

    GeneCards and IP:
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    GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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