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WDR46 Gene

protein-coding   GIFtS: 50
GCID: GC06M033246

WD Repeat Domain 46

(Previous name: chromosome 6 open reading frame 11)
(Previous symbol: C6orf11)
  Search for WDR46
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
WD Repeat Domain 461 2     Chromosome 6 Open Reading Frame 111
C6orf111 2 3     FP2212
BING42 3     UTP72
WD Repeat-Containing Protein BING42 3     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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for WDR46 Gene:
WDR46 (WD repeat domain 46) is a protein-coding gene.

Gene Wiki entry for WDR46 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 at NCBI GenBank:
NC_000006.11  NT_007592.16  NT_113891.3  NT_167245.2  NT_167247.2  NT_167248.2  NC_018917.2  
Regulatory elements:
   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 Chromatin IP Primers for WDR46

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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-,NT_113891.2 4,690,690-4,701,118      Chr6-,NT_167245 4,528,202-4,538,630      Chr6-,NT_167248 4,479,119-4,489,547     
Chr6-,NT_167247 4,720,654-4,731,048     

(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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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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

Explore proteomics data for WDR46 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See WDR46 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

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

    ENSEMBL proteins: 
     ENSP00000363746   ENSP00000405568  

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    Search eBioscience for ELISAs for WDR46 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    WDR: WD repeat domain containing

    4 InterPro protein domains:
     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 domain: IPB012952 BING4

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


    Find genes that share domains with WDR46           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0005515protein binding ----
    GO:0044822poly(A) RNA binding IDA--
         
    Find genes that share ontologies with WDR46           About GenesLikeMe


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

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for WDR46
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    miRNA
    Products:
        
    miRTarBase miRNAs that target WDR46:
    hsa-mir-324-3p (MIRT043007), hsa-let-7a-5p (MIRT052562), hsa-mir-345-5p (MIRT042736), hsa-mir-339-5p (MIRT042749), hsa-mir-760 (MIRT036786)

    Block miRNA regulation of human, mouse, rat WDR46 using miScript Target Protectors
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for WDR46


    (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 COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2

    Gene Ontology (GO): 1 cellular component term:    About this table

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

    Find genes that share ontologies with WDR46           About GenesLikeMe


    (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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for WDR46
    Interactions:

        Search GeneGlobe Interaction Network for WDR46

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

    Selected Interacting proteins for WDR46 (O152133 ENSP000003637464) via UniProtKB, MINT, STRING, and/or I2D (see all 154)
    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:    About this table

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

    Find genes that share ontologies with WDR46           About GenesLikeMe



    (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 WDR46



    (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,
    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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    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
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000473611 ENST00000461951 ENST00000374617(uc011dra.2 uc003ods.3 uc010juo.1)
    ENST00000489905 ENST00000444176 ENST00000488944 ENST00000477718 ENST00000468157
    ENST00000481025
    miRNA
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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat WDR46
      QuantiFast Probe-based Assays in human, mouse, rat WDR46

    Additional mRNA sequence: 

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

    22 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  DT.100822234 

    Selected AceView cDNA sequences (see all 447):

    BQ954602 CR597118 F06119 BX951566 BM810952 CR604572 CA310883 AI610795 
    AL579741 AA776348 AI421287 CR621799 BX283822 NM_005452 BX439421 CA430256 
    AL557009 BG574075 AL526244 AA306917 BG119460 AI866952 CR615634 BU633065 

    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™, 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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    WDR46 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GATGAGGAAC
    WDR46 Expression
    About this image


    WDR46 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Brain (Nervous System)    fully expand to see all 8 entries
             Cerebral Cortex
             Septum   
    WDR46 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    WDR46 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.520063
        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)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for WDR46 gene from Selected species (see all 19)    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 52.35(n)
    45.33(a)
      31732  NM_132213.1  NP_572441.1 
    worm
    (Caenorhabditis elegans)
    Secernentea wdr-461 wdr-46 52.78(n)
    48.71(a)
      178185  NM_069957.5  NP_502358.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes UTP7(YER082C)4
    UTP71
    Nucleolar protein, component of the small subunit (SSU) more4
    UTP71
    47.1(n)1
    44.02(a)1
      5(325936-324272)4
    8568151, 4  NP_011005.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT3G105301 AT3G10530 48.54(n)
    39.24(a)
      820218  NM_111889.3  NP_187664.2 
    rice
    (Oryza sativa)
    Liliopsida Os01g01831001 Os01g0183100 49.44(n)
    43.34(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)
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      --

    (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 WDR46 (see all 264)    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--------
    rs3761843611,2
    C--33247509(+) GAAGAC/TGGGCC 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

    HapMap Linkage Disequilibrium report for WDR46 (33246880 - 33257304 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for WDR46:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2731890CNV Deletion23290073
    nsv830634CNV Loss17160897
    nsv830635CNV Loss17160897
    nsv5249CNV Loss18451855
    esv29761CNV Loss19812545

    Site Specific Mutation Identification with PCR Assays
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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.)
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    OMIM gene information: 611440    OMIM disorders: --


    Find genes that share disorders with WDR46           About GenesLikeMe

    Genetic Association Database (GAD): WDR46
    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)
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    PubMed articles for WDR46 gene, integrated from 10 sources (see all 19):
    (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. (J. Mol. Biol. 1998)
    2. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PubMed id 19851445)1, 4 Barcellos L.F....Criswell L.A. (PLoS Genet. 2009)
    3. Large-scale cDNA transfection screening for genes related to cancer development and progression. (PubMed id 15498874)1, 2 Wan D....Gu J. (Proc. Natl. Acad. Sci. U.S.A. 2004)
    4. 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. (Genome Res. 2004)
    5. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (Nature 2003)
    6. 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. (Eur. J. Immunol. 1998)
    7. Nucleolar scaffold protein, WDR46, determines the granular compartmental localization of nucleolin and DDX21. (PubMed id 23848194)1 Hirai Y....Takeyasu K. (amp 2013)
    8. 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. (amp 2012)
    9. The proteomic analysis of endogenous FAT10 substrates identifies p62/SQSTM1 as a substrate of FAT10ylation. (PubMed id 22797925)1 Aichem A....Groettrup M. (J. Cell. Sci. 2012)
    10. Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription. (PubMed id 22586326)1 Tsai Y.C.... Cristea I.M. (Mol. Cell. Proteomics 2012)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 9277 HGNC: 13923 AceView: C6orf11 Ensembl:ENSG00000227057 euGenes: HUgn9277
    ECgene: WDR46 H-InvDB: WDR46

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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