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WDR88 Gene

protein-coding   GIFtS: 45
GCID: GC19P033622

WD Repeat Domain 88

(Previous name: PQQ repeat and WD repeat domain containing)
(Previous symbol: PQWD)
  Search for WDR88
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 881 2
PQWD1 2 3
PQQ Repeat And WD Repeat Domain Containing1 2
PQQ Repeat And WD Repeat-Containing Protein2 3
WD Repeat-Containing Protein 882

External Ids:    HGNC: 269991   Entrez Gene: 1262482   Ensembl: ENSG000001663597   UniProtKB: Q6ZMY63   

Export aliases for WDR88 gene to outside databases

Previous GC identifers: GC19P038316 GC19P030125


(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 WDR88 Gene:
WDR88 (WD repeat domain 88) is a protein-coding 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_000019.9  NT_011109.17  NC_018930.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the WDR88 gene promoter:
         SRF   GATA-3   SRF (504 AA)   GATA-1   GATA-2   FOXC1   FOXO4   HSF2   Ik-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidWDR88 promoter sequence
   Search Chromatin IP Primers for WDR88

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat WDR88


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

Entrez Gene cytogenetic band: 19q13.11   Ensembl cytogenetic band:  19q13.11   HGNC cytogenetic band: 19q13.11

WDR88 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
WDR88 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P033622:  view genomic region     (about GC identifiers)

Start:
33,622,996 bp from pter      End:
33,666,705 bp from pter
Size:
43,710 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, 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: WDR88_HUMAN, Q6ZMY6 (See protein sequence)
Recommended Name: WD repeat-containing protein 88  
Size: 472 amino acids; 52621 Da
Sequence caution: Sequence=AAH31227.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: Q8NEF8
Alternative splicing: 2 isoforms:  Q6ZMY6-1   Q6ZMY6-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for WDR88: NX_Q6ZMY6

Explore proteomics data for WDR88 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See WDR88 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_775750.3  
    ENSEMBL proteins: 
     ENSP00000467383   ENSP00000355148   ENSP00000348129  

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    (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

    Selected InterPro protein domains (see all 8):
     IPR019775 WD40_repeat_CS
     IPR002372 PQQ_repeat
     IPR011047 Quinonprotein_ADH-like_supfam
     IPR018391 PQQ_beta_propeller_repeat
     IPR001680 WD40_repeat

    Graphical View of Domain Structure for InterPro Entry Q6ZMY6

    ProtoNet protein and cluster: Q6ZMY6

    1 Blocks protein domain: IPB002372 Bacterial quinoprotein

    UniProtKB/Swiss-Prot: WDR88_HUMAN, Q6ZMY6
    Similarity: Contains 7 WD repeats


    Find genes that share domains with WDR88           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): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    Find genes that share ontologies with WDR88           About GenesLikeMe


    Animal Models:
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    (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
    cytosol3
    nucleus2
    extracellular1
    golgi apparatus1

    (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 WDR88
    Interactions:

        Search GeneGlobe Interaction Network for WDR88

    STRING Interaction Network Preview (showing 5 interactants - click image to see 14)

    Selected Interacting proteins for WDR88 (Q6ZMY63 ENSP000003481294) via UniProtKB, MINT, STRING, and/or I2D (see all 14)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBCP0CG483, ENSP000003448184I2D: score=1 STRING: ENSP00000344818
    ADRM1ENSP000002530034STRING: ENSP00000253003
    PSMA4ENSP000000444624STRING: ENSP00000044462
    PSMD13ENSP000003969374STRING: ENSP00000396937
    PSMD9ENSP000002618174STRING: ENSP00000261817
    About this table

    (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 WDR88



    (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 WDR88 gene: 
    NM_173479.3  

    Unigene Cluster for WDR88:

    WD repeat domain 88
    Hs.211046  [show with all ESTs]
    Unigene Representative Sequence: AK131444
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000592765 ENST00000361680 ENST00000355868(uc002nui.3)
    miRNA
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      QuantiFast Probe-based Assays in human, mouse, rat WDR88

    Additional mRNA sequence: 

    AK131444.1 BC031227.1 

    2 DOTS entries:

    DT.95359841  DT.75128521 

    9 AceView cDNA sequences:

    AI982942 AI825732 BC031227 BI826378 BI460849 BI560259 NM_173479 AK131444 
    BX109140 

    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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    WDR88 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGAAGCCTGA
    WDR88 Expression
    About this image

    WDR88 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    WDR88 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.211046
        Custom PCR Arrays for WDR88
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for WDR88

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for WDR88 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Wdr881 , 5 WD repeat domain 881, 5 74.65(n)1
    67.74(a)1
      7 (21.21 cM)5
    3846051  XM_001480144.31  XP_001480194.21 
     352362335 
    chicken
    (Gallus gallus)
    Aves WDR881 WD repeat domain 88 62.96(n)
    55.82(a)
      101752101  XM_004944228.1  XP_004944285.1 
    lizard
    (Anolis carolinensis)
    Reptilia WDR886
    WD repeat domain 88
    50(a)
    1 ↔ 1
    GL343469.1(664453-672445)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia wdr881 WD repeat domain 88 58.68(n)
    48.16(a)
      101732918  XM_004913556.1  XP_004913613.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes TUP16
    General repressor of transcription, forms complex ...
    14(a)
    1 ↔ 1
    III(260311-262452) YCR084C


    ENSEMBL Gene Tree for WDR88 (if available)
    TreeFam Gene Tree for WDR88 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for WDR88 gene
    7 SIMAP similar genes for WDR88 using alignment to 2 protein entries:     WDR88_HUMAN (see all proteins):
    WSB1    PF20    POC1B    WDR38    WDR5    WDR83
    DKFZp762M0115

    Find genes that share paralogs with WDR88           About GenesLikeMe



    (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 WDR88 (see all 1027)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0358924
    A breast cancer sample4--see VAR_0358922 D H mis40--------
    rs1883606951,2
    --33621957(+) GCACTC/TTGGGA 1 -- us2k10--------
    rs1931565781,2
    --33621967(+) AGGCCA/GAGGCC 1 -- us2k10--------
    rs1837067881,2
    --33622128(+) GAACCC/TTGGAG 1 -- us2k10--------
    rs1386628871,2
    C--33622186(+) TGACA-/AGAG  
            
    GACTC
    1 -- us2k10--------
    rs711761981,2
    C--33622188(+) ACAGAGAGA/-  
            
    CTCTT
    1 -- us2k11Minor allele frequency- -:0.00NA 2
    rs346590051,2
    C--33622223(+) AAAAA-/A/GGAAGG 1 -- us2k11NA 2
    rs1489016851,2
    --33622323(+) GCTGTC/TATCTG 1 -- us2k10--------
    rs790968331,2
    C--33622368(+) TTGGGC/GTTGTG 1 -- us2k10--------
    rs104114041,2
    H--33622374(+) TTGTGA/GCAGAT 1 -- us2k1 tfbs34Minor allele frequency- G:0.00NS EA 418

    HapMap Linkage Disequilibrium report for WDR88 (33622996 - 33666705 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for WDR88:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2677868CNV Deletion23128226
    esv2657217CNV Deletion23128226
    esv2718468CNV Deletion23290073
    nsv828525CNV Loss20364138
    nsv833808CNV Loss17160897

    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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    Find genes that share disorders with WDR88           About GenesLikeMe

    Genetic Association Database (GAD): WDR88

    Export disorders for WDR88 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 WDR88 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with WDR88)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    2. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)
    3. TLR8-dependent TNF-(alpha) overexpression in Fanconi anemia group C cells. (PubMed id 19850743)1 Vanderwerf S.M....Bagby G.C. (Blood 2009)
    4. The consensus coding sequences of human breast and colorectal cancers. (PubMed id 16959974)2 Sjoeblom T.... Velculescu V.E. (Science 2006)
    5. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)2 Grimwood J.... Lucas S.M. (Nature 2004)
    6. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    7. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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)
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    Entrez Gene: 126248 HGNC: 26999 AceView: LOC126248 Ensembl:ENSG00000166359 euGenes: HUgn126248
    ECgene: WDR88 H-InvDB: WDR88

    (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 WDR88 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 WDR88 gene:
    Search GeneIP for patents involving WDR88

    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
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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