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WDR34 Gene

protein-coding   GIFtS: 49
GCID: GC09M131395

WD Repeat Domain 34

  See WDR34-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)
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Aliases
WD Repeat Domain 341 2
SRTD112 5
DIC52
FAP1332
bA216B9.32
WD Repeat-Containing Protein 342

External Ids:    HGNC: 282961   Entrez Gene: 898912   Ensembl: ENSG000001193337   OMIM: 6133635   UniProtKB: Q96EX33   

Export aliases for WDR34 gene to outside databases

Previous GC identifers: GC09M126772 GC09M128475 GC09M130435 GC09M101007


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for WDR34 Gene:
This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of
approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation
of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular
processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. Defects in this
gene are a cause of short-rib thoracic dysplasia 11 with or without polydactyly. (provided by RefSeq, Mar 2014)

GeneCards Summary for WDR34 Gene:
WDR34 (WD repeat domain 34) is a protein-coding gene. Diseases associated with WDR34 include short-rib thoracic dysplasia 11 with or without polydactyly, and short-rib thoracic dysplasia 2 with or without polydactyly. An important paralog of this gene is DNAI1.

UniProtKB/Swiss-Prot: WDR34_HUMAN, Q96EX3
Function: Acts as a negative regulator of the Toll-like and IL-1R receptor signaling pathways. Inhibits the
MAP3K7-induced NF-kappa-B activation pathway. Inhibits MAP3K7 phosphorylation at 'Thr-184' and 'Thr-187' upon
Il-1 beta stimulation




(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_000009.11  NC_018920.2  NT_008470.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the WDR34 gene promoter:
         AP-1   ATF-2   HSF1 (long)   RelA   NF-kappaB   c-Rel   HSF1short   c-Jun   NF-kappaB1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidWDR34 promoter sequence
   Search Chromatin IP Primers for WDR34

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat WDR34


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

Entrez Gene cytogenetic band: 9q34.11   Ensembl cytogenetic band:  9q34.11   HGNC cytogenetic band: 9q34.11

WDR34 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
WDR34 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M131395:  view genomic region     (about GC identifiers)

Start:
131,395,940 bp from pter      End:
131,419,129 bp from pter
Size:
23,190 bases      Orientation:
minus 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: WDR34_HUMAN, Q96EX3 (See protein sequence)
Recommended Name: WD repeat-containing protein 34  
Size: 536 amino acids; 57801 Da
Subunit: Interacts (via the WD domains) with MAP3K7 and TAB3. Interacts (via WD domains) with TAB2 (via
C-terminus). Interacts (via WD domains) with TRAF6 (via TRAF-type domains)
Secondary accessions: Q5VXV4 Q9BV46

Explore the universe of human proteins at neXtProt for WDR34: NX_Q96EX3

Explore proteomics data for WDR34 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys361
  • Modification sites at PhosphoSitePlus

  • See WDR34 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_443076.2  
    ENSEMBL proteins: 
     ENSP00000361800   ENSP00000411370   ENSP00000415421  

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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

    3 InterPro protein domains:
     IPR001680 WD40_repeat
     IPR017986 WD40_repeat_dom
     IPR015943 WD40/YVTN_repeat-like_dom

    Graphical View of Domain Structure for InterPro Entry Q96EX3

    ProtoNet protein and cluster: Q96EX3

    UniProtKB/Swiss-Prot: WDR34_HUMAN, Q96EX3
    Similarity: Contains 5 WD repeats


    Find genes that share domains with WDR34           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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: WDR34_HUMAN, Q96EX3
    Function: Acts as a negative regulator of the Toll-like and IL-1R receptor signaling pathways. Inhibits the
    MAP3K7-induced NF-kappa-B activation pathway. Inhibits MAP3K7 phosphorylation at 'Thr-184' and 'Thr-187' upon
    Il-1 beta stimulation

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    Find genes that share ontologies with WDR34           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for WDR34:
     Decreased viability with pacli 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for WDR34
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    miRNA
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    miRTarBase miRNAs that target WDR34:
    hsa-mir-221-3p (MIRT046904)

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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 UniProtKB/Swiss-Prot
    WDR34_HUMAN, Q96EX3: Cytoplasm
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular2
    cytoskeleton1
    cytosol1
    lysosome1
    mitochondrion1
    nucleus1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IEA--

    Find genes that share ontologies with WDR34           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 WDR34
    Interactions:

        Search GeneGlobe Interaction Network for WDR34

    STRING Interaction Network Preview (showing 5 interactants - click image to see 15)

    Selected Interacting proteins for WDR34 (Q96EX32, 3 ENSP000003618004) via UniProtKB, MINT, STRING, and/or I2D (see all 20)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MAPK6Q166592, 3MINT-8262176 I2D: score=2 
    MAP3K7O433183I2D: score=1 
    TAB2Q9NYJ83I2D: score=1 
    TAB3Q8N5C83I2D: score=1 
    TRAF6Q9Y4K33I2D: score=1 
    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 WDR34



    (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 WDR34 gene: 
    NM_052844.3  

    Unigene Cluster for WDR34:

    WD repeat domain 34
    Hs.495240  [show with all ESTs]
    Unigene Representative Sequence: BM479044
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000372715(uc004bvq.1) ENST00000483181 ENST00000480613 ENST00000473486
    ENST00000451652(uc011mbi.2) ENST00000419989
    miRNA
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      QuantiTect SYBR Green Assays in human, mouse, rat WDR34
      QuantiFast Probe-based Assays in human, mouse, rat WDR34

    Additional mRNA sequence: 

    AK302098.1 BC001614.1 BC011874.2 

    Selected DOTS entries (see all 32):

    DT.315083  DT.100649581  DT.100847609  DT.101970090  DT.100847619  DT.75122514  DT.100847610  DT.100847612 
    DT.100847608  DT.100847622  DT.75198478  DT.100847603  DT.92452531  DT.121201303  DT.121201304  DT.92452529 
    DT.97776651  DT.100847623  DT.121201387  DT.97862136  DT.100847599  DT.100847607  DT.100847620  DT.100847598 

    Selected AceView cDNA sequences (see all 571):

    CA432295 AA027965 BX097489 CR621430 AW249989 CR605861 CR594160 AA040863 
    AI784427 CR604643 AA595541 CR625055 CR611062 BM008530 CR626799 AI275203 
    CR591802 AW002892 BE881379 CR615609 CR605290 AI473608 AI954975 AA329499 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for WDR34 (see all 14)    About this scheme

    ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c · 4d · 4e ^ 5a · 5b · 5c ^ 6a · 6b · 6c · 6d ^ 7a · 7b · 7c ^ 8a · 8b ·
    SP1:                                                        -                 -     -     -           -     -                                                   
    SP2:                                                        -                 -     -     -           -     -     -                                             
    SP3:                                                        -                 -     -     -           -     -     -                                             
    SP4:                                                        -                 -     -     -     -     -     -                                                   
    SP5:                                                        -                 -     -     -     -     -     -                                                   

    ExUns: 8c ^ 9
    SP1:            
    SP2:            
    SP3:            
    SP4:            
    SP5:            


    ECgene alternative splicing isoforms for WDR34

    (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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    WDR34 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTGCAGGCCC
    WDR34 Expression
    About this image

    WDR34 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    WDR34 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.495240

    UniProtKB/Swiss-Prot: WDR34_HUMAN, Q96EX3
    Tissue specificity: Expressed in several cell lines (at protein level)

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    In Situ
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    (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.

    Orthologs for WDR34 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Wdr341 , 5 WD repeat domain 341, 5 81.46(n)1
    83.15(a)1
      2 (21.04 cM)5
    718201  NM_001008498.21  NP_001008498.21 
     300315465 
    chicken
    (Gallus gallus)
    Aves WDR341 WD repeat domain 34 65.32(n)
    64.24(a)
      417211  XM_415494.4  XP_415494.2 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia wdr341 WD repeat domain 34 61.51(n)
    63.97(a)
      448417  NM_001006745.1  NP_001006746.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BG304270.12   -- 71.64(n)    BG304270.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG139306
    Dic61B6
    Dynein intermediate chain at 61B
    13(a)
    12(a)
    many → 1
    many → 1
    3L(1670407-1672727)
    3L(149679-152589)


    ENSEMBL Gene Tree for WDR34 (if available)
    TreeFam Gene Tree for WDR34 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for WDR34 gene
    DNAI12  DYNC1I12  DYNC1I22  WDR782  

    Find genes that share paralogs with WDR34           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 WDR34 (see all 596)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1465622251,2
    C,F--131396514(+) CCCAGA/GGGCAG 2 P S mis11Minor allele frequency- G:0.00NA 4524
    rs2000522391,2
    --131396527(+) GCAAAA/TACCAA 2 V syn10--------
    rs2017845481,2
    --131396550(+) GGACCA/GGCGCA 2 R W mis10--------
    rs2012022951,2
    --131396551(+) GACCAA/GCGCAC 2 R syn10--------
    rs1862364781,2
    C--131396567(+) ACAGAC/TACTTG 2 Y C mis10--------
    rs1468175841,2
    C--131396647(+) CCAGCG/ACTCAG 2 /S syn11Minor allele frequency- A:0.00NA 4538
    rs22980461,2
    C,F--131396771(-) GACCCG/AGGAGG 1 -- int11Minor allele frequency- A:0.02EA 120
    rs758504531,2
    C--131396795(+) TTGGTC/GCTCTC 1 -- int10--------
    rs557600031,2
    C,F--131396849(+) ACACGG/AGTCTC 1 -- int12Minor allele frequency- A:0.03WA 120
    rs562580871,2
    C--131397040(+) GGGCCC/TGCAGG 2 Q R mis10--------

    HapMap Linkage Disequilibrium report for WDR34 (131395940 - 131419129 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for WDR34 (see all 15):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv1002903CNV Deletion20482838
    esv2739075CNV Deletion23290073
    esv2677232CNV Deletion23128226
    nsv820577CNV Deletion20802225
    esv2436971CNV Deletion19546169
    esv1498928CNV Deletion17803354
    nsv825103CNV Loss20364138
    nsv825097CNV Loss20364138
    dgv1236n67CNV Loss20364138
    esv2591544CNV Loss19546169

    Human Gene Mutation Database (HGMD): WDR34
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing WDR34
    DNA2.0 Custom Variant and Variant Library Synthesis for WDR34

    (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: 613363   
    OMIM disorders: 615633  
    3 diseases for WDR34:    
    About MalaCards
    short-rib thoracic dysplasia 11 with or without polydactyly    short-rib thoracic dysplasia 2 with or without polydactyly    asphyxiating thoracic dystrophy


    Find genes that share disorders with WDR34           About GenesLikeMe


    Export disorders for WDR34 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 WDR34 gene, integrated from 10 sources (see all 15):
    (articles sorted by number of sources associating them with WDR34)
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    1. WDR34 is a novel TAK1-associated suppressor of the IL-1R/TLR3/TLR4- induced NF-kappaB activation pathway. (PubMed id 19521662)1, 2, 3 Gao D.... Chen D.Y. (Cell. Mol. Life Sci. 2009)
    2. Mutations in the gene encoding IFT dynein complex component WDR34 cause Jeune asphyxiating thoracic dystrophy. (PubMed id 24183451)1, 3 Schmidts M....Mitchison H.M. (Am. J. Hum. Genet. 2013)
    3. A unified taxonomy for ciliary dyneins. (PubMed id 21953912)1, 3 Hom E.F....King S.M. (Cytoskeleton (Hoboken) 2011)
    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. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)1, 2 Humphray S.J.... Dunham I. (Nature 2004)
    6. WDR34 mutations that cause short-rib polydactyly syndrome type III/severe asphyxiating thoracic dysplasia reveal a role for the NF-I_B pathway in cilia. (PubMed id 24183449)1 Huber C....Cormier-Daire V. (Am. J. Hum. Genet. 2013)
    7. Genetic variants associated with disordered eating. (PubMed id 23568457)1 Wade T.D....Martin N.G. (Int J Eat Disord 2013)
    8. Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error. (PubMed id 24144296)1 Cheng C.Y....Baird P.N. (Am. J. Hum. Genet. 2013)
    9. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)
    10. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)

    (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: 89891 HGNC: 28296 AceView: WDR34 Ensembl:ENSG00000119333 euGenes: HUgn89891
    ECgene: WDR34 H-InvDB: WDR34

    (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 WDR34 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 WDR34 gene:
    Search GeneIP for patents involving WDR34

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



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