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WDR90 Gene

protein-coding   GIFtS: 41
GCID: GC16P000699

WD Repeat Domain 90

(Previous names: chromosome 16 open reading frame 17, chromosome 16 open...)
(Previous symbols: C16orf17, C16orf15, C16orf16, C16orf19, C16orf18)
  Search for WDR90
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 901 2     Chromosome 16 Open Reading Frame 161
C16orf151 2 3     Chromosome 16 Open Reading Frame 171
C16orf161 2 3     Chromosome 16 Open Reading Frame 181
C16orf171 2 3     Chromosome 16 Open Reading Frame 191
C16orf181 2 3     WD Repeat-Containing Protein 902
C16orf191 2 3     KIAA19243
Chromosome 16 Open Reading Frame 151     

External Ids:    HGNC: 269601   Entrez Gene: 1973352   Ensembl: ENSG000001619967   UniProtKB: Q96KV73   

Export aliases for WDR90 gene to outside databases

Previous GC identifers: GC16P000644 GC16P000645 GC16P000624


(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 WDR90 Gene:
WDR90 (WD repeat domain 90) is a protein-coding gene. An important paralog of this gene is WDR16.


(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_000016.9  NT_010393.17  NC_018927.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the WDR90 gene promoter:
         STAT1   STAT1beta   AP-2alpha isoform 2   LCR-F1   STAT1alpha   E47   HEN1   Ik-2   AP-2alpha   AP-2alphaA   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for WDR90

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat WDR90


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

Entrez Gene cytogenetic band: 16p13.3   Ensembl cytogenetic band:  16p13.3   HGNC cytogenetic band: 16p13.3

WDR90 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
WDR90 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P000699:  view genomic region     (about GC identifiers)

Start:
699,311 bp from pter      End:
717,833 bp from pter
Size:
18,523 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: WDR90_HUMAN, Q96KV7 (See protein sequence)
Recommended Name: WD repeat-containing protein 90  
Size: 1748 amino acids; 187437 Da
Sequence caution: Sequence=AAK61239.1; Type=Erroneous gene model prediction; Sequence=BAB67817.1;
Type=Miscellaneous discrepancy; Note=Intron retention; Sequence=BAC03575.1; Type=Miscellaneous discrepancy;
Note=Unlikely isoform. Aberrant splicing; Sequence=BAC04225.1; Type=Erroneous initiation; Note=Translation
N-terminally extended; Sequence=BAC04225.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact;
Sequence=BAD18654.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact; Sequence=EAW85775.1;
Type=Erroneous gene model prediction;
Secondary accessions: Q0VA87 Q0VA88 Q6P048 Q6ZMS1 Q6ZTH1 Q8N202 Q8N221 Q8NBB8 Q96PW4 Q96S18
Alternative splicing: 5 isoforms:  Q96KV7-1   Q96KV7-10   Q96KV7-3   Q96KV7-7   Q96KV7-5   (No experimental confirmation available. Ref.6 (AAI21186) sequence differs from that shown due to a frameshift in position 697)

Explore the universe of human proteins at neXtProt for WDR90: NX_Q96KV7

Explore proteomics data for WDR90 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See WDR90 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_660337.3  
    ENSEMBL proteins: 
     ENSP00000448122   ENSP00000293879   ENSP00000448603   ENSP00000447435   ENSP00000449576  
     ENSP00000322808   ENSP00000450308   ENSP00000447915  

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    WDR90 Assay Products:

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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 7):
     IPR019775 WD40_repeat_CS
     IPR021717 Nucleoporin_Nup160
     IPR011047 Quinonprotein_ADH-like_supfam
     IPR001680 WD40_repeat
     IPR017986 WD40_repeat_dom

    Graphical View of Domain Structure for InterPro Entry Q96KV7

    ProtoNet protein and cluster: Q96KV7

    UniProtKB/Swiss-Prot: WDR90_HUMAN, Q96KV7
    Similarity: Contains 21 WD repeats


    Find genes that share domains with WDR90           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 WDR90           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for WDR90:
     Increased G2M DNA content 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for WDR90
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for WDR90


    (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
    nucleus2
    cytosol1
    mitochondrion1
    peroxisome1
    plasma membrane1

    (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 WDR90
    Interactions:

        Search GeneGlobe Interaction Network for WDR90

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

    Selected Interacting proteins for WDR90 (ENSP000002938794) via UniProtKB, MINT, STRING, and/or I2D (see all 15)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ADRM1ENSP000002530034STRING: ENSP00000253003
    PSMA4ENSP000000444624STRING: ENSP00000044462
    PSMD13ENSP000003969374STRING: ENSP00000396937
    PSMD9ENSP000002618174STRING: ENSP00000261817
    ELP3ENSP000002563984STRING: ENSP00000256398
    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 WDR90



    (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 WDR90 gene (2 alternative transcripts): 
    NM_145294.4  NM_153239.2  

    Unigene Cluster for WDR90:

    WD repeat domain 90
    Hs.511903  [show with all ESTs]
    Unigene Representative Sequence: NM_145294
    Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 25):
    ENST00000552943(uc002cig.1 uc002cih.1 uc002cij.1) ENST00000549091(uc002cii.1)
    ENST00000549648 ENST00000420061 ENST00000293879 ENST00000550593 ENST00000552648
    ENST00000546516(uc002cik.1 uc002cim.1) ENST00000547407 ENST00000552728(uc002cil.1)
    ENST00000548859 ENST00000552683 ENST00000548844 ENST00000550739 ENST00000549024(uc002cin.1)
    ENST00000550902 ENST00000546923 ENST00000548603
    miRNA
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    SwitchGear 3'UTR luciferase reporter plasmidWDR90 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for WDR90
    Predesigned siRNA for gene silencing in human, mouse, rat WDR90
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    GenScript: all cDNA clones in your preferred vector: WDR90 (NM_145294)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat WDR90
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      QuantiTect SYBR Green Assays in human, mouse, rat WDR90
      QuantiFast Probe-based Assays in human, mouse, rat WDR90

    Additional mRNA sequence: 

    AK092719.1 AK131510.1 BC062304.1 BC065836.1 BC121185.1 BC121186.1 

    12 DOTS entries:

    DT.97765830  DT.113593  DT.97827433  DT.75100565  DT.40311238  DT.120714617  DT.102836289  DT.70103140 
    DT.100677433  DT.121151992  DT.95343921  DT.97778329 

    Selected AceView cDNA sequences (see all 136):

    BQ898698 BU070227 BM703391 AI870474 BC065836 NM_153239 AW015205 CD518315 
    AI339873 AI634727 AA906707 AA262616 BM706508 AA448183 AB067511 AK092719 
    CA432568 BU734188 AA468572 AI797967 BX492640 BX492629 AI493534 CA843007 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for WDR90 (see all 13)    About this scheme

    ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14a · 14b · 14c ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^
    SP1:                                                                                                                                                            
    SP2:                                                                                                                                                            
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                              -                 -                                                                           

    ExUns: 21a · 21b ^ 22a · 22b ^ 23 ^ 24 ^ 25 ^ 26 ^ 27a · 27b ^ 28 ^ 29 ^ 30a · 30b ^ 31 ^ 32a · 32b · 32c ^ 33 ^ 34a · 34b · 34c ^ 35a · 35b ^ 36
    SP1:        -                                                                                                                       -                     
    SP2:                                                                                                                                -                     
    SP3:                                                                                                                                                      
    SP4:                                                                                                                                                      
    SP5:                                                                                                                                                      


    ECgene alternative splicing isoforms for WDR90

    (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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    WDR90 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGCATTTATT
    WDR90 Expression
    About this image

    WDR90 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    WDR90 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.511903
        Custom PCR Arrays for WDR90
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for WDR90

    (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 WDR90 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Wdr901 , 5 WD repeat domain 901, 5 75.62(n)1
    71.99(a)1
      17 (12.94 cM)5
    1066181  NM_001163766.11  NP_001157238.11 
     258447715 
    chicken
    (Gallus gallus)
    Aves WDR906
    WD repeat domain 90
    60(a)
    1 ↔ 1
    14(13096738-13106562)
    lizard
    (Anolis carolinensis)
    Reptilia WDR906
    WD repeat domain 90
    51(a)
    1 ↔ 1
    GL343263.1(974625-1029808)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia wdr901 WD repeat domain 90 60.97(n)
    56.32(a)
      100036617  NM_001097176.1  NP_001090645.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wdr901 WD repeat domain 90 55.28(n)
    49.65(a)
      100038787  XM_003201346.2  XP_003201394.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG100646
    --
    18(a)
    1 → many
    3L(6958360-6960997)


    ENSEMBL Gene Tree for WDR90 (if available)
    TreeFam Gene Tree for WDR90 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for WDR90 gene
    WDR162  

    Find genes that share paralogs with WDR90           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 WDR90 (see all 820)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs22728631,2
    C,F--699019(+) GGCAGG/AGTGAG 1 -- us2k15Minor allele frequency- A:0.14NA WA EA 362
    rs1916687641,2
    --699233(+) GCAACC/TCTGGA 1 -- us2k10--------
    rs22728641,2
    C,F--699236(+) ACCCTG/CGAGGC 1 -- us2k11Minor allele frequency- C:0.09EA 1494
    rs734874141,2
    C--699326(+) GTGGCC/ACCGTT 1 -- us2k11Minor allele frequency- A:0.50WA 2
    rs734874151,2
    C,F--699384(+) GCGCGG/AAGGCC 1 -- ut512Minor allele frequency- A:0.15WA EA 238
    rs129340861,2
    C,F,A--699456(+) CGAGGG/ATCCCG 1 -- int1 ese35Minor allele frequency- A:0.25NA WA EA 362
    rs1168017851,2
    F--699667(+) GAGCCC/GCGGCT 1 -- int11Minor allele frequency- G:0.13WA 118
    rs2016985071,2
    C--699940(+) GCCCCC/GGCTGC 1 -- int11Minor allele frequency- G:0.00EU 473
    rs1997193861,2
    C--699962(+) GTGCTG/TTCGGT 1 -- int10--------
    rs2001231731,2
    C--700046(+) CGCCAA/GCTACA 2 N S mis11Minor allele frequency- G:0.00EU 1307

    HapMap Linkage Disequilibrium report for WDR90 (699311 - 717833 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for WDR90 (see all 35):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv1011191CNV Deletion20482838
    esv2750220CNV Deletion23290073
    esv2750221CNV Deletion23290073
    esv2750223CNV Deletion23290073
    esv2750222CNV Deletion23290073
    esv2422427CNV Duplication17116639
    dgv2489n71CNV Loss21882294
    dgv2475n71CNV Loss21882294
    nsv904760CNV Loss21882294
    dgv334n27CNV Loss19166990

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing WDR90
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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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    (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 WDR90 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with WDR90)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins. (PubMed id 11572484)1, 2, 3 Nagase T.... Ohara O. (DNA Res. 2001)
    2. Sequence, structure and pathology of the fully annotated terminal 2 Mb of the short arm of human chromosome 16. (PubMed id 11157797)1, 2, 3 Daniels R.J....Higgs D.R. (Hum. Mol. Genet. 2001)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network. (PubMed id 23446634)1 Chen Z....Reiner A.P. (Hum. Mol. Genet. 2013)
    5. The sequence and analysis of duplication-rich human chromosome 16. (PubMed id 15616553)2 Martin J.... Pennacchio L.A. (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. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (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: 197335 HGNC: 26960 AceView: LOC197336 Ensembl:ENSG00000161996 euGenes: HUgn197335
    ECgene: WDR90 H-InvDB: WDR90

    (According to HUGE)
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    HUGE: KIAA1924

    (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 WDR90 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 WDR90 gene:
    Search GeneIP for patents involving WDR90

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



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