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WDR38 Gene

protein-coding   GIFtS: 38
GCID: GC09P127615

WD Repeat Domain 38

  Search for WDR38
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 381 2
WD Repeat-Containing Protein 382

External Ids:    HGNC: 237451   Entrez Gene: 4015512   Ensembl: ENSG000001369187   UniProtKB: Q5JTN63   

Export aliases for WDR38 gene to outside databases

Previous GC identifers: GC09P126657 GC09P097229


(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 WDR38 Gene:
WDR38 (WD repeat domain 38) is a protein-coding gene. An important paralog of this gene is NLE1.


(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:
NC_000009.12  NT_008470.20  NC_018920.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the WDR38 gene promoter:
         MyoD   AP-2gamma   GATA-2   PPAR-gamma1   CP2   AP-2beta   PPAR-gamma2   AP-2alpha   CBF(2)   AP-2alphaA   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for WDR38

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat WDR38


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

Entrez Gene cytogenetic band: 9q33.3   Ensembl cytogenetic band:  9q33.3   HGNC cytogenetic band: 9q33.3

WDR38 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
WDR38 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P127615:  view genomic region     (about GC identifiers)

Start:
127,615,755 bp from pter      End:
127,620,160 bp from pter
Size:
4,406 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: WDR38_HUMAN, Q5JTN6 (See protein sequence)
Recommended Name: WD repeat-containing protein 38  
Size: 314 amino acids; 34312 Da
Secondary accessions: A0PK24

Explore the universe of human proteins at neXtProt for WDR38: NX_Q5JTN6

Explore proteomics data for WDR38 at MOPED


See WDR38 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (4 alternative transcripts): 
NP_001038941.1  NP_001263303.1  NP_001263304.1  NP_001263305.1  

ENSEMBL proteins: 
 ENSP00000362677  

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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

5 InterPro protein domains:
 IPR019775 WD40_repeat_CS
 IPR001680 WD40_repeat
 IPR020472 G-protein_beta_WD-40_rep
 IPR017986 WD40_repeat_dom
 IPR015943 WD40/YVTN_repeat-like_dom

Graphical View of Domain Structure for InterPro Entry Q5JTN6

ProtoNet protein and cluster: Q5JTN6

UniProtKB/Swiss-Prot: WDR38_HUMAN, Q5JTN6
Similarity: Contains 7 WD repeats


Find genes that share domains with WDR38           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 WDR38           About GenesLikeMe


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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
cytosol2
nucleus2
extracellular1
peroxisome1

(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 WDR38
Interactions:

    Search GeneGlobe Interaction Network for WDR38

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

Selected Interacting proteins for WDR38 (ENSP000003626774) via UniProtKB, MINT, STRING, and/or I2D (see all 68)
InteractantInteraction Details
GeneCardExternal ID(s)
TADA3ENSP000003076844STRING: ENSP00000307684
TRRAPENSP000003477334STRING: ENSP00000347733
CCDC101ENSP000003161144STRING: ENSP00000316114
TADA2AENSP000002253964STRING: ENSP00000225396
TADA2BENSP000003080224STRING: ENSP00000308022
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(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
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  Browse compounds at ApexBio 

Browse Tocris compounds for WDR38



(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 WDR38 gene (4 alternative transcripts): 
NM_001045476.2  NM_001276374.1  NM_001276375.1  NM_001276376.1  

Unigene Cluster for WDR38:

WD repeat domain 38
Hs.343383  [show with all ESTs]
Unigene Representative Sequence: NM_001276374
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000373574(uc011lzn.2 uc011lzo.2 uc011lzp.2 uc004box.3)

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Additional mRNA sequence: 

BC127949.1 BC150645.1 BC171828.1 BC171830.1 BC171837.1 

4 DOTS entries:

DT.423949  DT.91749793  DT.95099885  DT.92002937 

14 AceView cDNA sequences:

AA478768 BF513871 BM981761 BI769504 BF515709 AI915356 AA478887 BX108090 
BM975209 AI139841 BU101832 BF941899 AI190548 AA867995 

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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WDR38 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GCCAGGACTC
WDR38 Expression
About this image

WDR38 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

WDR38 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.343383
    Custom PCR Arrays for WDR38
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for WDR38

(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 WDR38 gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Wdr381 , 5 WD repeat domain 381, 5 78.31(n)1
76.61(a)1
  2 (24.42 cM)5
766461  NM_029687.31  NP_083963.11 
 389974765 
tropical clawed frog
(Xenopus tropicalis)
Amphibia wdr381 WD repeat domain 38 59.6(n)
53(a)
  100493075  XM_002941647.2  XP_002941693.1 
zebrafish
(Danio rerio)
Actinopterygii wdr381 WD repeat domain 38 55.22(n)
50.51(a)
  550366  NM_001017672.1  NP_001017672.1 
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RSA46
WD-repeat protein involved in ribosome biogenesis;...
16(a)
1 → many
III(240805-242352) YCR072C


ENSEMBL Gene Tree for WDR38 (if available)
TreeFam Gene Tree for WDR38 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for WDR38 gene
NLE12  WDR832  POC1B2  WDR52  ATG16L12  SNRNP402  WDR5B2  PAFAH1B12  
SMU12  DAW12  ATG16L22  POC1A2  
18 SIMAP similar genes for WDR38 using alignment to 4 protein entries:     WDR38_HUMAN (see all proteins):
POC1B    PF20    WDR83    WSB1    DAW1    DKFZp434D199
WDR5B    GNB2    BUB3    DKFZp762M0115    NLE1    WDR88
WDR5    PLRG1    SNRNP40    WDR86    WDR61    WDSUB1

Find genes that share paralogs with WDR38           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 WDR38 (see all 219)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 9 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs676298891,2
C--97232127(+) CCCCT-/C/TC  
        
CCTTT
4 -- int11NA 2
rs109864641,2
C--127613733(+) TGATCT/CGCCTG 4 -- us2k1 tfbs34Minor allele frequency- C:0.32NA WA EA 360
rs1509011181,2
C--127613755(+) CAAAGA/TGCTAG 4 -- us2k10--------
rs1921453471,2
--127613814(+) TTGACA/GTGCGT 4 -- us2k10--------
rs1383991211,2
--127613817(+) ACATGC/TGTAGC 4 -- us2k10--------
rs751848831,2
F--127613890(+) AAAAGC/TCAGCG 4 -- us2k11Minor allele frequency- T:0.01NA 120
rs120012381,2
C,F,A,H--127614051(+) ATGATC/GCTCCG 4 -- us2k19Minor allele frequency- G:0.15NS EA NA CSA WA 640
rs727633561,2
C--127614117(+) GGTTTC/TGACCC 4 -- us2k10--------
rs48370021,2
C,F,H--127614169(+) ACAAGG/TTCTAC 4 -- us2k15Minor allele frequency- T:0.01NS NA 208
rs1928567371,2
--127614206(+) GGGCTG/TGGGAA 4 -- us2k10--------

HapMap Linkage Disequilibrium report for WDR38 (127615755 - 127620160 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for WDR38:    About this table    
Variant IDTypeSubtypePubMed ID
nsv831721CNV Gain17160897

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing WDR38
DNA2.0 Custom Variant and Variant Library Synthesis for WDR38

(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 WDR38 gene integrated from 10 sources:
(articles sorted by number of sources associating them with WDR38)
    Utopia: connect your pdf to the dynamic
world of online information

  1. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)2 Humphray S.J.... Dunham I. (Nature 2004)
  2. 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)
  3. 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: 401551 HGNC: 23745 AceView: LOC401551 Ensembl:ENSG00000136918 euGenes: HUgn401551
ECgene: WDR38 H-InvDB: WDR38

(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 WDR38 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 WDR38 gene:
Search GeneIP for patents involving WDR38

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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 Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for WDR38
 Browse SwitchGear 3'UTR luciferase reporter plasmids for WDR38
 Browse SwitchGear Promoter luciferase reporter plasmids for WDR38
 Search ThermoFisher Antibodies for WDR38
 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat WDR38
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for WDR38
 inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for WDR38
 Search LSBio for Antibodies for WDR38
Customized transgenic rodents for:
 Humanization
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 Off-target effect monitoring
 Translational medicine
 Tissue-specific gene expresssion
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 Browse compounds at ApexBio
 Search Addgene for plasmids for WDR38
  Search eBioscience for proteins for WDR38
  Search eBioscience for elisas for WDR38
  eBioscience FlowRNA Probe Sets
       
GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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