Human Gene WDR4 (uc002zci.4)
  Description: Homo sapiens WD repeat domain 4 (WDR4), transcript variant 2, mRNA.
RefSeq Summary (NM_033661): 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. This gene is excluded as a candidate for a form of nonsyndromic deafness (DFNB10), but is still a candidate for other disorders mapped to 21q22.3 as well as for the development of Down syndrome phenotypes. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, May 2012].
Transcript (Including UTRs)
   Position: hg19 chr21:44,263,190-44,299,693 Size: 36,504 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr21:44,270,159-44,299,605 Size: 29,447 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr21:44,263,190-44,299,693)mRNA (may differ from genome)Protein (412 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: WDR4_HUMAN
DESCRIPTION: RecName: Full=tRNA (guanine-N(7)-)-methyltransferase subunit WDR4; AltName: Full=WD repeat-containing protein 4;
FUNCTION: Required for the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. In the complex, it is required to stabilize and induce conformational change of the catalytic subunit.
PATHWAY: tRNA modification; N(7)-methylguanine-tRNA biosynthesis.
SUBUNIT: Forms a complex with METTL1.
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Belongs to the WD repeat TRM82 family.
SIMILARITY: Contains 4 WD repeats.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): WDR4
CDC HuGE Published Literature: WDR4
Positive Disease Associations: Hypertension
Related Studies:
  1. Hypertension
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: WDR4
Diseases sorted by gene-association score: growth hormone deficiency, isolated, type ia (4), nonsyndromic deafness (1), seckel syndrome (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D001564 Benzo(a)pyrene
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • C009505 4,4'-diaminodiphenylmethane
  • C075773 4-phenylbutyric acid
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D000082 Acetaminophen
  • D016604 Aflatoxin B1
  • D003300 Copper
  • D003375 Coumestrol
  • D004958 Estradiol
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.65 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 143.33 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -34.3088-0.390 Picture PostScript Text
3' UTR -57.82210-0.275 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR017986 - WD40_repeat_dom

Pfam Domains:
PF00400 - WD domain, G-beta repeat

SCOP Domains:
50952 - Soluble quinoprotein glucose dehydrogenase
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Prolyl oligopeptidase, N-terminal domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - Dipeptidyl peptidase IV/CD26, N-terminal domain

ModBase Predicted Comparative 3D Structure on P57081
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008176 tRNA (guanine-N7-)-methyltransferase activity

Biological Process:
GO:0006400 tRNA modification
GO:0008033 tRNA processing
GO:0036265 RNA (guanine-N7)-methylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0043527 tRNA methyltransferase complex


-  Descriptions from all associated GenBank mRNAs
  BC018866 - Homo sapiens WD repeat domain 4, mRNA (cDNA clone IMAGE:3141631).
AJ243912 - Homo sapiens short form mRNA for WD repeat domain 4 protein (WDR4 gene).
JD140296 - Sequence 121320 from Patent EP1572962.
JD339761 - Sequence 320785 from Patent EP1572962.
JD161722 - Sequence 142746 from Patent EP1572962.
AK056343 - Homo sapiens cDNA FLJ31781 fis, clone NT2RI2008233, highly similar to WD repeat protein 4.
BC006341 - Homo sapiens WD repeat domain 4, mRNA (cDNA clone MGC:12826 IMAGE:4080041), complete cds.
BC001074 - Homo sapiens WD repeat domain 4, mRNA (cDNA clone MGC:2706 IMAGE:2821060), complete cds.
AJ243913 - Homo sapiens long form mRNA for WD repeat domain 4 protein (WDR4 gene).
AK292923 - Homo sapiens cDNA FLJ77214 complete cds, highly similar to Homo sapiens WD repeat domain 4 (WDR4), transcript variant 2, mRNA.
AK298015 - Homo sapiens cDNA FLJ55518 complete cds, highly similar to WD repeat protein 4.
KJ902154 - Synthetic construct Homo sapiens clone ccsbBroadEn_11548 WDR4 gene, encodes complete protein.
KJ898287 - Synthetic construct Homo sapiens clone ccsbBroadEn_07681 WDR4 gene, encodes complete protein.
AK315008 - Homo sapiens cDNA, FLJ95938, highly similar to Homo sapiens WD repeat domain 4 (WDR4), transcript variant 3, mRNA.
DQ892967 - Synthetic construct clone IMAGE:100005597; FLH191251.01X; RZPDo839B0377D WD repeat domain 4 (WDR4) gene, encodes complete protein.
DQ896215 - Synthetic construct Homo sapiens clone IMAGE:100010675; FLH191247.01L; RZPDo839B0367D WD repeat domain 4 (WDR4) gene, encodes complete protein.
AB590172 - Synthetic construct DNA, clone: pFN21AE1441, Homo sapiens WDR4 gene for WD repeat domain 4, without stop codon, in Flexi system.
CU674538 - Synthetic construct Homo sapiens gateway clone IMAGE:100016931 5' read WDR4 mRNA.
DQ597158 - Homo sapiens piRNA piR-35224, complete sequence.
DQ601189 - Homo sapiens piRNA piR-39255, complete sequence.
CU675357 - Synthetic construct Homo sapiens gateway clone IMAGE:100019283 5' read WDR4 mRNA.
JD157881 - Sequence 138905 from Patent EP1572962.
JD493259 - Sequence 474283 from Patent EP1572962.
JD406797 - Sequence 387821 from Patent EP1572962.
JD090625 - Sequence 71649 from Patent EP1572962.
JD462210 - Sequence 443234 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P57081 (Reactome details) participates in the following event(s):

R-HSA-6782286 METTL1:WDR4 methylates guanosine-46 of tRNA(Phe) yielding 7-methylguanosine-46
R-HSA-6782315 tRNA modification in the nucleus and cytosol
R-HSA-72306 tRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: A8KA58, B2RCA3, B4DNQ7, D3DSK3, NM_033661, NP_001247406, P57081, Q9BVM5, Q9HCR3, uc002zci.3, WDR4_HUMAN
UCSC ID: uc002zci.4
RefSeq Accession: NM_033661
Protein: P57081 (aka WDR4_HUMAN)
CCDS: CCDS13691.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_033661.4
exon count: 12CDS single in 3' UTR: no RNA size: 1554
ORF size: 1239CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2568.00frame shift in genome: no % Coverage: 98.91
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.