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Aliases for WDR4 Gene

Aliases for WDR4 Gene

  • WD Repeat Domain 4 2 3 5
  • WD Repeat-Containing Protein 4 3 4
  • TRNA (Guanine-N(7)-)-Methyltransferase Non-Catalytic Subunit WDR4 3
  • TRM82 TRNA Methyltransferase 82 Homolog (S. Cerevisiae) 2
  • TRNA (Guanine-N(7)-)-Methyltransferase Subunit WDR4 3
  • TRM82 TRNA Methyltransferase 82 Homolog 3
  • TRMT82 3
  • TRM82 3

External Ids for WDR4 Gene

Previous GeneCards Identifiers for WDR4 Gene

  • GC21M040810
  • GC21M043157
  • GC21M043136
  • GC21M044263
  • GC21M029678

Summaries for WDR4 Gene

Entrez Gene Summary for WDR4 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. 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]

GeneCards Summary for WDR4 Gene

WDR4 (WD Repeat Domain 4) is a Protein Coding gene. Diseases associated with WDR4 include Isolated Growth Hormone Deficiency, Type Ia and Nonsyndromic Deafness. Among its related pathways are Gene Expression and tRNA processing. Gene Ontology (GO) annotations related to this gene include tRNA (guanine-N7-)-methyltransferase activity.

UniProtKB/Swiss-Prot for WDR4 Gene

  • 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 changes of the catalytic subunit.

Gene Wiki entry for WDR4 Gene

Additional gene information for WDR4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for WDR4 Gene

Genomics for WDR4 Gene

GeneHancer (GH) Regulatory Elements for WDR4 Gene

Promoters and enhancers for WDR4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH21I042878 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 626.5 +0.1 117 2.8 HDGF PKNOX1 CLOCK SMAD1 MLX ARNT ARID4B NEUROD1 SIN3A DMAP1 WDR4 NDUFV3 LOC105372817 PRDM15 RRP1B U2AF1 ENSG00000233754 ENSG00000235772 ZBTB21 GC21M042796
GH21I043158 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 107.7 -283.0 -282967 7.7 HDGF PKNOX1 FOXA2 MLX ARNT ZFP64 ARID4B YBX1 DMAP1 IRF4 ENSG00000228120 WDR4 RRP1B U2AF1 ENSG00000233754 PWP2 SIK1 TRAPPC10 HSF2BP CRYAA
GH21I041952 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 60.1 +925.3 925293 4.3 HDGF PKNOX1 ARNT NEUROD1 SIN3A DMAP1 ZBTB7B POLR2B ZNF207 FOS C2CD2 PRDM15 WDR4 ENSG00000233754 ZBTB21 ZNF295-AS1 ENSG00000251778 ENSG00000227698 ENSG00000236545 UMODL1
GH21I043724 Promoter/Enhancer 2.3 FANTOM5 Ensembl ENCODE dbSUPER 61.8 -853.3 -853310 17.4 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 WDR4 RRP1B U2AF1 PWP2 ENSG00000233754 HSF2BP TRPM2 SIK1 PDXK TRAPPC10
GH21I042923 Enhancer 1.3 Ensembl ENCODE 99.7 -49.4 -49439 11.9 HDGF PKNOX1 CLOCK ARNT ARID4B SIN3A ZNF2 ZBTB7B POLR2B ZNF766 U2AF1 WDR4 ENSG00000233754 RRP1B NDUFV3 SIK1 ENSG00000224100 PKNOX1 FRGCA UBASH3A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around WDR4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the WDR4 gene promoter:

Genomic Locations for WDR4 Gene

Genomic Locations for WDR4 Gene
chr21:42,843,080-42,879,589
(GRCh38/hg38)
Size:
36,510 bases
Orientation:
Minus strand
chr21:44,263,204-44,299,678
(GRCh37/hg19)

Genomic View for WDR4 Gene

Genes around WDR4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
WDR4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for WDR4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for WDR4 Gene

Proteins for WDR4 Gene

  • Protein details for WDR4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P57081-WDR4_HUMAN
    Recommended name:
    tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4
    Protein Accession:
    P57081
    Secondary Accessions:
    • A8KA58
    • B2RCA3
    • B4DNQ7
    • D3DSK3
    • Q9BVM5
    • Q9HCR3

    Protein attributes for WDR4 Gene

    Size:
    412 amino acids
    Molecular mass:
    45490 Da
    Quaternary structure:
    • Forms a heterodimer with the catalytic subunit METTL1.

    Alternative splice isoforms for WDR4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for WDR4 Gene

Post-translational modifications for WDR4 Gene

No Post-translational modifications

No data available for DME Specific Peptides for WDR4 Gene

Domains & Families for WDR4 Gene

Gene Families for WDR4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for WDR4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P57081

UniProtKB/Swiss-Prot:

WDR4_HUMAN :
  • Belongs to the WD repeat TRM82 family.
Family:
  • Belongs to the WD repeat TRM82 family.
genes like me logo Genes that share domains with WDR4: view

Function for WDR4 Gene

Molecular function for WDR4 Gene

UniProtKB/Swiss-Prot 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 changes of the catalytic subunit.

Phenotypes From GWAS Catalog for WDR4 Gene

Gene Ontology (GO) - Molecular Function for WDR4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15861136
GO:0008176 contributes_to tRNA (guanine-N7-)-methyltransferase activity IDA 12403464
genes like me logo Genes that share ontologies with WDR4: view
genes like me logo Genes that share phenotypes with WDR4: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for WDR4 Gene

Localization for WDR4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for WDR4 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for WDR4 gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 2
mitochondrion 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleus (3)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for WDR4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 15861136
GO:0005654 nucleoplasm HDA,IDA 16780588
GO:0005829 cytosol IDA,IBA --
GO:0043527 tRNA methyltransferase complex IDA 12403464
genes like me logo Genes that share ontologies with WDR4: view

Pathways & Interactions for WDR4 Gene

genes like me logo Genes that share pathways with WDR4: view

Pathways by source for WDR4 Gene

UniProtKB/Swiss-Prot P57081-WDR4_HUMAN

  • Pathway: tRNA modification; N(7)-methylguanine-tRNA biosynthesis.

Gene Ontology (GO) - Biological Process for WDR4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006400 tRNA modification IDA 15861136
GO:0008033 tRNA processing IEA --
GO:0036265 RNA (guanine-N7)-methylation IEA --
GO:0106004 tRNA (guanine-N7)-methylation IEA --
genes like me logo Genes that share ontologies with WDR4: view

No data available for SIGNOR curated interactions for WDR4 Gene

Drugs & Compounds for WDR4 Gene

No Compound Related Data Available

Transcripts for WDR4 Gene

Unigene Clusters for WDR4 Gene

WD repeat domain 4:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for WDR4 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14
SP1: - - - -
SP2: - - - - -
SP3: - - -
SP4: - -
SP5:
SP6: -

Relevant External Links for WDR4 Gene

GeneLoc Exon Structure for
WDR4
ECgene alternative splicing isoforms for
WDR4

Expression for WDR4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for WDR4 Gene

Protein differential expression in normal tissues from HIPED for WDR4 Gene

This gene is overexpressed in Lung (56.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for WDR4 Gene



NURSA nuclear receptor signaling pathways regulating expression of WDR4 Gene:

WDR4

SOURCE GeneReport for Unigene cluster for WDR4 Gene:

Hs.248815

Evidence on tissue expression from TISSUES for WDR4 Gene

  • Lung(4.2)
  • Nervous system(2.3)
genes like me logo Genes that share expression patterns with WDR4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for WDR4 Gene

Orthologs for WDR4 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for WDR4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia WDR4 33 34
  • 98.86 (n)
dog
(Canis familiaris)
Mammalia WDR4 33 34
  • 83 (n)
cow
(Bos Taurus)
Mammalia WDR4 33 34
  • 81.46 (n)
mouse
(Mus musculus)
Mammalia Wdr4 33 16 34
  • 79.92 (n)
rat
(Rattus norvegicus)
Mammalia Wdr4 33
  • 79.87 (n)
oppossum
(Monodelphis domestica)
Mammalia WDR4 34
  • 69 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia WDR4 34
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves WDR4 33 34
  • 62.43 (n)
lizard
(Anolis carolinensis)
Reptilia WDR4 34
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.4956 33
African clawed frog
(Xenopus laevis)
Amphibia wdr4-prov 33
zebrafish
(Danio rerio)
Actinopterygii LOC100536637 33
  • 53.14 (n)
FP017279.3 34
  • 43 (a)
OneToMany
wdr4 34
  • 43 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta wuho 34
  • 24 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea Y102E9.2 34
  • 21 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TRM82 34 36
  • 20 (a)
OneToOne
Species where no ortholog for WDR4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for WDR4 Gene

ENSEMBL:
Gene Tree for WDR4 (if available)
TreeFam:
Gene Tree for WDR4 (if available)

Paralogs for WDR4 Gene

Pseudogenes.org Pseudogenes for WDR4 Gene

genes like me logo Genes that share paralogs with WDR4: view

No data available for Paralogs for WDR4 Gene

Variants for WDR4 Gene

Sequence variations from dbSNP and Humsavar for WDR4 Gene

SNP ID Clin Chr 21 pos Variation AA Info Type
rs1000098449 -- 42,858,561(-) G/C intron_variant
rs1000102023 -- 42,842,962(-) C/G downstream_transcript_variant
rs1000102522 -- 42,872,825(-) T/C intron_variant
rs1000164003 -- 42,867,205(-) A/C intron_variant
rs1000232962 -- 42,868,127(-) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for WDR4 Gene

Variant ID Type Subtype PubMed ID
nsv834105 CNV loss 17160897
nsv587659 CNV loss 21841781
nsv587657 CNV gain 21841781
nsv1135908 CNV deletion 24896259
esv3647095 CNV loss 21293372
esv3647094 CNV loss 21293372
esv3584478 CNV gain 24956385
esv3568210 CNV loss 25503493
esv2723579 CNV deletion 23290073
esv2723578 CNV deletion 23290073
esv2723577 CNV deletion 23290073
esv2723576 CNV deletion 23290073
esv2666871 CNV deletion 23128226

Variation tolerance for WDR4 Gene

Residual Variation Intolerance Score: 60.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.03; 90.06% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for WDR4 Gene

Human Gene Mutation Database (HGMD)
WDR4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
WDR4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for WDR4 Gene

Disorders for WDR4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for WDR4 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
isolated growth hormone deficiency, type ia
  • ighd1a
nonsyndromic deafness
  • nonsyndromic hearing loss
- elite association - COSMIC cancer census association via MalaCards
Search WDR4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for WDR4

genes like me logo Genes that share disorders with WDR4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for WDR4 Gene

Publications for WDR4 Gene

  1. Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. (PMID: 12403464) Alexandrov A … Phizicky EM (RNA (New York, N.Y.) 2002) 2 3 4 22 58
  2. Isolation and characterization of a human chromosome 21q22.3 gene (WDR4) and its mouse homologue that code for a WD-repeat protein. (PMID: 10950928) Michaud J … Scott HS (Genomics 2000) 3 4 22 58
  3. The tRNA methylase METTL1 is phosphorylated and inactivated by PKB and RSK in vitro and in cells. (PMID: 15861136) Cartlidge RA … Cohen P (The EMBO journal 2005) 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for WDR4 Gene

Sources for WDR4 Gene

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