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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 Seckel Syndrome 1. Among its related pathways are tRNA processing and Gene Expression. 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

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

Genomics for WDR4 Gene

Regulatory Elements for WDR4 Gene

Enhancers for WDR4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH21F042226 1.8 FANTOM5 Ensembl ENCODE 50.9 +646.6 646619 13.7 MLX CREB3L1 ZFP64 DMAP1 FEZF1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 PRDM15 WDR4 U2AF1 ABCG1 ENSG00000233754 UMODL1 ZBTB21 TFF2 ENSG00000235772 C2CD2
GH21F043105 1.6 FANTOM5 ENCODE 46.7 -228.8 -228758 5.1 HDGF PKNOX1 CREB3L1 MLX ZFP64 ARID4B SIN3A DMAP1 YBX1 ZNF2 WDR4 U2AF1 ENSG00000233754 NDUFV3 FRGCA PWP2 GC21P043111 LOC101928369
GH21F043158 1.6 FANTOM5 Ensembl ENCODE 38.4 -283.0 -282967 7.7 HDGF PKNOX1 MLX ZFP64 ARID4B SIN3A YBX1 DMAP1 ZNF766 ZNF302 WDR4 U2AF1 ENSG00000233754 SIK1 HSF2BP RRP1B PWP2 CRYAA LINC01678 ENSG00000228120
GH21F042923 1.4 Ensembl ENCODE 38.4 -49.4 -49439 11.9 HDGF PKNOX1 ARNT ARID4B ZNF2 ZNF143 ZNF207 MCM3 SP3 MCM5 U2AF1 WDR4 NDUFV3 ENSG00000233754 ENSG00000224100 PKNOX1 FRGCA ERVH48-1 MIR5692B
GH21F042878 1.2 ENCODE 44.1 +0.1 117 2.8 HDGF PKNOX1 ARNT MLX CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 WDR4 PRDM15 U2AF1 NDUFV3 ENSG00000233754 ENSG00000235772 ZBTB21 GC21M042796
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around WDR4 on UCSC Golden Path with GeneCards custom track

Promoters for WDR4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000614353 389 2801 MLX CREB3L1 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC TBX21 ZNF610

Genomic Location for WDR4 Gene

Chromosome:
21
Start:
42,843,080 bp from pter
End:
42,879,589 bp from pter
Size:
36,510 bases
Orientation:
Minus strand

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

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Abcam antibodies for WDR4
  • Santa Cruz Biotechnology (SCBT) Antibodies for WDR4

No data available for DME Specific Peptides for WDR4 Gene

Domains & Families for WDR4 Gene

Gene Families for WDR4 Gene

Protein Domains for WDR4 Gene

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.
  • Contains 7 WD repeats.
Family:
  • Belongs to the WD repeat TRM82 family.
Similarity:
  • Contains 7 WD repeats.
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.

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

Inhibitory RNA Products

Flow Cytometry 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

Gene Ontology (GO) - Cellular Components for WDR4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 15861136
GO:0005654 nucleoplasm IDA 16780588
GO:0005737 cytoplasm IDA --
GO:0005829 cytosol IBA --
GO:0043527 tRNA methyltransferase complex IBA --
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:0030488 tRNA methylation IEA --
GO:0036265 RNA (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

Transcripts for WDR4 Gene

Unigene Clusters for WDR4 Gene

WD repeat domain 4:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry 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 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
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 and mRNA Expression by UniProt/SwissProt 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 34 35
  • 98.86 (n)
dog
(Canis familiaris)
Mammalia WDR4 34 35
  • 83 (n)
cow
(Bos Taurus)
Mammalia WDR4 34 35
  • 81.46 (n)
mouse
(Mus musculus)
Mammalia Wdr4 34 16 35
  • 79.92 (n)
rat
(Rattus norvegicus)
Mammalia Wdr4 34
  • 79.87 (n)
oppossum
(Monodelphis domestica)
Mammalia WDR4 35
  • 69 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia WDR4 35
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves WDR4 34 35
  • 62.43 (n)
lizard
(Anolis carolinensis)
Reptilia WDR4 35
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.4956 34
African clawed frog
(Xenopus laevis)
Amphibia wdr4-prov 34
zebrafish
(Danio rerio)
Actinopterygii LOC100536637 34
  • 53.14 (n)
FP017279.3 35
  • 43 (a)
OneToMany
wdr4 35
  • 43 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta wuho 35
  • 24 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea Y102E9.2 35
  • 21 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TRM82 35 37
  • 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 Sequence Context AA Info Type
rs10709007 -- 42,847,038(+) GTCTC(-/A)AAAAA intron-variant
rs1107829 -- 42,855,014(-) TGTGC(A/C)CGGCC intron-variant
rs1107830 -- 42,854,987(-) TATTT(C/T)CTCTG intron-variant
rs1107831 -- 42,854,735(-) TTCCT(C/T)GATAT intron-variant
rs111167046 -- 42,848,871(+) CTCAC(A/T)CACAC intron-variant, downstream-variant-500B

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

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

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)

Relevant External Links 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

(1) MalaCards diseases for WDR4 Gene - From: DISEASES

Disorder Aliases PubMed IDs
seckel syndrome 1
  • seckel syndrome
- elite association - COSMIC cancer census association via MalaCards
Search WDR4 in MalaCards View complete list of genes associated with diseases

Relevant External Links for WDR4

Genetic Association Database (GAD)
WDR4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 E.M. (RNA 2002) 2 3 4 22 64
  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 H.S. (Genomics 2000) 3 4 22 64
  3. The tRNA methylase METTL1 is phosphorylated and inactivated by PKB and RSK in vitro and in cells. (PMID: 15861136) Cartlidge R.A. … Cohen P. (EMBO J. 2005) 3 4 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for WDR4 Gene

Sources for WDR4 Gene

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