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WDR4 WD repeat domain 4 [ Homo sapiens (human) ]

Gene ID: 10785, updated on 5-Jul-2020

Summary

Official Symbol
WDR4provided by HGNC
Official Full Name
WD repeat domain 4provided by HGNC
Primary source
HGNC:HGNC:12756
See related
Ensembl:ENSG00000160193 MIM:605924
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
hWH; MIGSB; TRM82; GAMOS6; TRMT82
Summary
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]
Expression
Ubiquitous expression in lymph node (RPKM 3.3), appendix (RPKM 3.2) and 25 other tissues See more
Orthologs

Genomic context

See WDR4 in Genome Data Viewer
Location:
21q22.3
Exon count:
15
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 21 NC_000021.9 (42843075..42891695, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (44263190..44299699, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1668 Neighboring gene uncharacterized LOC107985479 Neighboring gene uncharacterized LOC105372817 Neighboring gene NADH:ubiquinone oxidoreductase subunit V3 Neighboring gene endogenous retrovirus group 48 member 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
GALLOWAY-MOWAT SYNDROME 6
MedGen: C5193043 OMIM: 618347 GeneReviews: Not available
Compare labs
MICROCEPHALY, GROWTH DEFICIENCY, SEIZURES, AND BRAIN MALFORMATIONS
MedGen: C5193042 OMIM: 618346 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association study of selenium concentrations.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
contributes_to tRNA (guanine-N7-)-methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
contributes_to tRNA (guanine-N7-)-methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
cellular response to DNA damage stimulus IEA
Inferred from Electronic Annotation
more info
 
tRNA (guanine-N7)-methylation IEA
Inferred from Electronic Annotation
more info
 
tRNA modification IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
chromosome IEA
Inferred from Electronic Annotation
more info
 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
nucleoplasm HDA PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
tRNA methyltransferase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
tRNA methyltransferase complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4
Names
TRM82 tRNA methyltransferase 82 homolog
WD repeat-containing protein 4
protein Wuho homolog
tRNA (guanine-N(7)-)-methyltransferase subunit WDR4

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001260474.1NP_001247403.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame acceptor splice site at an internal coding exon compared to variant 1, resulting in a shorter isoform (2) missing a single aa compared to isoform 1.
    Source sequence(s)
    AJ243913, AK292923, BC006341, DC303088
    UniProtKB/Swiss-Prot
    P57081
    Conserved Domains (3) summary
    COG2319
    Location:25231
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:65102
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:20299
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  2. NM_001260475.1NP_001247404.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform 3

    See identical proteins and their annotated locations for NP_001247404.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate donor splice site at an exon in the 5' region compared to variant 1, resulting in translation initiation from an in-frame downstream AUG and an isoform (3) with a shorter N-terminus compared to isoform 1. Variants 4-6 encode the same isoform.
    Source sequence(s)
    AJ243913, AK315008, BC006341, DC303088
    UniProtKB/Swiss-Prot
    P57081
    Conserved Domains (2) summary
    sd00039
    Location:338
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:4154
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  3. NM_001260476.1NP_001247405.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform 3

    See identical proteins and their annotated locations for NP_001247405.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses alternate donor splice sites at the 5' terminal exon and at another exon in the 5' region compared to variant 1, resulting in translation initiation from an in-frame downstream AUG and an isoform (3) with a shorter N-terminus compared to isoform 1. Variants 4-6 encode the same isoform.
    Source sequence(s)
    AJ243913, AK298015, AK315008, BC001074, BC006341
    UniProtKB/Swiss-Prot
    P57081
    Related
    ENST00000476326.5
    Conserved Domains (2) summary
    sd00039
    Location:338
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:4154
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  4. NM_001260477.1NP_001247406.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform 3

    See identical proteins and their annotated locations for NP_001247406.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains an alternate 5' terminal exon and uses an alternate donor splice site at an exon in the 5' region compared to variant 1, resulting in translation initiation from an in-frame downstream AUG and an isoform (3) with a shorter N-terminus compared to isoform 1. Variants 4-6 encode the same isoform.
    Source sequence(s)
    AJ243913, AK056343, AK315008, AP001629, BC006341, DA029985
    UniProtKB/Swiss-Prot
    P57081
    Related
    ENST00000492742.5
    Conserved Domains (2) summary
    sd00039
    Location:338
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:4154
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  5. NM_018669.6NP_061139.2  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform 1

    See identical proteins and their annotated locations for NP_061139.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1). Variants 1 and 2 both encode the same isoform.
    Source sequence(s)
    AP001628, AP001629
    Consensus CDS
    CCDS13691.1
    UniProtKB/Swiss-Prot
    P57081
    Related
    ENSP00000381266.2, ENST00000398208.3
    Conserved Domains (2) summary
    sd00039
    Location:65102
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:20300
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  6. NM_033661.4NP_387510.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform 1

    See identical proteins and their annotated locations for NP_387510.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AJ243912, AK298015, BQ447230, DC303088
    Consensus CDS
    CCDS13691.1
    UniProtKB/Swiss-Prot
    P57081
    Related
    ENSP00000328671.2, ENST00000330317.6
    Conserved Domains (2) summary
    sd00039
    Location:65102
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:20300
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RNA

  1. NR_048535.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) uses an alternate donor splice site at the 5' terminal exon compared to variant 1. It is represented as non-coding due to the presence of an upstream ORF (with a strong Kozak signal) that is predicted to interfere with the translation of the longest ORF; translation of the upstream ORF renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AJ243913, AK298015, BC006341

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p13 Primary Assembly

    Range
    42843075..42891695 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017028264.1XP_016883753.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X3

  2. XM_024452048.1XP_024307816.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X4

    Conserved Domains (2) summary
    sd00039
    Location:338
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:4154
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  3. XM_017028262.1XP_016883751.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X2

  4. XM_024452049.1XP_024307817.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X4

    Conserved Domains (2) summary
    sd00039
    Location:338
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:4154
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  5. XM_024452047.1XP_024307815.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X4

    Conserved Domains (2) summary
    sd00039
    Location:338
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:4154
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  6. XM_011529433.1XP_011527735.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X1

    Conserved Domains (3) summary
    COG2319
    Location:23227
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:655
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:139296
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  7. XM_017028263.1XP_016883752.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X3

  8. XM_024452050.1XP_024307818.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X4

    Conserved Domains (2) summary
    sd00039
    Location:338
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:4154
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
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