U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from MedGen

    • Showing Current items.

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

    Gene ID: 10785, updated on 25-Jan-2024

    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; AllianceGenome:HGNC:12756
    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; Wuho; 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See WDR4 in Genome Data Viewer
    Location:
    21q22.3
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (42843094..42892998, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (41231676..41281371, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (44263204..44299699, complement)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene phosphodiesterase 9A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:44195549-44196050 Neighboring gene uncharacterized LOC107985504 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18530 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44197711-44198660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44199612-44200561 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:44201049-44201772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:44202497-44203220 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44203221-44203942 Neighboring gene long intergenic non-protein coding RNA 1668 Neighboring gene NANOG hESC enhancer GRCh37_chr21:44220991-44221572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:44254625-44255576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18531 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18532 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44268253-44268818 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44268819-44269384 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44280271-44280829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:44285917-44286612 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44297711-44298674 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44298675-44299639 Neighboring gene uncharacterized LOC105372817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13353 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:44334874-44335381 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:44335382-44335888 Neighboring gene NADH:ubiquinone oxidoreductase subunit V3 Neighboring gene endogenous retrovirus group 48 member 1, envelope

    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?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables enzyme activator activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables tRNA methyltransferase activator activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in DNA damage response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in tRNA (guanine-N7)-methylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in tRNA modification IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in tRNA modification IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm HDA PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of tRNA (m7G46) methyltransferase complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of tRNA methyltransferase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of 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)

    NEW Try the new Transcript table

    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_001260474.2NP_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)
      AP001628, AP001629
      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_001260475.2NP_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)
      AP001628, AP001629
      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_001260476.2NP_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)
      AP001628, AP001629
      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_001260477.2NP_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)
      AP001628, AP001629
      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
      A8KA58, B2RCA3, B4DNQ7, D3DSK3, P57081, Q9BVM5, Q9HCR3
      Related
      ENSP00000381266.2, ENST00000398208.3
      Conserved Domains (2) summary
      sd00039
      Location:65102
      7WD40; WD40 repeat [structural motif]
      cl29593
      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_033661.5NP_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, DC303088
      Consensus CDS
      CCDS13691.1
      UniProtKB/Swiss-Prot
      A8KA58, B2RCA3, B4DNQ7, D3DSK3, P57081, Q9BVM5, Q9HCR3
      Related
      ENSP00000328671.2, ENST00000330317.6
      Conserved Domains (2) summary
      sd00039
      Location:65102
      7WD40; WD40 repeat [structural motif]
      cl29593
      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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      42843094..42892998 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017028264.2XP_016883753.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X2

    2. XM_011529433.2XP_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 ...
    3. XM_024452048.2XP_024307816.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X3

      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. XM_024452047.2XP_024307815.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X3

      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_017028263.2XP_016883752.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      41231676..41281371 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324315.1XP_054180290.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X1

    2. XM_054324317.1XP_054180292.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X2

    3. XM_054324319.1XP_054180294.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X3

    4. XM_054324318.1XP_054180293.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X3

    5. XM_054324316.1XP_054180291.1  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X2