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WDR38 WD repeat domain 38 [ Homo sapiens (human) ]

Gene ID: 401551, updated on 2-Nov-2024

Summary

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Official Symbol
WDR38provided by HGNC
Official Full Name
WD repeat domain 38provided by HGNC
Primary source
HGNC:HGNC:23745
See related
Ensembl:ENSG00000136918 AllianceGenome:HGNC:23745
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Predicted to act upstream of or within hematopoietic progenitor cell differentiation. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in lung (RPKM 2.9), testis (RPKM 2.5) and 7 other tissues See more
Orthologs
mouse all
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Genomic context

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See WDR38 in Genome Data Viewer
Location:
9q33.3
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (124853460..124857878)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (137051771..137056188)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (127615739..127620157)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:127533372-127533939 Neighboring gene uncharacterized LOC107987126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20266 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20267 Neighboring gene olfactomedin like 2A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127561206-127561720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127561721-127562234 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:127573487-127573987 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:127573988-127574490 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:127574992-127575493 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28990 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127596476-127597087 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127597088-127597698 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:127602031-127602634 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:127602635-127603237 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20268 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:127618044-127618212 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:127620824-127621106 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127621747-127622248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127622249-127622748 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:127623737-127624360 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28993 Neighboring gene ribosomal protein L35 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28994 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20270 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20271 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28995 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28996 Neighboring gene actin related protein 2/3 complex subunit 5 like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127634813-127635313

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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Related articles in PubMed

  1. WDR38, a novel equatorial segment protein, interacts with the GTPase protein RAB19 and Golgi protein GM130 to play roles in acrosome biogenesis. Gao Q, et al. Acta Biochim Biophys Sin (Shanghai), 2023 Oct 25. PMID 37635409, Free PMC Article
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. WDR38, a novel equatorial segment protein, interacts with the GTPase protein RAB19 and Golgi protein GM130 to play roles in acrosome biogenesis.
    Title: WDR38, a novel equatorial segment protein, interacts with the GTPase protein RAB19 and Golgi protein GM130 to play roles in acrosome biogenesis.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

General gene information

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Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in hematopoietic progenitor cell differentiation IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
WD repeat-containing protein 38

NCBI Reference Sequences (RefSeq)

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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_001045476.3 → NP_001038941.1  WD repeat-containing protein 38 isoform 2

    See identical proteins and their annotated locations for NP_001038941.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has an alternate splice site in the 3' coding region, compared to variant 1. The resulting isoform (2) lacks an internal aa, compared to isoform 1.
    Source sequence(s)
    AA867995, AL354928, BC150645
    Consensus CDS
    CCDS43876.1
    UniProtKB/Swiss-Prot
    A0PK24, Q5JTN6
    UniProtKB/TrEMBL
    B9EK65
    Related
    ENSP00000362677.1, ENST00000373574.2
    Conserved Domains (3) summary
    COG2319
    Location:11 → 298
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:20 → 300
    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 ...
    sd00039
    Location:26 → 61
    7WD40; WD40 repeat [structural motif]

  2. NM_001276374.2 → NP_001263303.1  WD repeat-containing protein 38 isoform 1

    See identical proteins and their annotated locations for NP_001263303.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AA867995, AL354928, BC171828, BC171830
    Consensus CDS
    CCDS75898.1
    UniProtKB/TrEMBL
    A0A087X0D8, B7ZW23
    Related
    ENSP00000483312.1, ENST00000613760.4
    Conserved Domains (3) summary
    COG2319
    Location:11 → 299
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:20 → 301
    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 ...
    sd00039
    Location:26 → 61
    7WD40; WD40 repeat [structural motif]

  3. NM_001276375.2 → NP_001263304.1  WD repeat-containing protein 38 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has an alternate splice site in the 5' coding region, compared to variant 1. The resulting isoform (3) lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AA867995, AL354928, BC171830
    UniProtKB/TrEMBL
    B7ZW24
    Conserved Domains (2) summary
    cd00200
    Location:11 → 290
    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 ...
    sd00039
    Location:56 → 92
    7WD40; WD40 repeat [structural motif]

  4. NM_001276376.2 → NP_001263305.1  WD repeat-containing protein 38 isoform 4

    See identical proteins and their annotated locations for NP_001263305.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) initiates translation at an alternate downstream start codon and has a distinct and shorter internal segment in the CDS, compared to variant 1. The resulting isoform (4) has a shorter and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AA867995, AL354928, BC171837
    Consensus CDS
    CCDS75899.1
    UniProtKB/TrEMBL
    A0A087X0J1
    Related
    ENSP00000483432.1, ENST00000618744.4
    Conserved Domains (2) summary
    cd00200
    Location:54 → 250
    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 ...
    sd00039
    Location:60 → 96
    7WD40; WD40 repeat [structural motif]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    124853460..124857878
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005251987.5 → XP_005252044.1  WD repeat-containing protein 38 isoform X1

    UniProtKB/TrEMBL
    B7ZW23
    Conserved Domains (3) summary
    COG2319
    Location:11 → 272
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:20 → 274
    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 ...
    sd00039
    Location:26 → 61
    7WD40; WD40 repeat [structural motif]

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    137051771..137056188
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054362974.1 → XP_054218949.1  WD repeat-containing protein 38 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5JTN6.1 GenPept UniProtKB/Swiss-Prot:Q5JTN6

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