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WDR48 WD repeat domain 48 [ Homo sapiens (human) ]

Gene ID: 57599, updated on 6-Oct-2019

Summary

Official Symbol
WDR48provided by HGNC
Official Full Name
WD repeat domain 48provided by HGNC
Primary source
HGNC:HGNC:30914
See related
Ensembl:ENSG00000114742 MIM:612167
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
P80; UAF1; SPG60
Summary
The protein encoded by this gene has been shown to interact with ubiquitin specific peptidase 1 (USP1), activating the deubiquitinating activity of USP1 and allowing it to remove the ubiquitin moiety from monoubiquitinated FANCD2. FANCD2 is ubiquitinated in response to DNA damage. [provided by RefSeq, Sep 2016]
Expression
Ubiquitous expression in testis (RPKM 33.3), bone marrow (RPKM 19.8) and 25 other tissues See more
Orthologs

Genomic context

See WDR48 in Genome Data Viewer
Location:
3p22.2
Exon count:
22
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (39052002..39096671)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (39093477..39138155)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986042 Neighboring gene sodium voltage-gated channel alpha subunit 11 Neighboring gene RNA, U6 small nuclear 1227, pseudogene Neighboring gene golgi reassembly stacking protein 1 Neighboring gene tetratricopeptide repeat domain 21A Neighboring gene uncharacterized LOC101928263 Neighboring gene microRNA 6822 Neighboring gene cysteine and serine rich nuclear protein 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

NHGRI GWAS Catalog

Description
Variability in the common genetic architecture of social-communication spectrum phenotypes during childhood and adolescence.
NHGRI GWA Catalog

Pathways from BioSystems

  • Deubiquitination, organism-specific biosystem (from REACTOME)
    Deubiquitination, organism-specific biosystemUbiquitination, the modification of proteins by the covalent attachment of ubiquitin (Ub), is a key regulatory mechanism for many many cellular processes, including protein degradation by the 26S pro...
  • Fanconi anemia pathway, organism-specific biosystem (from KEGG)
    Fanconi anemia pathway, organism-specific biosystemThe Fanconi anemia pathway is required for the efficient repair of damaged DNA, especially interstrand cross-links (ICLs). DNA ICL is directly recognized by FANCM and associated proteins, that recrui...
  • Fanconi anemia pathway, conserved biosystem (from KEGG)
    Fanconi anemia pathway, conserved biosystemThe Fanconi anemia pathway is required for the efficient repair of damaged DNA, especially interstrand cross-links (ICLs). DNA ICL is directly recognized by FANCM and associated proteins, that recrui...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Ub-specific processing proteases, organism-specific biosystem (from REACTOME)
    Ub-specific processing proteases, organism-specific biosystemUb-specific processing proteases (USPs) are the largest of the DUB families with more than 50 members in humans. The USP catalytic domain varies considerably in size and consists of six conserved mo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1449, DKFZp686G1794

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
DNA damage response, detection of DNA damage TAS
Traceable Author Statement
more info
 
double-strand break repair via homologous recombination IEA
Inferred from Electronic Annotation
more info
 
embryonic organ development IEA
Inferred from Electronic Annotation
more info
 
homeostasis of number of cells IEA
Inferred from Electronic Annotation
more info
 
interstrand cross-link repair TAS
Traceable Author Statement
more info
 
multicellular organism growth IEA
Inferred from Electronic Annotation
more info
 
positive regulation of epithelial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of protein deubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein deubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein deubiquitination TAS
Traceable Author Statement
more info
 
regulation of protein monoubiquitination IEA
Inferred from Electronic Annotation
more info
 
seminiferous tubule development IEA
Inferred from Electronic Annotation
more info
 
single fertilization IEA
Inferred from Electronic Annotation
more info
 
skeletal system morphogenesis IEA
Inferred from Electronic Annotation
more info
 
skin development IEA
Inferred from Electronic Annotation
more info
 
spermatogenesis IEA
Inferred from Electronic Annotation
more info
 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
late endosome IEA
Inferred from Electronic Annotation
more info
 
lysosome IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
WD repeat-containing protein 48
Names
USP1 associated factor 1
WD repeat endosomal protein
testicular tissue protein Li 224

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.

Genomic

  1. NG_051663.1 RefSeqGene

    Range
    5031..49679
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001303402.2NP_001290331.1  WD repeat-containing protein 48 isoform 2

    See identical proteins and their annotated locations for NP_001290331.1

    Status: REVIEWED

    Source sequence(s)
    AB040882
    UniProtKB/Swiss-Prot
    Q8TAF3
    Conserved Domains (3) summary
    cd00200
    Location:3204
    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:3878
    7WD40; WD40 repeat [structural motif]
    pfam11816
    Location:427591
    DUF3337; Domain of unknown function (DUF3337)
  2. NM_001303403.2NP_001290332.1  WD repeat-containing protein 48 isoform 3

    See identical proteins and their annotated locations for NP_001290332.1

    Status: REVIEWED

    Source sequence(s)
    AB040882
    UniProtKB/Swiss-Prot
    Q8TAF3
    Conserved Domains (3) summary
    cd00200
    Location:30277
    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:3573
    7WD40; WD40 repeat [structural motif]
    pfam11816
    Location:500664
    DUF3337; Domain of unknown function (DUF3337)
  3. NM_001346225.2NP_001333154.1  WD repeat-containing protein 48 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) encodes the longest isoform (4).
    Source sequence(s)
    AC123903, AC138124
    Conserved Domains (3) summary
    cd00200
    Location:30324
    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:3573
    7WD40; WD40 repeat [structural motif]
    pfam11816
    Location:547711
    DUF3337; Domain of unknown function (DUF3337)
  4. NM_001346226.2NP_001333155.1  WD repeat-containing protein 48 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC123903, AC138124
    Conserved Domains (3) summary
    cd00200
    Location:17229
    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:2258
    7WD40; WD40 repeat [structural motif]
    pfam11816
    Location:452616
    DUF3337; Domain of unknown function (DUF3337)
  5. NM_001346227.2NP_001333156.1  WD repeat-containing protein 48 isoform 6

    Status: REVIEWED

    Source sequence(s)
    AC123903, AC138124
    UniProtKB/Swiss-Prot
    Q8TAF3
    Conserved Domains (3) summary
    sd00039
    Location:232
    7WD40; WD40 repeat [structural motif]
    pfam11816
    Location:334498
    DUF3337; Domain of unknown function (DUF3337)
    cl25539
    Location:5111
    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_001346228.1NP_001333157.1  WD repeat-containing protein 48 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AC123903, AC138124
    UniProtKB/Swiss-Prot
    Q8TAF3
    Conserved Domains (3) summary
    cd00200
    Location:4216
    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:945
    7WD40; WD40 repeat [structural motif]
    pfam11816
    Location:439603
    DUF3337; Domain of unknown function (DUF3337)
  7. NM_020839.4NP_065890.1  WD repeat-containing protein 48 isoform 1

    See identical proteins and their annotated locations for NP_065890.1

    Status: REVIEWED

    Source sequence(s)
    AB040882
    Consensus CDS
    CCDS33738.1
    UniProtKB/Swiss-Prot
    Q8TAF3
    UniProtKB/TrEMBL
    A0A024R2L1
    Related
    ENSP00000307491.5, ENST00000302313.10
    Conserved Domains (3) summary
    cd00200
    Location:30286
    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:3573
    7WD40; WD40 repeat [structural motif]
    pfam11816
    Location:509673
    DUF3337; Domain of unknown function (DUF3337)

RNA

  1. NR_144399.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    BC037168, DA414095
    Related
    ENST00000420940.6
  2. NR_144400.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC123903, AC138124
  3. NR_144401.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC123903, AC138124

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    39052002..39096671
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005265346.4XP_005265403.1  WD repeat-containing protein 48 isoform X1

    Conserved Domains (4) summary
    COG2319
    Location:29328
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:30286
    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 ...
    pfam11816
    Location:509647
    DUF3337; Domain of unknown function (DUF3337)
    sd00039
    Location:3573
    7WD40; WD40 repeat [structural motif]
  2. XM_011533971.2XP_011532273.1  WD repeat-containing protein 48 isoform X2

    Conserved Domains (4) summary
    COG2319
    Location:4321
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:4216
    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 ...
    pfam11816
    Location:439577
    DUF3337; Domain of unknown function (DUF3337)
    sd00039
    Location:945
    7WD40; WD40 repeat [structural motif]
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