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Aliases for WDR48 Gene

Aliases for WDR48 Gene

  • WD Repeat Domain 48 2 3 5
  • WD Repeat Endosomal Protein 3 4
  • UAF1 3 4
  • P80 3 4
  • Testicular Tissue Protein Li 224 3
  • WD Repeat-Containing Protein 48 3
  • USP1 Associated Factor 1 3
  • USP1-Associated Factor 1 4
  • KIAA1449 4
  • SPG60 3

External Ids for WDR48 Gene

Previous GeneCards Identifiers for WDR48 Gene

  • GC03P039069

Summaries for WDR48 Gene

Entrez Gene Summary for WDR48 Gene

  • 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]

GeneCards Summary for WDR48 Gene

WDR48 (WD Repeat Domain 48) is a Protein Coding gene. Diseases associated with WDR48 include Autosomal Recessive Spastic Paraplegia Type 60 and Congenital Hypoplastic Anemia. Among its related pathways are Metabolism of proteins and Deubiquitination. An important paralog of this gene is STRN.

UniProtKB/Swiss-Prot for WDR48 Gene

  • Regulator of deubiquitinating complexes. Acts as a strong activator of USP1 and USP46 (PubMed:18082604, PubMed:19075014, PubMed:26388029). Enhances the USP1-mediated deubiquitination of FANCD2; USP1 being almost inactive by itself (PubMed:18082604). Also activates deubiquitinating activity of complexes containing USP12 (PubMed:19075014). Activates deubiquitination by increasing the catalytic turnover without increasing the affinity of deubiquitinating enzymes for the substrate. In case of infection by Herpesvirus saimiri, may play a role in vesicular transport or membrane fusion events necessary for transport to lysosomes. Induces lysosomal vesicle formation via interaction with Herpesvirus saimiri tyrosine kinase-interacting protein (TIP). Subsequently, TIP recruits tyrosine-protein kinase LCK, resulting in down-regulation of T-cell antigen receptor TCR. May play a role in generation of enlarged endosomal vesicles via interaction with TIP. In case of infection by papillomavirus HPV11, promotes the maintenance of the viral genome via its interaction with HPV11 helicase E1.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for WDR48 Gene

Genomics for WDR48 Gene

Regulatory Elements for WDR48 Gene

Enhancers for WDR48 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
GH03F038722 1.3 Ensembl ENCODE 10.6 -327.5 -327479 4.6 PKNOX1 ATF1 ARNT SIN3A GATA2 FOS KDM4B NCOA1 REST SMARCB1 ENSG00000231243 WDR48 RNU6-1227P SCN10A SCN5A
GH03F039124 1.2 Ensembl ENCODE 10.8 +74.7 74739 3.8 HDGF PKNOX1 YY1 ZNF766 FOS ZNF263 MCM3 NCOA1 REST MBD2 TTC21A CSRNP1 WDR48 XIRP1 CX3CR1 GORASP1 LOC101928263
GH03F039280 0.9 Ensembl 10.7 +229.1 229115 2.6 PTRF ZNF766 GATA2 ZBTB11 USF2 ELF1 HDAC8 CREB3 TFDP1 POLR2H WDR48 RPSA CX3CR1 LOC102724104
GH03F038985 0.8 Ensembl ENCODE 10.8 -65.7 -65681 1.8 ZNF316 PYGO2 FOS SPI1 GORASP1 TTC21A RNU6-1227P WDR48 SCN11A PIR61629
GH03F039808 0.8 ENCODE 10.5 +757.3 757339 1.2 RING1 SUZ12 KLF17 ZIC2 RAD21 E2F1 CCNT2 GLIS2 ZBTB48 POLR2A WDR48 GORASP1 MYRIP GC03M039810
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around WDR48 on UCSC Golden Path with GeneCards custom track

Promoters for WDR48 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001361510 314 2201 HDGF PKNOX1 CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1

Genomic Location for WDR48 Gene

Chromosome:
3
Start:
39,051,986 bp from pter
End:
39,096,671 bp from pter
Size:
44,686 bases
Orientation:
Plus strand

Genomic View for WDR48 Gene

Genes around WDR48 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
WDR48 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for WDR48 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for WDR48 Gene

Proteins for WDR48 Gene

  • Protein details for WDR48 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TAF3-WDR48_HUMAN
    Recommended name:
    WD repeat-containing protein 48
    Protein Accession:
    Q8TAF3
    Secondary Accessions:
    • B4DM86
    • B4DQI2
    • B4DY84
    • Q63HJ2
    • Q658Y1
    • Q8N3Z1
    • Q9NSK8
    • Q9P279

    Protein attributes for WDR48 Gene

    Size:
    677 amino acids
    Molecular mass:
    76210 Da
    Quaternary structure:
    • Interacts with USP46 (PubMed:26388029, PubMed:19075014). Interacts with USP1 (PubMed:18082604, PubMed:26388029). Interacts with USP12 (PubMed:19075014). Interacts with Saimiriine herpesvirus TIP protein (PubMed:12196293, PubMed:12885920). Interacts with papillomavirus HPV11 E1 protein (PubMed:18032488).
    SequenceCaution:
    • Sequence=AAH37168.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA95973.2; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAH56182.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAH56300.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for WDR48 Gene

    Alternative splice isoforms for WDR48 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for WDR48 Gene

Post-translational modifications for WDR48 Gene

  • Ubiquitination at Lys 106, Lys 327, and Lys 578
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Abcam antibodies for WDR48
  • Santa Cruz Biotechnology (SCBT) Antibodies for WDR48

No data available for DME Specific Peptides for WDR48 Gene

Domains & Families for WDR48 Gene

Gene Families for WDR48 Gene

Suggested Antigen Peptide Sequences for WDR48 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8TAF3

UniProtKB/Swiss-Prot:

WDR48_HUMAN :
  • N-terminal WD region interacts with TIP and C-terminal region mediates lysosomal localization (Probable). The WD repeats are required for the interaction with deubiquitinating enzymes USP1, USP12 and USP46.
  • Belongs to the WD repeat WDR48 family.
  • Contains 8 WD repeats.
Domain:
  • N-terminal WD region interacts with TIP and C-terminal region mediates lysosomal localization (Probable). The WD repeats are required for the interaction with deubiquitinating enzymes USP1, USP12 and USP46.
Family:
  • Belongs to the WD repeat WDR48 family.
Similarity:
  • Contains 8 WD repeats.
genes like me logo Genes that share domains with WDR48: view

Function for WDR48 Gene

Molecular function for WDR48 Gene

UniProtKB/Swiss-Prot Function:
Regulator of deubiquitinating complexes. Acts as a strong activator of USP1 and USP46 (PubMed:18082604, PubMed:19075014, PubMed:26388029). Enhances the USP1-mediated deubiquitination of FANCD2; USP1 being almost inactive by itself (PubMed:18082604). Also activates deubiquitinating activity of complexes containing USP12 (PubMed:19075014). Activates deubiquitination by increasing the catalytic turnover without increasing the affinity of deubiquitinating enzymes for the substrate. In case of infection by Herpesvirus saimiri, may play a role in vesicular transport or membrane fusion events necessary for transport to lysosomes. Induces lysosomal vesicle formation via interaction with Herpesvirus saimiri tyrosine kinase-interacting protein (TIP). Subsequently, TIP recruits tyrosine-protein kinase LCK, resulting in down-regulation of T-cell antigen receptor TCR. May play a role in generation of enlarged endosomal vesicles via interaction with TIP. In case of infection by papillomavirus HPV11, promotes the maintenance of the viral genome via its interaction with HPV11 helicase E1.

Gene Ontology (GO) - Molecular Function for WDR48 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 18082604
genes like me logo Genes that share ontologies with WDR48: view
genes like me logo Genes that share phenotypes with WDR48: view

Animal Model Products

miRNA for WDR48 Gene

miRTarBase miRNAs that target WDR48

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 WDR48 Gene

Localization for WDR48 Gene

Subcellular locations from UniProtKB/Swiss-Prot for WDR48 Gene

Nucleus. Cytoplasm. Lysosome. Late endosome. Note=Mainly in cytoplasmic compartments (PubMed:12196293, PubMed:18032488). In case of infection by papillomavirus HPV11, translocates to the nucleus via its interaction with papillomavirus HPV11 (PubMed:18032488). {ECO:0000269 PubMed:12196293, ECO:0000269 PubMed:18032488}.

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 WDR48 gene
Compartment Confidence
nucleus 5
lysosome 3
endosome 3
mitochondrion 2
peroxisome 1
cytosol 1

Gene Ontology (GO) - Cellular Components for WDR48 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 18082604
GO:0005737 cytoplasm IEA --
GO:0005764 lysosome IEA --
GO:0005768 endosome IEA --
GO:0005770 late endosome IEA --
genes like me logo Genes that share ontologies with WDR48: view

Pathways & Interactions for WDR48 Gene

genes like me logo Genes that share pathways with WDR48: view

Pathways by source for WDR48 Gene

Gene Ontology (GO) - Biological Process for WDR48 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000724 double-strand break repair via homologous recombination IEA --
GO:0006974 cellular response to DNA damage stimulus IEA --
GO:0007283 spermatogenesis IEA --
GO:0007338 single fertilization IEA --
GO:0008584 male gonad development IEA --
genes like me logo Genes that share ontologies with WDR48: view

No data available for SIGNOR curated interactions for WDR48 Gene

Transcripts for WDR48 Gene

Unigene Clusters for WDR48 Gene

WD repeat domain 48:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for WDR48 Gene

No ASD Table

Relevant External Links for WDR48 Gene

GeneLoc Exon Structure for
WDR48
ECgene alternative splicing isoforms for
WDR48

Expression for WDR48 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for WDR48 Gene

Protein differential expression in normal tissues from HIPED for WDR48 Gene

This gene is overexpressed in Breast (21.1) and Lymph node (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for WDR48 Gene



Protein tissue co-expression partners for WDR48 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of WDR48 Gene:

WDR48

SOURCE GeneReport for Unigene cluster for WDR48 Gene:

Hs.109778

mRNA Expression by UniProt/SwissProt for WDR48 Gene:

Q8TAF3-WDR48_HUMAN
Tissue specificity: Ubiquitous.
genes like me logo Genes that share expression patterns with WDR48: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for WDR48 Gene

Orthologs for WDR48 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for WDR48 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia WDR48 34 35
  • 99.8 (n)
dog
(Canis familiaris)
Mammalia WDR48 34 35
  • 95.08 (n)
oppossum
(Monodelphis domestica)
Mammalia WDR48 35
  • 95 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia WDR48 35
  • 95 (a)
OneToOne
cow
(Bos Taurus)
Mammalia WDR48 34 35
  • 93.99 (n)
rat
(Rattus norvegicus)
Mammalia Wdr48 34
  • 88.91 (n)
mouse
(Mus musculus)
Mammalia Wdr48 34 16 35
  • 88.56 (n)
chicken
(Gallus gallus)
Aves WDR48 34 35
  • 86.71 (n)
lizard
(Anolis carolinensis)
Reptilia WDR48 35
  • 96 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia wdr48 34
  • 81.54 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.33731 34
zebrafish
(Danio rerio)
Actinopterygii WDR48 (3 of 3) 35
  • 91 (a)
OneToMany
WDR48 (2 of 3) 35
  • 90 (a)
OneToMany
wdr48 34 35
  • 77.6 (n)
wufd19a04 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001361 34
  • 58.05 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG9062 34 35
  • 57.6 (n)
worm
(Caenorhabditis elegans)
Secernentea F35G12.4 34
  • 55.04 (n)
wdr-48 35
  • 45 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CAF4 35
  • 16 (a)
OneToMany
MDV1 35
  • 13 (a)
OneToMany
DUF1 37
thale cress
(Arabidopsis thaliana)
eudicotyledons LRS1 34
  • 49.64 (n)
rice
(Oryza sativa)
Liliopsida Os12g0165000 34
  • 49.72 (n)
Species where no ortholog for WDR48 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for WDR48 Gene

ENSEMBL:
Gene Tree for WDR48 (if available)
TreeFam:
Gene Tree for WDR48 (if available)

Paralogs for WDR48 Gene

Paralogs for WDR48 Gene

genes like me logo Genes that share paralogs with WDR48: view

Variants for WDR48 Gene

Sequence variations from dbSNP and Humsavar for WDR48 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs1000541 -- 39,069,237(-) AGCAC(G/T)CTGGG intron-variant
rs10428189 -- 39,062,184(+) tgcct(A/G)tgtcc intron-variant
rs1043170 -- 39,096,673(-) ACTAC(A/C)CTTTG nc-transcript-variant, downstream-variant-500B, utr-variant-3-prime, splice-donor-variant
rs10510698 -- 39,066,502(+) AAGTT(G/T)TAAGT intron-variant
rs1053489 -- 39,095,787(+) ACTTT(A/C)ATAGA nc-transcript-variant, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for WDR48 Gene

Variant ID Type Subtype PubMed ID
esv2759141 CNV loss 17122850
nsv1007100 CNV loss 25217958

Variation tolerance for WDR48 Gene

Residual Variation Intolerance Score: 7.51% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.83; 17.41% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for WDR48 Gene

Human Gene Mutation Database (HGMD)
WDR48
SNPedia medical, phenotypic, and genealogical associations of SNPs for
WDR48

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for WDR48 Gene

Disorders for WDR48 Gene

MalaCards: The human disease database

(3) MalaCards diseases for WDR48 Gene - From: Orphanet and DISEASES

Disorder Aliases PubMed IDs
autosomal recessive spastic paraplegia type 60
  • spg60
congenital hypoplastic anemia
  • congenital aplastic anemia
fanconi anemia, complementation group a
  • fanconi's anemia
- elite association - COSMIC cancer census association via MalaCards
Search WDR48 in MalaCards View complete list of genes associated with diseases

Relevant External Links for WDR48

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
WDR48
genes like me logo Genes that share disorders with WDR48: view

No data available for UniProtKB/Swiss-Prot and Genatlas for WDR48 Gene

Publications for WDR48 Gene

  1. Human papillomavirus E1 helicase interacts with the WD repeat protein p80 to promote maintenance of the viral genome in keratinocytes. (PMID: 18032488) Cote-Martin A. … Archambault J. (J. Virol. 2008) 3 4 22 64
  2. Herpesviral protein targets a cellular WD repeat endosomal protein to downregulate T lymphocyte receptor expression. (PMID: 12196293) Park J. … Jung J.U. (Immunity 2002) 2 3 4 64
  3. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10819331) Nagase T. … Ohara O. (DNA Res. 2000) 2 3 4 64
  4. Structural Insights into WD-Repeat 48 Activation of Ubiquitin-Specific Protease 46. (PMID: 26388029) Yin J. … Harris S.F. (Structure 2015) 3 4 64
  5. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. (PMID: 24482476) Novarino G. … Gleeson J.G. (Science 2014) 2 3 64

Products for WDR48 Gene

Sources for WDR48 Gene

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