Human Gene WDR48 (uc003cit.3) Description and Page Index
  Description: Homo sapiens WD repeat domain 48 (WDR48), mRNA.
RefSeq Summary (NM_020839): 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]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AK025513.1, AB040882.2 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000302313.10/ ENSP00000307491.5 RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr3:39,093,507-39,137,881 Size: 44,375 Total Exon Count: 19 Strand: +
Coding Region
   Position: hg19 chr3:39,093,517-39,136,234 Size: 42,718 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:39,093,507-39,137,881)mRNA (may differ from genome)Protein (677 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKB

-  Comments and Description Text from UniProtKB
  ID: WDR48_HUMAN
DESCRIPTION: RecName: Full=WD repeat-containing protein 48; AltName: Full=USP1-associated factor 1; AltName: Full=WD repeat endosomal protein; AltName: Full=p80;
FUNCTION: Regulator of deubiquitinating complexes. Acts as a strong activator of USP1 by enhancing the USP1-mediated deubiquitination of FANCD2; USP1 being almost inactive by itself. Also activates deubiquitinating activity of complexes containing USP12 and USP46, respectively. 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.
SUBUNIT: Interacts with USP1, USP12 and USP46. Interacts with Saimiriine herpesvirus TIP protein. Interacts with papillomavirus HPV11 E1 protein.
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Lysosome. Note=Mainly cytoplasmic. In case of infection by papillomavirus HPV11, translocates to the nucleus via its interaction with papillomavirus HPV11.
TISSUE SPECIFICITY: Ubiquitous.
DOMAIN: N-terminal WD region interacts with TIP and C-terminal region mediates lysosomal localization. The WD repeats are required for the interaction with deubiquitinating enzymes USP1, USP12 and USP46.
SIMILARITY: Belongs to the WD repeat WDR48 family.
SIMILARITY: Contains 8 WD repeats.
SEQUENCE CAUTION: Sequence=AAH37168.1; Type=Erroneous initiation; Sequence=BAA95973.2; Type=Erroneous initiation; Sequence=CAH56182.1; Type=Erroneous initiation; Sequence=CAH56300.1; Type=Erroneous initiation;

-  MalaCards Disease Associations
  MalaCards Gene Search: WDR48
Diseases sorted by gene-association score: autosomal recessive spastic paraplegia type 60* (350), fanconi anemia, complementation group a (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.07 RPKM in Testis
Total median expression: 167.31 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -503.521647-0.306 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR021772 - DUF3337
IPR020472 - G-protein_beta_WD-40_rep
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR019775 - WD40_repeat_CS
IPR017986 - WD40_repeat_dom

Pfam Domains:
PF00400 - WD domain, G-beta repeat
PF11816 - Domain of unknown function (DUF3337)

SCOP Domains:
50952 - Soluble quinoprotein glucose dehydrogenase
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
50965 - Galactose oxidase, central domain
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Prolyl oligopeptidase, N-terminal domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - Dipeptidyl peptidase IV/CD26, N-terminal domain

ModBase Predicted Comparative 3D Structure on Q8TAF3
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  EnsemblFlyBaseWormBase 
  Protein SequenceProtein SequenceProtein Sequence 
  AlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0036459 thiol-dependent ubiquitinyl hydrolase activity

Biological Process:
GO:0000724 double-strand break repair via homologous recombination
GO:0006974 cellular response to DNA damage stimulus
GO:0007283 spermatogenesis
GO:0007338 single fertilization
GO:0008584 male gonad development
GO:0016032 viral process
GO:0016579 protein deubiquitination
GO:0035264 multicellular organism growth
GO:0042769 DNA damage response, detection of DNA damage
GO:0043588 skin development
GO:0048568 embryonic organ development
GO:0048705 skeletal system morphogenesis
GO:0048872 homeostasis of number of cells
GO:0050679 positive regulation of epithelial cell proliferation
GO:0072520 seminiferous tubule development
GO:1902525 regulation of protein monoubiquitination

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005768 endosome
GO:0005770 late endosome
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  AB040882 - Homo sapiens KIAA1449 mRNA for KIAA1449 protein.
HM005537 - Homo sapiens clone HTL-T-224 testicular tissue protein Li 224 mRNA, complete cds.
AK302307 - Homo sapiens cDNA FLJ56174 complete cds, highly similar to WD repeat protein 48.
AK297349 - Homo sapiens cDNA FLJ55492 complete cds, highly similar to WD repeat protein 48.
AK298810 - Homo sapiens cDNA FLJ55498 complete cds, highly similar to WD repeat protein 48.
BC026353 - Homo sapiens WD repeat domain 48, mRNA (cDNA clone MGC:26819 IMAGE:4812745), complete cds.
AK025513 - Homo sapiens cDNA: FLJ21860 fis, clone HEP02307.
BC037168 - Homo sapiens WD repeat domain 48, mRNA (cDNA clone MGC:29487 IMAGE:4843736), complete cds.
AB385469 - Synthetic construct DNA, clone: pF1KA1449, Homo sapiens WDR48 gene for WD repeat protein 48, complete cds, without stop codon, in Flexi system.
AF468833 - Homo sapiens WD repeat endosomal protein mRNA, complete cds.
AL832926 - Homo sapiens mRNA; cDNA DKFZp666A1410 (from clone DKFZp666A1410).
KJ902979 - Synthetic construct Homo sapiens clone ccsbBroadEn_12373 WDR48 gene, encodes complete protein.
AK074278 - Homo sapiens cDNA FLJ23698 fis, clone HEP10558.
AL162064 - Homo sapiens mRNA; cDNA DKFZp762E115 (from clone DKFZp762E115).
BX649170 - Homo sapiens mRNA; cDNA DKFZp686G1794 (from clone DKFZp686G1794).
BC012861 - Homo sapiens WD repeat domain 48, mRNA (cDNA clone IMAGE:3864503), with apparent retained intron.
JD066400 - Sequence 47424 from Patent EP1572962.
JD381528 - Sequence 362552 from Patent EP1572962.
JD333526 - Sequence 314550 from Patent EP1572962.
JD253112 - Sequence 234136 from Patent EP1572962.
JD389034 - Sequence 370058 from Patent EP1572962.
JD436333 - Sequence 417357 from Patent EP1572962.
JD043354 - Sequence 24378 from Patent EP1572962.
JD553013 - Sequence 534037 from Patent EP1572962.
JD561882 - Sequence 542906 from Patent EP1572962.
JD114629 - Sequence 95653 from Patent EP1572962.
JD050426 - Sequence 31450 from Patent EP1572962.
JD318669 - Sequence 299693 from Patent EP1572962.
JD087646 - Sequence 68670 from Patent EP1572962.
JD549232 - Sequence 530256 from Patent EP1572962.
JD518656 - Sequence 499680 from Patent EP1572962.
JD508500 - Sequence 489524 from Patent EP1572962.
JD139456 - Sequence 120480 from Patent EP1572962.
JD087808 - Sequence 68832 from Patent EP1572962.
JD084945 - Sequence 65969 from Patent EP1572962.
JD469282 - Sequence 450306 from Patent EP1572962.
JD563782 - Sequence 544806 from Patent EP1572962.
JD503350 - Sequence 484374 from Patent EP1572962.
JD294553 - Sequence 275577 from Patent EP1572962.
JD207862 - Sequence 188886 from Patent EP1572962.
JD124613 - Sequence 105637 from Patent EP1572962.
JD102625 - Sequence 83649 from Patent EP1572962.
JD195288 - Sequence 176312 from Patent EP1572962.
JD241414 - Sequence 222438 from Patent EP1572962.
JD349050 - Sequence 330074 from Patent EP1572962.
JD343009 - Sequence 324033 from Patent EP1572962.
JD220974 - Sequence 201998 from Patent EP1572962.
JD500305 - Sequence 481329 from Patent EP1572962.
JD539010 - Sequence 520034 from Patent EP1572962.
JD042792 - Sequence 23816 from Patent EP1572962.
JD258134 - Sequence 239158 from Patent EP1572962.
JD501098 - Sequence 482122 from Patent EP1572962.
JD168410 - Sequence 149434 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8TAF3 (Reactome details) participates in the following event(s):

R-HSA-5655481 USP1:WDR48 binds monoUb:K164-PCNA
R-HSA-5655483 USP1 autocleavage
R-HSA-5655466 USP1:WDR48 deubiquitinates monoUb:K164-PCNA
R-HSA-6786171 FANCD2 deubiquitination by USP1:WDR48
R-HSA-5696605 USP12, USP26 deubiquitinate AR
R-HSA-110314 Recognition of DNA damage by PCNA-containing replication complex
R-HSA-73893 DNA Damage Bypass
R-HSA-6783310 Fanconi Anemia Pathway
R-HSA-73894 DNA Repair
R-HSA-5689880 Ub-specific processing proteases
R-HSA-5688426 Deubiquitination
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: B4DM86, B4DQI2, B4DY84, KIAA1449, NM_020839, NP_065890, Q63HJ2, Q658Y1, Q8N3Z1, Q8TAF3, Q9NSK8, Q9P279, UAF1, WDR48_HUMAN
UCSC ID: uc003cit.3
RefSeq Accession: NM_020839
Protein: Q8TAF3 (aka WDR48_HUMAN)
CCDS: CCDS33738.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene WDR48:
hsp (Hereditary Spastic Paraplegia Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_020839.2
exon count: 19CDS single in 3' UTR: no RNA size: 3705
ORF size: 2034CDS single in intron: no Alignment % ID: 99.95
txCdsPredict score: 4261.00frame shift in genome: no % Coverage: 99.62
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.