Human Gene WDR48 (uc011ayt.1)
  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].
Transcript (Including UTRs)
   Position: hg19 chr3:39,093,507-39,136,905 Size: 43,399 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 LinksPrimersMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:39,093,507-39,136,905)mRNA (may differ from genome)Protein (668 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMalacardsMGI
OMIMPubMedReactomeTreefamUniProtKBBioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  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 -186.12671-0.277 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
  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 Q8TAF3-3
FrontTopSide
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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  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.

-  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: AK302307, KIAA1449, NM_020839, NP_065890, Q8TAF3-3, UAF1
UCSC ID: uc011ayt.1
RefSeq Accession: NM_020839
Protein: Q8TAF3-3, splice isoform of Q8TAF3 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: AK302307.1
exon count: 19CDS single in 3' UTR: no RNA size: 2134
ORF size: 2007CDS single in intron: no Alignment % ID: 99.77
txCdsPredict score: 4207.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # 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.