Human Gene WDR3 (ENST00000349139.6_4) from GENCODE V47lift37
  Description: WD repeat domain 3 (from RefSeq NM_006784.3)
Gencode Transcript: ENST00000349139.6_4
Gencode Gene: ENSG00000065183.16_7
Transcript (Including UTRs)
   Position: hg19 chr1:118,472,362-118,509,166 Size: 36,805 Total Exon Count: 27 Strand: +
Coding Region
   Position: hg19 chr1:118,475,943-118,502,070 Size: 26,128 Coding Exon Count: 26 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:118,472,362-118,509,166)mRNA (may differ from genome)Protein (943 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: WDR3_HUMAN
DESCRIPTION: RecName: Full=WD repeat-containing protein 3;
SUBCELLULAR LOCATION: Nucleus, nucleolus.
TISSUE SPECIFICITY: Ubiquitous.
SIMILARITY: Belongs to the WD repeat WDR3/UTP12 family.
SIMILARITY: Contains 13 WD repeats.

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 20.50 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 264.71 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
5' UTR -20.3076-0.267 Picture PostScript Text
3' UTR -2030.097096-0.286 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
IPR020472 - G-protein_beta_WD-40_rep
IPR007148 - SSU_processome_Utp12
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
PF04003 - Dip2/Utp12 Family
PF12894 - Anaphase-promoting complex subunit 4 WD40 domain

SCOP Domains:
50952 - Soluble quinoprotein glucose dehydrogenase
50956 - Thermostable phytase (3-phytase)
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
117289 - Nucleoporin domain
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Peptidase/esterase 'gauge' domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - DPP6 N-terminal domain-like

ModBase Predicted Comparative 3D Structure on Q9UNX4
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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 orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0030515 snoRNA binding

Biological Process:
GO:0006364 rRNA processing
GO:0030490 maturation of SSU-rRNA

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0031965 nuclear membrane
GO:0032040 small-subunit processome
GO:0034388 Pwp2p-containing subcomplex of 90S preribosome


-  Descriptions from all associated GenBank mRNAs
  LF206258 - JP 2014500723-A/13761: Polycomb-Associated Non-Coding RNAs.
LP895151 - Sequence 15 from Patent EP3253886.
AK292438 - Homo sapiens cDNA FLJ77605 complete cds, highly similar to Homo sapiens WD repeat domain 3 (WDR3), mRNA.
AF083217 - Homo sapiens WD repeat protein WDR3 (WDR3) mRNA, complete cds.
BC128385 - Homo sapiens cDNA clone IMAGE:40123306.
BC128454 - Homo sapiens cDNA clone IMAGE:40123297.
BC148244 - Homo sapiens cDNA clone IMAGE:40123299.
AK022858 - Homo sapiens cDNA FLJ12796 fis, clone NT2RP2002058, highly similar to WD repeat protein 3.
MA441835 - JP 2018138019-A/13761: Polycomb-Associated Non-Coding RNAs.
BC058836 - Homo sapiens WD repeat domain 3, mRNA (cDNA clone IMAGE:6745281), complete cds.
KJ902170 - Synthetic construct Homo sapiens clone ccsbBroadEn_11564 WDR3 gene, encodes complete protein.
LF352720 - JP 2014500723-A/160223: Polycomb-Associated Non-Coding RNAs.
LF352718 - JP 2014500723-A/160221: Polycomb-Associated Non-Coding RNAs.
LF352717 - JP 2014500723-A/160220: Polycomb-Associated Non-Coding RNAs.
LF352716 - JP 2014500723-A/160219: Polycomb-Associated Non-Coding RNAs.
MA588297 - JP 2018138019-A/160223: Polycomb-Associated Non-Coding RNAs.
MA588295 - JP 2018138019-A/160221: Polycomb-Associated Non-Coding RNAs.
MA588294 - JP 2018138019-A/160220: Polycomb-Associated Non-Coding RNAs.
MA588293 - JP 2018138019-A/160219: Polycomb-Associated Non-Coding RNAs.
AB209201 - Homo sapiens mRNA for WD repeat-containing protein 3 variant protein.
LF352714 - JP 2014500723-A/160217: Polycomb-Associated Non-Coding RNAs.
LF352713 - JP 2014500723-A/160216: Polycomb-Associated Non-Coding RNAs.
LF352712 - JP 2014500723-A/160215: Polycomb-Associated Non-Coding RNAs.
LF352711 - JP 2014500723-A/160214: Polycomb-Associated Non-Coding RNAs.
LF352709 - JP 2014500723-A/160212: Polycomb-Associated Non-Coding RNAs.
JD203968 - Sequence 184992 from Patent EP1572962.
JD183429 - Sequence 164453 from Patent EP1572962.
JD218028 - Sequence 199052 from Patent EP1572962.
LF352708 - JP 2014500723-A/160211: Polycomb-Associated Non-Coding RNAs.
JD102433 - Sequence 83457 from Patent EP1572962.
JD411027 - Sequence 392051 from Patent EP1572962.
JD434182 - Sequence 415206 from Patent EP1572962.
AK055194 - Homo sapiens cDNA FLJ30632 fis, clone CTONG2002417.
MA588291 - JP 2018138019-A/160217: Polycomb-Associated Non-Coding RNAs.
MA588290 - JP 2018138019-A/160216: Polycomb-Associated Non-Coding RNAs.
MA588289 - JP 2018138019-A/160215: Polycomb-Associated Non-Coding RNAs.
MA588288 - JP 2018138019-A/160214: Polycomb-Associated Non-Coding RNAs.
MA588286 - JP 2018138019-A/160212: Polycomb-Associated Non-Coding RNAs.
MA588285 - JP 2018138019-A/160211: Polycomb-Associated Non-Coding RNAs.

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

Protein Q9UNX4 (Reactome details) participates in the following event(s):

R-HSA-6790906 EMG1 of the SSU processome methylates pseudouridine-1248 of 18S rRNA yielding N(1)-methylpseudouridine-1248
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-6790901 rRNA modification in the nucleus and cytosol
R-HSA-8868773 rRNA processing in the nucleus and cytosol
R-HSA-72312 rRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000349139.1, ENST00000349139.2, ENST00000349139.3, ENST00000349139.4, ENST00000349139.5, NM_006784, Q9UNX4, uc317xud.1, uc317xud.2, WDR3 , WDR3_HUMAN
UCSC ID: ENST00000349139.6_4
RefSeq Accession: NM_006784.3
Protein: Q9UNX4 (aka WDR3_HUMAN)

-  Gene Model Information
  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.