Human Gene WDR46 (uc003ods.3) Description and Page Index
  Description: Homo sapiens WD repeat domain 46 (WDR46), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr6:33,246,880-33,257,304 Size: 10,425 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr6:33,247,053-33,256,947 Size: 9,895 Coding Exon Count: 15 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:33,246,880-33,257,304)mRNA (may differ from genome)Protein (610 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: WDR46_HUMAN
DESCRIPTION: RecName: Full=WD repeat-containing protein 46; AltName: Full=WD repeat-containing protein BING4;
SIMILARITY: Contains 6 WD repeats.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): WDR46
CDC HuGE Published Literature: WDR46

-  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: 26.26 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 825.96 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -106.02357-0.297 Picture PostScript Text
3' UTR -66.70173-0.386 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
IPR012952 - BING4_C_dom
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR017986 - WD40_repeat_dom

Pfam Domains:
PF00400 - WD domain, G-beta repeat
PF08149 - BING4CT (NUC141) domain

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 O15213
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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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

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

Biological Process:
GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0006364 rRNA processing

Cellular Component:
GO:0005575 cellular_component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0030686 90S preribosome
GO:0032040 small-subunit processome


-  Descriptions from all associated GenBank mRNAs
  BC000388 - Homo sapiens WD repeat domain 46, mRNA (cDNA clone MGC:8435 IMAGE:2821198), complete cds.
AF447870 - Homo sapiens FP221 mRNA, complete cds.
AK297925 - Homo sapiens cDNA FLJ51004 complete cds, highly similar to WD repeat protein 46.
AK292616 - Homo sapiens cDNA FLJ77639 complete cds.
AK292171 - Homo sapiens cDNA FLJ77705 complete cds.
JD222501 - Sequence 203525 from Patent EP1572962.
JD203161 - Sequence 184185 from Patent EP1572962.
JD539121 - Sequence 520145 from Patent EP1572962.
JD555091 - Sequence 536115 from Patent EP1572962.
JD305229 - Sequence 286253 from Patent EP1572962.
JD323217 - Sequence 304241 from Patent EP1572962.
AK298151 - Homo sapiens cDNA FLJ51014 complete cds, highly similar to WD repeat protein 46.
JD221069 - Sequence 202093 from Patent EP1572962.
JD078187 - Sequence 59211 from Patent EP1572962.
AK315616 - Homo sapiens cDNA, FLJ96697.
KJ897991 - Synthetic construct Homo sapiens clone ccsbBroadEn_07385 WDR46 gene, encodes complete protein.
AK311388 - Homo sapiens cDNA, FLJ18430.
AK308534 - Homo sapiens cDNA, FLJ98575.
CU674188 - Synthetic construct Homo sapiens gateway clone IMAGE:100017738 5' read WDR46 mRNA.
JD460716 - Sequence 441740 from Patent EP1572962.

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

Protein O15213 (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: A6NDP5, BING4, C6orf11, FP221, NM_005452, NP_005443, O15213, Q5HYZ0, Q5STK5, Q5STR3, WDR46_HUMAN
UCSC ID: uc003ods.3
RefSeq Accession: NM_005452
Protein: O15213 (aka WDR46_HUMAN)
CCDS: CCDS4772.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005452.5
exon count: 15CDS single in 3' UTR: no RNA size: 2363
ORF size: 1833CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3607.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 5
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.