Human Gene WDR46 (ENST00000374617.9_7) from GENCODE V47lift37
  Description: WD repeat domain 46, transcript variant 1 (from RefSeq NM_005452.6)
Gencode Transcript: ENST00000374617.9_7
Gencode Gene: ENSG00000227057.10_10
Transcript (Including UTRs)
   Position: hg19 chr6:33,246,885-33,257,016 Size: 10,132 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 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 (chr6:33,246,885-33,257,016)mRNA (may differ from genome)Protein (610 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  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.

-  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: 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
  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 -17.3069-0.251 Picture PostScript Text
3' UTR -65.50168-0.390 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
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 O15213
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-  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

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, ENST00000374617.1, ENST00000374617.2, ENST00000374617.3, ENST00000374617.4, ENST00000374617.5, ENST00000374617.6, ENST00000374617.7, ENST00000374617.8, FP221, NM_005452, O15213, Q5HYZ0, Q5STK5, Q5STR3, uc318lsb.1, uc318lsb.2, WDR46_HUMAN
UCSC ID: ENST00000374617.9_7
RefSeq Accession: NM_005452.6
Protein: O15213 (aka WDR46_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.