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    WDR46 WD repeat domain 46 [ Homo sapiens (human) ]

    Gene ID: 9277, updated on 5-May-2024

    Summary

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    Official Symbol
    WDR46provided by HGNC
    Official Full Name
    WD repeat domain 46provided by HGNC
    Primary source
    HGNC:HGNC:13923
    See related
    Ensembl:ENSG00000227057 MIM:611440; AllianceGenome:HGNC:13923
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    UTP7; BING4; FP221; C6orf11
    Summary
    Enables RNA binding activity. Predicted to be involved in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Predicted to be located in nucleoplasm. Predicted to be part of small-subunit processome. Predicted to be active in nucleolus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in appendix (RPKM 10.6), testis (RPKM 10.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    6p21.32
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (33279108..33289239, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (33100470..33110601, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (33246885..33257016, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein S18 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33244298-33245030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33245765-33246496 Neighboring gene beta-1,3-galactosyltransferase 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33255009-33255542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33255543-33256076 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33256611-33257144 Neighboring gene microRNA 6873 Neighboring gene microRNA 6834 Neighboring gene prefoldin subunit 6 Neighboring gene ral guanine nucleotide dissociation stimulator like 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33265070-33265597 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33265684-33266184 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:33266952-33267130 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33267887-33268394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33268395-33268900 Neighboring gene TAP binding protein

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Nucleolar scaffold protein, WDR46, determines the granular compartmental localization of nucleolin and DDX21. Hirai Y, et al. Genes Cells, 2013 Sep. PMID 23848194
    2. WDR46 is a Genetic Risk Factor for Aspirin-Exacerbated Respiratory Disease in a Korean Population. Pasaje CF, et al. Allergy Asthma Immunol Res, 2012 Jul. PMID 22754713, Free PMC Article
    3. Dynamics of WD-repeat containing proteins in SSU processome components. Wada K, et al. Biochem Cell Biol, 2014 Jun. PMID 24754225
    4. Genomic analysis of the Tapasin gene, located close to the TAP loci in the MHC. Herberg JA, et al. Eur J Immunol, 1998 Feb. PMID 9521053
    5. TAPASIN, DAXX, RGL2, HKE2 and four new genes (BING 1, 3 to 5) form a dense cluster at the centromeric end of the MHC. Herberg JA, et al. J Mol Biol, 1998 Apr 10. PMID 9545376

    See all (51) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. When WDR46 was knocked down, nucleolin and DDX21 were mislocalized from the granular component to the edges of the nucleoli.
      Title: Nucleolar scaffold protein, WDR46, determines the granular compartmental localization of nucleolin and DDX21.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    Process Evidence Code Pubs
    involved_in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ribosomal small subunit biogenesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    part_of small-subunit processome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of small-subunit processome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    WD repeat-containing protein 46
    Names
    WD repeat-containing protein BING4

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001164267.2 → NP_001157739.1  WD repeat-containing protein 46 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AK292171, AK298151, BC000388, BX439421
      UniProtKB/TrEMBL
      A0A1U9X8U7, A0A1U9X8W1
      Conserved Domains (3) summary
      smart01033
      Location:386 → 464
      BING4CT; BING4CT (NUC141) domain
      sd00039
      Location:145 → 181
      7WD40; WD40 repeat [structural motif]
      cl25539
      Location:154 → 333
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    2. NM_005452.6 → NP_005443.3  WD repeat-containing protein 46 isoform 1

      See identical proteins and their annotated locations for NP_005443.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK292171, BC000388, DB272479
      Consensus CDS
      CCDS4772.1
      UniProtKB/Swiss-Prot
      A6NDP5, O15213, Q5HYZ0, Q5STK5, Q5STR3
      UniProtKB/TrEMBL
      B0UZZ8, E7EM79
      Related
      ENSP00000363746.4, ENST00000374617.9
      Conserved Domains (4) summary
      smart01033
      Location:440 → 518
      BING4CT; BING4CT (NUC141) domain
      COG2319
      Location:203 → 396
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:199 → 235
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:208 → 387
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      33279108..33289239 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047419523.1 → XP_047275479.1  WD repeat-containing protein 46 isoform X1

    2. XM_047419524.1 → XP_047275480.1  WD repeat-containing protein 46 isoform X2

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      4690589..4700724 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329929.1 → XP_054185904.1  WD repeat-containing protein 46 isoform X1

    2. XM_054329930.1 → XP_054185905.1  WD repeat-containing protein 46 isoform X2

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      4522622..4532757 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330422.1 → XP_054186397.1  WD repeat-containing protein 46 isoform X1

    2. XM_054330423.1 → XP_054186398.1  WD repeat-containing protein 46 isoform X2

    Reference GRCh38.p14 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

      Range
      4715074..4725175 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330915.1 → XP_054186890.1  WD repeat-containing protein 46 isoform X1

    2. XM_054330916.1 → XP_054186891.1  WD repeat-containing protein 46 isoform X2

    Reference GRCh38.p14 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

      Range
      4473279..4483663 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331195.1 → XP_054187170.1  WD repeat-containing protein 46 isoform X4

    2. XM_054331194.1 → XP_054187169.1  WD repeat-containing protein 46 isoform X3

    3. XM_054331196.1 → XP_054187171.1  WD repeat-containing protein 46 isoform X1

    4. XM_054331197.1 → XP_054187172.1  WD repeat-containing protein 46 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      33100470..33110601 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356755.1 → XP_054212730.1  WD repeat-containing protein 46 isoform X1

    2. XM_054356756.1 → XP_054212731.1  WD repeat-containing protein 46 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O15213.3 GenPept UniProtKB/Swiss-Prot:O15213

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