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    RRP9 ribosomal RNA processing 9, U3 small nucleolar RNA binding protein [ Homo sapiens (human) ]

    Gene ID: 9136, updated on 10-Dec-2024

    Summary

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    Official Symbol
    RRP9provided by HGNC
    Official Full Name
    ribosomal RNA processing 9, U3 small nucleolar RNA binding proteinprovided by HGNC
    Primary source
    HGNC:HGNC:16829
    See related
    Ensembl:ENSG00000114767 MIM:620013; AllianceGenome:HGNC:16829
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    U3-55K; RNU3IP2
    Summary
    This gene encodes a member of the WD-repeat protein family. The encoded protein is a component of the nucleolar small nuclear ribonucleoprotein particle (snoRNP) and is essential for 18s rRNA processing during ribosome synthesis. It contains seven WD domains required for nucleolar localization and specific interaction with the U3 small nucleolar RNA (U3 snoRNA). [provided by RefSeq, Oct 2012]
    Expression
    Ubiquitous expression in appendix (RPKM 6.7), adrenal (RPKM 6.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RRP9 in Genome Data Viewer
    Location:
    3p21.2
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (51933429..51941904, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (51966348..51974823, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (51967445..51975920, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene IQCF5 antisense RNA 1 Neighboring gene IQ motif containing F5 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:51935927-51937126 Neighboring gene IQ motif containing F1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:51975282-51975930 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19921 Neighboring gene poly(ADP-ribose) polymerase family member 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:51990057-51990645 Neighboring gene G protein-coupled receptor 62 Neighboring gene poly(rC) binding protein 4

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Anti-U3 RNP autoantibodies in systemic sclerosis. Aggarwal R, et al. Arthritis Rheum, 2009 Apr. PMID 19333934
    2. The hU3-55K protein requires 15.5K binding to the box B/C motif as well as flanking RNA elements for its association with the U3 small nucleolar RNA in Vitro. Granneman S, et al. J Biol Chem, 2002 Dec 13. PMID 12381732
    3. Interaction of the U3-55k protein with U3 snoRNA is mediated by the box B/C motif of U3 and the WD repeats of U3-55k. Lukowiak AA, et al. Nucleic Acids Res, 2000 Sep 15. PMID 10982864, Free PMC Article
    4. cDNA cloning and characterization of the human U3 small nucleolar ribonucleoprotein complex-associated 55-kilodalton protein. Pluk H, et al. Mol Cell Biol, 1998 Jan. PMID 9418896, Free PMC Article
    5. A weak C' box renders U3 snoRNA levels dependent on hU3-55K binding. Knox AA, et al. Mol Cell Biol, 2011 Jun. PMID 21505065, Free PMC Article

    See all (96) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Joint effect of RRP9 and DDX21 on development of colorectal cancer and keloid.
      Title: Joint effect of RRP9 and DDX21 on development of colorectal cancer and keloid.
    2. RRP9 and DDX21 as new biomarkers of colorectal cancer.
      Title: RRP9 and DDX21 as new biomarkers of colorectal cancer.
    3. Neddylation modification of the U3 snoRNA-binding protein RRP9 by Smurf1 promotes tumorigenesis.
      Title: Neddylation modification of the U3 snoRNA-binding protein RRP9 by Smurf1 promotes tumorigenesis.
    4. Data show that U3 snoRNP assembly, and therefore U3 snoRNA accumulation, is regulated through the U3-specific protein hU3-55K.
      Title: A weak C' box renders U3 snoRNA levels dependent on hU3-55K binding.
    5. the frequencies of African American race and male sex are greater among systemic sclerosis patients with anti-U3 RNP antibody than those without
      Title: Anti-U3 RNP autoantibodies in systemic sclerosis.
    6. Mammalian and yeast U3 snoRNPs are matured in specific and related nuclear compartments.
      Title: Mammalian and yeast U3 snoRNPs are matured in specific and related nuclear compartments.
    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)

    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 
    contributes_to U3 snoRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables U3 snoRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables snoRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in rRNA processing IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in rRNA processing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in ribosomal small subunit biogenesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of box C/D methylation guide snoRNP complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    U3 small nucleolar RNA-interacting protein 2
    Names
    RNA, U3 small nucleolar interacting protein 2
    RRP9 homolog
    RRP9, small subunit (SSU) processome component, homolog
    U3 small nucleolar ribonucleoprotein-associated 55 kDa protein
    U3 snoRNP-associated 55-kDa protein
    ribosomal RNA processing 9, small subunit (SSU) processome component, homolog

    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_004704.5 → NP_004695.1  U3 small nucleolar RNA-interacting protein 2

      See identical proteins and their annotated locations for NP_004695.1

      Status: REVIEWED

      Source sequence(s)
      AA465355, AC115284, BC010048
      Consensus CDS
      CCDS2837.1
      UniProtKB/Swiss-Prot
      B2R996, O43818, Q8IZ30
      Related
      ENSP00000232888.6, ENST00000232888.7
      Conserved Domains (2) summary
      cd00200
      Location:139 → 439
      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 ...
      sd00039
      Location:149 → 197
      7WD40; WD40 repeat [structural motif]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      51933429..51941904 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047449172.1 → XP_047305128.1  U3 small nucleolar RNA-interacting protein 2 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      51966348..51974823 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348335.1 → XP_054204310.1  U3 small nucleolar RNA-interacting protein 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O43818.1 GenPept UniProtKB/Swiss-Prot:O43818

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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