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    RIBOSOMAL RNA PROCESSING 5 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 820370, updated on 18-Sep-2024

    Summary

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    Official Full Name
    RIBOSOMAL RNA PROCESSING 5
    Primary source
    TAIR:AT3G11964
    Locus tag
    AT3G11964
    See related
    Araport:AT3G11964
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    Ribosomal RNA Processing 5; RRP5
    Summary
    Encodes a nucleolar protein that is a ribosome biogenesis co-factor. Mutants display aberrant RNA processing and female gametophyte development.
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    Genomic context

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    Location:
    chromosome: 3
    Exon count:
    40
    Sequence:
    Chromosome: 3; NC_003074.8 (3793731..3806743, complement)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene TRAF-like superfamily protein Neighboring gene Cleavage and polyadenylation specificity factor (CPSF) A subunit protein Neighboring gene pseudo Neighboring gene Jojoba acyl CoA reductase-related male sterility protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003074.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. 40S ribosome biogenesis co-factors are essential for gametophyte and embryo development. Missbach S, et al. PLoS One, 2013. PMID 23382868, Free PMC Article
    2. Large-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry. Nühse TS, et al. Mol Cell Proteomics, 2003 Nov. PMID 14506206
    3. Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions. Pendle AF, et al. Mol Biol Cell, 2005 Jan. PMID 15496452, Free PMC Article
    4. Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism. Ito J, et al. J Proteome Res, 2011 Apr 1. PMID 21166475
    5. Advanced proteomic analyses yield a deep catalog of ubiquitylation targets in Arabidopsis. Kim DY, et al. Plant Cell, 2013 May. PMID 23667124, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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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    NM_112030.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within embryo sac development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within rRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    NOT located_in cytosol RCA
    inferred from Reviewed Computational Analysis
    more info
    		 PubMed 
    located_in nucleolus HDA PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  
    located_in plasma membrane HDA PubMed 

    General protein information

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    Preferred Names
    RIBOSOMAL RNA PROCESSING 5
    NP_187803.4
    • RNA binding;RNA binding; FUNCTIONS IN: RNA binding; INVOLVED IN: mRNA processing, RNA processing; LOCATED IN: nucleolus, plasma membrane; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Nucleic acid-binding, OB-fold (InterPro:IPR012340), Nucleic acid-binding, OB-fold-like (InterPro:IPR016027), Ribosomal protein S1, RNA-binding domain (InterPro:IPR003029), RNA-processing protein, HAT helix (InterPro:IPR003107), Suppressor of forked (InterPro:IPR008847); BEST Arabidopsis thaliana protein match is: Tetratricopeptide repeat (TPR)-like superfamily protein (TAIR:AT3G51110.1); Has 43836 Blast hits to 19683 proteins in 2824 species: Archae - 141; Bacteria - 33398; Metazoa - 1103; Fungi - 905; Plants - 756; Viruses - 0; Other Eukaryotes - 7533 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

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

    Reference assembly

    Genomic

    1. NC_003074.8 Reference assembly

      Range
      3793731..3806743 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001337968.1 → NP_001326789.1  RIBOSOMAL RNA PROCESSING 5 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      F4J8K6, Q9C7B6, Q9LHM6, Q9SF02
      UniProtKB/TrEMBL
      A0A5S9XCN5
      Conserved Domains (10) summary
      COG0539
      Location:1052 → 1530
      RpsA; Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
      COG5107
      Location:1595 → 1913
      RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
      cd04461
      Location:740 → 821
      S1_Rrp5_repeat_hs8_sc7; Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal ...
      cd05693
      Location:125 → 215
      S1_Rrp5_repeat_hs1_sc1; Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces ...
      cd05694
      Location:222 → 296
      S1_Rrp5_repeat_hs2_sc2; Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces ...
      cd05695
      Location:314 → 382
      S1_Rrp5_repeat_hs3; Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces ...
      cd05698
      Location:577 → 646
      S1_Rrp5_repeat_hs6_sc5; Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces ...
      cd05708
      Location:1457 → 1533
      S1_Rrp5_repeat_sc12; Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces ...
      TIGR00717
      Location:307 → 644
      rpsA; ribosomal protein S1
      sd00006
      Location:1707 → 1740
      TPR; TPR repeat [structural motif]

    2. NM_112030.4 → NP_187803.4  RIBOSOMAL RNA PROCESSING 5 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_187803.4

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VK80, A0A5S9XCN5
      Conserved Domains (13) summary
      smart00316
      Location:473 → 542
      S1; Ribosomal protein S1-like RNA-binding domain
      COG0539
      Location:561 → 1106
      RpsA; Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
      COG5107
      Location:1571 → 1889
      RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
      cd04461
      Location:714 → 795
      S1_Rrp5_repeat_hs8_sc7; S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct ...
      cd05693
      Location:125 → 215
      S1_Rrp5_repeat_hs1_sc1; S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
      cd05694
      Location:222 → 296
      S1_Rrp5_repeat_hs2_sc2; S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
      cd05695
      Location:314 → 382
      S1_Rrp5_repeat_hs3; S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
      cd05698
      Location:562 → 628
      S1_Rrp5_repeat_hs6_sc5; S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
      cd05702
      Location:1028 → 1098
      S1_Rrp5_repeat_hs11_sc8; S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
      cd05703
      Location:1129 → 1200
      S1_Rrp5_repeat_hs12_sc9; S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
      cd05708
      Location:1433 → 1509
      S1_Rrp5_repeat_sc12; S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
      sd00006
      Location:1683 → 1716
      TPR; TPR repeat [structural motif]
      cl09927
      Location:1348 → 1412
      S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    F4J8K6.2

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