U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    RARE1 Pentatricopeptide repeat (PPR) superfamily protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 831168, updated on 18-Sep-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    RARE1
    Official Full Name
    Pentatricopeptide repeat (PPR) superfamily protein
    Primary source
    TAIR:AT5G13270
    Locus tag
    AT5G13270
    See related
    Araport:AT5G13270
    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
    REQUIRED FOR ACCD RNA EDITING 1; T31B5.90; T31B5_90
    Summary
    Encodes RARE1 (Required for accD RNA Editing 1), a trans-factor essential for C-to-U editing of the chloroplast accD transcript. RARE1 carries 15 PPR (pentatricopeptide repeat) motifs, an E/E+ and a DYW domain (C-terminal tripeptide).
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See RARE1 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    1
    Sequence:
    Chromosome: 5; NC_003076.8 (4246954..4249307, complement)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene RING finger protein Neighboring gene ncRNA Neighboring gene myosin Neighboring gene aspartate kinase 1 Neighboring gene uncharacterized protein Neighboring gene Protein kinase superfamily protein

    Genomic regions, transcripts, and products

    Go to the top of the page Help
    Genomic Sequence:
    NC_003076.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. The DYW domain of RARE1 plays an indispensable role in regulating accD-C794 RNA editing in Arabidopsis thaliana. Liu D, et al. Plant Sci, 2023 Sep. PMID 37263527
    2. The PPR protein RARE1-mediated editing of chloroplast accD transcripts is required for fatty acid biosynthesis and heat tolerance in Arabidopsis. Huang C, et al. Plant Commun, 2023 Jan 9. PMID 36221851, Free PMC Article
    3. RIP1, a member of an Arabidopsis protein family, interacts with the protein RARE1 and broadly affects RNA editing. Bentolila S, et al. Proc Natl Acad Sci U S A, 2012 May 29. PMID 22566615, Free PMC Article
    4. A comparative genomics approach identifies a PPR-DYW protein that is essential for C-to-U editing of the Arabidopsis chloroplast accD transcript. Robbins JC, et al. RNA, 2009 Jun. PMID 19395655, Free PMC Article
    5. Discovering the RNA-Binding Proteome of Plant Leaves with an Improved RNA Interactome Capture Method. Bach-Pages M, et al. Biomolecules, 2020 Apr 24. PMID 32344669, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The DYW domain of RARE1 plays an indispensable role in regulating accD-C794 RNA editing in Arabidopsis thaliana.
      Title: The DYW domain of RARE1 plays an indispensable role in regulating accD-C794 RNA editing in Arabidopsis thaliana.
    2. The PPR protein RARE1-mediated editing of chloroplast accD transcripts is required for fatty acid biosynthesis and heat tolerance in Arabidopsis.
      Title: The PPR protein RARE1-mediated editing of chloroplast accD transcripts is required for fatty acid biosynthesis and heat tolerance in Arabidopsis.
    3. Data show that the presence RIP1 (At3g15000.1) in a protein complex with chloroplast editing factor RARE1 (At5g13270.1) indicates that RIP1 is an important component of the RNA editing apparatus that acts on many chloroplast and mitochondrial C targets.
      Title: RIP1, a member of an Arabidopsis protein family, interacts with the protein RARE1 and broadly affects RNA editing.
    Submit: New GeneRIF Correction

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help
    NM_121330.2

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables cytidine deaminase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables mRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in RNA modification IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within RNA modification IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in mitochondrion ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    Pentatricopeptide repeat (PPR) superfamily protein
    NP_196831.1
    • REQUIRED FOR ACCD RNA EDITING 1 (RARE1); CONTAINS InterPro DOMAIN/s: Pentatricopeptide repeat (InterPro:IPR002885); BEST Arabidopsis thaliana protein match is: Tetratricopeptide repeat (TPR)-like superfamily protein (TAIR:AT3G49170.1); Has 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 0; Metazoa - 736; Fungi - 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    Genome Annotation

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

    Reference assembly

    Genomic

    1. NC_003076.8 Reference assembly

      Range
      4246954..4249307 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_121330.2 → NP_196831.1  Pentatricopeptide repeat (PPR) superfamily protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_196831.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9LYU9
      UniProtKB/TrEMBL
      A0A5S9Y418
      Conserved Domains (5) summary
      TIGR00756
      Location:454 → 488
      PPR; pentatricopeptide repeat domain (PPR motif)
      sd00004
      Location:455 → 482
      PPR; PPR repeat [structural motif]
      pfam01535
      Location:352 → 381
      PPR; PPR repeat
      pfam13041
      Location:451 → 500
      PPR_2; PPR repeat family
      pfam14432
      Location:627 → 742
      DYW_deaminase; DYW family of nucleic acid deaminases
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9LYU9.1

    Gene LinkOut

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

    Molecular Biology Databases
    Research Materials
    Tools