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    CAF2 RNA-binding CRS1 / YhbY (CRM) domain-containing protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 838948, updated on 18-Sep-2024

    Summary

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    Official Symbol
    CAF2
    Official Full Name
    RNA-binding CRS1 / YhbY (CRM) domain-containing protein
    Primary source
    TAIR:AT1G23400
    Locus tag
    AT1G23400
    See related
    Araport:AT1G23400
    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
    ARABIDOPSIS THALIANA HOMOLOG OF MAIZE CAF2; ATCAF2; F26F24.27; F26F24_27
    Summary
    Promotes the splicing of chloroplast group II introns.
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    Genomic context

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    See CAF2 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    6
    Sequence:
    Chromosome: 1; NC_003070.9 (8311984..8315876, complement)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene Kelch repeat-containing F-box family protein Neighboring gene Ribosomal protein S27a / Ubiquitin family protein Neighboring gene Plant-specific transcription factor YABBY family protein Neighboring gene ncRNA

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003070.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. CAF Proteins Help SOT1 Regulate the Stability of Chloroplast ndhA Transcripts. Li X, et al. Int J Mol Sci, 2021 Nov 23. PMID 34884441, Free PMC Article
    2. Arabidopsis orthologs of maize chloroplast splicing factors promote splicing of orthologous and species-specific group II introns. Asakura Y, et al. Plant Physiol, 2006 Dec. PMID 17071648, Free PMC Article
    3. Formation of the CRS2-CAF2 group II intron splicing complex is mediated by a 22-amino acid motif in the COOH-terminal region of CAF2. Ostheimer GJ, et al. J Biol Chem, 2006 Feb 24. PMID 16379013
    4. 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
    5. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Theologis A, et al. Nature, 2000 Dec 14. PMID 11130712

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The mutant phenotype associated with T-DNA insertions in the Arabidopsis gene AtCAF2, encoding the ortholog of the maize chloroplast splicing factor CAF2, was examined.
      Title: Arabidopsis orthologs of maize chloroplast splicing factors promote splicing of orthologous and species-specific group II introns.
    2. a 22-amino acid motif in the COOH-terminal region of CAF2 mediates formation of the CRS2-CAF2 group II intron splicing complex [CAF2]
      Title: Formation of the CRS2-CAF2 group II intron splicing complex is mediated by a 22-amino acid motif in the COOH-terminal region of CAF2.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    NM_102189.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables mRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within Group II intron splicing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chloroplast ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    RNA-binding CRS1 / YhbY (CRM) domain-containing protein
    NP_173754.2
    • CAF2; FUNCTIONS IN: RNA binding; INVOLVED IN: Group II intron splicing; LOCATED IN: chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: RNA-binding, CRM domain (InterPro:IPR001890); BEST Arabidopsis thaliana protein match is: RNA-binding CRS1 / YhbY (CRM) domain-containing protein (TAIR:AT2G20020.1); Has 265 Blast hits to 223 proteins in 15 species: Archae - 0; Bacteria - 0; Metazoa - 1; Fungi - 2; Plants - 261; Viruses - 0; Other Eukaryotes - 1 (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_003070.9 Reference assembly

      Range
      8311984..8315876 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_102189.4 → NP_173754.2  RNA-binding CRS1 / YhbY (CRM) domain-containing protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_173754.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9LDA9
      UniProtKB/TrEMBL
      A0A178WC04, A0A5S9VMW9, A0A7G2DYH7
      Conserved Domains (1) summary
      smart01103
      Location:203 → 286
      CRS1_YhbY; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9LDA9.1

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