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    XRN3 5'-3' exoribonuclease 3 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 843900, updated on 18-Sep-2024

    Summary

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    Official Symbol
    XRN3
    Official Full Name
    5'-3' exoribonuclease 3
    Primary source
    TAIR:AT1G75660
    Locus tag
    AT1G75660
    See related
    Araport:AT1G75660
    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
    5'-3' exoribonuclease 3; 5'-3' EXORIBONUCLEASE 3; AtXRN3; F10A5.15; F10A5_15
    Summary
    Encodes a protein with similarity to yeast 5'-3'exonucleases and can functionally complement the yeast mutations. In Arabidopsis XRN3 acts as a suppressor of posttranscriptional gene silencing. Mutants accumulate excised miRNA products suggesting that XRN3 is involved in degradation of these products.
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    Genomic context

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    See XRN3 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    23
    Sequence:
    Chromosome: 1; NC_003070.9 (28408134..28415118)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene Leucine-rich receptor-like protein kinase family protein Neighboring gene tRNA-Glu Neighboring gene DNA-directed RNA polymerase Neighboring gene glycosyl hydrolase 9B7

    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. Defective XRN3-mediated transcription termination in Arabidopsis affects the expression of protein-coding genes. Krzyszton M, et al. Plant J, 2018 Mar. PMID 29356198
    2. Arabidopsis thaliana XRN2 is required for primary cleavage in the pre-ribosomal RNA. Zakrzewska-Placzek M, et al. Nucleic Acids Res, 2010 Jul. PMID 20338880, Free PMC Article
    3. RNA Polymerase II Read-Through Promotes Expression of Neighboring Genes in SAL1-PAP-XRN Retrograde Signaling. Crisp PA, et al. Plant Physiol, 2018 Dec. PMID 30301775, Free PMC Article
    4. Arabidopsis FIERY1, XRN2, and XRN3 are endogenous RNA silencing suppressors. Gy I, et al. Plant Cell, 2007 Nov. PMID 17993620, Free PMC Article
    5. Novel features of the XRN-family in Arabidopsis: evidence that AtXRN4, one of several orthologs of nuclear Xrn2p/Rat1p, functions in the cytoplasm. Kastenmayer JP, et al. Proc Natl Acad Sci U S A, 2000 Dec 5. PMID 11106401, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. XRN3 expression affects RNA polymerase II termination.
      Title: RNA Polymerase II Read-Through Promotes Expression of Neighboring Genes in SAL1-PAP-XRN Retrograde Signaling.
    2. data suggest that 5'-3' exoribonuclease 3 (XRN3)-mediated changes in the expression of a subset of genes are caused by upstream read-through transcription and these effects are enhanced by RNA-mRNA chimeras generated in xrn3 plants.
      Title: Defective XRN3-mediated transcription termination in Arabidopsis affects the expression of protein-coding genes.
    3. The nuclear exoribonucleases XRN2 and XRN3 the nucleotidase/phosphatase FIERY1 are endogenous posttranscriptional gene silencing suppressors.
      Title: Arabidopsis FIERY1, XRN2, and XRN3 are endogenous RNA silencing suppressors.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    NM_106217.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables 5'-3' RNA exonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables 5'-3' RNA exonuclease activity IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within miRNA catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of post-transcriptional gene silencing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nuclear polyadenylation-dependent rRNA catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in rRNA 5'-end processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    5'-3' exoribonuclease 3
    NP_565114.1
    • 5'-3' exoribonuclease 3 (XRN3); CONTAINS InterPro DOMAIN/s: 5'-3' exoribonuclease 2 (InterPro:IPR017151), Zinc finger, CCHC-type (InterPro:IPR001878), Putative 5-3 exonuclease (InterPro:IPR004859); BEST Arabidopsis thaliana protein match is: exoribonuclease 2 (TAIR:AT5G42540.1); Has 4264 Blast hits to 3505 proteins in 442 species: Archae - 2; Bacteria - 295; Metazoa - 1361; Fungi - 725; Plants - 751; Viruses - 31; Other Eukaryotes - 1099 (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
      28408134..28415118
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_106217.3 → NP_565114.1  5'-3' exoribonuclease 3 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_565114.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8L7A3, Q9FQ03, Q9LR05
      UniProtKB/TrEMBL
      A0A5S9WUP9, A0A654EPI4
      Conserved Domains (1) summary
      COG5049
      Location:1 → 823
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9FQ03.1

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