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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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