UPF3 Smg-4/UPF3 family protein [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: UPF3
Official Full Name: Smg-4/UPF3 family protein
Primary source: TAIR:AT1G33980
Locus tag: AT1G33980
See related: Araport:AT1G33980
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: ATUPF3; F12G12.20; F12G12_20
Summary: Involved in mRNA surveillance, detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD)
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Genomic context

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See UPF3 in Genome Data Viewer

Location:: chromosome: 1

Exon count:: 13

Sequence:: Chromosome: 1; NC_003070.9 (12351566..12355173)

Chromosome 1 - NC_003070.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003070.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The results demonstrate that, in contrast to mammalian cells, a delicate balance of UPF3 transcript levels by its feedback loop and by restriction of its transcription, are crucial for proper nonsense-mediated-decay regulation in Arabidopsis.
Title: The feedback control of UPF3 is crucial for RNA surveillance in plants.
The involvement of UPF1, UPF2, and UPF3 in development and in response to stresses, wounding and infection by Pseudomonas syringae pv. tomato strain DC3000, were examined.
Title: Arabidopsis plants having defects in nonsense-mediated mRNA decay factors UPF1, UPF2, and UPF3 show photoperiod-dependent phenotypes in development and stress responses.
UPF1 and UPF3, which are key nonsense-mediated mRNA decay factors, may act as defense-related regulators associated with plant immunity.
Title: Nonsense-mediated mRNA decay factors, UPF1 and UPF3, contribute to plant defense.
Here, we analyzed the abundances of all splice variants for each alternatively spliced gene in an Arabidopsis mutant that lacks UPF3, one of the core components of NMD machinery, to determine if the PTC-containing transcripts are degraded by NMD.
Title: Extensive coupling of alternative splicing of pre-mRNAs of serine/arginine (SR) genes with nonsense-mediated decay.
The nonsense-mediated decay factor UPF3 localize to the nucleolus, suggesting that the Arabidopsis nucleolus is therefore involved in identifying aberrant mRNAs and NMD.
Title: Aberrant mRNA transcripts and the nonsense-mediated decay proteins UPF2 and UPF3 are enriched in the Arabidopsis nucleolus.
Data show that in mutants impaired in the nonsense-mediated decay (NMD) components UPF3, levels of the alternatively spliced AtGRP7 and AtGRP8 transcripts are strongly elevated, implicating UPF3 in the decay of these clock-regulated transcripts.
Title: Auto-regulation of the circadian slave oscillator component AtGRP7 and regulation of its targets is impaired by a single RNA recognition motif point mutation.
Our results indicate that the AtUPF3 gene is required by the plant nonsense-mediated mRNA decay system to obviate aberrantly spliced mRNA.
Title: UPF3 suppresses aberrant spliced mRNA in Arabidopsis.

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Pathways from PubChem

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General gene information

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NM_001123934.1

Supported by ESTs:

NM_103120.4

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables mRNA binding	HDA more info	PubMed

Process	Evidence Code	Pubs
involved_in defense response to bacterium	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in jasmonic acid mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in long-day photoperiodism	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to wounding	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in salicylic acid mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	HDA more info	PubMed
located_in nucleus	ISM Inferred from Sequence Model more info

General protein information

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Preferred Names: Smg-4/UPF3 family protein

NP_001117406.1

UPF3; FUNCTIONS IN: nucleotide binding; INVOLVED IN: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; LOCATED IN: cellular_component unknown; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Nucleotide-binding, alpha-beta plait (InterPro:IPR012677), Regulator of nonsense-mediated decay, UPF3 (InterPro:IPR005120); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink).

NP_174660.2

UPF3; FUNCTIONS IN: nucleotide binding; INVOLVED IN: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; LOCATED IN: cellular_component unknown; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Nucleotide-binding, alpha-beta plait (InterPro:IPR012677), Regulator of nonsense-mediated decay, UPF3 (InterPro:IPR005120); Has 779 Blast hits to 748 proteins in 191 species: Archae - 0; Bacteria - 17; Metazoa - 416; Fungi - 147; Plants - 73; Viruses - 0; Other Eukaryotes - 126 (source: NCBI BLink).