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    regulator of nonsense transcripts UPF2 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 818511, updated on 18-Sep-2024

    Summary

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    Official Full Name
    regulator of nonsense transcripts UPF2
    Primary source
    TAIR:AT2G39260
    Locus tag
    AT2G39260
    See related
    Araport:AT2G39260
    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
    T16B24.10; T16B24_10
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    Genomic context

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    Location:
    chromosome: 2
    Exon count:
    17
    Sequence:
    Chromosome: 2; NC_003071.7 (16391924..16399812, complement)

    Chromosome 2 - NC_003071.7Genomic Context describing neighboring genes Neighboring gene RNA polymerase I specific transcription initiation factor RRN3 protein Neighboring gene Integrase-type DNA-binding superfamily protein Neighboring gene P-loop containing nucleoside triphosphate hydrolases superfamily protein Neighboring gene ncRNA Neighboring gene Ypt/Rab-GAP domain of gyp1p superfamily protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003071.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Pathogen-Associated Molecular Pattern-Triggered Immunity Involves Proteolytic Degradation of Core Nonsense-Mediated mRNA Decay Factors During the Early Defense Response. Jung HW, et al. Plant Cell, 2020 Apr. PMID 32086363, Free PMC Article
    2. Arabidopsis plants having defects in nonsense-mediated mRNA decay factors UPF1, UPF2, and UPF3 show photoperiod-dependent phenotypes in development and stress responses. Shi C, et al. J Integr Plant Biol, 2012 Feb. PMID 22353561
    3. Aberrant mRNA transcripts and the nonsense-mediated decay proteins UPF2 and UPF3 are enriched in the Arabidopsis nucleolus. Kim SH, et al. Plant Cell, 2009 Jul. PMID 19602621, Free PMC Article
    4. In Planta Determination of the mRNA-Binding Proteome of Arabidopsis Etiolated Seedlings. Reichel M, et al. Plant Cell, 2016 Oct. PMID 27729395, Free PMC Article
    5. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Lin X, et al. Nature, 1999 Dec 16. PMID 10617197

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Data suggests a complex regulatory network, likely composed of light signaling and NMD factor-mediated pathways involving NMD factor proteins, UPF1, UPF2, and UPF3, in influencing plant development and adaption to environmental stresses. [UPF2]
      Title: Arabidopsis plants having defects in nonsense-mediated mRNA decay factors UPF1, UPF2, and UPF3 show photoperiod-dependent phenotypes in development and stress responses.
    2. The nonsense-mediated decay factor UPF2 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.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    NM_129484.5

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables mRNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    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 
    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 cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm ISM
    Inferred from Sequence Model
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    regulator of nonsense transcripts UPF2
    NP_181459.4
    • binding;RNA binding; FUNCTIONS IN: RNA binding, binding; INVOLVED IN: translation, RNA metabolic process; LOCATED IN: cellular_component unknown; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Armadillo-type fold (InterPro:IPR016024), MIF4G-like, type 3 (InterPro:IPR003890), Up-frameshift suppressor 2 (InterPro:IPR007193), MIF4-like, type 1/2/3 (InterPro:IPR016021); Has 8683 Blast hits to 5464 proteins in 545 species: Archae - 34; Bacteria - 610; Metazoa - 3010; Fungi - 1047; Plants - 271; Viruses - 134; Other Eukaryotes - 3577 (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_003071.7 Reference assembly

      Range
      16391924..16399812 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_129484.5 → NP_181459.4  regulator of nonsense transcripts UPF2 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_181459.4

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      F4IUX6, O80955
      UniProtKB/TrEMBL
      A0A178W2N7, A0A5S9X5E5, A0A7G2EIJ2
      Conserved Domains (3) summary
      smart00543
      Location:671 → 872
      MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
      pfam04050
      Location:992 → 1122
      Upf2; Up-frameshift suppressor 2
      cl02652
      Location:57 → 196
      MIF4G; MIF4G domain
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    F4IUX6.1

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