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    upf1 ATP-dependent RNA helicase Upf1 [ Schizosaccharomyces pombe (fission yeast) ]

    Gene ID: 2542327, updated on 18-Sep-2024

    Summary

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    Official Symbol
    upf1
    Official Full Name
    ATP-dependent RNA helicase Upf1
    Primary source
    PomBase:SPAC16C9.06c
    Locus tag
    SPOM_SPAC16C9.06C
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Schizosaccharomyces pombe (strain: 972h-)
    Lineage
    Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces
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    Genomic context

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    See upf1 in Genome Data Viewer
    Location:
    chromosome: I
    Exon count:
    1
    Sequence:
    Chromosome: I; NC_003424.3 (801141..804133, complement)

    Chromosome I - NC_003424.3Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene CCR4-Not complex subunit Mot2 Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene Clr6 histone deacetylase-associated PHD protein-1 Cph1 Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene DYRK family protein kinase Pom2

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003424.3

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Genome-wide chromosomal association of Upf1 is linked to Pol II transcription in Schizosaccharomyces pombe. De S, et al. Nucleic Acids Res, 2022 Jan 11. PMID 34928380, Free PMC Article
    2. Functional characterization of Upf1 targets in Schizosaccharomyces pombe. Matia-González AM, et al. RNA Biol, 2013 Jun. PMID 23619768, Free PMC Article
    3. Upf1, an RNA helicase required for nonsense-mediated mRNA decay, modulates the transcriptional response to oxidative stress in fission yeast. Rodríguez-Gabriel MA, et al. Mol Cell Biol, 2006 Sep. PMID 16914721, Free PMC Article
    4. Schizosaccharomyces pombe centromere protein Mis19 links Mis16 and Mis18 to recruit CENP-A through interacting with NMD factors and the SWI/SNF complex. Hayashi T, et al. Genes Cells, 2014 Jul. PMID 24774534
    5. The S. pombe translation initiation factor eIF4G is Sumoylated and associates with the SUMO protease Ulp2. Jongjitwimol J, et al. PLoS One, 2014. PMID 24818994, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Genome-wide chromosomal association of Upf1 is linked to Pol II transcription in Schizosaccharomyces pombe.
      Title: Genome-wide chromosomal association of Upf1 is linked to Pol II transcription in Schizosaccharomyces pombe.
    2. study defined a population of mRNAs specifically regulated by Upf1; showed Upf2 and Upf3 are required for binding of Upf1 to its RNA targets and for proper response to oxidative stress; demonstrated that Upf1-dependent downregulation of some of its direct targets is necessary for resistance to oxidative stress
      Title: Functional characterization of Upf1 targets in Schizosaccharomyces pombe.
    3. upf1Delta and csx1Delta strains are similarly sensitive to oxidative stress, and the effects of the mutations are not additive, suggesting that Upf1 and Csx1 work in the same pathway to stabilize atf1(+) mRNA during oxidative stress.
      Title: Upf1, an RNA helicase required for nonsense-mediated mRNA decay, modulates the transcriptional response to oxidative stress in fission yeast.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by PomBase

    Function Evidence Code Pubs
    enables ATP binding IC
    Inferred by Curator
    more info
    		  
    enables ATP hydrolysis activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA helicase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables double-stranded DNA helicase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables single-stranded DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of mRNA stability involved in response to oxidative stress IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytosol HDA PubMed 

    General protein information

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    Preferred Names
    ATP-dependent RNA helicase Upf1

    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_003424.3 Reference assembly

      Range
      801141..804133 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001018477.3 → NP_593080.1  ATP-dependent RNA helicase Upf1 [Schizosaccharomyces pombe]

      See identical proteins and their annotated locations for NP_593080.1

      Status: PROVISIONAL

      UniProtKB/Swiss-Prot
      Q09820
      Conserved Domains (4) summary
      COG1112
      Location:66 → 839
      DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
      pfam09416
      Location:44 → 193
      UPF1_Zn_bind; RNA helicase (UPF2 interacting domain)
      pfam13087
      Location:608 → 805
      AAA_12; AAA domain
      cl21455
      Location:392 → 597
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
    Nucleotide Protein
    Heading Accession and Version

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