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    Upf1 Upf1 RNA helicase [ Drosophila melanogaster (fruit fly) ]

    Gene ID: 32153, updated on 17-Dec-2024

    Summary

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    Official Symbol
    Upf1provided by FlyBase
    Official Full Name
    Upf1 RNA helicaseprovided by FlyBase
    Primary source
    FLYBASE:FBgn0030354
    Locus tag
    Dmel_CG1559
    See related
    AllianceGenome:FB:FBgn0030354
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Drosophila melanogaster
    Lineage
    Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora
    Also known as
    CG1559; Dm-Upf1; Dmel\CG1559; DmUpf1; dUPF1; smg-2; upf1; UPF1; Upf1p
    Summary
    Predicted to enable ATP hydrolysis activity; RNA binding activity; and helicase activity. Involved in cellular response to hypoxia; nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; and positive regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay. Located in neuronal ribonucleoprotein granule. Is expressed in adult head. Orthologous to human UPF1 (UPF1 RNA helicase and ATPase). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See Upf1 in Genome Data Viewer
    Location:
    10F4-10F4; 1-37 cM
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    Release 6.54 current Release 6 plus ISO1 MT (GCF_000001215.4) X NC_004354.4 (11899996..11905371, complement)
    Release 5.57 previous assembly Release 5 (GCF_000001215.2) X NC_004354.3 (11794029..11799404, complement)

    Chromosome X - NC_004354.4Genomic Context describing neighboring genes Neighboring gene severe impairment of CI with lengthened youth Neighboring gene wispy Neighboring gene uncharacterized protein Neighboring gene papillote

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Evidence of slightly increased Pol II pausing in UPF1-depleted Drosophila melanogaster cells. Singh AK, et al. MicroPubl Biol, 2020 Oct 16. PMID 33274326, Free PMC Article
    2. A Hox gene mutation that triggers nonsense-mediated RNA decay and affects alternative splicing during Drosophila development. Alonso CR, et al. Nucleic Acids Res, 2003 Jul 15. PMID 12853602, Free PMC Article
    3. UPF1 reduces C9orf72 HRE-induced neurotoxicity in the absence of nonsense-mediated decay dysfunction. Zaepfel BL, et al. Cell Rep, 2021 Mar 30. PMID 33789100, Free PMC Article
    4. The protein Mago provides a link between splicing and mRNA localization. Le Hir H, et al. EMBO Rep, 2001 Dec. PMID 11743026, Free PMC Article
    5. Diverse forms of RPS9 splicing are part of an evolving autoregulatory circuit. Plocik AM, et al. PLoS Genet, 2012. PMID 22479208, Free PMC Article

    See all (82) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Here the authors offer evidence, obtained from Drosophila, that UPF1 constantly moves between the nucleus and cytoplasm by a mechanism that requires its RNA helicase activity. Cells depleted of UPF1 show defects in the release of mRNAs from transcription sites and their export from the nucleus.
      Title: The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from gene loci.
    2. the lethality of upf1 and upf2 mutants is not due to disrupting their roles during Nonsense-mediated RNA decay (NMD) -independent processes, but to their function in the degradation of specific mRNAs by the NMD pathway.
      Title: Drosophila Upf1 and Upf2 loss of function inhibits cell growth and causes animal death in a Upf3-independent manner.
    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 FlyBase

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA helicase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables double-stranded DNA helicase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA duplex unwinding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cellular response to hypoxia IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    NOT involved_in miRNA-mediated post-transcriptional gene silencing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    NOT involved_in regulatory ncRNA-mediated post-transcriptional gene silencing 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
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in neuronal ribonucleoprotein granule IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    Upf1 RNA helicase
    Names
    CG1559-PA
    CG1559-PB
    Upf1-PA
    Upf1-PB
    up-frameshift suppressor 1
    NP_001285145.1
    NP_572767.1

    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_004354.4 Reference assembly

      Range
      11899996..11905371 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_132539.3 → NP_572767.1  Upf1 RNA helicase, isoform A [Drosophila melanogaster]

      See identical proteins and their annotated locations for NP_572767.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q95RG9, Q9VYS3
      UniProtKB/TrEMBL
      X2JBC1
      Related
      FBpp0073433
      Conserved Domains (5) summary
      COG1112
      Location:122 → 897
      DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
      pfam05859
      Location:210 → 299
      Mis12; Mis12 protein
      pfam09416
      Location:98 → 249
      UPF1_Zn_bind; RNA helicase (UPF2 interacting domain)
      pfam13087
      Location:661 → 857
      AAA_12; AAA domain
      pfam13245
      Location:458 → 515
      AAA_19; Part of AAA domain

    2. NM_001298216.1 → NP_001285145.1  Upf1 RNA helicase, isoform B [Drosophila melanogaster]

      See identical proteins and their annotated locations for NP_001285145.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q95RG9, Q9VYS3
      UniProtKB/TrEMBL
      X2JBC1
      Conserved Domains (5) summary
      COG1112
      Location:122 → 897
      DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
      pfam05859
      Location:210 → 299
      Mis12; Mis12 protein
      pfam09416
      Location:98 → 249
      UPF1_Zn_bind; RNA helicase (UPF2 interacting domain)
      pfam13087
      Location:661 → 857
      AAA_12; AAA domain
      pfam13245
      Location:458 → 515
      AAA_19; Part of AAA domain
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9VYS3.2 Q9VYS3
    X2JBC1 X2JBC1

    Gene LinkOut

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