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

Gene ID: 32153, updated on 4-Jan-2025

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, Jan 2025]
Orthologs
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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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