U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

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

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help
Genomic Sequence:
NC_003424.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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

Go to the top of the page Help
Preferred Names
ATP-dependent RNA helicase Upf1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases
Research Materials
Miscellaneous