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Upf1 UPF1 RNA helicase and ATPase [ Mus musculus (house mouse) ]

Gene ID: 19704, updated on 9-May-2024

Summary

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Official Symbol
Upf1provided by MGI
Official Full Name
UPF1 RNA helicase and ATPaseprovided by MGI
Primary source
MGI:MGI:107995
See related
Ensembl:ENSMUSG00000058301 AllianceGenome:MGI:107995
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
NORF1; Rent1; Upflp; PNORF-1; B430202H16Rik
Summary
Predicted to enable RNA helicase activity; chromatin binding activity; and nucleic acid binding activity. Acts upstream of or within dosage compensation by inactivation of X chromosome. Predicted to be located in chromatin; chromosome, telomeric region; and nucleoplasm. Predicted to be part of exon-exon junction complex and supraspliceosomal complex. Predicted to be active in cytoplasm. Is expressed in cerebral cortex ventricular layer; embryo; and oocyte. Orthologous to human UPF1 (UPF1 RNA helicase and ATPase). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thymus adult (RPKM 29.6), adrenal adult (RPKM 22.9) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
8 B3.3; 8 34.15 cM
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (70784143..70806418, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (70331493..70353423, complement)

Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene homer scaffolding protein 3 Neighboring gene STARR-positive B cell enhancer ABC_E8240 Neighboring gene DEAD box helicase 49 Neighboring gene coatomer protein complex, subunit epsilon Neighboring gene ceramide synthase 1 Neighboring gene growth differentiation factor 1 Neighboring gene STARR-seq mESC enhancer starr_21770 Neighboring gene predicted gene, 51533 Neighboring gene cartilage oligomeric matrix protein Neighboring gene CREB regulated transcription coactivator 1

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. Dysregulated Up-Frameshift Protein 1 Promotes Ulcerative Colitis Pathogenesis Through the TNFR1-NF-κB/MAPKs Pathway. Zhu H, et al. Dig Dis Sci, 2018 Oct. PMID 29959727
  2. Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay. Hurt JA, et al. Genome Res, 2013 Oct. PMID 23766421, Free PMC Article
  3. Rent1, a trans-effector of nonsense-mediated mRNA decay, is essential for mammalian embryonic viability. Medghalchi SM, et al. Hum Mol Genet, 2001 Jan 15. PMID 11152657
  4. Translation-dependent unwinding of stem-loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs. Mino T, et al. Nucleic Acids Res, 2019 Sep 19. PMID 31329944, Free PMC Article
  5. Upf1 regulates neurite outgrowth and branching by transcriptional and post-transcriptional modulation of Arc. Ryu HG, et al. J Cell Sci, 2019 Jan 18. PMID 30584064

See all (54) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. BMSC-Derived Exosomes Carrying lncRNA-ZFAS1 Alleviate Pulmonary Ischemia/Reperfusion Injury by UPF1-Mediated mRNA Decay of FOXD1.
    Title: BMSC-Derived Exosomes Carrying lncRNA-ZFAS1 Alleviate Pulmonary Ischemia/Reperfusion Injury by UPF1-Mediated mRNA Decay of FOXD1.
  2. Aberrant expression of the UPF1 RNA surveillance gene disturbs keratinocyte homeostasis by stabilizing AREG.
    Title: Aberrant expression of the UPF1 RNA surveillance gene disturbs keratinocyte homeostasis by stabilizing AREG.
  3. C9orf72 arginine-rich dipeptide repeats inhibit UPF1-mediated RNA decay via translational repression.
    Title: C9orf72 arginine-rich dipeptide repeats inhibit UPF1-mediated RNA decay via translational repression.
  4. these data reveal that multiple levels of Upf1-mediated inhibition of Arc gene expression may allow neurons to more effectively respond to changes in neuronal activity.
    Title: Upf1 regulates neurite outgrowth and branching by transcriptional and post-transcriptional modulation of Arc.
  5. Translation-dependent unwinding of stem-loops by UPF1 triggers Regnase-1 to degrade inflammatory mRNAs.
    Title: Translation-dependent unwinding of stem-loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs.
  6. Status epilepticus led to increased protein levels of Up-frameshift suppressor 1 homolog (Upf1) within the mouse hippocampus. Upf1 protein levels were also higher in resected hippocampus from patients with intractable temporal lobe epilepsy.
    Title: RNA sequencing of synaptic and cytoplasmic Upf1-bound transcripts supports contribution of nonsense-mediated decay to epileptogenesis.
  7. Downregulation of UPF1 activated the TNFR1-dependent NF-kappaB/MAPKs pathway, and promoting inflammatory responses in colon might act as a causal role in Ulcerative Colitis.
    Title: Dysregulated Up-Frameshift Protein 1 Promotes Ulcerative Colitis Pathogenesis Through the TNFR1-NF-κB/MAPKs Pathway.
  8. Upon removal of TDRD6, the association of several mRNAs with UPF1 and UPF2 is disturbed, and the long 3' UTR-stimulated but not the downstream exon-exon junction triggered pathway of NMD is impaired.This function depends on TDRD6-promoted assembly of mRNA and decay enzymes in Chromatoid bodies .
    Title: Chromatoid Body Protein TDRD6 Supports Long 3' UTR Triggered Nonsense Mediated mRNA Decay.
  9. results identify novel nonsense-mediated mRNA decay (NMD) determinants and targets and provide context for understanding the impact of UPF1 and NMD on the murine embryonic stem cell transcriptome
    Title: Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (1)  1 citation
  • Endonuclease-mediated (2) 

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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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP hydrolysis activity ISO
Inferred from Sequence Orthology
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 ISO
Inferred from Sequence Orthology
more info
  
enables RNA helicase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA helicase activity ISO
Inferred from Sequence Orthology
more info
  
enables chromatin binding ISO
Inferred from Sequence Orthology
more info
  
enables double-stranded DNA helicase activity ISO
Inferred from Sequence Orthology
more info
  
enables helicase activity IEA
Inferred from Electronic Annotation
more info
  
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-containing complex binding ISO
Inferred from Sequence Orthology
more info
  
enables telomeric DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in 3'-UTR-mediated mRNA destabilization ISO
Inferred from Sequence Orthology
more info
  
involved_in DNA duplex unwinding ISO
Inferred from Sequence Orthology
more info
  
involved_in DNA repair ISO
Inferred from Sequence Orthology
more info
  
involved_in DNA replication ISO
Inferred from Sequence Orthology
more info
  
involved_in cell cycle phase transition ISO
Inferred from Sequence Orthology
more info
  
involved_in histone mRNA catabolic process ISO
Inferred from Sequence Orthology
more info
  
involved_in nuclear-transcribed mRNA catabolic process 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 ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of mRNA catabolic process ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within positive regulation of mRNA cis splicing, via spliceosome IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of telomere maintenance ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of translational termination ISO
Inferred from Sequence Orthology
more info
  
involved_in telomere maintenance via semi-conservative replication ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of chromatin ISO
Inferred from Sequence Orthology
more info
  
located_in chromosome, telomeric region ISO
Inferred from Sequence Orthology
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
part_of exon-exon junction complex ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
part_of supraspliceosomal complex ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
regulator of nonsense transcripts 1
Names
ATP-dependent helicase RENT1
UPF1 regulator of nonsense transcripts homolog
regulator of nonsense transcripts 1 (Nonsense mRNA reducing factor 1) (NORF1) (Up-frameshift suppressor 1 homolog)
NP_001116301.1
NP_109605.2
XP_006509667.1
XP_006509668.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001122829.3 → NP_001116301.1  regulator of nonsense transcripts 1 isoform a

    See identical proteins and their annotated locations for NP_001116301.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AC158553
    Consensus CDS
    CCDS52572.1
    UniProtKB/Swiss-Prot
    Q3UG00, Q6GYP5, Q6PHQ5, Q8K0N4, Q99PR4, Q9EPU0
    Related
    ENSMUSP00000075089.7, ENSMUST00000075666.8
    Conserved Domains (2) summary
    COG1112
    Location:140 → 915
    DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
    cd18039
    Location:476 → 709
    DEXXQc_UPF1; DEXXQ-box helicase domain of UPF1

  2. NM_030680.4 → NP_109605.2  regulator of nonsense transcripts 1 isoform b

    See identical proteins and their annotated locations for NP_109605.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (b) is shorter compared to isoform a.
    Source sequence(s)
    AC158553
    Consensus CDS
    CCDS90409.1
    UniProtKB/Swiss-Prot
    Q9EPU0
    Related
    ENSMUSP00000148927.2, ENSMUST00000215817.2
    Conserved Domains (2) summary
    COG1112
    Location:140 → 904
    DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
    cd18039
    Location:465 → 698
    DEXXQc_UPF1; DEXXQ-box helicase domain of UPF1

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000074.7 Reference GRCm39 C57BL/6J

    Range
    70784143..70806418 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006509604.5 → XP_006509667.1  regulator of nonsense transcripts 1 isoform X1

    See identical proteins and their annotated locations for XP_006509667.1

    UniProtKB/Swiss-Prot
    Q3UG00, Q6GYP5, Q6PHQ5, Q8K0N4, Q99PR4, Q9EPU0
    Conserved Domains (2) summary
    COG1112
    Location:140 → 915
    DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
    cd18039
    Location:476 → 709
    DEXXQc_UPF1; DEXXQ-box helicase domain of UPF1

  2. XM_006509605.5 → XP_006509668.1  regulator of nonsense transcripts 1 isoform X1

    See identical proteins and their annotated locations for XP_006509668.1

    UniProtKB/Swiss-Prot
    Q3UG00, Q6GYP5, Q6PHQ5, Q8K0N4, Q99PR4, Q9EPU0
    Conserved Domains (2) summary
    COG1112
    Location:140 → 915
    DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
    cd18039
    Location:476 → 709
    DEXXQc_UPF1; DEXXQ-box helicase domain of UPF1
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9EPU0.2 GenPept UniProtKB/Swiss-Prot:Q9EPU0

Gene LinkOut

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

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