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UPF1 UPF1, RNA helicase and ATPase [ Homo sapiens (human) ]

Gene ID: 5976, updated on 20-Jan-2019

Summary

Official Symbol
UPF1provided by HGNC
Official Full Name
UPF1, RNA helicase and ATPaseprovided by HGNC
Primary source
HGNC:HGNC:9962
See related
Ensembl:ENSG00000005007 MIM:601430
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HUPF1; NORF1; RENT1; smg-2; pNORF1
Summary
This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMD to degrade mRNAs containing premature stop codons. This protein is located only in the cytoplasm. When translation ends, it interacts with the protein that is a functional homolog of yeast Upf2p to trigger mRNA decapping. Use of multiple polyadenylation sites has been noted for this gene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
Expression
Ubiquitous expression in testis (RPKM 26.0), kidney (RPKM 17.5) and 25 other tissues See more
Orthologs

Genomic context

See UPF1 in Genome Data Viewer
Location:
19p13.11
Exon count:
24
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 19 NC_000019.10 (18831405..18868232)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (18942744..18979039)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985321 Neighboring gene cartilage oligomeric matrix protein Neighboring gene ceramide synthase 1 Neighboring gene growth differentiation factor 1 Neighboring gene coatomer protein complex subunit epsilon

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
HIV-1 requires UPF1 for nuclear export of viral RNA as shown through siRNA depletion PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify regulator of nonsense transcripts homolog (UPF1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify regulator of nonsense transcripts homolog (UPF1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify regulator of nonsense transcripts homolog (UPF1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify regulator of nonsense transcripts homolog (UPF1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
gag Depletion of UPF1 by siRNA results in a dramatic reduction in steady-state HIV-1 RNA and pr55(Gag), while overexpression of UPF1 leads to a dramatic up-regulation of HIV-1 RNA expression and Gag protein synthesis PubMed
gag The effects given by UPF1 on HIV-1 RNA expression and Gag protein synthesis are dependent on its ATPase activity PubMed
retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human regulator of nonsense transcripts homolog (yeast) (UPF1) at amino acid residues 727-728 by the HIV-1 protease PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Exon junction complex (EJC), organism-specific biosystem (from KEGG)
    Exon junction complex (EJC), organism-specific biosystemStructural complex; Genetic information processing; RNA processing
  • Exon junction complex (EJC), conserved biosystem (from KEGG)
    Exon junction complex (EJC), conserved biosystemStructural complex; Genetic information processing; RNA processing
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC), organism-specific biosystem (from REACTOME)
    Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC), organism-specific biosystemDuring normal translation termination eRF3 associates with the ribosome and then interacts with PABP bound to the polyadenylate tail of the mRNA to release the ribosome and allow a new round of trans...
  • Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC), organism-specific biosystem (from REACTOME)
    Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC), organism-specific biosystemNonsense-mediated decay has been observed with mRNAs that do not have an exon junction complex (EJC) downstream of the termination codon (reviewed in Isken and Maquat 2007, Chang et al. 2007, Behm-An...
  • Nonsense-Mediated Decay (NMD), organism-specific biosystem (from REACTOME)
    Nonsense-Mediated Decay (NMD), organism-specific biosystemThe Nonsense-Mediated Decay (NMD) pathway activates the destruction of mRNAs containing premature termination codons (PTCs) (reviewed in Isken and Maquat 2007, Chang et al. 2007, Behm-Ansmant et al. ...
  • RNA transport, organism-specific biosystem (from KEGG)
    RNA transport, organism-specific biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
  • RNA transport, conserved biosystem (from KEGG)
    RNA transport, conserved biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
  • mRNA surveillance pathway, organism-specific biosystem (from KEGG)
    mRNA surveillance pathway, organism-specific biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...
  • mRNA surveillance pathway, conserved biosystem (from KEGG)
    mRNA surveillance pathway, conserved biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ43809, FLJ46894, KIAA0221

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
ATP-dependent RNA helicase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ATP-dependent RNA helicase activity IDA
Inferred from Direct Assay
more info
PubMed 
RNA binding HDA PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA binding NAS
Non-traceable Author Statement
more info
PubMed 
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
helicase activity NAS
Non-traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
telomeric DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
3'-UTR-mediated mRNA destabilization IDA
Inferred from Direct Assay
more info
PubMed 
3'-UTR-mediated mRNA destabilization IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA repair IDA
Inferred from Direct Assay
more info
PubMed 
DNA replication IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell cycle phase transition IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to interleukin-1 IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to lipopolysaccharide IDA
Inferred from Direct Assay
more info
PubMed 
dosage compensation by inactivation of X chromosome IEA
Inferred from Electronic Annotation
more info
 
histone mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
mRNA export from nucleus TAS
Traceable Author Statement
more info
PubMed 
nuclear-transcribed mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay IMP
Inferred from Mutant Phenotype
more info
PubMed 
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IDA
Inferred from Direct Assay
more info
PubMed 
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IMP
Inferred from Mutant Phenotype
more info
PubMed 
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay NAS
Non-traceable Author Statement
more info
PubMed 
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS
Traceable Author Statement
more info
PubMed 
positive regulation of mRNA catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of telomere maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of translational termination IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of translational termination NAS
Non-traceable Author Statement
more info
PubMed 
telomere maintenance via semi-conservative replication IDA
Inferred from Direct Assay
more info
PubMed 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
P-body IEA
Inferred from Electronic Annotation
more info
 
chromatin IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm NAS
Non-traceable Author Statement
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
exon-exon junction complex IDA
Inferred from Direct Assay
more info
PubMed 
nuclear chromosome, telomeric region IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
supraspliceosomal complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
regulator of nonsense transcripts 1
Names
ATP-dependent helicase RENT1
UPF1 regulator of nonsense transcripts homolog
delta helicase
nonsense mRNA reducing factor 1
smg-2 homolog, nonsense mediated mRNA decay factor
up-frameshift mutation 1 homolog
up-frameshift suppressor 1 homolog
yeast Upf1p homolog

NCBI Reference Sequences (RefSeq)

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_001297549.1NP_001284478.1  regulator of nonsense transcripts 1 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK128727, BE243084, BM969672, BX331580, BX364728, D86988, U65533
    Consensus CDS
    CCDS74315.1
    UniProtKB/Swiss-Prot
    Q92900
    UniProtKB/TrEMBL
    A0A024R7L8, B3KY55
    Related
    ENSP00000470142.1, ENST00000599848.5
    Conserved Domains (1) summary
    COG1112
    Location:145920
    DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
  2. NM_002911.3NP_002902.2  regulator of nonsense transcripts 1 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
    Source sequence(s)
    BC039817, BQ950083, CB960545
    Consensus CDS
    CCDS12386.1
    UniProtKB/Swiss-Prot
    Q92900
    UniProtKB/TrEMBL
    A0A024R7L5
    Related
    ENSP00000262803.4, ENST00000262803.9
    Conserved Domains (1) summary
    COG1112
    Location:145909
    DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p12 Primary Assembly

    Range
    18831405..18868232
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017027105.2XP_016882594.1  regulator of nonsense transcripts 1 isoform X1

    Conserved Domains (4) summary
    COG1112
    Location:145928
    DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
    pfam09416
    Location:121272
    UPF1_Zn_bind; RNA helicase (UPF2 interacting domain)
    pfam13087
    Location:699896
    AAA_12; AAA domain
    pfam13245
    Location:496553
    AAA_19; Part of AAA domain
  2. XM_017027106.2XP_016882595.1  regulator of nonsense transcripts 1 isoform X2

    Conserved Domains (4) summary
    COG1112
    Location:145917
    DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
    pfam09416
    Location:121272
    UPF1_Zn_bind; RNA helicase (UPF2 interacting domain)
    pfam13087
    Location:688885
    AAA_12; AAA domain
    pfam13245
    Location:485542
    AAA_19; Part of AAA domain
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