U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 5976, updated on 6-Nov-2022

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; AllianceGenome:HGNC:9962
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
UTF; 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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See UPF1 in Genome Data Viewer
Location:
19p13.11
Exon count:
25
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (18831959..18868230)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (18967570..19003847)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (18942768..18979039)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene CREB regulated transcription coactivator 1 Neighboring gene cartilage oligomeric matrix protein Neighboring gene ceramide synthase 1 Neighboring gene growth differentiation factor 1 Neighboring gene COPI coat 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 Functions

What'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 PubChem

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
enables ATP binding IEA
Inferred from Electronic Annotation
more info
 
enables ATP hydrolysis activity IDA
Inferred from Direct Assay
more info
PubMed 
enables RNA binding HDA PubMed 
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables RNA binding NAS
Non-traceable Author Statement
more info
PubMed 
enables RNA helicase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables RNA helicase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables double-stranded DNA helicase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables helicase activity NAS
Non-traceable Author Statement
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein-containing complex binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables telomeric DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in 3'-UTR-mediated mRNA destabilization IDA
Inferred from Direct Assay
more info
PubMed 
involved_in 3'-UTR-mediated mRNA destabilization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in DNA duplex unwinding IDA
Inferred from Direct Assay
more info
PubMed 
involved_in DNA repair IDA
Inferred from Direct Assay
more info
PubMed 
involved_in DNA replication IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cell cycle phase transition IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cellular response to interleukin-1 IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cellular response to lipopolysaccharide IDA
Inferred from Direct Assay
more info
PubMed 
involved_in histone mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in mRNA export from nucleus TAS
Traceable Author Statement
more info
PubMed 
involved_in nuclear-transcribed mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay 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
PubMed 
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IDA
Inferred from Direct Assay
more info
PubMed 
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay NAS
Non-traceable Author Statement
more info
PubMed 
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS
Traceable Author Statement
more info
PubMed 
involved_in positive regulation of mRNA catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of telomere maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of translational termination IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of translational termination NAS
Non-traceable Author Statement
more info
PubMed 
involved_in telomere maintenance via semi-conservative replication IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
located_in P-body IEA
Inferred from Electronic Annotation
more info
 
located_in chromatin IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromosome, telomeric region IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in cytoplasm NAS
Non-traceable Author Statement
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in cytosol TAS
Traceable Author Statement
more info
 
part_of exon-exon junction complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
 
part_of 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
NP_001284478.1
NP_002902.2
XP_016882594.1
XP_016882595.1
XP_047295147.1

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001297549.2NP_001284478.1  regulator of nonsense transcripts 1 isoform 1

    See identical proteins and their annotated locations for NP_001284478.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK128727, BE243084, BM969672, BX364728, D86988, U65533
    Consensus CDS
    CCDS74315.1
    UniProtKB/Swiss-Prot
    Q92842, Q92900
    UniProtKB/TrEMBL
    A0A024R7L8, B3KY55
    Related
    ENSP00000470142.1, ENST00000599848.5
    Conserved Domains (2) summary
    COG1112
    Location:145920
    DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
    cd18039
    Location:481714
    DEXXQc_UPF1; DEXXQ-box helicase domain of UPF1
  2. NM_002911.4NP_002902.2  regulator of nonsense transcripts 1 isoform 2

    See identical proteins and their annotated locations for NP_002902.2

    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
    ENSP00000262803.5, ENST00000262803.10
    Conserved Domains (2) summary
    COG1112
    Location:145909
    DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
    cd18039
    Location:470703
    DEXXQc_UPF1; DEXXQ-box helicase domain of UPF1

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    18831959..18868230
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017027105.3XP_016882594.1  regulator of nonsense transcripts 1 isoform X1

    Conserved Domains (2) summary
    COG1112
    Location:145928
    DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
    cd18039
    Location:489722
    DEXXQc_UPF1; DEXXQ-box helicase domain of UPF1
  2. XM_017027106.3XP_016882595.1  regulator of nonsense transcripts 1 isoform X2

    Conserved Domains (2) summary
    COG1112
    Location:145917
    DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
    cd18039
    Location:478711
    DEXXQc_UPF1; DEXXQ-box helicase domain of UPF1
  3. XM_047439191.1XP_047295147.1  regulator of nonsense transcripts 1 isoform X3

    Related
    ENST00000601981.6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    18967570..19003847
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)