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

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: mouse all
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Genomic context

Location:: 19p13.11

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (18831959..18868230)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (18967570..19003847)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (18942768..18979039)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

UPF1 helicase orchestrates mutually exclusive interactions with the SMG6 endonuclease and UPF2.
Title: UPF1 helicase orchestrates mutually exclusive interactions with the SMG6 endonuclease and UPF2.
UPF1 ATPase autoinhibition and activation modulate RNA binding kinetics and NMD efficiency.
Title: UPF1 ATPase autoinhibition and activation modulate RNA binding kinetics and NMD efficiency.
UPF1 regulates mRNA stability by sensing poorly translated coding sequences.
Title: UPF1 regulates mRNA stability by sensing poorly translated coding sequences.
LncRNA GAS5 regulated by FTO-mediated m6A demethylation promotes autophagic cell death in NSCLC by targeting UPF1/BRD4 axis.
Title: LncRNA GAS5 regulated by FTO-mediated m6A demethylation promotes autophagic cell death in NSCLC by targeting UPF1/BRD4 axis.
Nonsense-mediated mRNA decay affects hyperactive root formation in oculo-facio-cardio-dental syndrome via up-frameshift protein 1.
Title: Nonsense-mediated mRNA decay affects hyperactive root formation in oculo-facio-cardio-dental syndrome via up-frameshift protein 1.
LINC02561 promotes metastasis in HCC via HIF1-alpha/NDRG1/UPF1 axis.
Title: LINC02561 promotes metastasis in HCC via HIF1-α/NDRG1/UPF1 axis.
Role of UPF1-LIN28A interaction during early differentiation of pluripotent stem cells.
Title: Role of UPF1-LIN28A interaction during early differentiation of pluripotent stem cells.
YTHDF2 facilitates aggresome formation via UPF1 in an m[6]A-independent manner.
Title: YTHDF2 facilitates aggresome formation via UPF1 in an m(6)A-independent manner.
Synergistic Binding of ATP and Nucleic Acids Necessitates UPF1's ATPase Functional Cycle.
Title: Synergistic Binding of ATP and Nucleic Acids Necessitates UPF1's ATPase Functional Cycle.
UPF1 regulates FOXO1 protein expression by promoting PBK transcription in non-small cell lung cancer.
Title: UPF1 regulates FOXO1 protein expression by promoting PBK transcription in non-small cell lung cancer.

Submit: New GeneRIF Correction See all GeneRIFs (109)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

A006H36 (e-PCR)
- UniSTS:63779

D19S842E (e-PCR)
- UniSTS:153964

RH25427 (e-PCR)
- UniSTS:40837

RH36847 (e-PCR)
- UniSTS:86171

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 ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	PubMed
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
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
enables RNA helicase activity	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
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	TAS Traceable Author Statement 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	TAS Traceable Author Statement more info	PubMed
involved_in cellular response to lipopolysaccharide	TAS Traceable Author Statement more info	PubMed
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
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, nonsense-mediated decay	IBA Inferred from Biological aspect of Ancestor more info
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 positive regulation of mRNA cis splicing, via spliceosome	IEA Inferred from Electronic Annotation more info
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
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

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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

EC 3.6.4.12

EC 3.6.4.13

NP_002902.2

EC 3.6.4.12

EC 3.6.4.13

XP_016882594.1

EC 3.6.4.12

EC 3.6.4.13

XP_016882595.1

EC 3.6.4.12

EC 3.6.4.13

XP_047295147.1

EC 3.6.4.12

EC 3.6.4.13

XP_054177645.1

EC 3.6.4.12

EC 3.6.4.13

XP_054177646.1

EC 3.6.4.12

EC 3.6.4.13

XP_054177647.1

EC 3.6.4.12

EC 3.6.4.13

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)

NM_001297549.2 → NP_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

O00239, O43343, Q86Z25, Q92842, Q92900

UniProtKB/TrEMBL

A0A994J4L7

Related

ENSP00000470142.1, ENST00000599848.5

Conserved Domains (2) summary

COG1112
Location:145 → 920

DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]

cd18039
Location:481 → 714

DEXXQc_UPF1; DEXXQ-box helicase domain of UPF1
NM_002911.4 → NP_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/TrEMBL

A0A024R7L5, A0A994J4L7

Related

ENSP00000262803.5, ENST00000262803.10

Conserved Domains (2) summary

COG1112
Location:145 → 909

DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]

cd18039
Location:470 → 703

DEXXQc_UPF1; DEXXQ-box helicase domain of UPF1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

18831959..18868230

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A994J4L7

Conserved Domains (2) summary

COG1112
Location:145 → 928

DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]

cd18039
Location:489 → 722

DEXXQc_UPF1; DEXXQ-box helicase domain of UPF1
XM_017027106.3 → XP_016882595.1 regulator of nonsense transcripts 1 isoform X2

UniProtKB/TrEMBL

A0A994J4L7

Conserved Domains (2) summary

COG1112
Location:145 → 917

DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]

cd18039
Location:478 → 711

DEXXQc_UPF1; DEXXQ-box helicase domain of UPF1
XM_047439191.1 → XP_047295147.1 regulator of nonsense transcripts 1 isoform X3

UniProtKB/TrEMBL

A0A994J4L7

Related

ENST00000601981.6

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

18967570..19003847

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054321670.1 → XP_054177645.1 regulator of nonsense transcripts 1 isoform X1

UniProtKB/TrEMBL

A0A994J4L7
XM_054321671.1 → XP_054177646.1 regulator of nonsense transcripts 1 isoform X2

UniProtKB/TrEMBL

A0A994J4L7
XM_054321672.1 → XP_054177647.1 regulator of nonsense transcripts 1 isoform X3

UniProtKB/TrEMBL

A0A994J4L7