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

Summary

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 several functions, including ATP hydrolysis activity; helicase activity; and nucleic acid binding activity. Acts upstream of or within positive regulation of mRNA cis splicing, via spliceosome. Predicted to be located in chromosome; cytosol; 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; cumulus oophorus; embryo; and oocyte. Orthologous to human UPF1 (UPF1 RNA helicase and ATPase). [provided by Alliance of Genome Resources, Nov 2024]
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

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_000074.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

UPF1 plays critical roles in early B cell development.
Title: UPF1 plays critical roles in early B cell development.
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.
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.
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.
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.
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.
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.
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.
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.
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.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (4)
Targeted (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH139099 (e-PCR)
- UniSTS:221185

Gdf1 (e-PCR), detects polymorphism
- UniSTS:496651

AI385651 (e-PCR)
- UniSTS:159770

NoName (e-PCR)
- UniSTS:235917

Rent1 (e-PCR), detects polymorphism
- UniSTS:259246

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 ATP hydrolysis activity	ISS Inferred from Sequence or Structural Similarity more info
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	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables RNA binding	ISS Inferred from Sequence or Structural Similarity 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 RNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
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	ISO Inferred from Sequence Orthology more info
enables double-stranded DNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IEA Inferred from Electronic Annotation more info
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info
enables telomeric DNA binding	IEA Inferred from Electronic Annotation 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 3'-UTR-mediated mRNA destabilization	ISS Inferred from Sequence or Structural Similarity more info
involved_in DNA duplex unwinding	ISO Inferred from Sequence Orthology more info
involved_in DNA duplex unwinding	ISS Inferred from Sequence or Structural Similarity more info
involved_in DNA repair	ISO Inferred from Sequence Orthology more info
involved_in DNA repair	ISS Inferred from Sequence or Structural Similarity more info
involved_in DNA replication	ISO Inferred from Sequence Orthology more info
involved_in DNA replication	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell cycle phase transition	ISO Inferred from Sequence Orthology more info
involved_in cell cycle phase transition	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to interleukin-1	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to lipopolysaccharide	ISS Inferred from Sequence or Structural Similarity more info
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	ISO Inferred from Sequence Orthology more info
involved_in histone mRNA catabolic process	ISS Inferred from Sequence or Structural Similarity 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 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	ISS Inferred from Sequence or Structural Similarity 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	IEA Inferred from Electronic Annotation more info
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 regulation of translational termination	ISS Inferred from Sequence or Structural Similarity more info
involved_in telomere maintenance via semi-conservative replication	IEA Inferred from Electronic Annotation more info
involved_in telomere maintenance via semi-conservative replication	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in P-body	IEA Inferred from Electronic Annotation more info
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in chromatin	ISS Inferred from Sequence or Structural Similarity more info
located_in chromosome, telomeric region	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation more info
part_of exon-exon junction complex	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
part_of supraspliceosomal complex	IEA Inferred from Electronic Annotation 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

EC 3.6.4.12

EC 3.6.4.13

NP_109605.2

EC 3.6.4.12

EC 3.6.4.13

XP_006509667.1

EC 3.6.4.12

EC 3.6.4.13

XP_006509668.1

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_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
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

NC_000074.7 Reference GRCm39 C57BL/6J

Range

70784143..70806418 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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