Upf1 UPF1, RNA helicase and ATPase [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Upf1provided by RGD
Official Full Name: UPF1, RNA helicase and ATPaseprovided by RGD
Primary source: RGD:1589127
See related: EnsemblRapid:ENSRNOG00000020134 AllianceGenome:RGD:1589127
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable several functions, including ATP hydrolysis activity; helicase activity; and nucleic acid binding activity. Predicted to be involved in several processes, including chromosome organization; regulation of gene expression; and regulation of telomere maintenance. Predicted to act 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. Orthologous to human UPF1 (UPF1 RNA helicase and ATPase). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Adrenal (RPKM 155.4), Thymus (RPKM 140.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 16p14

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	16	NC_086034.1 (19110531..19131327)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	16	NC_051351.1 (19076594..19097365)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	16	NC_005115.4 (20824888..20845632)

Chromosome 16 - NC_086034.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Here, we describe a new role for the ATP-dependent helicase UPF1 and its interaction with the RNA localization protein STAU2 in mediating mGluR-LTD through the regulation of mRNA translation complexes stalled at the level of elongation and/or termination.
Title: UPF1 Governs Synaptic Plasticity through Association with a STAU2 RNA Granule.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

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

Gene Ontology Provided by RGD

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 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 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	ISO Inferred from Sequence Orthology 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 telomere maintenance via semi-conservative replication	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in 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	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology 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
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: UPF1 regulator of nonsense transcripts homolog

NP_001414288.1

EC 3.6.4.-

EC 3.6.4.12

EC 3.6.4.13

XP_063131800.1

EC 3.6.4.-

EC 3.6.4.12

EC 3.6.4.13

XP_063131801.1

EC 3.6.4.-

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.