Upf3a UPF3A, regulator of nonsense mediated mRNA decay [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Upf3aprovided by RGD
Official Full Name: UPF3A, regulator of nonsense mediated mRNA decayprovided by RGD
Primary source: RGD:1308778
See related: EnsemblRapid:ENSRNOG00000017397 AllianceGenome:RGD:1308778
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable mRNA binding activity and telomeric DNA binding activity. Predicted to be involved in negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay and positive regulation of translation. Predicted to act upstream of or within positive regulation of mRNA cis splicing, via spliceosome. Predicted to be located in cytosol; neuron projection; and nucleoplasm. Predicted to be part of exon-exon junction complex. Predicted to be active in cytoplasm and nucleolus. Orthologous to human UPF3A (UPF3A regulator of nonsense mediated mRNA decay). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Lung (RPKM 57.1), Brain (RPKM 53.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 16q12.5

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	16	NC_086034.1 (82459651..82470686, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	16	NC_051351.1 (75757442..75768478, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	16	NC_005115.4 (81521084..81532512)

Chromosome 16 - NC_086034.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: 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?

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General gene information

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Markers

RH136670 (e-PCR)
- UniSTS:218761

BE099587 (e-PCR)
- UniSTS:245695

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables mRNA binding	ISO Inferred from Sequence Orthology more info
enables telomeric DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables telomeric DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of in utero embryonic development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	ISO Inferred from Sequence Orthology more info
NOT involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	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 positive regulation of translation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of translation	ISO Inferred from Sequence Orthology more info
acts_upstream_of spermatogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
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 intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in neuron projection	ISO Inferred from Sequence Orthology more info
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: regulator of nonsense transcripts 3A

Names: UPF3 regulator of nonsense transcripts homolog A

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.