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Upf3a UPF3 regulator of nonsense transcripts homolog A (yeast) [ Mus musculus (house mouse) ]

Gene ID: 67031, updated on 2-Nov-2024

Summary

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Official Symbol
Upf3aprovided by MGI
Official Full Name
UPF3 regulator of nonsense transcripts homolog A (yeast)provided by MGI
Primary source
MGI:MGI:1914281
See related
Ensembl:ENSMUSG00000038398 AllianceGenome:MGI:1914281
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
UPF3; RENT3A; 2600001C03Rik; 4930546M19Rik
Summary
Predicted to enable mRNA binding activity; protein sequestering activity; and telomeric DNA binding activity. Involved in negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay. Acts upstream of or within positive regulation of mRNA cis splicing, via spliceosome. Located in neuron projection. Is expressed in central nervous system. Orthologous to human UPF3A (UPF3A regulator of nonsense mediated mRNA decay). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in testis adult (RPKM 45.2), CNS E11.5 (RPKM 14.6) and 19 other tissues See more
Orthologs
human all
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Genomic context

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See Upf3a in Genome Data Viewer
Location:
8 A1.1; 8 6.38 cM
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (13834636..13848723)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (13785055..13798723)

Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 46032 Neighboring gene STARR-positive B cell enhancer mm9_chr8:13753700-13754000 Neighboring gene 3-phosphoglycerate dehydrogenase pseudogene Neighboring gene CDC16 cell division cycle 16 Neighboring gene SUMO/sentrin specific peptidase 2-like 2A Neighboring gene predicted gene, 53400

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data 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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Related articles in PubMed

  1. UPF3A is dispensable for nonsense-mediated mRNA decay in mouse pluripotent and somatic cells. Chen C, et al. Life Sci Alliance, 2023 Jun. PMID 36997282, Free PMC Article
  2. Spatial expression of the nonsense-mediated mRNA decay factors UPF3A and UPF3B among mouse tissues. Ma X, et al. J Zhejiang Univ Sci B, 2023 Nov 15. PMID 37961809, Free PMC Article
  3. The UPF3B gene, implicated in intellectual disability, autism, ADHD and childhood onset schizophrenia regulates neural progenitor cell behaviour and neuronal outgrowth. Jolly LA, et al. Hum Mol Genet, 2013 Dec 1. PMID 23821644
  4. Nuclear mRNA degradation pathway(s) are implicated in Xist regulation and X chromosome inactivation. Ciaudo C, et al. PLoS Genet, 2006 Jun. PMID 16789828, Free PMC Article
  5. Dynamic expression pattern and subcellular localization of the Rhox10 homeobox transcription factor during early germ cell development. Song HW, et al. Reproduction, 2012 May. PMID 22393026

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Spatial expression of the nonsense-mediated mRNA decay factors UPF3A and UPF3B among mouse tissues.
    Title: Spatial expression of the nonsense-mediated mRNA decay factors UPF3A and UPF3B among mouse tissues.
  2. UPF3A is dispensable for nonsense-mediated mRNA decay in mouse pluripotent and somatic cells.
    Title: UPF3A is dispensable for nonsense-mediated mRNA decay in mouse pluripotent and somatic cells.
  3. Analysis revealed that UPF3A is a broadly acting nonsense-mediated RNA decay inhibitor. This discovery implies that UPF3A and UPF3B do not primarily work in a complementary or redundant manner as previously supposed; instead, they oppose each other, allowing this paralog pair to serve as a molecular rheostat to modulate the level of gene expression during development.
    Title: The Antagonistic Gene Paralogs Upf3a and Upf3b Govern Nonsense-Mediated RNA Decay.
Submit: New GeneRIF Correction

Variation

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Alleles

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

General gene information

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Markers

Homology

Clone Names

  • MGC151365

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables mRNA binding ISO
Inferred from Sequence Orthology
more info
  
enables protein sequestering activity 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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of 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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
located_in intracellular membrane-bounded organelle ISO
Inferred from Sequence Orthology
more info
  
located_in neuron projection IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
regulator of nonsense transcripts 3A

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)

  1. NM_025924.2 → NP_080200.1  regulator of nonsense transcripts 3A

    See identical proteins and their annotated locations for NP_080200.1

    Status: VALIDATED

    Source sequence(s)
    BC116988
    Consensus CDS
    CCDS40235.1
    UniProtKB/TrEMBL
    Q3ULJ3
    Related
    ENSMUSP00000037354.8, ENSMUST00000043767.9
    Conserved Domains (1) summary
    pfam03467
    Location:63 → 223
    Smg4_UPF3; Smg-4/UPF3 family

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

  1. NC_000074.7 Reference GRCm39 C57BL/6J

    Range
    13834636..13848723
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006508860.5 → XP_006508923.1  regulator of nonsense transcripts 3A isoform X1

    Conserved Domains (1) summary
    pfam03467
    Location:66 → 223
    Smg4_UPF3; Smg-4/UPF3 family
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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