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

    Gene ID: 67031, updated on 9-Dec-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, Dec 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
    • 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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