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    Upf2 UPF2 regulator of nonsense transcripts homolog (yeast) [ Mus musculus (house mouse) ]

    Gene ID: 326622, updated on 4-Jan-2025

    Summary

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    Official Symbol
    Upf2provided by MGI
    Official Full Name
    UPF2 regulator of nonsense transcripts homolog (yeast)provided by MGI
    Primary source
    MGI:MGI:2449307
    See related
    Ensembl:ENSMUSG00000043241 AllianceGenome:MGI:2449307
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Summary
    Predicted to enable telomeric DNA binding activity. Acts upstream of or within animal organ regeneration and liver development. Predicted to be located in several cellular components, including cytoplasmic ribonucleoprotein granule; cytosol; and perinuclear region of cytoplasm. Predicted to be part of exon-exon junction complex. Predicted to be active in cytoplasm. Is expressed in several structures, including liver; lung; pancreas; spleen; and testis. Orthologous to human UPF2 (UPF2 regulator of nonsense mediated mRNA decay). [provided by Alliance of Genome Resources, Jan 2025]
    Expression
    Broad expression in CNS E11.5 (RPKM 6.1), bladder adult (RPKM 4.3) and 23 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Upf2 in Genome Data Viewer
    Location:
    2 A1; 2 3.62 cM
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (5956218..6061514)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (5951447..6056703)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_03579 Neighboring gene SEC61 translocon subunit alpha 2 Neighboring gene STARR-positive B cell enhancer mm9_chr2:5816293-5816594 Neighboring gene predicted gene 13267 Neighboring gene dehydrogenase E1 and transketolase domain containing 1 Neighboring gene STARR-seq mESC enhancer starr_03580 Neighboring gene STARR-positive B cell enhancer ABC_E2029 Neighboring gene STARR-seq mESC enhancer starr_03581 Neighboring gene STARR-seq mESC enhancer starr_03584 Neighboring gene predicted gene, 30136 Neighboring gene STARR-seq mESC enhancer starr_03586 Neighboring gene proline and serine rich 2

    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. UPF2 leads to degradation of dendritically targeted mRNAs to regulate synaptic plasticity and cognitive function. Notaras M, et al. Mol Psychiatry, 2020 Dec. PMID 31636381, Free PMC Article
    2. NMD is essential for hematopoietic stem and progenitor cells and for eliminating by-products of programmed DNA rearrangements. Weischenfeldt J, et al. Genes Dev, 2008 May 15. PMID 18483223, Free PMC Article
    3. Upf1/Upf2 regulation of 3' untranslated region splice variants of AUF1 links nonsense-mediated and A+U-rich element-mediated mRNA decay. Banihashemi L, et al. Mol Cell Biol, 2006 Dec. PMID 17000771, Free PMC Article
    4. Inhibition of Upf2-Dependent Nonsense-Mediated Decay Leads to Behavioral and Neurophysiological Abnormalities by Activating the Immune Response. Johnson JL, et al. Neuron, 2019 Nov 20. PMID 31585809, Free PMC Article
    5. Nonsense in the testis: multiple roles for nonsense-mediated decay revealed in male reproduction. MacDonald CC, et al. Biol Reprod, 2017 May 1. PMID 28444146, Free PMC Article

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Progression of the pluripotent epiblast depends upon the NMD factor UPF2.
      Title: Progression of the pluripotent epiblast depends upon the NMD factor UPF2.
    2. Immunotherapy for breast cancer using EpCAM aptamer tumor-targeted gene knockdown.
      Title: Immunotherapy for breast cancer using EpCAM aptamer tumor-targeted gene knockdown.
    3. UPF2 leads to degradation of dendritically targeted mRNAs to regulate synaptic plasticity and cognitive function.
      Title: UPF2 leads to degradation of dendritically targeted mRNAs to regulate synaptic plasticity and cognitive function.
    4. our findings indicate that impaired UPF2-dependent nonsense-mediated decay leads to neurodevelopmental dysfunction
      Title: Inhibition of Upf2-Dependent Nonsense-Mediated Decay Leads to Behavioral and Neurophysiological Abnormalities by Activating the Immune Response.
    5. we report that UPF2-mediated nonsense-mediated mRNA decay (NMD) plays an essential role in male germ cells by eliminating ubiquitous genes-derived, longer 3'UTR transcripts, and that this role is independent of its canonical role in degrading "premature termination codon" (PTC)-containing transcripts in somatic cell lineages
      Title: UPF2-Dependent Nonsense-Mediated mRNA Decay Pathway Is Essential for Spermatogenesis by Selectively Eliminating Longer 3'UTR Transcripts.
    6. 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.
    7. UPF2, a nonsense-mediated mRNA decay factor, is required for prepubertal Sertoli cell development and male fertility by ensuring fidelity of the transcriptome.
      Title: UPF2, a nonsense-mediated mRNA decay factor, is required for prepubertal Sertoli cell development and male fertility by ensuring fidelity of the transcriptome.
    8. Study find that loss of Upf2 during fetal liver development is incompatible with postnatal life due to failure of terminal differentiation. Moreover, deletion of Upf2 in the adult liver results in hepatosteatosis and disruption of liver homeostasis.
      Title: UPF2 is a critical regulator of liver development, function and regeneration.
    9. Hematopoietic-specific deletion of Upf2, a core NMD factor, led to the rapid, complete, and lasting cell-autonomous extinction of all hematopoietic stem and progenitor populations.
      Title: NMD is essential for hematopoietic stem and progenitor cells and for eliminating by-products of programmed DNA rearrangements.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (2)  1 citation

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables telomeric DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables telomeric DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within animal organ regeneration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within liver development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within response to unfolded protein 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 cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasmic ribonucleoprotein granule IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasmic ribonucleoprotein granule ISO
    Inferred from Sequence Orthology
    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 IBA
    Inferred from Biological aspect of Ancestor
    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 nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    regulator of nonsense transcripts 2
    Names
    nonsense mRNA reducing factor 2
    up-frameshift suppressor 2 homolog

    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_001081132.1 → NP_001074601.1  regulator of nonsense transcripts 2

      Status: PROVISIONAL

      Source sequence(s)
      AL928735, AL928924, CR388026
      Consensus CDS
      CCDS38041.1
      UniProtKB/Swiss-Prot
      A2AT37
      Related
      ENSMUSP00000058375.7, ENSMUST00000060092.13
      Conserved Domains (4) summary
      smart00543
      Location:569 → 756
      MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
      pfam02854
      Location:774 → 984
      MIF4G; MIF4G domain
      pfam04050
      Location:1091 → 1215
      Upf2; Up-frameshift suppressor 2
      cl19727
      Location:357 → 420
      DUF1451; Zinc-ribbon containing domain

    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_000068.8 Reference GRCm39 C57BL/6J

      Range
      5956218..6061514
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006497486.2 → XP_006497549.1  regulator of nonsense transcripts 2 isoform X2

      Conserved Domains (3) summary
      smart00543
      Location:771 → 984
      MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
      pfam04050
      Location:1086 → 1214
      Upf2; Up-frameshift suppressor 2
      cl19727
      Location:357 → 420
      DUF1451; Zinc-ribbon containing domain

    2. XM_006497487.2 → XP_006497550.1  regulator of nonsense transcripts 2 isoform X3

      Conserved Domains (3) summary
      smart00543
      Location:771 → 984
      MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
      pfam04050
      Location:1086 → 1215
      Upf2; Up-frameshift suppressor 2
      cl19727
      Location:357 → 420
      DUF1451; Zinc-ribbon containing domain

    3. XM_006497488.5 → XP_006497551.1  regulator of nonsense transcripts 2 isoform X4

      Conserved Domains (2) summary
      smart00543
      Location:167 → 362
      MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
      cl19727
      Location:357 → 420
      DUF1451; Zinc-ribbon containing domain

    4. XM_006497485.5 → XP_006497548.1  regulator of nonsense transcripts 2 isoform X1

      UniProtKB/Swiss-Prot
      A2AT37
      Conserved Domains (4) summary
      smart00543
      Location:569 → 756
      MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
      pfam02854
      Location:774 → 984
      MIF4G; MIF4G domain
      pfam04050
      Location:1091 → 1215
      Upf2; Up-frameshift suppressor 2
      cl19727
      Location:357 → 420
      DUF1451; Zinc-ribbon containing domain

    RNA

    1. XR_001783050.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A2AT37.1 GenPept UniProtKB/Swiss-Prot:A2AT37

    Gene LinkOut

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