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    Upf2 UPF2, regulator of nonsense mediated mRNA decay [ Rattus norvegicus (Norway rat) ]

    Gene ID: 361271, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Upf2provided by RGD
    Official Full Name
    UPF2, regulator of nonsense mediated mRNA decayprovided by RGD
    Primary source
    RGD:1309178
    See related
    EnsemblRapid:ENSRNOG00000023593 AllianceGenome:RGD:1309178
    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 telomeric DNA binding activity. Predicted to be involved in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay. Predicted to act upstream of or within animal organ regeneration and liver development. Predicted to be located in cytoplasmic ribonucleoprotein granule; cytosol; and nucleus. Predicted to be part of exon-exon junction complex. Predicted to be active in cytoplasm. Orthologous to human UPF2 (UPF2 regulator of nonsense mediated mRNA decay). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Spleen (RPKM 135.8), Thymus (RPKM 132.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Upf2 in Genome Data Viewer
    Location:
    17q12.3
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 17 NC_086035.1 (77133975..77245266, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 17 NC_051352.1 (72224575..72335896, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 17 NC_005116.4 (76176379..76287246, complement)

    Chromosome 17 - NC_086035.1Genomic Context describing neighboring genes Neighboring gene enoyl CoA hydratase domain containing 3 Neighboring gene proline and serine rich 2 Neighboring gene cytochrome c oxidase subunit VIb polypeptide 1-like Neighboring gene dehydrogenase E1 and transketolase domain containing 1 Neighboring gene large ribosomal subunit protein eL37-like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. NMD resulting from encephalomyocarditis virus IRES-directed translation initiation seems to be restricted to CBP80/20-bound mRNA. Woeller CF, et al. EMBO Rep, 2008 May. PMID 18369367, Free PMC Article
    2. Human UPF1 interacts with TPP1 and telomerase and sustains telomere leading-strand replication. Chawla R, et al. EMBO J, 2011 Aug 9. PMID 21829167, Free PMC Article
    3. Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7. Ohnishi T, et al. Mol Cell, 2003 Nov. PMID 14636577
    4. Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends. Azzalin CM, et al. Science, 2007 Nov 2. PMID 17916692
    5. Functions of hUpf3a and hUpf3b in nonsense-mediated mRNA decay and translation. Kunz JB, et al. RNA, 2006 Jun. PMID 16601204, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA 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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within liver development 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
    		  
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of exon-exon junction complex IBA
    Inferred from Biological aspect of Ancestor
    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
    		  

    General protein information

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    Preferred Names
    regulator of nonsense transcripts 2
    Names
    UPF2 regulator of nonsense transcripts 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_001108421.1 → NP_001101891.1  regulator of nonsense transcripts 2

      See identical proteins and their annotated locations for NP_001101891.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473990
      UniProtKB/TrEMBL
      A0A0U1RRS6, A6JLX5
      Related
      ENSRNOP00000075795.3, ENSRNOT00000092693.3
      Conserved Domains (3) summary
      smart00543
      Location:771 → 984
      MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
      pfam04050
      Location:1072 → 1214
      Upf2; Up-frameshift suppressor 2
      cl19727
      Location:357 → 420
      DUF1451; Zinc-ribbon containing domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086035.1 Reference GRCr8

      Range
      77133975..77245266 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039095923.2 → XP_038951851.1  regulator of nonsense transcripts 2 isoform X1

      UniProtKB/TrEMBL
      A0A0U1RRS6, A0A0U1RRY8
      Related
      ENSRNOP00000075866.2, ENSRNOT00000092452.3
      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

    2. XM_039095924.2 → XP_038951852.1  regulator of nonsense transcripts 2 isoform X1

      UniProtKB/TrEMBL
      A0A0U1RRS6, A0A0U1RRY8
      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

    3. XM_063276633.1 → XP_063132703.1  regulator of nonsense transcripts 2 isoform X1

      UniProtKB/TrEMBL
      A0A0U1RRS6, A0A0U1RRY8

    4. XM_063276632.1 → XP_063132702.1  regulator of nonsense transcripts 2 isoform X1

      UniProtKB/TrEMBL
      A0A0U1RRS6, A0A0U1RRY8

    5. XM_063276631.1 → XP_063132701.1  regulator of nonsense transcripts 2 isoform X1

      UniProtKB/TrEMBL
      A0A0U1RRS6, A0A0U1RRY8

    6. XM_039095926.2 → XP_038951854.1  regulator of nonsense transcripts 2 isoform X1

      UniProtKB/TrEMBL
      A0A0U1RRS6, A0A0U1RRY8
      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

    7. XM_039095929.2 → XP_038951857.1  regulator of nonsense transcripts 2 isoform X3

      Conserved Domains (3) summary
      smart00543
      Location:167 → 354
      MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
      pfam02854
      Location:372 → 582
      MIF4G; MIF4G domain
      pfam04050
      Location:689 → 813
      Upf2; Up-frameshift suppressor 2

    8. XM_039095928.2 → XP_038951856.1  regulator of nonsense transcripts 2 isoform X2

      UniProtKB/TrEMBL
      A0A0U1RRS6
      Related
      ENSRNOP00000054878.6, ENSRNOT00000058070.6
      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

    9. XM_063276634.1 → XP_063132704.1  regulator of nonsense transcripts 2 isoform X5

    10. XM_039095930.2 → XP_038951858.1  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
    Nucleotide Protein Strain
    Heading Accession and Version

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