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

Gene ID: 361271, updated on 2-Nov-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, Nov 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 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
    A0A0U1RRY8

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

    UniProtKB/TrEMBL
    A0A0U1RRY8

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

    UniProtKB/TrEMBL
    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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