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    Upf3b UPF3B, regulator of nonsense mediated mRNA decay [ Rattus norvegicus (Norway rat) ]

    Gene ID: 313449, updated on 13-Apr-2024

    Summary

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    Official Symbol
    Upf3bprovided by RGD
    Official Full Name
    UPF3B, regulator of nonsense mediated mRNA decayprovided by RGD
    Primary source
    RGD:1560264
    See related
    Ensembl:ENSRNOG00000039994 AllianceGenome:RGD:1560264
    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
    Also known as
    RGD1560264
    Summary
    Predicted to enable mRNA binding activity. Predicted to be involved in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay and positive regulation of translation. Predicted to be located in centriolar satellite; cytosol; and nucleoplasm. Predicted to be part of exon-exon junction complex. Predicted to be active in cytoplasm and nucleolus. Human ortholog(s) of this gene implicated in non-syndromic X-linked intellectual disability 82 and syndromic X-linked intellectual disability 14. Orthologous to human UPF3B (UPF3B regulator of nonsense mediated mRNA decay). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 84.1), Spleen (RPKM 71.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Upf3b in Genome Data Viewer
    Location:
    Xq35
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) X NC_086039.1 (121200993..121219059, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) X NC_051356.1 (116335308..116353332, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) X NC_005120.4 (123713327..123731431, complement)

    Chromosome X - NC_086039.1Genomic Context describing neighboring genes Neighboring gene sosondowah ankyrin repeat domain family member D Neighboring gene small nucleolar RNA SNORA69 Neighboring gene ribosomal protein L39 Neighboring gene NFKB activating protein Neighboring gene A-kinase anchoring protein 14 Neighboring gene uncharacterized LOC134484097

    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. Y14 and hUpf3b form an NMD-activating complex. Gehring NH, et al. Mol Cell, 2003 Apr. PMID 12718880
    2. Role of the nonsense-mediated decay factor hUpf3 in the splicing-dependent exon-exon junction complex. Kim VN, et al. Science, 2001 Sep 7. PMID 11546873
    3. 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
    4. Functions of hUpf3a and hUpf3b in nonsense-mediated mRNA decay and translation. Kunz JB, et al. RNA, 2006 Jun. PMID 16601204, Free PMC Article
    5. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Baltz AG, et al. Mol Cell, 2012 Jun 8. PMID 22681889

    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 mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables mRNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of brain development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of neuron projection 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
    		  
    acts_upstream_of_or_within nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in 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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of positive regulation of neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    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
    		  
    Component Evidence Code Pubs
    located_in centriolar satellite ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of exon-exon junction complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in neuronal cell body ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    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 3B
    Names
    UPF3 regulator of nonsense transcripts homolog B

    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_001135873.1 → NP_001129345.1  regulator of nonsense transcripts 3B

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      D3ZBE8
      Related
      ENSRNOP00000029696.4, ENSRNOT00000032618.6
      Conserved Domains (1) summary
      cd12728
      Location:50 → 137
      RRM_like_Smg4_UPF3B; RNA recognition motif-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog B on chromosome X (Upf3B)

    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_086039.1 Reference GRCr8

      Range
      121200993..121219059 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063279990.1 → XP_063136060.1  regulator of nonsense transcripts 3B isoform X3

    2. XM_017602038.3 → XP_017457527.1  regulator of nonsense transcripts 3B isoform X2

      Conserved Domains (1) summary
      cd12728
      Location:50 → 137
      RRM_like_Smg4_UPF3B; RNA recognition motif (RRM)-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog B on chromosome X (Upf3B)

    3. XM_006257455.5 → XP_006257517.1  regulator of nonsense transcripts 3B isoform X1

      See identical proteins and their annotated locations for XP_006257517.1

      UniProtKB/TrEMBL
      A0A0U1RRP3, A6JMH6
      Related
      ENSRNOP00000075758.1
      Conserved Domains (1) summary
      cd12728
      Location:50 → 137
      RRM_like_Smg4_UPF3B; RNA recognition motif-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog B on chromosome X (Upf3B)

    4. XM_063279991.1 → XP_063136061.1  regulator of nonsense transcripts 3B isoform X4

    Nucleotide Protein Strain
    Heading Accession and Version

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