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

    Gene ID: 313449, updated on 9-Dec-2024

    Summary

    Official Symbol
    Upf3bprovided by RGD
    Official Full Name
    UPF3B, regulator of nonsense mediated mRNA decayprovided by RGD
    Primary source
    RGD:1560264
    See related
    EnsemblRapid: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 act upstream of or within positive regulation of mRNA cis splicing, via spliceosome. Predicted to be located in several cellular components, including centriolar satellite; neuronal cell body; 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 syndromic X-linked intellectual disability 14. Orthologous to human UPF3B (UPF3B regulator of nonsense mediated mRNA decay). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 84.1), Spleen (RPKM 71.1) and 9 other tissues See more
    Orthologs
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    Genomic context

    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

    Expression

    • 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

    General gene information

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables mRNA binding  
    enables mRNA binding  
    Component Evidence Code Pubs
    located_in centriolar satellite  
    is_active_in cytoplasm  
    located_in cytosol  
    part_of exon-exon junction complex  
    located_in neuronal cell body  
    is_active_in nucleolus  
    located_in nucleolus  
    located_in nucleoplasm  
    located_in nucleus  

    General protein information

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

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      D3ZBE8
      Related
      ENSRNOP00000029696.4, ENSRNOT00000032618.7
      Conserved Domains (1) summary
      cd12728
      Location:50137
      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_063279990.1XP_063136060.1  regulator of nonsense transcripts 3B isoform X3

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

      Conserved Domains (1) summary
      cd12728
      Location:50137
      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_006257455.5XP_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, ENSRNOT00000092574.3
      Conserved Domains (1) summary
      cd12728
      Location:50137
      RRM_like_Smg4_UPF3B; RNA recognition motif-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog B on chromosome X (Upf3B)
    4. XM_063279991.1XP_063136061.1  regulator of nonsense transcripts 3B isoform X4

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