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

Gene ID: 313449, updated on 4-Jan-2025

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
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, Jan 2025]
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, ENSRNOT00000032618.7
    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, ENSRNOT00000092574.3
    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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