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Upf3b UPF3 regulator of nonsense transcripts homolog B (yeast) [ Mus musculus (house mouse) ]

Gene ID: 68134, updated on 5-Mar-2024

Summary

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Official Symbol
Upf3bprovided by MGI
Official Full Name
UPF3 regulator of nonsense transcripts homolog B (yeast)provided by MGI
Primary source
MGI:MGI:1915384
See related
Ensembl:ENSMUSG00000036572 AllianceGenome:MGI:1915384
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
UPF3X; RENT3B; 5730594O13Rik
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 response to unfolded protein. 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. Is expressed in several structures, including central nervous system. 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
Broad expression in CNS E11.5 (RPKM 8.6), CNS E14 (RPKM 7.2) and 22 other tissues See more
Orthologs
human all
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Genomic context

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Location:
X A3.3; X 21.51 cM
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (36355331..36374124, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (37091678..37110471, complement)

Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene predicted gene, 26099 Neighboring gene small nucleolar RNA, H/ACA box 69 Neighboring gene ribosomal protein L39 Neighboring gene STARR-positive B cell enhancer ABC_E5721 Neighboring gene CapStarr-seq enhancer MGSCv37_chrX:34666661-34666844 Neighboring gene NFKB activating protein Neighboring gene A kinase anchor protein 14 Neighboring gene predicted gene, 39503 Neighboring gene NADH:ubiquinone oxidoreductase subunit A1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. A Upf3b-mutant mouse model with behavioral and neurogenesis defects. Huang L, et al. Mol Psychiatry, 2018 Aug. PMID 28948974, Free PMC Article
  2. The unfolded protein response is shaped by the NMD pathway. Karam R, et al. EMBO Rep, 2015 May. PMID 25807986, Free PMC Article
  3. RNA homeostasis governed by cell type-specific and branched feedback loops acting on NMD. Huang L, et al. Mol Cell, 2011 Sep 16. PMID 21925383, Free PMC Article
  4. The role of the NMD factor UPF3B in olfactory sensory neurons. Tan K, et al. Elife, 2020 Aug 10. PMID 32773035, Free PMC Article
  5. Disorders with similar clinical phenotypes reveal underlying genetic interaction: SATB2 acts as an activator of the UPF3B gene. Leoyklang P, et al. Hum Genet, 2013 Dec. PMID 23925499, Free PMC Article

See all (21) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Spatial expression of the nonsense-mediated mRNA decay factors UPF3A and UPF3B among mouse tissues.
    Title: Spatial expression of the nonsense-mediated mRNA decay factors UPF3A and UPF3B among mouse tissues.
  2. The role of the NMD factor UPF3B in olfactory sensory neurons.
    Title: The role of the NMD factor UPF3B in olfactory sensory neurons.
  3. Study reports the generation and characterization of mice harboring a null Upf3b allele. These Upf3b-null mice exhibit deficits in fear-conditioned learning, but not spatial learning. Upf3b-null mice also have a profound defect in prepulse inhibition. Cortical pyramidal neurons from Upf3b-null mice display deficient dendritic spine maturation in vivo.
    Title: A Upf3b-mutant mouse model with behavioral and neurogenesis defects.
  4. Analysis revealed that UPF3A is a broadly acting nonsense-mediated RNA decay inhibitor. This discovery implies that UPF3A and UPF3B do not primarily work in a complementary or redundant manner as previously supposed; instead, they oppose each other, allowing this paralog pair to serve as a molecular rheostat to modulate the level of gene expression during development.
    Title: The Antagonistic Gene Paralogs Upf3a and Upf3b Govern Nonsense-Mediated RNA Decay.
  5. Evidence suggests Upf3b-dependent nonsense-mediated mRNA decay is regulated at multiple levels during development including regulation of expression and sub-cellular localization of Upf3b.
    Title: The UPF3B gene, implicated in intellectual disability, autism, ADHD and childhood onset schizophrenia regulates neural progenitor cell behaviour and neuronal outgrowth.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Gene trapped (1) 
  • Endonuclease-mediated (3) 

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of neuron projection development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of positive regulation of neuron differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
 PubMed 
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
hUPF3B

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_026573.3 → NP_080849.1  regulator of nonsense transcripts 3B

    See identical proteins and their annotated locations for NP_080849.1

    Status: VALIDATED

    Source sequence(s)
    AK145431, BC047049
    Consensus CDS
    CCDS30068.1
    UniProtKB/TrEMBL
    Q3ULL6, Q80UI8
    Related
    ENSMUSP00000075614.7, ENSMUST00000076265.13
    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_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000086.8 Reference GRCm39 C57BL/6J

    Range
    36355331..36374124 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006541394.4 → XP_006541457.1  regulator of nonsense transcripts 3B isoform X1

    See identical proteins and their annotated locations for XP_006541457.1

    UniProtKB/TrEMBL
    Q80UI8
    Conserved Domains (1) summary
    pfam03467
    Location:51 → 208
    Smg4_UPF3; Smg-4/UPF3 family

  2. XM_036162085.1 → XP_036017978.1  regulator of nonsense transcripts 3B isoform X3

  3. XM_036162083.1 → XP_036017976.1  regulator of nonsense transcripts 3B isoform X2

  4. XM_036162084.1 → XP_036017977.1  regulator of nonsense transcripts 3B isoform X2

RNA

  1. XR_001782759.2 RNA Sequence

  2. XR_004940361.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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