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

    Gene ID: 68134, updated on 2-Nov-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. Acts upstream of or within nuclear-transcribed mRNA catabolic process, nonsense-mediated decay and positive regulation of mRNA cis splicing, via spliceosome. Located in neuronal cell body and nucleus. Is expressed in several structures, including central nervous system. 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, Nov 2024]
    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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    See Upf3b in Genome Data Viewer
    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 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. Spatial expression of the nonsense-mediated mRNA decay factors UPF3A and UPF3B among mouse tissues. Ma X, et al. J Zhejiang Univ Sci B, 2023 Nov 15. PMID 37961809, Free PMC Article
    5. The role of the NMD factor UPF3B in olfactory sensory neurons. Tan K, et al. Elife, 2020 Aug 10. PMID 32773035, Free PMC Article

    See all (26) 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)
    • Endonuclease-mediated (3) 
    • Gene trapped (1) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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