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

Gene ID: 68134, updated on 7-May-2024

Summary

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
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Genomic context

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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

General gene information

Markers

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
 
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

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_026573.3NP_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: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_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_006541394.4XP_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:51208
    Smg4_UPF3; Smg-4/UPF3 family
  2. XM_036162085.1XP_036017978.1  regulator of nonsense transcripts 3B isoform X3

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

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

RNA

  1. XR_001782759.2 RNA Sequence

  2. XR_004940361.1 RNA Sequence