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    UPF3B UPF3B regulator of nonsense mediated mRNA decay [ Homo sapiens (human) ]

    Gene ID: 65109, updated on 17-Jun-2024

    Summary

    Official Symbol
    UPF3Bprovided by HGNC
    Official Full Name
    UPF3B regulator of nonsense mediated mRNA decayprovided by HGNC
    Primary source
    HGNC:HGNC:20439
    See related
    Ensembl:ENSG00000125351 MIM:300298; AllianceGenome:HGNC:20439
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MRX62; MRX82; UPF3X; HUPF3B; MRXS14; RENT3B; UPF3BP1; UPF3BP2; UPF3BP3; Upf3p-X
    Summary
    This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. The encoded protein is one of two functional homologs to yeast Upf3p. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMD to degrade mRNAs containing premature stop codons. This protein binds to the mRNA and remains bound after nuclear export, acting as a nucleocytoplasmic shuttling protein. It forms with Y14 a complex that binds specifically 20 nt upstream of exon-exon junctions. This gene is located on the long arm of chromosome X. Two splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in lymph node (RPKM 5.0), brain (RPKM 4.7) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See UPF3B in Genome Data Viewer
    Location:
    Xq24
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (119805311..119852963, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (118180438..118228084, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (118967985..118986926, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29896 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29897 Neighboring gene sosondowah ankyrin repeat domain family member D Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:118902711-118903910 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29899 Neighboring gene uncharacterized LOC107985694 Neighboring gene small nucleolar RNA, H/ACA box 69 Neighboring gene ribosomal protein L39 Neighboring gene Sharpr-MPRA regulatory region 4463 Neighboring gene UPF3B, regulator of nonsense mediated mRNA decay pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29902 Neighboring gene ring finger protein 113A Neighboring gene NADH:ubiquinone oxidoreductase subunit A1

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Syndromic X-linked intellectual disability 14
    MedGen: C1970822 OMIM: 300676 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2021-02-09)

    ClinGen Genome Curation PagePubMed
    Triplosensitivity

    No evidence available (Last evaluated 2021-02-09)

    ClinGen Genome Curation Page

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of UPF3 regulator of nonsense transcripts homolog B (UPF3B) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify UPF3 regulator of nonsense transcripts homolog B (UPF3B), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify UPF3 regulator of nonsense transcripts homolog B (UPF3B), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Nef nef Tandem affinity purification and mass spectrometry analysis identify UPF3 regulator of nonsense transcripts homolog B (UPF3B), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify UPF3 regulator of nonsense transcripts homolog B (UPF3B), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables mRNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in centriolar satellite IDA
    Inferred from Direct Assay
    more info
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    part_of exon-exon junction complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in neuronal cell body IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    regulator of nonsense transcripts 3B
    Names
    UPF3 regulator of nonsense transcripts homolog B
    UPF3B pseudogene 1
    UPF3B pseudogene 2
    UPF3B pseudogene 3
    nonfunctional UPF3B regulator of nonsense mediated mRNA decay
    nonsense mRNA reducing factor 3B
    up-frameshift suppressor 3 homolog B
    up-frameshift suppressor 3 homolog on chromosome X

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_009241.2 RefSeqGene

      Range
      5000..23941
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_023010.4NP_075386.1  regulator of nonsense transcripts 3B isoform 2

      See identical proteins and their annotated locations for NP_075386.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate coding segment, compared to variant 1, and encodes the shorter protein (isoform 2).
      Source sequence(s)
      AC002477, AY013251, BC121017
      Consensus CDS
      CCDS14587.1
      UniProtKB/TrEMBL
      B3KSJ3
      Related
      ENSP00000245418.2, ENST00000345865.6
      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)
    2. NM_080632.3NP_542199.1  regulator of nonsense transcripts 3B isoform 1

      See identical proteins and their annotated locations for NP_542199.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer protein (isoform 1), also known as hUpf3-X.
      Source sequence(s)
      AA657616, AF318576, BC121017
      Consensus CDS
      CCDS14588.1
      UniProtKB/Swiss-Prot
      D3DWI3, D3DWI4, Q0VAK8, Q9BZI7, Q9H1J0
      UniProtKB/TrEMBL
      B3KSJ3
      Related
      ENSP00000276201.3, ENST00000276201.7
      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_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      119805311..119852963 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017029738.2XP_016885227.1  regulator of nonsense transcripts 3B isoform X2

    2. XM_047442375.1XP_047298331.1  regulator of nonsense transcripts 3B isoform X2

    3. XM_017029739.2XP_016885228.1  regulator of nonsense transcripts 3B isoform X3

    4. XM_017029740.2XP_016885229.1  regulator of nonsense transcripts 3B isoform X4

    5. XM_017029737.2XP_016885226.1  regulator of nonsense transcripts 3B isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      118180438..118228084 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054327596.1XP_054183571.1  regulator of nonsense transcripts 3B isoform X2

    2. XM_054327595.1XP_054183570.1  regulator of nonsense transcripts 3B isoform X2

    3. XM_054327597.1XP_054183572.1  regulator of nonsense transcripts 3B isoform X3

    4. XM_054327598.1XP_054183573.1  regulator of nonsense transcripts 3B isoform X4

    5. XM_054327594.1XP_054183569.1  regulator of nonsense transcripts 3B isoform X1