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

Gene ID: 65109, updated on 20-Dec-2019

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
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

Genomic context

See UPF3B in Genome Data Viewer
Location:
Xq24
Exon count:
16
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (119805311..119853028, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (118941115..118986991, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene sosondowah ankyrin repeat domain family member D 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 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
Mental retardation, syndromic 14, X-linked
MedGen: C1970822 OMIM: 300676 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-05-10)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-05-10)

ClinGen Genome Curation PagePubMed

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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
structural constituent of nuclear pore NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
centriolar satellite IDA
Inferred from Direct Assay
more info
 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm NAS
Non-traceable Author Statement
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
exon-exon junction complex IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
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
mental retardation, X-linked 62
nonsense mRNA reducing factor 3B
up-frameshift suppressor 3 homolog B
up-frameshift suppressor 3 homolog on chromosome X

NCBI Reference Sequences (RefSeq)

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_009241.1 RefSeqGene

    Range
    4978..23980
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_023010.3NP_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)
    AY013251, BC121017, DA949746
    Consensus CDS
    CCDS14587.1
    UniProtKB/Swiss-Prot
    Q9BZI7
    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
    Q9BZI7
    Related
    ENSP00000276201.2, ENST00000276201.6
    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)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    119805311..119853028 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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

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

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

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