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UPF3B UPF3 regulator of nonsense transcripts homolog B (yeast) [ Homo sapiens (human) ]

Gene ID: 65109, updated on 8-May-2016
Official Symbol
UPF3Bprovided by HGNC
Official Full Name
UPF3 regulator of nonsense transcripts homolog B (yeast)provided by HGNC
Primary source
HGNC:HGNC:20439
See related
Ensembl:ENSG00000125351 HPRD:02247; MIM:300298; Vega:OTTHUMG00000022282
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; 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]
Orthologs
Location:
Xq24
Exon count:
16
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 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 small nucleolar RNA, H/ACA box 69 Neighboring gene ribosomal protein L39 Neighboring gene UPF3 regulator of nonsense transcripts homolog B (yeast) pseudogene Neighboring gene ring finger protein 113A Neighboring gene NADH:ubiquinone oxidoreductase subunit A1 Neighboring gene A-kinase anchoring protein 14

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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

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

  • Cleavage of Growing Transcript in the Termination Region, organism-specific biosystem (from REACTOME)
    Cleavage of Growing Transcript in the Termination Region, organism-specific biosystemThis section includes the cleavage of both polyadenylated and non-polyadenylated transcripts. In the former case polyadenylation has to precede transcript cleavage, while in the latter case there is ...
  • Exon junction complex (EJC), organism-specific biosystem (from KEGG)
    Exon junction complex (EJC), organism-specific biosystemStructural complex; Genetic information processing; RNA processing
  • Exon junction complex (EJC), conserved biosystem (from KEGG)
    Exon junction complex (EJC), conserved biosystemStructural complex; Genetic information processing; RNA processing
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC), organism-specific biosystem (from REACTOME)
    Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC), organism-specific biosystemDuring normal translation termination eRF3 associates with the ribosome and then interacts with PABP bound to the polyadenylate tail of the mRNA to release the ribosome and allow a new round of trans...
  • Nonsense-Mediated Decay (NMD), organism-specific biosystem (from REACTOME)
    Nonsense-Mediated Decay (NMD), organism-specific biosystemThe Nonsense-Mediated Decay (NMD) pathway activates the destruction of mRNAs containing premature termination codons (PTCs) (reviewed in Isken and Maquat 2007, Chang et al. 2007, Behm-Ansmant et al. ...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • RNA Polymerase II Transcription, organism-specific biosystem (from REACTOME)
    RNA Polymerase II Transcription, organism-specific biosystem
    RNA Polymerase II Transcription
  • RNA Polymerase II Transcription Termination, organism-specific biosystem (from REACTOME)
    RNA Polymerase II Transcription Termination, organism-specific biosystemThe detailed annotation of this section will be completed in the next release.
  • RNA transport, organism-specific biosystem (from KEGG)
    RNA transport, organism-specific biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
  • RNA transport, conserved biosystem (from KEGG)
    RNA transport, conserved biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
  • Transport of Mature Transcript to Cytoplasm, organism-specific biosystem (from REACTOME)
    Transport of Mature Transcript to Cytoplasm, organism-specific biosystemTransport of mRNA through the Nuclear Pore Complex (NPC) is a dynamic process involving distinct machinery and receptor subsets. The separation of the two compartments and the regulation of this tran...
  • Transport of Mature mRNA derived from an Intron-Containing Transcript, organism-specific biosystem (from REACTOME)
    Transport of Mature mRNA derived from an Intron-Containing Transcript, organism-specific biosystemTransport of mRNA from the nucleus to the cytoplasm, where it is translated into protein, is highly selective and closely coupled to correct RNA processing. This coupling is achieved by the nuclear p...
  • mRNA 3'-end processing, organism-specific biosystem (from REACTOME)
    mRNA 3'-end processing, organism-specific biosystemThe 3' ends of eukaryotic mRNAs are generated by posttranscriptional processing of an extended primary transcript. For almost all RNAs, 3'-end processing consists of two steps: (i) the mRNA is first ...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...
  • mRNA surveillance pathway, organism-specific biosystem (from KEGG)
    mRNA surveillance pathway, organism-specific biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...
  • mRNA surveillance pathway, conserved biosystem (from KEGG)
    mRNA surveillance pathway, conserved biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
mRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
nucleocytoplasmic transporter activity NAS
Non-traceable Author Statement
more info
PubMed 
nucleotide binding IEA
Inferred from Electronic Annotation
more info
 
poly(A) RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
 
cytoplasm NAS
Non-traceable Author Statement
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
exon-exon junction complex IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with exon-exon junction complex IDA
Inferred from Direct Assay
more info
PubMed 
microtubule organizing center IDA
Inferred from Direct Assay
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 
nucleus NAS
Non-traceable Author Statement
more info
PubMed 
Preferred Names
regulator of nonsense transcripts 3B
Names
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

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, OTTHUMP00000023924, ENST00000345865, OTTHUMT00000058069
    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_080632.2NP_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)
    AF318576, CN412717, DA949746
    Consensus CDS
    CCDS14588.1
    UniProtKB/Swiss-Prot
    Q9BZI7
    Related
    ENSP00000276201, OTTHUMP00000023923, ENST00000276201, OTTHUMT00000058068
    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 Annotation Release 107 details...

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p2 Primary Assembly

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

mRNA and Protein(s)

  1. XM_011531379.1XP_011529681.1  

    Conserved Domains (2) summary
    smart00360
    Location:52123
    RRM; RNA recognition motif
    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. XM_005262458.3XP_005262515.1  

    Conserved Domains (2) summary
    smart00360
    Location:52123
    RRM; RNA recognition motif
    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)
  3. XM_006724780.2XP_006724843.1  

    Conserved Domains (2) summary
    smart00360
    Location:52123
    RRM; RNA recognition motif
    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)
  4. XM_006724781.2XP_006724844.1  

    Conserved Domains (2) summary
    smart00360
    Location:52123
    RRM; RNA recognition motif
    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)
  5. XM_011531378.1XP_011529680.1  

    Conserved Domains (2) summary
    smart00360
    Location:52123
    RRM; RNA recognition motif
    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)

Alternate CHM1_1.1

Genomic

  1. NC_018934.2 Alternate CHM1_1.1

    Range
    118879087..118898087 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)