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UPF2 UPF2, regulator of nonsense mediated mRNA decay [ Homo sapiens (human) ]

Gene ID: 26019, updated on 7-Dec-2018

Summary

Official Symbol
UPF2provided by HGNC
Official Full Name
UPF2, regulator of nonsense mediated mRNA decayprovided by HGNC
Primary source
HGNC:HGNC:17854
See related
Ensembl:ENSG00000151461 MIM:605529
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
HUPF2; RENT2; smg-3
Summary
This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. 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 is located in the perinuclear area. It interacts with translation release factors and the proteins that are functional homologs of yeast Upf1p and Upf3p. Two splice variants have been found for this gene; both variants encode the same protein. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 11.8), lymph node (RPKM 8.5) and 25 other tissues See more
Orthologs

Genomic context

See UPF2 in Genome Data Viewer
Location:
10p14
Exon count:
24
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 10 NC_000010.11 (11920022..12043170, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (11962021..12085169, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376415 Neighboring gene proline and serine rich 2 Neighboring gene PROSER2 antisense RNA 1 Neighboring gene RNA, U6 small nuclear 1095, pseudogene Neighboring gene uncharacterized LOC105376416 Neighboring gene dehydrogenase E1 and transketolase domain containing 1 Neighboring gene RNA, U6 small nuclear 88, pseudogene

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants.
NHGRI GWA Catalog

Pathways from BioSystems

  • 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. ...
  • 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) ...
  • 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 ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1408, MGC138834, MGC138835, DKFZp434D222

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
telomeric DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
animal organ regeneration IEA
Inferred from Electronic Annotation
more info
 
liver development IEA
Inferred from Electronic Annotation
more info
 
mRNA export from nucleus TAS
Traceable Author Statement
more info
PubMed 
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IMP
Inferred from Mutant Phenotype
more info
PubMed 
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic ribonucleoprotein granule IDA
Inferred from Direct Assay
more info
 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
exon-exon junction complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
exon-exon junction complex IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
 
polysome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
regulator of nonsense transcripts 2
Names
FRS2/UPF2/LEMD3 fusion
LEMD3/UPF2 fusion
UPF2 regulator of nonsense transcripts homolog
nonsense mRNA reducing factor 2
smg-3 homolog, nonsense mediated mRNA decay factor
up-frameshift suppressor 2 homolog
yeast Upf2p homolog

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_033936.1 RefSeqGene

    Range
    5001..128149
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_015542.4NP_056357.1  regulator of nonsense transcripts 2

    See identical proteins and their annotated locations for NP_056357.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains a different 5' UTR than variant 1 and is the shorter transcript.
    Source sequence(s)
    AF301013, BC114964, DA188353
    Consensus CDS
    CCDS7086.1
    UniProtKB/Swiss-Prot
    Q9HAU5
    Related
    ENSP00000350221.5, ENST00000357604.9
    Conserved Domains (3) summary
    smart00543
    Location:773986
    MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
    pfam04050
    Location:10951218
    Upf2; Up-frameshift suppressor 2
    cl19727
    Location:358421
    DUF1451; Zinc-ribbon containing domain
  2. NM_080599.2NP_542166.1  regulator of nonsense transcripts 2

    See identical proteins and their annotated locations for NP_542166.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) contains a different 5' UTR than variant 2 and is the longer transcript.
    Source sequence(s)
    AF301013, BC114964, DB065422
    Consensus CDS
    CCDS7086.1
    UniProtKB/Swiss-Prot
    Q9HAU5
    Related
    ENSP00000380244.2, ENST00000397053.6
    Conserved Domains (3) summary
    smart00543
    Location:773986
    MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
    pfam04050
    Location:10951218
    Upf2; Up-frameshift suppressor 2
    cl19727
    Location:358421
    DUF1451; Zinc-ribbon containing domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p12 Primary Assembly

    Range
    11920022..12043170 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011519449.3XP_011517751.1  regulator of nonsense transcripts 2 isoform X1

    Conserved Domains (2) summary
    smart00543
    Location:168363
    MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
    cl19727
    Location:358421
    DUF1451; Zinc-ribbon containing domain

RNA

  1. XR_930489.3 RNA Sequence

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