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

    Gene ID: 26019, updated on 3-Nov-2024

    Summary

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    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; AllianceGenome:HGNC:17854
    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
    mouse all
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    Genomic context

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    See UPF2 in Genome Data Viewer
    Location:
    10p14
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (11920022..12043170, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (11931338..12054461, complement)
    RS_2024_09 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 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:11835512-11836711 Neighboring gene proline and serine rich 2 Neighboring gene PROSER2 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:11917739-11918586 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:11923543-11924742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3027 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:11940130-11941329 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3028 Neighboring gene RNA, U6 small nuclear 1095, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2133 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3029 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2135 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3031 Neighboring gene uncharacterized LOC105376416 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2136 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2137 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3033 Neighboring gene dehydrogenase E1 and transketolase domain containing 1 Neighboring gene RNA, U6 small nuclear 88, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. Insights into the assembly and architecture of a Staufen-mediated mRNA decay (SMD)-competent mRNP. Gowravaram M, et al. Nat Commun, 2019 Nov 7. PMID 31699982, Free PMC Article
    2. An alternative spliced UPF2 transcript in pancreatic inflammatory myofibroblastic tumors. Jiang H, et al. Biochem Biophys Res Commun, 2024 Jan 8. PMID 38056247
    3. Structural and functional analysis of the three MIF4G domains of nonsense-mediated decay factor UPF2. Clerici M, et al. Nucleic Acids Res, 2014 Feb. PMID 24271394, Free PMC Article
    4. hUPF2 silencing identifies physiologic substrates of mammalian nonsense-mediated mRNA decay. Wittmann J, et al. Mol Cell Biol, 2006 Feb. PMID 16449641, Free PMC Article
    5. Results of the determination of serum markers in patients with malignant melanoma. Lugović L, et al. Coll Antropol, 2007 Jan. PMID 17469741

    See all (117) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. UPF1 helicase orchestrates mutually exclusive interactions with the SMG6 endonuclease and UPF2.
      Title: UPF1 helicase orchestrates mutually exclusive interactions with the SMG6 endonuclease and UPF2.
    2. An alternative spliced UPF2 transcript in pancreatic inflammatory myofibroblastic tumors.
      Title: An alternative spliced UPF2 transcript in pancreatic inflammatory myofibroblastic tumors.
    3. Modulation of RNA-binding properties of the RNA helicase UPF1 by its activator UPF2.
      Title: Modulation of RNA-binding properties of the RNA helicase UPF1 by its activator UPF2.
    4. Structures of nonsense-mediated mRNA decay factors UPF3B and UPF3A in complex with UPF2 reveal molecular basis for competitive binding and for neurodevelopmental disorder-causing mutation.
      Title: Structures of nonsense-mediated mRNA decay factors UPF3B and UPF3A in complex with UPF2 reveal molecular basis for competitive binding and for neurodevelopmental disorder-causing mutation.
    5. our findings indicate that impaired UPF2-dependent nonsense-mediated decay leads to neurodevelopmental dysfunction
      Title: Inhibition of Upf2-Dependent Nonsense-Mediated Decay Leads to Behavioral and Neurophysiological Abnormalities by Activating the Immune Response.
    6. UPF2 acts as an adaptor between Stau1 and UPF1, stimulates the catalytic activity of UPF1 and plays a central role in the formation of an Staufen-mediated mRNA decay-competent mRNP.
      Title: Insights into the assembly and architecture of a Staufen-mediated mRNA decay (SMD)-competent mRNP.
    7. we find that the interaction of UPF2 with UPF3b interferes with the assembly of the UPF2-eRF3 complex, and that UPF2 binds UPF3b more strongly than eRF3
      Title: Human nonsense-mediated mRNA decay factor UPF2 interacts directly with eRF3 and the SURF complex.
    8. UPF2 binds the FRB domain of SMG1, a region that regulates the related mTOR kinase.
      Title: Structures of SMG1-UPFs complexes: SMG1 contributes to regulate UPF2-dependent activation of UPF1 in NMD.
    9. This study demonstrated the quantitative regulation of Upf1 and Upf2 proteins by ubiquitin-proteasome system and SMG1.
      Title: Proteasome inhibitors and knockdown of SMG1 cause accumulation of Upf1 and Upf2 in human cells.
    10. UPF2 MIF4G-1 and MIF4G-2 domains appear to have a crucial scaffolding role, while the MIF4G-3 domain is the key module required for triggering nonsense-mediated decay.
      Title: Structural and functional analysis of the three MIF4G domains of nonsense-mediated decay factor UPF2.
    Submit: New GeneRIF Correction See all GeneRIFs (19)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2019-02-13)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2019-02-13)

    ClinGen Genome Curation Page

    EBI GWAS Catalog

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

    Variation

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    See Variation Viewer (GRCh37.p13)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1408, MGC138834, MGC138835, DKFZp434D222

    Gene Ontology Provided by GOA

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

    General protein information

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    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)

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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.

    Genomic

    1. NG_033936.1 RefSeqGene

      Range
      5362..128149
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_015542.4 → NP_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
      A6NLJ5, D3DRS0, Q14BM1, Q5W0J4, Q8N8U1, Q9H1J2, Q9HAU5, Q9NWL1, Q9P2D9, Q9Y4M9
      Related
      ENSP00000350221.5, ENST00000357604.10
      Conserved Domains (3) summary
      smart00543
      Location:773 → 986
      MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
      pfam04050
      Location:1095 → 1218
      Upf2; Up-frameshift suppressor 2
      cl19727
      Location:358 → 421
      DUF1451; Zinc-ribbon containing domain

    2. NM_080599.3 → NP_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
      A6NLJ5, D3DRS0, Q14BM1, Q5W0J4, Q8N8U1, Q9H1J2, Q9HAU5, Q9NWL1, Q9P2D9, Q9Y4M9
      Related
      ENSP00000380244.2, ENST00000397053.6
      Conserved Domains (3) summary
      smart00543
      Location:773 → 986
      MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
      pfam04050
      Location:1095 → 1218
      Upf2; Up-frameshift suppressor 2
      cl19727
      Location:358 → 421
      DUF1451; Zinc-ribbon containing domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_047424986.1 → XP_047280942.1  regulator of nonsense transcripts 2 isoform X3

    2. XM_047424987.1 → XP_047280943.1  regulator of nonsense transcripts 2 isoform X2

    3. XM_011519449.4 → XP_011517751.1  regulator of nonsense transcripts 2 isoform X1

      Conserved Domains (2) summary
      smart00543
      Location:168 → 363
      MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
      cl19727
      Location:358 → 421
      DUF1451; Zinc-ribbon containing domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      11931338..12054461 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054365447.1 → XP_054221422.1  regulator of nonsense transcripts 2 isoform X2

    2. XM_054365446.1 → XP_054221421.1  regulator of nonsense transcripts 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HAU5.1 GenPept UniProtKB/Swiss-Prot:Q9HAU5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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