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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

UPF1 Gene

protein-coding   GIFtS: 61
GCID: GC19P018942

UPF1 Regulator Of Nonsense Transcripts Homolog (Yeast)

(Previous name: regulator of nonsense transcripts 1)
(Previous symbol: RENT1)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
UPF1 Regulator Of Nonsense Transcripts Homolog (Yeast)1 2     Delta Helicase2
RENT11 2 3 5     pNORF12
Regulator Of Nonsense Transcripts 11 2     smg-22
UP Frameshift 11 2     Smg-2 Homolog, Nonsense Mediated MRNA Decay Factor2
Nonsense MRNA Reducing Factor 12 3     Up-Frameshift Mutation 1 Homolog2
Up-Frameshift Suppressor 1 Homolog2 3     Yeast Upf1p Homolog2
NORF12 3     EC 3.6.4.-3
ATP-Dependent Helicase RENT12 3     KIAA02213
Nonsense Mediated MRNA Decay Factor (C. Elegans)1     hUpf13
Smg-2 Homolog1     EC 3.6.18
HUPF12     

External Ids:    HGNC: 99621   Entrez Gene: 59762   Ensembl: ENSG000000050077   OMIM: 6014305   UniProtKB: Q929003   

Export aliases for UPF1 gene to outside databases

Previous GC identifers: GC19P018804 GC19P018507


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for UPF1 Gene:
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 only in the
cytoplasm. When translation ends, it interacts with the protein that is a functional homolog of yeast Upf2p to
trigger mRNA decapping. Use of multiple polyadenylation sites has been noted for this gene. (provided by RefSeq,
Jul 2008)

GeneCards Summary for UPF1 Gene: 
UPF1 (UPF1 regulator of nonsense transcripts homolog (yeast)) is a protein-coding gene. Diseases associated with UPF1 include ullrich congenital muscular dystrophy, and congenital muscular dystrophy, and among its related super-pathways are Eukaryotic Translation Termination and Metabolism of RNA. GO annotations related to this gene include RNA binding and helicase activity. An important paralog of this gene is HELZ.

UniProtKB/Swiss-Prot: RENT1_HUMAN, Q92900
Function: RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing
premature stop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of
phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. Recruited by release
factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF
(SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex
(EJC) (located 50-55 or more nucleotides downstream from the termination codon) through UPF2 and allows the
formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Phosphorylated UPF1 is
recognized by EST1B/SMG5, SMG6 and SMG7 which are thought to provide a link to the mRNA degradation machinery
involving exonucleolytic and endonucleolytic pathways, and to serve as adapters to protein phosphatase 2A (PP2A),
thereby triggering UPF1 dephosphorylation and allowing the recycling of NMD factors. UPF1 can also activate NMD
without UPF2 or UPF3, and in the absence of the NMD-enhancing downstream EJC indicative for alternative NMD
pathways. Plays a role in replication-dependent histone mRNA degradation at the end of phase S; the function is
independent of UPF2. For the recognition of premature termination codons (PTC) and initiation of NMD a
competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed. The ATPase
activity of UPF1 is required for disassembly of mRNPs undergoing NMD. Essential for embryonic viability

Gene Wiki entry for UPF1 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000019.9  NT_011295.11  NC_018930.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the UPF1 gene promoter:
         Nkx2-5   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidUPF1 promoter sequence
   Search SABiosciences Chromatin IP Primers for UPF1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat UPF1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19p13.2-p13.11   Ensembl cytogenetic band:  19p13.11   HGNC cytogenetic band: 19p13.2-p13.11

UPF1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
UPF1 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P018942:  view genomic region     (about GC identifiers)

Start:
18,942,744 bp from pter      End:
18,979,045 bp from pter
Size:
36,302 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: RENT1_HUMAN, Q92900 (See protein sequence)
Recommended Name: Regulator of nonsense transcripts 1  
Size: 1129 amino acids; 124345 Da
Subunit: Found in a post-splicing messenger ribonucleoprotein (mRNP) complex. Associates with the exon junction
complex (EJC). Associates with the SGM1C complex; is phosphorylated by the complex kinase component SGM1.
Interacts with UPF2, UPF3A and UPF3B. Interacts with EST1A and SLBP. Interacts (when hyperphosphorylated) with
PNRC2. Interacts with AGO1, AGO2 and GSPT2. Interacts with isoform 1 and isoform 5 of ADAR/ADAR1
Subcellular location: Cytoplasm. Cytoplasm, P-body. Nucleus. Note=Hyperphosphorylated form is targeted to the
P-body, while unphosphorylated protein is distributed throughout the cytoplasm
Sequence caution: Sequence=BAA19664.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;
6/8 PDB 3D structures from and Proteopedia for UPF1 (see all 8):
2GJK (3D)        2GK6 (3D)        2GK7 (3D)        2IYK (3D)        2WJV (3D)        2WJY (3D)    
Secondary accessions: O00239 O43343 Q86Z25 Q92842
Alternative splicing: 2 isoforms:  Q92900-1   Q92900-2   

Explore the universe of human proteins at neXtProt for UPF1: NX_Q92900

Explore proteomics data for UPF1 at MOPED 

Post-translational modifications:

  • UniProtKB: Phosphorylated by SMG1; required for formation of mRNA surveillance complexes
  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q92900

  • 4/17 DME Specific Peptides for UPF1 (Q92900) (see all 17)
     LVCAPSN  IILSCVR  EHQGIGF  YHKLLGH 

    UPF1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    UPF1 Protein Expression
    REFSEQ proteins: NP_002902.2  
    ENSEMBL proteins: 
     ENSP00000262803   ENSP00000470142  
    Reactome Protein details: Q92900
    Human Recombinant Protein Products for UPF1: 
    Browse Purified and Recombinant Proteins at EMD Millipore
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Browse OriGene full length recombinant human proteins expressed in human HEK293 cells
    OriGene Protein Over-expression Lysate for UPF1
    OriGene Custom MassSpec 
    OriGene Custom Protein Services for UPF1
    GenScript Custom Purified and Recombinant Proteins Services for UPF1
    Novus Biologicals UPF1 Protein
    Novus Biologicals UPF1 Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 5/7 cellular component terms (GO ID links to tree view) (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000785chromatin IDA16488880
    GO:0000932cytoplasmic mRNA processing body IEA--
    GO:0005634nucleus IDA18362360
    GO:0005737cytoplasm NAS9064659
    GO:0005829cytosol TAS--

    UPF1 for ontologies           About GeneDecksing



    UPF1 Antibody Products: 
    EMD Millipore Mono- and Polyclonal Antibodies for the study of UPF1
    R&D Systems Antibodies for UPF1 (RENT1/UPF1)
    Cell Signaling Technology (CST) Antibodies for UPF1  (RENT1)
    OriGene Antibodies for UPF1
    OriGene Custom Antibody Services for UPF1
    GenScript Custom Superior Antibodies Services for UPF1
    Novus Biologicals UPF1 Antibodies
    Abcam antibodies for UPF1
    Browse Antibodies at Cloud-Clone Corp. 
    ThermoFisher Antibodies for UPF1
    LSBio Antibodies in human, mouse, rat for UPF1 

    Assay Products for UPF1: 
    Browse Kits and Assays available from EMD Millipore
    OriGene Custom Assay Services for UPF1
    Browse R&D Systems for biochemical assays
    GenScript Custom Assay Services for UPF1
    Browse Enzo Life Sciences for kits & assays
    Browse ELISAs at Cloud-Clone Corp. 
    Browse CLIAs at Cloud-Clone Corp.


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    2 InterPro protein domains:
     IPR027417 P-loop_NTPase
     IPR018999 RNA-helicase_UPF1_UPF2-interct

    Graphical View of Domain Structure for InterPro Entry Q92900

    ProtoNet protein and cluster: Q92900

    UniProtKB/Swiss-Prot: RENT1_HUMAN, Q92900
    Domain: The [ST]-Q motif constitutes a recognition sequence for kinases from the PI3/PI4-kinase family
    Similarity: Belongs to the DNA2/NAM7 helicase family
    Similarity: Contains 1 UPF1-type zinc finger


    UPF1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RENT1_HUMAN, Q92900
    Function: RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing
    premature stop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of
    phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. Recruited by release
    factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF
    (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex
    (EJC) (located 50-55 or more nucleotides downstream from the termination codon) through UPF2 and allows the
    formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Phosphorylated UPF1 is
    recognized by EST1B/SMG5, SMG6 and SMG7 which are thought to provide a link to the mRNA degradation machinery
    involving exonucleolytic and endonucleolytic pathways, and to serve as adapters to protein phosphatase 2A (PP2A),
    thereby triggering UPF1 dephosphorylation and allowing the recycling of NMD factors. UPF1 can also activate NMD
    without UPF2 or UPF3, and in the absence of the NMD-enhancing downstream EJC indicative for alternative NMD
    pathways. Plays a role in replication-dependent histone mRNA degradation at the end of phase S; the function is
    independent of UPF2. For the recognition of premature termination codons (PTC) and initiation of NMD a
    competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed. The ATPase
    activity of UPF1 is required for disassembly of mRNPs undergoing NMD. Essential for embryonic viability

         Enzyme Numbers (IUBMB): EC 3.6.12 EC 3.6.4.-1

         Gene Ontology (GO): 5/9 molecular function terms (GO ID links to tree view) (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0003682chromatin binding IDA16488880
    GO:0003723RNA binding NAS10999600
    GO:0004004ATP-dependent RNA helicase activity IDA12554878
    GO:0004386helicase activity NAS9064659
         
    UPF1 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for UPF1:
     Increased cell number in G2M,   Synthetic lethal with Ras 

         4 MGI mutant phenotypes (inferred from 1 allele(MGI details for Upf1):
     cellular  embryogenesis  mortality/aging  reproductive system 

    UPF1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Upf1tm1Hcd for UPF1

       inGenious Targeting Laboratory - Custom generated mouse model solutions for UPF1 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for UPF1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for UPF1 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for UPF1 

    miRNA
    Products:
        
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat UPF1
    8/42 QIAGEN miScript miRNA Assays for microRNAs that regulate UPF1 (see all 42):
    hsa-miR-3130-5p hsa-miR-4328 hsa-miR-128 hsa-miR-3138 hsa-miR-3921 hsa-miR-3916 hsa-miR-570 hsa-miR-4274
    SwitchGear 3'UTR luciferase reporter plasmidUPF1 3' UTR sequence
    Inhib. RNA
    Products:
        
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for UPF1
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat UPF1

    Gene Editing
    Products:
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    Sirion Biotech Customized adenovirus for overexpression of UPF1

    Clone
    Products:
         
    Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
    OriGene clones in human, mouse for UPF1 (see all 9)
    OriGene ORF clones in mouse, rat for UPF1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: UPF1 (NM_002911)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for UPF1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat UPF1
    Sirion Biotech Customized lentivirus for stable overexpression of UPF1 
                         Customized lentivirus expression plasmids for stable overexpression of UPF1 

    Cell Line
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    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for UPF1


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for UPF1 About   (see all 6)                                                                                              See pathways by source

    SuperPathContained pathways About
    1Viral mRNA Translation
    Nonsense Mediated Decay Independent of the Exon Junction Complex0.94
    Nonsense Mediated Decay Enhanced by the Exon Junction Complex0.84
    Nonsense-Mediated Decay0.84
    2Metabolism of mRNA
    Metabolism of mRNA0.92
    Metabolism of RNA0.92
    3Generic Transcription Pathway
    Gene Expression0.47
    4mRNA surveillance pathway
    mRNA surveillance pathway
    5RNA transport
    RNA transport

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Cell Signaling Technology (CST) Pathway for UPF1
        Translational Control

    5/6        Reactome Pathways for UPF1 (see all 6)
        Nonsense Mediated Decay Independent of the Exon Junction Complex
    Nonsense-Mediated Decay
    Nonsense Mediated Decay Enhanced by the Exon Junction Complex
    Metabolism of RNA
    Metabolism of mRNA


    2         Kegg Pathways  (Kegg details for UPF1):
        RNA transport
    mRNA surveillance pathway


    UPF1 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for UPF1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/1008 Interacting proteins for UPF1 (Q929001, 2, 3 ENSP000002628034) via UniProtKB, MINT, STRING, and/or I2D (see all 1008)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UPF2Q9HAU51, 2, 3, ENSP000003487084EBI-373471,EBI-372073 MINT-6539840 MINT-7904432 MINT-6539908 MINT-7904445 MINT-7945693 MINT-7904564 MINT-4791496 MINT-7904530 MINT-6539883 MINT-7904547 MINT-7904417 MINT-7904495 MINT-7904598 MINT-7947479 MINT-6539859 MINT-7904478 MINT-7904581 MINT-7904403 MINT-7904512 MINT-7904458 I2D: score=9 STRING: ENSP00000348708
    CSNK2BP678702, 3MINT-8253748 I2D: score=2 
    ENSG00000206406P678702, 3MINT-8253748 I2D: score=2 
    ENSG00000224398P678702, 3MINT-8253748 I2D: score=2 
    ENSG00000224774P678702, 3MINT-8253748 I2D: score=2 
    About this table

    Gene Ontology (GO): 5/12 biological process terms (GO ID links to tree view) (see all 12):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000184nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS8855285
    GO:0006260DNA replication IMP16488880
    GO:0006281DNA repair IDA16488880
    GO:0006406mRNA export from nucleus TAS16488880
    GO:0006449regulation of translational termination NAS10999600

    UPF1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    UPF1 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for UPF1 (RENT1)

    4 Novoseek inferred chemical compound relationships for UPF1 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    nitrobenzylthioinosine 73.2 2 9353301 (1), 11139404 (1)
    nucleoside 48.1 4 9353301 (1), 11463208 (1), 10428086 (1), 11139404 (1)
    uridine 47.4 4 11139404 (2), 9353301 (1)
    zinc 0 1 9064659 (1)

    Search CenterWatch for drugs/clinical trials and news about UPF1 / RENT1

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for UPF1 gene: 
    NM_002911.3  

    Unigene Cluster for UPF1:

    UPF1 regulator of nonsense transcripts homolog (yeast)
    Hs.515266  [show with all ESTs]
    Unigene Representative Sequence: NM_002911
    13 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000262803(uc002nkf.3 uc002nkg.3 uc002nkh.3) ENST00000599848
    ENST00000601981 ENST00000594504 ENST00000600012 ENST00000600868 ENST00000598209
    ENST00000600310 ENST00000598471 ENST00000601689 ENST00000594243 ENST00000596842
    ENST00000600689
    miRNA
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat UPF1

    Additional mRNA sequence: 

    AF074016.1 AK125797.1 AK128727.1 BC034291.1 BC039817.1 D86988.1 U59323.1 U65533.1 

    23 DOTS entries:

    DT.100822434  DT.456245  DT.97802108  DT.100801983  DT.92441421  DT.40289544  DT.121468677  DT.95190426 
    DT.100822424  DT.100822429  DT.100822431  DT.102828678  DT.121468685  DT.121468688  DT.121468701  DT.121468708 
    DT.121468718  DT.91947800  DT.91968174  DT.92441407  DT.97801452  DT.100822428  DT.92441406 

    24/431 AceView cDNA sequences (see all 431):

    CD364377 CA310849 BM725972 AK125797 BG231960 BF508927 BQ029905 BM764737 
    CA946823 AI129317 BQ439866 BM742246 CF138243 BG288234 AI569472 AI085481 
    BM016503 AJ711993 AA412091 BU790211 CK430617 BM772767 BM472526 BQ883810 

    GeneLoc Exon Structure

    5/13 Alternative Splicing Database (ASD) splice patterns (SP) for UPF1 (see all 13)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b · 12c · 12d · 12e ^ 13a · 13b · 13c ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^
    SP1:              -                 -     -     -     -                 -                                               -                                       
    SP2:              -                 -     -     -     -                 -                                                                                       
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 19 ^ 20 ^ 21 ^ 22a · 22b ^ 23a · 23b ^ 24 ^ 25a · 25b ^ 26a · 26b ^ 27 ^ 28 ^ 29 ^ 30 ^ 31
    SP1:                    -           -                             -                                       
    SP2:                    -           -                             -                                       
    SP3:                                -                             -                                       
    SP4:                    -           -                                                                     
    SP5:                                                                                                      


    ECgene alternative splicing isoforms for UPF1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    UPF1 expression in normal human tissues (normalized intensities)      UPF1 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CACCGGGTAG
    UPF1 Expression
    About this image


    UPF1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/28 selected tissues (see all 28) fully expand
     
     Epithelium
             vagina ; squamous epithelial cells   
     
     Testis (Reproductive System)    fully expand to see all 4 entries
             Leydig Cells Testis Interstitium
             seminal vesicle ; glandular cells   
     
     Colon (Gastrointestinal Tract)    fully expand to see all 4 entries
             colon ; peripheral nerve/ganglion   
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Uterus
             uterus, post-menopause ; glandular cells   

    See UPF1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for UPF1

    SOURCE GeneReport for Unigene cluster: Hs.515266

    UniProtKB/Swiss-Prot: RENT1_HUMAN, Q92900
    Tissue specificity: Ubiquitous

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for UPF1 gene from 9/26 species (see all 26)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Upf11 , 5 UPF1 regulator of nonsense transcripts homolog (yeast) less1, 5 88.92(n)1
    98.92(a)1
      8 (34.15 cM)5
    197041  NM_001122829.11  NP_001116301.11 
     703315225 
    chicken
    (Gallus gallus)
    Aves UPF11 UPF1 regulator of nonsense transcripts homolog (yeast) less 81.08(n)
    97.87(a)
      420119  XM_418237.3  XP_418237.3 
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.105472 Xenopus laevis transcribed sequence with strong similarity to protein spQ92900 (H.sapiens) RNT1_HUMAN Regulator of nonsense transcripts 1 (Nonsense mRNA reducing factor 1) (NORF1) (Up-frameshift suppressor 1 homolog) less 79.67(n)    BU914294.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.135942 Danio rerio mRNA similar to regulator of nonsense transcripts 1 (cDNA clone MGC55472 IMAGE2640133), complete cds less 82.95(n)    BC045353.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Upf11 CG1559-PA 68.46(n)
    71.44(a)
      32153  NM_132539.2  NP_572767.1 
    worm
    (Caenorhabditis elegans)
    Secernentea smg-21 Protein SMG-2 54.6(n)
    52.86(a)
      171696  NM_058428.3  NP_490829.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes NAM7(YMR080C)4
    NAM71
    ATP-dependent RNA helicase of the SFI superfamily involved in nonsense mediated mRNA decay; required for efficient translation termination at nonsense codons and targeting of NMD substrates to P-bodies; involved in telomere maintenance less4
    Nam7p1
    53.86(n)1
    56.88(a)1
      13(429627-426712)4
    8551041, 4  NP_013797.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons LBA11 Regulator of nonsense transcripts 1-like protein 58.41(n)
    63.94(a)
      834747  NM_124072.2  NP_199512.2 
    rice
    (Oryza sativa)
    Liliopsida Os.188372 Oryza sativa (japonica cultivar-group) cDNA cloneJ023105F12, full insert sequence less 72.8(n)    AK067729.1 


    ENSEMBL Gene Tree for UPF1 (if available)
    TreeFam Gene Tree for UPF1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for UPF1 gene
    HELZ2  HELZ22  MOV10L12  MOV102  C4orf212  

    UPF1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/795 SNPs in UPF1 are shown (see all 795)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1996001581,2
    --18940921(+) ATTTC-/GGGGGG 1 -- us2k10--------
    rs1852443611,2
    --18941199(+) ACACCA/GCACCG 1 -- us2k10--------
    rs1897606851,2
    --18941312(+) TAATAC/TACACA 1 -- us2k10--------
    rs1820623521,2
    --18941338(+) TCTGTC/TACCCA 1 -- us2k10--------
    rs1157719961,2
    F--18941340(+) TGTCAC/TCCAGG 1 -- us2k11Minor allele frequency- T:0.03WA 118
    rs801999401,2
    C,F--18941447(+) GGAAAG/AAGCCA 1 -- us2k11Minor allele frequency- A:0.09WA 118
    rs1167062771,2
    C,F--18941459(+) CTTGCC/TCAGGC 1 -- us2k11Minor allele frequency- T:0.04WA 118
    rs1439732301,2
    --18941586(+) TCCAGC/TTGTTT 1 -- us2k10--------
    rs1459736861,2
    --18941659(+) AGAGGC/TATCAG 1 -- us2k10--------
    rs1875699031,2
    --18941700(+) AGGCCC/TAGTAC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for UPF1 (18942744 - 18979045 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for UPF1:    About this table     
    Variant IDTypeSubtypePubMed ID
    dgv3787n71CNV Loss21882294
    nsv833777CNV Loss17160897
    nsv470132CNV Loss18288195
    nsv911299CNV Loss21882294
    dgv3786n71CNV Loss21882294
    nsv828473CNV Gain20364138
    nsv828477CNV Gain20364138
    nsv828474CNV Gain20364138

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 601430    OMIM disorders: --

    12 diseases for UPF1:    About MalaCards
    ullrich congenital muscular dystrophy    congenital muscular dystrophy    long qt syndrome    muscular dystrophy
    lateral sclerosis    amyotrophic lateral sclerosis    colon cancer    gastric cancer
    colorectal cancer    prostate cancer    prostatitis    breast cancer

    1 disease from the University of Copenhagen DISEASES database for UPF1:
    Ullrich congenital muscular dystrophy

    UPF1 for disorders           About GeneDecksing


    Export disorders for UPF1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for UPF1 gene, integrated from 9 sources (see all 135):
    (articles sorted by number of sources associating them with UPF1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning and characterization of HUPF1, a human homolog of the Saccharomyces cerevisiae nonsense mRNA-reducing UPF1 protein. (PubMed id 9064659)1, 2, 3, 9 Applequist S.E.... Jaeck H.-M. (1997)
    2. Mammalian orthologues of a yeast regulator of nonsense transcript stability. (PubMed id 8855285)1, 2, 3, 9 Perlick H.A....Dietz H.C. (1996)
    3. Characterization of human Smg5/7a: a protein with similarities to Caenorhabditis elegans SMG5 and SMG7 that functions in the dephosphorylation of Upf1. (PubMed id 12554878)1, 2, 9 Chiu S.-Y.... Maquat L.E. (2003)
    4. Binding of a novel SMG-1-Upf1-eRF1-eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay. (PubMed id 16452507)1, 2, 9 Kashima I....Ohno S. (2006)
    5. SMG7 is a 14-3-3-like adaptor in the nonsense-mediated mRNA decay pathway. (PubMed id 15721257)1, 2, 9 Fukuhara N....Conti E. (2005)
    6. SMG-8 and SMG-9, two novel subunits of the SMG-1 complex, regulate remodeling of the mRNA surveillance complex during nonsense-mediated mRNA decay. (PubMed id 19417104)1, 2, 9 Yamashita A....Ohno S. (2009)
    7. Characterization of the biochemical properties of the human Upf1 gene product that is involved in nonsense-mediated mRNA decay. (PubMed id 10999600)1, 2, 9 Bhattacharya A....Peltz S.W. (2000)
    8. Human proline-rich nuclear receptor coregulatory protein 2 mediates an interaction between mRNA surveillance machinery and decapping complex. (PubMed id 19150429)1, 2, 9 Cho H.... Kim Y.K. (2009)
    9. Regulated degradation of replication-dependent histone mRNAs requires both ATR and Upf1. (PubMed id 16086026)1, 2, 9 Kaygun H. and Marzluff W.F. (2005)
    10. Cloning of a novel phosphatidylinositol kinase-related kinase: characterization of the human SMG-1 RNA surveillance protein. (PubMed id 11331269)1, 2, 9 Denning G.... Fields A.P. (2001)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 5976 HGNC: 9962 AceView: RENT1 Ensembl:ENSG00000005007 euGenes: HUgn5976
    ECgene: UPF1 Kegg: 5976 H-InvDB: UPF1

    (According to HUGE)
    About This Section
    HUGE: KIAA0221

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for UPF1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for UPF1 gene:
    Search GeneIP for patents involving UPF1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    About This Section

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