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UPF1 Gene

protein-coding   GIFtS: 62
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)
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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     H5
HUPF12     EC 3.6.18

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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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. 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000019.10  NT_011295.12  NC_018930.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the UPF1 gene promoter:
         Nkx2-5   
         Other transcription factors

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

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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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
Sequence caution: Sequence=BAA19664.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Selected 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: 

  • Phosphorylated by SMG1; required for formation of mRNA surveillance complexes1
  • Ubiquitination2 at Lys220, Lys264, Lys378, Lys386, Lys439, Lys587, Lys638, Lys688, Lys926, Lys929
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for UPF1 (Q92900) (see all 17)
     LVCAPSN  IILSCVR  EHQGIGF  YHKLLGH 


    See UPF1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_002902.2  
    ENSEMBL proteins: 
     ENSP00000262803   ENSP00000470142  
    Reactome Protein details: Q92900

    UPF1 Human Recombinant Protein Products:

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    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.

    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
    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

    UPF1 Assay Products:

    EMD Millipore Kits and Assays for the Analysis of UPF1
    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)
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    2 InterPro protein domains:
     IPR018999 RNA-helicase_UPF1_UPF2-interct
     IPR027417 P-loop_NTPase

    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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    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): Selected molecular function terms (see all 10):    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: Let us create your new Knockout/Knockin mouse model for UPF1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models 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:
        
    miRTarBase miRNAs that target UPF1:
    hsa-mir-423-3p (MIRT042554), hsa-mir-93-5p (MIRT048857)

    Block miRNA regulation of human, mouse, rat UPF1 using miScript Target Protectors
    Selected qRT-PCR 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:
        
    OriGene RNAi products in human, mouse, rat for UPF1
    Predesigned siRNA for gene silencing in human, mouse, rat UPF1

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for UPF1

    Clone
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    OriGene clones in human, mouse for UPF1 (see all 8)
    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

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for UPF1 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for UPF1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    RENT1_HUMAN, Q92900: Cytoplasm. Cytoplasm, P-body. Nucleus. Note=Hyperphosphorylated form is targeted to the
    P-body, while unphosphorylated protein is distributed throughout the cytoplasm
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol4
    golgi apparatus1
    mitochondrion1
    peroxisome1

    Gene Ontology (GO): Selected cellular component terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000785chromatin IDA16488880
    GO:0000932cytoplasmic mRNA processing body IEA--
    GO:0005634nucleus IDA--
    GO:0005730NOT nucleolus IDA--
    GO:0005737cytoplasm NAS9064659

    UPF1 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    SuperPaths for UPF1 About    
    See pathways by source

    SuperPathContained pathways About
    1Influenza Viral RNA Transcription and Replication
    Nonsense Mediated Decay Independent of the Exon Junction Complex0.94
    Nonsense Mediated Decay Enhanced by the Exon Junction Complex0.89
    Nonsense-Mediated Decay0.89
    2Gene Expression
    Gene Expression0.40
    3Translational Control
    Translational Control
    4RNA transport
    RNA transport
    5mRNA surveillance pathway
    mRNA surveillance pathway

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


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

    2 Reactome Pathways for UPF1
        Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
    Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)


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


    UPF1 for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for UPF1
    Interactions:

        GeneGlobe Interaction Network for UPF1

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

    Selected Interacting proteins for UPF1 (Q929001, 2, 3 ENSP000002628034) via UniProtKB, MINT, STRING, and/or I2D (see all 1045)
    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
    GSPT1P151701, 2, 3, ENSP000003981314EBI-373471,EBI-948993 MINT-6539771 MINT-6539822 MINT-7945693 MINT-6539753 I2D: score=1 STRING: ENSP00000398131
    TERTO147461, 2, 3, ENSP000003095724EBI-373471,EBI-1772203 MINT-8286561 MINT-8286551 MINT-8286579 I2D: score=1 STRING: ENSP00000309572
    CSNK2BP678702, 3MINT-8253748 I2D: score=2 
    ENSG00000206406P678702, 3MINT-8253748 I2D: score=2 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 12):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000184nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS8855285
    GO:0000956nuclear-transcribed mRNA catabolic process IMP--
    GO:0006200ATP catabolic process IDA12554878
    GO:0006260DNA replication IMP16488880
    GO:0006281DNA repair IDA16488880

    UPF1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    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)



    UPF1 for compounds           About GeneDecksing



    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    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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    Selected qRT-PCR 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
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    GenScript: all cDNA clones in your preferred vector: UPF1 (NM_002911)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat UPF1
    Primer
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    OriGene qPCR primer pairs and template standards for UPF1
    OriGene qSTAR qPCR primer pairs in human, mouse for UPF1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat UPF1
      QuantiTect SYBR Green Assays in human, mouse, rat UPF1
      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 

    Selected AceView cDNA sequences (see all 431):

    AW303603 CF138243 BU790211 D86988 CA394879 BM693677 AI569472 NM_002911 
    AW009890 BQ950083 BM772626 BM765204 AI085481 AK125797 BM742246 BG288234 
    BF508927 BM670820 AW272624 CR614589 BU752038 BM855397 BX417965 CA447202 

    GeneLoc Exon Structure

    Selected 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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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    UPF1 expression in normal human tissues (normalized intensities)
    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
     selected tissues (see all 6) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Ovary (Reproductive System)
             Oviduct
     
     Pancreas (Endocrine System)
             Islets of Langerhans
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
    UPF1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    UPF1 Protein Expression

    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)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for UPF1 gene from Selected species (see all 27)    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)1, 5 88.65(n)1
    98.38(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) 80.68(n)
    97.23(a)
      420119  XM_418237.4  XP_418237.3 
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.105472 Xenopus laevis transcribed sequence with strong similarity more 79.67(n)    BU914294.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.135942 Danio rerio mRNA similar to regulator of nonsense transcripts more 82.95(n)    BC045353.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Upf11 Upf1 68.5(n)
    71.54(a)
      32153  NM_132539.2  NP_572767.1 
    worm
    (Caenorhabditis elegans)
    Secernentea smg-21 smg-2 54.63(n)
    52.19(a)
      171696  NM_058428.4  NP_490829.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes NAM7(YMR080C)4
    NAM71
    ATP-dependent RNA helicase of the SFI superfamily involved more4
    NAM71
    53.77(n)1
    56.97(a)1
      13(429627-426712)4
    8551041, 4  NP_013797.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons LBA11 LBA1 58.52(n)
    63.56(a)
      834747  NM_124072.2  NP_199512.2 
    rice
    (Oryza sativa)
    Liliopsida Os.188372 Oryza sativa (japonica cultivar-group) cDNA cloneJ more 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)
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    Paralogs for UPF1 gene
    HELZ2  HELZ22  MOV10L12  MOV102  ZGRF12  

    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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
    About This Section

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    Selected SNPs for UPF1 (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

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing UPF1
    DNA2.0 Custom Variant and Variant Library Synthesis for UPF1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

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    OMIM gene information: 601430    OMIM disorders: --

    17 diseases for UPF1:    
    About MalaCards
    ullrich congenital muscular dystrophy    congenital muscular dystrophy    long qt syndrome    muscular dystrophy
    conjunctivitis    lateral sclerosis    amyotrophic lateral sclerosis    tonsillitis
    colorectal cancer    prostatitis    hiv-1    prostate cancer
    thyroiditis    breast cancer    cerebritis    malaria
    endotheliitis

    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)
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    PubMed articles for UPF1 gene, integrated from 10 sources (see all 141):
    (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. (Nucleic Acids Res. 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. (Proc. Natl. Acad. Sci. U.S.A. 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. (RNA 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. (Genes Dev. 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. (Mol. Cell 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. (Genes Dev. 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. (RNA 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. (Mol. Cell 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. (Nat. Struct. Mol. Biol. 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. (J. Biol. Chem. 2001)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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)
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    Entrez Gene: 5976 HGNC: 9962 AceView: RENT1 Ensembl:ENSG00000005007 euGenes: HUgn5976
    ECgene: UPF1 Kegg: 5976 H-InvDB: UPF1

    (According to HUGE)
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    HUGE: KIAA0221

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    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

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    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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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