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Fusion gene ID: 40850 |
FusionGeneSummary for UPF1_UPF1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: UPF1_UPF1 | Fusion gene ID: 40850 | Hgene | Tgene | Gene symbol | UPF1 | UPF1 | Gene ID | 5976 | 5976 |
| Gene name | UPF1, RNA helicase and ATPase | UPF1, RNA helicase and ATPase | |
| Synonyms | HUPF1|NORF1|RENT1|pNORF1|smg-2 | HUPF1|NORF1|RENT1|pNORF1|smg-2 | |
| Cytomap | 19p13.11 | 19p13.11 | |
| Type of gene | protein-coding | protein-coding | |
| Description | regulator of nonsense transcripts 1ATP-dependent helicase RENT1UPF1 regulator of nonsense transcripts homologdelta helicasenonsense mRNA reducing factor 1smg-2 homolog, nonsense mediated mRNA decay factorup-frameshift mutation 1 homologup-frameshif | regulator of nonsense transcripts 1ATP-dependent helicase RENT1UPF1 regulator of nonsense transcripts homologdelta helicasenonsense mRNA reducing factor 1smg-2 homolog, nonsense mediated mRNA decay factorup-frameshift mutation 1 homologup-frameshif | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | Q92900 | Q92900 | |
| Ensembl transtripts involved in fusion gene | ENST00000262803, ENST00000599848, ENST00000600310, | ENST00000262803, ENST00000599848, ENST00000600310, | |
| Fusion gene scores | * DoF score | 5 X 6 X 4=120 | 4 X 5 X 3=60 |
| # samples | 5 | 5 | |
| ** MAII score | log2(5/120*10)=-1.26303440583379 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(5/60*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: UPF1 [Title/Abstract] AND UPF1 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | |||
| * DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Hgene | UPF1 | GO:0000184 | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | 17468741 |
| Hgene | UPF1 | GO:0006281 | DNA repair | 16488880 |
| Hgene | UPF1 | GO:0032201 | telomere maintenance via semi-conservative replication | 21829167 |
| Hgene | UPF1 | GO:0071222 | cellular response to lipopolysaccharide | 26255671 |
| Hgene | UPF1 | GO:0071347 | cellular response to interleukin-1 | 26255671 |
| Tgene | UPF1 | GO:0000184 | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | 17468741 |
| Tgene | UPF1 | GO:0006281 | DNA repair | 16488880 |
| Tgene | UPF1 | GO:0032201 | telomere maintenance via semi-conservative replication | 21829167 |
| Tgene | UPF1 | GO:0071222 | cellular response to lipopolysaccharide | 26255671 |
| Tgene | UPF1 | GO:0071347 | cellular response to interleukin-1 | 26255671 |
| Fusion gene information from three resources (ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018)) * All genome coordinats were lifted-over on hg19. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| Data type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChiTaRS3.1 | AA532713 | UPF1 | chr19 | 18979030 | + | UPF1 | chr19 | 18978977 | - | ||
| ChiTaRS3.1 | CN406978 | UPF1 | chr19 | 18976159 | - | UPF1 | chr19 | 18976160 | + |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| 3UTR-3UTR | ENST00000262803 | ENST00000262803 | UPF1 | chr19 | 18979030 | + | UPF1 | chr19 | 18978977 | - |
| 3UTR-3UTR | ENST00000262803 | ENST00000599848 | UPF1 | chr19 | 18979030 | + | UPF1 | chr19 | 18978977 | - |
| 3UTR-intron | ENST00000262803 | ENST00000600310 | UPF1 | chr19 | 18979030 | + | UPF1 | chr19 | 18978977 | - |
| 3UTR-3UTR | ENST00000599848 | ENST00000262803 | UPF1 | chr19 | 18979030 | + | UPF1 | chr19 | 18978977 | - |
| 3UTR-3UTR | ENST00000599848 | ENST00000599848 | UPF1 | chr19 | 18979030 | + | UPF1 | chr19 | 18978977 | - |
| 3UTR-intron | ENST00000599848 | ENST00000600310 | UPF1 | chr19 | 18979030 | + | UPF1 | chr19 | 18978977 | - |
| intron-3UTR | ENST00000600310 | ENST00000262803 | UPF1 | chr19 | 18979030 | + | UPF1 | chr19 | 18978977 | - |
| intron-3UTR | ENST00000600310 | ENST00000599848 | UPF1 | chr19 | 18979030 | + | UPF1 | chr19 | 18978977 | - |
| intron-intron | ENST00000600310 | ENST00000600310 | UPF1 | chr19 | 18979030 | + | UPF1 | chr19 | 18978977 | - |
| In-frame | ENST00000262803 | ENST00000262803 | UPF1 | chr19 | 18976159 | - | UPF1 | chr19 | 18976160 | + |
| In-frame | ENST00000262803 | ENST00000599848 | UPF1 | chr19 | 18976159 | - | UPF1 | chr19 | 18976160 | + |
| 5CDS-intron | ENST00000262803 | ENST00000600310 | UPF1 | chr19 | 18976159 | - | UPF1 | chr19 | 18976160 | + |
| In-frame | ENST00000599848 | ENST00000262803 | UPF1 | chr19 | 18976159 | - | UPF1 | chr19 | 18976160 | + |
| In-frame | ENST00000599848 | ENST00000599848 | UPF1 | chr19 | 18976159 | - | UPF1 | chr19 | 18976160 | + |
| 5CDS-intron | ENST00000599848 | ENST00000600310 | UPF1 | chr19 | 18976159 | - | UPF1 | chr19 | 18976160 | + |
| intron-3CDS | ENST00000600310 | ENST00000262803 | UPF1 | chr19 | 18976159 | - | UPF1 | chr19 | 18976160 | + |
| intron-3CDS | ENST00000600310 | ENST00000599848 | UPF1 | chr19 | 18976159 | - | UPF1 | chr19 | 18976160 | + |
| intron-intron | ENST00000600310 | ENST00000600310 | UPF1 | chr19 | 18976159 | - | UPF1 | chr19 | 18976160 | + |
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FusionProtFeatures for UPF1_UPF1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| UPF1 | UPF1 |
| RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Isrecruited to mRNAs upon translation termination and undergoes acycle of phosphorylation and dephosphorylation; itsphosphorylation appears to be a key step in NMD. Recruited byrelease factors to stalled ribosomes together with the SMG1Cprotein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associateswith the exon junction complex (EJC) (located 50-55 or morenucleotides downstream from the termination codon) through UPF2and allows the formation of an UPF1-UPF2-UPF3 surveillance complexwhich is believed to activate NMD. Phosphorylated UPF1 isrecognized by EST1B/SMG5, SMG6 and SMG7 which are thought toprovide a link to the mRNA degradation machinery involvingexonucleolytic and endonucleolytic pathways, and to serve asadapters to protein phosphatase 2A (PP2A), thereby triggering UPF1dephosphorylation and allowing the recycling of NMD factors. UPF1can also activate NMD without UPF2 or UPF3, and in the absence ofthe NMD-enhancing downstream EJC indicative for alternative NMDpathways. Plays a role in replication-dependent histone mRNAdegradation at the end of phase S; the function is independent ofUPF2. For the recognition of premature termination codons (PTC)and initiation of NMD a competitive interaction between UPF1 andPABPC1 with the ribosome-bound release factors is proposed. TheATPase activity of UPF1 is required for disassembly of mRNPsundergoing NMD. Essential for embryonic viability.{ECO:0000269|PubMed:11163187, ECO:0000269|PubMed:16086026,ECO:0000269|PubMed:18172165, ECO:0000269|PubMed:21145460,ECO:0000269|PubMed:21419344}. | RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Isrecruited to mRNAs upon translation termination and undergoes acycle of phosphorylation and dephosphorylation; itsphosphorylation appears to be a key step in NMD. Recruited byrelease factors to stalled ribosomes together with the SMG1Cprotein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associateswith the exon junction complex (EJC) (located 50-55 or morenucleotides downstream from the termination codon) through UPF2and allows the formation of an UPF1-UPF2-UPF3 surveillance complexwhich is believed to activate NMD. Phosphorylated UPF1 isrecognized by EST1B/SMG5, SMG6 and SMG7 which are thought toprovide a link to the mRNA degradation machinery involvingexonucleolytic and endonucleolytic pathways, and to serve asadapters to protein phosphatase 2A (PP2A), thereby triggering UPF1dephosphorylation and allowing the recycling of NMD factors. UPF1can also activate NMD without UPF2 or UPF3, and in the absence ofthe NMD-enhancing downstream EJC indicative for alternative NMDpathways. Plays a role in replication-dependent histone mRNAdegradation at the end of phase S; the function is independent ofUPF2. For the recognition of premature termination codons (PTC)and initiation of NMD a competitive interaction between UPF1 andPABPC1 with the ribosome-bound release factors is proposed. TheATPase activity of UPF1 is required for disassembly of mRNPsundergoing NMD. Essential for embryonic viability.{ECO:0000269|PubMed:11163187, ECO:0000269|PubMed:16086026,ECO:0000269|PubMed:18172165, ECO:0000269|PubMed:21145460,ECO:0000269|PubMed:21419344}. |
| Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at . * Minus value of BPloci means that the break pointn is located before the CDS. |
| - In-frame and retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| - In-frame and not-retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
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FusionGeneSequence for UPF1_UPF1 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. (nt: nucleotides, aa: amino acids) |
| * Fusion amino acid sequences. |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| * Fusion transcript sequences (Full-length transcript). |
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FusionGenePPI for UPF1_UPF1 |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in . |
| Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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RelatedDrugs for UPF1_UPF1 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for UPF1_UPF1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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