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Fusion Protein:CYP2S1-UPF1 |
Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: CYP2S1-UPF1 | FusionPDB ID: 21065 | FusionGDB2.0 ID: 21065 | Hgene | Tgene | Gene symbol | CYP2S1 | UPF1 | Gene ID | 29785 | 5976 |
| Gene name | cytochrome P450 family 2 subfamily S member 1 | UPF1 RNA helicase and ATPase | |
| Synonyms | CYPIIS1 | HUPF1|NORF1|RENT1|pNORF1|smg-2 | |
| Cytomap | 19q13.2 | 19p13.11 | |
| Type of gene | protein-coding | protein-coding | |
| Description | cytochrome P450 2S1cytochrome P450, family 2, subfamily S, polypeptide 1cytochrome P540, subfamily IIS, polypeptide 1hydroperoxy icosatetraenoate dehydratasethromboxane-A synthase | 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 | 20200313 | 20200313 | |
| UniProtAcc | Q96SQ9 | . | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000310054, ENST00000542619, | ENST00000600310, ENST00000262803, ENST00000599848, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 1 X 1 X 1=1 | 8 X 7 X 5=280 |
| # samples | 1 | 9 | |
| ** MAII score | log2(1/1*10)=3.32192809488736 | log2(9/280*10)=-1.63742992061529 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context (manual curation of fusion genes in FusionPDB) | PubMed: CYP2S1 [Title/Abstract] AND UPF1 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | CYP2S1(41703833)-UPF1(18976098), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | CYP2S1-UPF1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. CYP2S1-UPF1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. CYP2S1-UPF1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. CYP2S1-UPF1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. | ||
| * 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 | CYP2S1 | GO:0006690 | icosanoid metabolic process | 21068195 |
| Hgene | CYP2S1 | GO:0006693 | prostaglandin metabolic process | 21068195 |
| Hgene | CYP2S1 | GO:0042573 | retinoic acid metabolic process | 12711469 |
| 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:0061014 | positive regulation of mRNA catabolic process | 24726324 |
| Tgene | UPF1 | GO:0061158 | 3'-UTR-mediated mRNA destabilization | 24726324 |
| Tgene | UPF1 | GO:0071222 | cellular response to lipopolysaccharide | 26255671 |
| Tgene | UPF1 | GO:0071347 | cellular response to interleukin-1 | 26255671 |
| Fusion gene breakpoints across CYP2S1 (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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| Fusion gene breakpoints across UPF1 (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Fusion Gene Sample Information |
| Fusion gene information from FusionGDB2.0. |
| Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0) * 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. |
| Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChimerDB4 | LUSC | TCGA-34-5240-01A | CYP2S1 | chr19 | 41703833 | + | UPF1 | chr19 | 18976098 | + |
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Fusion ORF Analysis |
| Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
| ENST00000310054 | CYP2S1 | chr19 | 41703833 | + | ENST00000262803 | UPF1 | chr19 | 18976098 | + | 2928 | 709 | 105 | 1208 | 367 |
| ENST00000310054 | CYP2S1 | chr19 | 41703833 | + | ENST00000599848 | UPF1 | chr19 | 18976098 | + | 2921 | 709 | 105 | 1208 | 367 |
| DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
| ENST00000310054 | ENST00000262803 | CYP2S1 | chr19 | 41703833 | + | UPF1 | chr19 | 18976098 | + | 0.009518466 | 0.99048156 |
| ENST00000310054 | ENST00000599848 | CYP2S1 | chr19 | 41703833 | + | UPF1 | chr19 | 18976098 | + | 0.009434285 | 0.9905657 |
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Fusion Amino Acid Sequences |
| For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
| >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP >21065_21065_1_CYP2S1-UPF1_CYP2S1_chr19_41703833_ENST00000310054_UPF1_chr19_18976098_ENST00000262803_length(amino acids)=367AA_BP=43 MPRPAPDFVGEGDARLPPLTSPAARSAWERRRSRPAEMEATGTWALLLALALLLLLTLALSGTRARGHLPPGPTPLPLLGNLLQLRPGAL YSGLMRLSKKYGPVFTIYLGPWRPVVVLVGQEAVREALGGQAEEFSGRGTVAMLEGTFDGHGVFFSNGERWRQLRKFTMLALRDLGMGKR EGEELIQAEARCLVETFQGTEGRPSSMYFQTHDQIGMISAGPSHVAAMNIPIPFNLVMPPMPPPGYFGQANGPAAGRGTPKGKTGRGGRQ KNRFGLPGPSQTNLPNSQASQDVASQPFSQGALTQGYISMSQPSQMSQPGLSQPELSQDSYLGDEFKSQIDVALSQDSTYQGERAYQHGG -------------------------------------------------------------- >21065_21065_2_CYP2S1-UPF1_CYP2S1_chr19_41703833_ENST00000310054_UPF1_chr19_18976098_ENST00000599848_length(amino acids)=367AA_BP=43 MPRPAPDFVGEGDARLPPLTSPAARSAWERRRSRPAEMEATGTWALLLALALLLLLTLALSGTRARGHLPPGPTPLPLLGNLLQLRPGAL YSGLMRLSKKYGPVFTIYLGPWRPVVVLVGQEAVREALGGQAEEFSGRGTVAMLEGTFDGHGVFFSNGERWRQLRKFTMLALRDLGMGKR EGEELIQAEARCLVETFQGTEGRPSSMYFQTHDQIGMISAGPSHVAAMNIPIPFNLVMPPMPPPGYFGQANGPAAGRGTPKGKTGRGGRQ KNRFGLPGPSQTNLPNSQASQDVASQPFSQGALTQGYISMSQPSQMSQPGLSQPELSQDSYLGDEFKSQIDVALSQDSTYQGERAYQHGG -------------------------------------------------------------- |
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Fusion Protein Functional Features |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:41703833/chr19:18976098) - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. - How to search 1. Put your fusion gene symbol. 2. Press the tab key until there will be shown the breakpoint information filled. 4. Go down and press 'Search' tab twice. 4. Go down to have the hyperlink of the search result. 5. Click the hyperlink. 6. See the FGviewer result for your fusion gene. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| CYP2S1 | . |
| FUNCTION: A cytochrome P450 monooxygenase involved in the metabolism of retinoids and eicosanoids (PubMed:12711469, PubMed:21068195). In epidermis, may contribute to the oxidative metabolism of all-trans-retinoic acid. For this activity, uses molecular oxygen inserting one oxygen atom into a substrate, and reducing the second into a water molecule, with two electrons provided by NADPH via cytochrome P450 reductase (NADPH--hemoprotein reductase) (PubMed:12711469). Additionally, displays peroxidase and isomerase activities toward various oxygenated eicosanoids such as prostaglandin H2 (PGH2) and hydroperoxyeicosatetraenoates (HPETEs) (PubMed:21068195). Independently of cytochrome P450 reductase, NADPH, and O2, catalyzes the breakdown of PGH2 to hydroxyheptadecatrienoic acid (HHT) and malondialdehyde (MDA), which is known to act as a mediator of DNA damage (PubMed:21068195). {ECO:0000269|PubMed:12711469, ECO:0000269|PubMed:21068195}. | FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes. |
| 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. |
| - 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 |
| Tgene | UPF1 | chr19:41703833 | chr19:18976098 | ENST00000262803 | 19 | 24 | 1042_1129 | 952.3333333333334 | 1523.3333333333333 | Compositional bias | Note=Gln/Ser-rich | |
| Tgene | UPF1 | chr19:41703833 | chr19:18976098 | ENST00000599848 | 19 | 24 | 1042_1129 | 963.3333333333334 | 1553.0 | Compositional bias | Note=Gln/Ser-rich | |
| Tgene | UPF1 | chr19:41703833 | chr19:18976098 | ENST00000262803 | 19 | 24 | 1089_1090 | 952.3333333333334 | 1523.3333333333333 | Motif | Note=[ST]-Q motif 1 | |
| Tgene | UPF1 | chr19:41703833 | chr19:18976098 | ENST00000262803 | 19 | 24 | 1107_1108 | 952.3333333333334 | 1523.3333333333333 | Motif | Note=[ST]-Q motif 2 | |
| Tgene | UPF1 | chr19:41703833 | chr19:18976098 | ENST00000599848 | 19 | 24 | 1089_1090 | 963.3333333333334 | 1553.0 | Motif | Note=[ST]-Q motif 1 | |
| Tgene | UPF1 | chr19:41703833 | chr19:18976098 | ENST00000599848 | 19 | 24 | 1107_1108 | 963.3333333333334 | 1553.0 | Motif | Note=[ST]-Q motif 2 |
| - 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 |
| Tgene | UPF1 | chr19:41703833 | chr19:18976098 | ENST00000262803 | 19 | 24 | 47_80 | 952.3333333333334 | 1523.3333333333333 | Compositional bias | Note=Ala/Gly/Pro-rich | |
| Tgene | UPF1 | chr19:41703833 | chr19:18976098 | ENST00000599848 | 19 | 24 | 47_80 | 963.3333333333334 | 1553.0 | Compositional bias | Note=Ala/Gly/Pro-rich | |
| Tgene | UPF1 | chr19:41703833 | chr19:18976098 | ENST00000262803 | 19 | 24 | 506_510 | 952.3333333333334 | 1523.3333333333333 | Nucleotide binding | Note=ATP | |
| Tgene | UPF1 | chr19:41703833 | chr19:18976098 | ENST00000599848 | 19 | 24 | 506_510 | 963.3333333333334 | 1553.0 | Nucleotide binding | Note=ATP | |
| Tgene | UPF1 | chr19:41703833 | chr19:18976098 | ENST00000262803 | 19 | 24 | 121_272 | 952.3333333333334 | 1523.3333333333333 | Zinc finger | Note=UPF1-type | |
| Tgene | UPF1 | chr19:41703833 | chr19:18976098 | ENST00000599848 | 19 | 24 | 121_272 | 963.3333333333334 | 1553.0 | Zinc finger | Note=UPF1-type |
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Fusion Protein-Protein Interaction |
| 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 from validated records (BIOGRID-3.4.160) |
| Gene | PPI interactors |
| Protein-protein interactors based on sequence similarity (STRING) |
| Gene | STRING network |
| CYP2S1 | |
| UPF1 |
| - Retained interactions in fusion protein (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost interactions due to fusion (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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Related Drugs to CYP2S1-UPF1 |
| Drugs used for this fusion-positive patient. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to CYP2S1-UPF1 |
| Diseases that have this fusion gene. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Disease | Source | PMID |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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