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Fusion Protein:CYP4F3-PTMS |
Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: CYP4F3-PTMS | FusionPDB ID: 21097 | FusionGDB2.0 ID: 21097 | Hgene | Tgene | Gene symbol | CYP4F3 | PTMS | Gene ID | 4051 | 5763 |
| Gene name | cytochrome P450 family 4 subfamily F member 3 | parathymosin | |
| Synonyms | CPF3|CYP4F|CYPIVF3|LTB4H | ParaT | |
| Cytomap | 19p13.12 | 12p13.31 | |
| Type of gene | protein-coding | protein-coding | |
| Description | cytochrome P450 4F320-HETE synthase20-hydroxyeicosatetraenoic acid synthasecytochrome P-450cytochrome P450, family 4, subfamily F, polypeptide 3cytochrome P450, subfamily IVF, polypeptide 3 (leukotriene B4 omega hydroxylase)cytochrome P450-LTB-omega | parathymosin | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | Q08477 | . | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000221307, ENST00000585846, ENST00000586182, ENST00000591058, ENST00000588886, | ENST00000538057, ENST00000309083, ENST00000389462, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 1 X 1 X 1=1 | 16 X 10 X 10=1600 |
| # samples | 1 | 16 | |
| ** MAII score | log2(1/1*10)=3.32192809488736 | log2(16/1600*10)=-3.32192809488736 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context (manual curation of fusion genes in FusionPDB) | PubMed: CYP4F3 [Title/Abstract] AND PTMS [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | CYP4F3(15752423)-PTMS(6878769), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | CYP4F3-PTMS 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. CYP4F3-PTMS 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 |
| Fusion gene breakpoints across CYP4F3 (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 PTMS (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 | LIHC | TCGA-EP-A2KB-01A | CYP4F3 | chr19 | 15752423 | + | PTMS | chr12 | 6878769 | + |
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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) |
| ENST00000586182 | CYP4F3 | chr19 | 15752423 | + | ENST00000389462 | PTMS | chr12 | 6878769 | + | 629 | 232 | 564 | 1 | 188 |
| ENST00000586182 | CYP4F3 | chr19 | 15752423 | + | ENST00000309083 | PTMS | chr12 | 6878769 | + | 997 | 232 | 567 | 1 | 189 |
| ENST00000591058 | CYP4F3 | chr19 | 15752423 | + | ENST00000389462 | PTMS | chr12 | 6878769 | + | 642 | 245 | 577 | 2 | 192 |
| ENST00000591058 | CYP4F3 | chr19 | 15752423 | + | ENST00000309083 | PTMS | chr12 | 6878769 | + | 1010 | 245 | 580 | 2 | 193 |
| ENST00000221307 | CYP4F3 | chr19 | 15752423 | + | ENST00000389462 | PTMS | chr12 | 6878769 | + | 642 | 245 | 577 | 2 | 192 |
| ENST00000221307 | CYP4F3 | chr19 | 15752423 | + | ENST00000309083 | PTMS | chr12 | 6878769 | + | 1010 | 245 | 580 | 2 | 193 |
| ENST00000585846 | CYP4F3 | chr19 | 15752423 | + | ENST00000389462 | PTMS | chr12 | 6878769 | + | 702 | 305 | 637 | 83 | 184 |
| ENST00000585846 | CYP4F3 | chr19 | 15752423 | + | ENST00000309083 | PTMS | chr12 | 6878769 | + | 1070 | 305 | 858 | 292 | 188 |
| 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 |
| ENST00000586182 | ENST00000389462 | CYP4F3 | chr19 | 15752423 | + | PTMS | chr12 | 6878769 | + | 0.025140723 | 0.97485936 |
| ENST00000586182 | ENST00000309083 | CYP4F3 | chr19 | 15752423 | + | PTMS | chr12 | 6878769 | + | 0.003724387 | 0.99627566 |
| ENST00000591058 | ENST00000389462 | CYP4F3 | chr19 | 15752423 | + | PTMS | chr12 | 6878769 | + | 0.026985902 | 0.9730142 |
| ENST00000591058 | ENST00000309083 | CYP4F3 | chr19 | 15752423 | + | PTMS | chr12 | 6878769 | + | 0.003055219 | 0.9969447 |
| ENST00000221307 | ENST00000389462 | CYP4F3 | chr19 | 15752423 | + | PTMS | chr12 | 6878769 | + | 0.026985902 | 0.9730142 |
| ENST00000221307 | ENST00000309083 | CYP4F3 | chr19 | 15752423 | + | PTMS | chr12 | 6878769 | + | 0.003055219 | 0.9969447 |
| ENST00000585846 | ENST00000389462 | CYP4F3 | chr19 | 15752423 | + | PTMS | chr12 | 6878769 | + | 0.03468168 | 0.96531826 |
| ENST00000585846 | ENST00000309083 | CYP4F3 | chr19 | 15752423 | + | PTMS | chr12 | 6878769 | + | 0.003566206 | 0.99643373 |
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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 >21097_21097_1_CYP4F3-PTMS_CYP4F3_chr19_15752423_ENST00000221307_PTMS_chr12_6878769_ENST00000309083_length(amino acids)=193AA_BP=1 MDLAAPTPTSRPREASQPQPVGRGSRRCPIFCLLPFGIRFILLFGSSLQRGPFIILFFFFLIFFFPFIFLLSILGSFFFFLLSPVLLLLH HFFLSLFPACLLLHLLLLLLQVQAQVTQEPIPFRGLRETPEAAAVVIEGIGPGQDAGQEPGGPNQQQEQPRGCCHWPKAQRGQAQLWHPS -------------------------------------------------------------- >21097_21097_2_CYP4F3-PTMS_CYP4F3_chr19_15752423_ENST00000221307_PTMS_chr12_6878769_ENST00000389462_length(amino acids)=192AA_BP=0 MPHFLSSAVWDPLHPPLRQLSSARALHHPLLLLPHLLLPLHLPPLHPRQFLLLPPQPRSPPPVGTRRGSSLRLAACLAHHHHQWDWSLHH FFLSLFPACLLLHLLLLLLQVQAQVTQEPIPFRGLRETPEAAAVVIEGIGPGQDAGQEPGGPNQQQEQPRGCCHWPKAQRGQAQLWHPSV -------------------------------------------------------------- >21097_21097_3_CYP4F3-PTMS_CYP4F3_chr19_15752423_ENST00000585846_PTMS_chr12_6878769_ENST00000309083_length(amino acids)=188AA_BP=0 MRLVGEGEREQRERGAIGGQLESSDGAGQEVEQWQSEGGGRSVWRGGNEKAGEKEEGGSSGAGPRAGSQVKSGWTWLPPPPPPGPERPPN PSLLAGAHADAPFSVFCRLGSASSSSSAALFSAGPSSSSSSSSSSSSSPSSSSSPSSAVSSSSSSAPFSSSSTTSFFRSFRLAFSSTFSF -------------------------------------------------------------- >21097_21097_4_CYP4F3-PTMS_CYP4F3_chr19_15752423_ENST00000585846_PTMS_chr12_6878769_ENST00000389462_length(amino acids)=184AA_BP=0 MPHFLSSAVWDPLHPPLRQLSSARALHHPLLLLPHLLLPLHLPPLHPRQFLLLPPQPRSPPPVGTRRGSSLRLAACLAHHHHQWDWSLHH FFLSLFPACLLLHLLLLLLQVQAQVTQEPIPFRGLRETPEAAAVVIEGIGPGQDAGQEPGGPNQQQEQPRGCCHWPKAQRGQAQLWHPAG -------------------------------------------------------------- >21097_21097_5_CYP4F3-PTMS_CYP4F3_chr19_15752423_ENST00000586182_PTMS_chr12_6878769_ENST00000309083_length(amino acids)=189AA_BP=1 MDLAAPTPTSRPREASQPQPVGRGSRRCPIFCLLPFGIRFILLFGSSLQRGPFIILFFFFLIFFFPFIFLLSILGSFFFFLLSPVLLLLH HFFLSLFPACLLLHLLLLLLQVQAQVTQEPIPFRGLRETPEAAAVVIEGIGPGQDAGQEPGGPNQQQEQPRGCCHWPKAQRGQAQLWHPC -------------------------------------------------------------- >21097_21097_6_CYP4F3-PTMS_CYP4F3_chr19_15752423_ENST00000586182_PTMS_chr12_6878769_ENST00000389462_length(amino acids)=188AA_BP=0 MPHFLSSAVWDPLHPPLRQLSSARALHHPLLLLPHLLLPLHLPPLHPRQFLLLPPQPRSPPPVGTRRGSSLRLAACLAHHHHQWDWSLHH FFLSLFPACLLLHLLLLLLQVQAQVTQEPIPFRGLRETPEAAAVVIEGIGPGQDAGQEPGGPNQQQEQPRGCCHWPKAQRGQAQLWHPCP -------------------------------------------------------------- >21097_21097_7_CYP4F3-PTMS_CYP4F3_chr19_15752423_ENST00000591058_PTMS_chr12_6878769_ENST00000309083_length(amino acids)=193AA_BP=1 MDLAAPTPTSRPREASQPQPVGRGSRRCPIFCLLPFGIRFILLFGSSLQRGPFIILFFFFLIFFFPFIFLLSILGSFFFFLLSPVLLLLH HFFLSLFPACLLLHLLLLLLQVQAQVTQEPIPFRGLRETPEAAAVVIEGIGPGQDAGQEPGGPNQQQEQPRGCCHWPKAQRGQAQLWHPS -------------------------------------------------------------- >21097_21097_8_CYP4F3-PTMS_CYP4F3_chr19_15752423_ENST00000591058_PTMS_chr12_6878769_ENST00000389462_length(amino acids)=192AA_BP=0 MPHFLSSAVWDPLHPPLRQLSSARALHHPLLLLPHLLLPLHLPPLHPRQFLLLPPQPRSPPPVGTRRGSSLRLAACLAHHHHQWDWSLHH FFLSLFPACLLLHLLLLLLQVQAQVTQEPIPFRGLRETPEAAAVVIEGIGPGQDAGQEPGGPNQQQEQPRGCCHWPKAQRGQAQLWHPSV -------------------------------------------------------------- |
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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/chr19:15752423/chr12:6878769) - 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 |
| CYP4F3 | . |
| FUNCTION: A cytochrome P450 monooxygenase involved in the metabolism of various endogenous substrates, including fatty acids and their oxygenated derivatives (oxylipins) (PubMed:8486631, PubMed:9675028, PubMed:11461919, PubMed:15145985, PubMed:16547005, PubMed:16820285, PubMed:18182499, PubMed:18065749, PubMed:18577768). Mechanistically, 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 (CPR; NADPH-ferrihemoprotein reductase) (PubMed:9675028). May play a role in inactivation of proinflammatory and anti-inflammatory oxylipins during the resolution of inflammation (PubMed:8486631, PubMed:9675028, PubMed:11461919, PubMed:15145985, PubMed:15364545, PubMed:16547005, PubMed:16820285, PubMed:18182499, PubMed:18065749, PubMed:18577768). {ECO:0000269|PubMed:11461919, ECO:0000269|PubMed:15145985, ECO:0000269|PubMed:15364545, ECO:0000269|PubMed:16547005, ECO:0000269|PubMed:16820285, ECO:0000269|PubMed:18065749, ECO:0000269|PubMed:18182499, ECO:0000269|PubMed:18577768, ECO:0000269|PubMed:8486631, ECO:0000269|PubMed:9675028}.; FUNCTION: [Isoform CYP4F3A]: Catalyzes predominantly the oxidation of the terminal carbon (omega-oxidation) of oxylipins in myeloid cells, displaying higher affinity for arachidonate metabolite leukotriene B4 (LTB4) (PubMed:8486631, PubMed:9675028, PubMed:11461919, PubMed:15364545). Inactivates LTB4 via three successive oxidative transformations to 20-hydroxy-LTB4, then to 20-oxo-LTB4 and to 20-carboxy-LTB4 (PubMed:9675028). Has omega-hydroxylase activity toward long-chain fatty acid epoxides with preference for 8,9-epoxy-(5Z,11Z,14Z)-eicosatrienoate (EET) and 9,10-epoxyoctadecanoate (PubMed:15145985). Omega-hydroxylates monohydroxy polyunsaturated fatty acids (PUFAs), including hydroxyeicosatetraenoates (HETEs) and hydroxyeicosapentaenoates (HEPEs), to dihydroxy compounds (PubMed:15364545, PubMed:9675028). Contributes to the degradation of saturated very long-chain fatty acids (VLCFAs) such as docosanoic acid, by catalyzing successive omega-oxidations to the corresponding dicarboxylic acid, thereby initiating chain shortening (PubMed:18182499). Has low hydroxylase activity toward PUFAs (PubMed:18577768, PubMed:11461919). {ECO:0000269|PubMed:11461919, ECO:0000269|PubMed:15145985, ECO:0000269|PubMed:15364545, ECO:0000269|PubMed:18182499, ECO:0000269|PubMed:18577768, ECO:0000269|PubMed:8486631, ECO:0000269|PubMed:9675028}.; FUNCTION: [Isoform CYP4F3B]: Catalyzes predominantly the oxidation of the terminal carbon (omega-oxidation) of polyunsaturated fatty acids (PUFAs) (PubMed:11461919, PubMed:16820285, PubMed:18577768). Participates in the conversion of arachidonic acid to 20-hydroxyeicosatetraenoic acid (20-HETE), a signaling molecule acting both as vasoconstrictive and natriuretic with overall effect on arterial blood pressure (PubMed:11461919, PubMed:16820285, PubMed:18577768). Has high omega-hydroxylase activity toward other PUFAs, including eicosatrienoic acid (ETA), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) (PubMed:16820285, PubMed:18577768). Can also catalyze the oxidation of the penultimate carbon (omega-1 oxidation) of PUFAs with lower efficiency (PubMed:18577768). Contributes to the degradation of saturated very long-chain fatty acids (VLCFAs) such as docosanoic acid and hexacosanoic acid, by catalyzing successive omega-oxidations to the corresponding dicarboxylic acids, thereby initiating chain shortening (PubMed:16547005, PubMed:18182499). Omega-hydroxylates long-chain 3-hydroxy fatty acids, likely initiating the oxidative conversion to the corresponding 3-hydroxydicarboxylic fatty acids (PubMed:18065749). Has omega-hydroxylase activity toward long-chain fatty acid epoxides with preference for 8,9-epoxy-(5Z,11Z,14Z)-eicosatrienoate (EET) and 9,10-epoxyoctadecanoate (PubMed:15145985). {ECO:0000269|PubMed:11461919, ECO:0000269|PubMed:15145985, ECO:0000269|PubMed:16547005, ECO:0000269|PubMed:16820285, ECO:0000269|PubMed:18065749, ECO:0000269|PubMed:18182499, ECO:0000269|PubMed:18577768}. | 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 |
| Hgene | CYP4F3 | chr19:15752423 | chr12:6878769 | ENST00000221307 | + | 2 | 13 | 11_31 | 66.0 | 521.0 | Transmembrane | Helical |
| Hgene | CYP4F3 | chr19:15752423 | chr12:6878769 | ENST00000585846 | + | 1 | 12 | 11_31 | 66.0 | 521.0 | Transmembrane | Helical |
| Hgene | CYP4F3 | chr19:15752423 | chr12:6878769 | ENST00000586182 | + | 2 | 13 | 11_31 | 66.0 | 521.0 | Transmembrane | Helical |
| Hgene | CYP4F3 | chr19:15752423 | chr12:6878769 | ENST00000591058 | + | 2 | 13 | 11_31 | 66.0 | 521.0 | Transmembrane | Helical |
| Tgene | PTMS | chr19:15752423 | chr12:6878769 | ENST00000309083 | 0 | 5 | 36_90 | 15.0 | 103.0 | Compositional bias | Note=Asp/Glu-rich (acidic) |
| - 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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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 |
| CYP4F3 | |
| PTMS |
| - 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 CYP4F3-PTMS |
| 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 CYP4F3-PTMS |
| 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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