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 | Fusion Gene Summary |
| Fusion Gene ORF analysis |
| Fusion Genomic Features |
| Fusion Protein Features |
| Fusion Gene Sequence |
| Fusion Gene PPI analysis |
| Related Drugs |
| Related Diseases |
Fusion gene:EDF1-KCNQ3 (FusionGDB2 ID:HG8721TG3786) |
Fusion Gene Summary for EDF1-KCNQ3 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: EDF1-KCNQ3 | Fusion gene ID: hg8721tg3786 | Hgene | Tgene | Gene symbol | EDF1 | KCNQ3 | Gene ID | 8721 | 3786 |
| Gene name | endothelial differentiation related factor 1 | potassium voltage-gated channel subfamily Q member 3 | |
| Synonyms | CFAP280|EDF-1|MBF1 | BFNC2|EBN2|KV7.3 | |
| Cytomap | ('EDF1')('KCNQ3') 9q34.3 | 8q24.22 | |
| Type of gene | protein-coding | protein-coding | |
| Description | endothelial differentiation-related factor 1multiprotein bridging factor 1 | potassium voltage-gated channel subfamily KQT member 3potassium channel subunit alpha KvLQT3potassium channel, voltage gated KQT-like subfamily Q, member 3potassium channel, voltage-gated, subfamily Q, member 3potassium voltage-gated channel, KQT-like | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | O60869 | O43525 | |
| Ensembl transtripts involved in fusion gene | ENST00000224073, ENST00000371649, ENST00000371648, | ENST00000224073, ENST00000371648, ENST00000371649, | |
| Fusion gene scores | * DoF score | 12 X 9 X 8=864 | 5 X 3 X 2=30 |
| # samples | 14 | 5 | |
| ** MAII score | log2(14/864*10)=-2.6256044852185 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(5/30*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: EDF1 [Title/Abstract] AND KCNQ3 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | EDF1(139756571)-KCNQ3(133393172), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | |||
| * 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 | EDF1 | GO:0043388 | positive regulation of DNA binding | 10567391 |
| Tgene | KCNQ3 | GO:0071805 | potassium ion transmembrane transport | 11159685|27564677 |
| Fusion gene information * 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 |
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Fusion Gene ORF analysis for EDF1-KCNQ3 |
| 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 |
| ORFfinder result based on the fusion transcript sequence of in-frame fusion genes. |
| 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) |
| 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 |
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Fusion Genomic Features for EDF1-KCNQ3 |
| FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints. |
| Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | 1-p | p (fusion gene breakpoint) |
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Fusion Protein Features for EDF1-KCNQ3 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:139756571/:133393172) - 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 |
| EDF1 | KCNQ3 |
| FUNCTION: Transcriptional coactivator stimulating NR5A1 and ligand-dependent NR1H3/LXRA and PPARG transcriptional activities. Enhances the DNA-binding activity of ATF1, ATF2, CREB1 and NR5A1. Regulates nitric oxid synthase activity probably by sequestering calmodulin in the cytoplasm. May function in endothelial cells differentiation, hormone-induced cardiomyocytes hypertrophy and lipid metabolism. {ECO:0000269|PubMed:10567391, ECO:0000269|PubMed:12040021, ECO:0000269|PubMed:15112053, ECO:0000269|PubMed:9813014}. | FUNCTION: Associates with KCNQ2 or KCNQ5 to form a potassium channel with essentially identical properties to the channel underlying the native M-current, a slowly activating and deactivating potassium conductance which plays a critical role in determining the subthreshold electrical excitability of neurons as well as the responsiveness to synaptic inputs. Therefore, it is important in the regulation of neuronal excitability. {ECO:0000269|PubMed:11159685, ECO:0000269|PubMed:14534157, ECO:0000269|PubMed:16319223, ECO:0000269|PubMed:9872318}. |
| 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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Fusion Gene Sequence for EDF1-KCNQ3 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
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Fusion Gene PPI Analysis for EDF1-KCNQ3 |
| 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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Related Drugs for EDF1-KCNQ3 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.8 2021-05-08) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Tgene | KCNQ3 | O43525 | DB00321 | Amitriptyline | Inhibitor | Small molecule | Approved |
| Tgene | KCNQ3 | O43525 | DB00996 | Gabapentin | Activator | Small molecule | Approved|Investigational |
| Tgene | KCNQ3 | O43525 | DB04953 | Ezogabine | Small molecule | Approved|Investigational | |
| Tgene | KCNQ3 | O43525 | DB00939 | Meclofenamic acid | Other | Small molecule | Approved|Vet_approved |
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Related Diseases for EDF1-KCNQ3 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | C1852581 | EPILEPSY, BENIGN NEONATAL, 2 | 5 | CTD_human;GENOMICS_ENGLAND;UNIPROT | |
| Tgene | C0220669 | Familial benign neonatal epilepsy | 2 | ORPHANET | |
| Tgene | C0005586 | Bipolar Disorder | 1 | PSYGENET | |
| Tgene | C0036341 | Schizophrenia | 1 | PSYGENET | |
| Tgene | C0270853 | Juvenile Myoclonic Epilepsy | 1 | ORPHANET |
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