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Fusion Protein:ATG3-EPHB1 |
Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: ATG3-EPHB1 | FusionPDB ID: 7559 | FusionGDB2.0 ID: 7559 | Hgene | Tgene | Gene symbol | ATG3 | EPHB1 | Gene ID | 64422 | 2047 |
| Gene name | autophagy related 3 | EPH receptor B1 | |
| Synonyms | APG3|APG3-LIKE|APG3L|PC3-96 | ELK|EPHT2|Hek6|NET | |
| Cytomap | 3q13.2 | 3q22.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | ubiquitin-like-conjugating enzyme ATG32610016C12RikAPG3 autophagy 3-likeATG3 autophagy related 3 homologautophagy-related protein 3hApg3 | ephrin type-B receptor 1EK6EPH-like kinase 6eph tyrosine kinase 2neuronally-expressed EPH-related tyrosine kinasesoluble EPHB1 variant 1tyrosine-protein kinase receptor EPH-2 | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | Q9NT62 | P54762 | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000283290, ENST00000402314, ENST00000495756, | ENST00000488154, ENST00000493838, ENST00000398015, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 5 X 5 X 2=50 | 5 X 5 X 3=75 |
| # samples | 5 | 5 | |
| ** MAII score | log2(5/50*10)=0 | log2(5/75*10)=-0.584962500721156 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context (manual curation of fusion genes in FusionPDB) | PubMed: ATG3 [Title/Abstract] AND EPHB1 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | ATG3(112277222)-EPHB1(134880858), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | ATG3-EPHB1 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. ATG3-EPHB1 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. ATG3-EPHB1 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. ATG3-EPHB1 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 | ATG3 | GO:0006464 | cellular protein modification process | 11825910 |
| Hgene | ATG3 | GO:0016567 | protein ubiquitination | 11825910 |
| Tgene | EPHB1 | GO:0001525 | angiogenesis | 9499402 |
| Tgene | EPHB1 | GO:0031589 | cell-substrate adhesion | 9430661 |
| Tgene | EPHB1 | GO:0046328 | regulation of JNK cascade | 9430661 |
| Tgene | EPHB1 | GO:0046777 | protein autophosphorylation | 18034775 |
| Tgene | EPHB1 | GO:0048013 | ephrin receptor signaling pathway | 12925710|18034775 |
| Tgene | EPHB1 | GO:0060326 | cell chemotaxis | 12925710 |
| Tgene | EPHB1 | GO:0070372 | regulation of ERK1 and ERK2 cascade | 12925710|18034775 |
| Fusion gene breakpoints across ATG3 (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 EPHB1 (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 |
| ChiTaRS5.0 | N/A | LQ657557 | ATG3 | chr3 | 112277222 | - | EPHB1 | chr3 | 134880858 | + |
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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) |
| ENST00000283290 | ATG3 | chr3 | 112277222 | - | ENST00000398015 | EPHB1 | chr3 | 134880858 | + | 3429 | 549 | 363 | 2081 | 572 |
| ENST00000402314 | ATG3 | chr3 | 112277222 | - | ENST00000398015 | EPHB1 | chr3 | 134880858 | + | 3382 | 502 | 316 | 2034 | 572 |
| 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 |
| ENST00000283290 | ENST00000398015 | ATG3 | chr3 | 112277222 | - | EPHB1 | chr3 | 134880858 | + | 0.00069877 | 0.9993012 |
| ENST00000402314 | ENST00000398015 | ATG3 | chr3 | 112277222 | - | EPHB1 | chr3 | 134880858 | + | 0.000700732 | 0.9992993 |
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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 >7559_7559_1_ATG3-EPHB1_ATG3_chr3_112277222_ENST00000283290_EPHB1_chr3_134880858_ENST00000398015_length(amino acids)=572AA_BP=62 MTPWPLTRLHFPSRRGAGRYSGPRMQNVINTVKGKALEVAEYLTPVLKESKFKETGVITPEEEHNEFNSSMARSQTNTARIDGLRPGMVY VVQVRARTVAGYGKFSGKMCFQTLTDDDYKSELREQLPLIAGSAAAGVVFVVSLVAISIVCSRKRAYSKEAVYSDKLQHYSTGRGSPGMK IYIDPFTYEDPNEAVREFAKEIDVSFVKIEEVIGAGEFGEVYKGRLKLPGKREIYVAIKTLKAGYSEKQRRDFLSEASIMGQFDHPNIIR LEGVVTKSRPVMIITEFMENGALDSFLRQNDGQFTVIQLVGMLRGIAAGMKYLAEMNYVHRDLAARNILVNSNLVCKVSDFGLSRYLQDD TSDPTYTSSLGGKIPVRWTAPEAIAYRKFTSASDVWSYGIVMWEVMSFGERPYWDMSNQDVINAIEQDYRLPPPMDCPAALHQLMLDCWQ KDRNSRPRFAEIVNTLDKMIRNPASLKTVATITAVPSQPLLDRSIPDFTAFTTVDDWLSAIKMVQYRDSFLTAGFTSLQLVTQMTSEDLL -------------------------------------------------------------- >7559_7559_2_ATG3-EPHB1_ATG3_chr3_112277222_ENST00000402314_EPHB1_chr3_134880858_ENST00000398015_length(amino acids)=572AA_BP=62 MTPWPLTRLHFPSRRGAGRYSGPRMQNVINTVKGKALEVAEYLTPVLKESKFKETGVITPEEEHNEFNSSMARSQTNTARIDGLRPGMVY VVQVRARTVAGYGKFSGKMCFQTLTDDDYKSELREQLPLIAGSAAAGVVFVVSLVAISIVCSRKRAYSKEAVYSDKLQHYSTGRGSPGMK IYIDPFTYEDPNEAVREFAKEIDVSFVKIEEVIGAGEFGEVYKGRLKLPGKREIYVAIKTLKAGYSEKQRRDFLSEASIMGQFDHPNIIR LEGVVTKSRPVMIITEFMENGALDSFLRQNDGQFTVIQLVGMLRGIAAGMKYLAEMNYVHRDLAARNILVNSNLVCKVSDFGLSRYLQDD TSDPTYTSSLGGKIPVRWTAPEAIAYRKFTSASDVWSYGIVMWEVMSFGERPYWDMSNQDVINAIEQDYRLPPPMDCPAALHQLMLDCWQ KDRNSRPRFAEIVNTLDKMIRNPASLKTVATITAVPSQPLLDRSIPDFTAFTTVDDWLSAIKMVQYRDSFLTAGFTSLQLVTQMTSEDLL -------------------------------------------------------------- |
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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/chr3:112277222/chr3:134880858) - 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 |
| ATG3 | EPHB1 |
| FUNCTION: E2 conjugating enzyme required for the cytoplasm to vacuole transport (Cvt), autophagy, and mitochondrial homeostasis. Responsible for the E2-like covalent binding of phosphatidylethanolamine to the C-terminal Gly of ATG8-like proteins (GABARAP, GABARAPL1, GABARAPL2 or MAP1LC3A). The ATG12-ATG5 conjugate plays a role of an E3 and promotes the transfer of ATG8-like proteins from ATG3 to phosphatidylethanolamine (PE). This step is required for the membrane association of ATG8-like proteins. The formation of the ATG8-phosphatidylethanolamine conjugates is essential for autophagy and for the cytoplasm to vacuole transport (Cvt). Preferred substrate is MAP1LC3A. Also acts as an autocatalytic E2-like enzyme, catalyzing the conjugation of ATG12 to itself, ATG12 conjugation to ATG3 playing a role in mitochondrial homeostasis but not in autophagy. ATG7 (E1-like enzyme) facilitates this reaction by forming an E1-E2 complex with ATG3. Promotes primary ciliogenesis by removing OFD1 from centriolar satellites via the autophagic pathway. {ECO:0000269|PubMed:11825910, ECO:0000269|PubMed:12207896, ECO:0000269|PubMed:12890687, ECO:0000269|PubMed:16704426, ECO:0000269|PubMed:20723759}. | FUNCTION: Receptor tyrosine kinase which binds promiscuously transmembrane ephrin-B family ligands residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. The signaling pathway downstream of the receptor is referred to as forward signaling while the signaling pathway downstream of the ephrin ligand is referred to as reverse signaling. Cognate/functional ephrin ligands for this receptor include EFNB1, EFNB2 and EFNB3. During nervous system development, regulates retinal axon guidance redirecting ipsilaterally ventrotemporal retinal ganglion cells axons at the optic chiasm midline. This probably requires repulsive interaction with EFNB2. In the adult nervous system together with EFNB3, regulates chemotaxis, proliferation and polarity of the hippocampus neural progenitors. In addition to its role in axon guidance plays also an important redundant role with other ephrin-B receptors in development and maturation of dendritic spines and synapse formation. May also regulate angiogenesis. More generally, may play a role in targeted cell migration and adhesion. Upon activation by EFNB1 and probably other ephrin-B ligands activates the MAPK/ERK and the JNK signaling cascades to regulate cell migration and adhesion respectively. Involved in the maintenance of the pool of satellite cells (muscle stem cells) by promoting their self-renewal and reducing their activation and differentiation (By similarity). {ECO:0000250|UniProtKB:Q8CBF3, ECO:0000269|PubMed:12223469, ECO:0000269|PubMed:12925710, ECO:0000269|PubMed:18034775, ECO:0000269|PubMed:9430661, ECO:0000269|PubMed:9499402}. |
| 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 | EPHB1 | chr3:112277222 | chr3:134880858 | ENST00000398015 | 5 | 16 | 619_882 | 474.0 | 985.0 | Domain | Protein kinase | |
| Tgene | EPHB1 | chr3:112277222 | chr3:134880858 | ENST00000398015 | 5 | 16 | 911_975 | 474.0 | 985.0 | Domain | SAM | |
| Tgene | EPHB1 | chr3:112277222 | chr3:134880858 | ENST00000398015 | 5 | 16 | 982_984 | 474.0 | 985.0 | Motif | PDZ-binding | |
| Tgene | EPHB1 | chr3:112277222 | chr3:134880858 | ENST00000398015 | 5 | 16 | 625_633 | 474.0 | 985.0 | Nucleotide binding | ATP | |
| Tgene | EPHB1 | chr3:112277222 | chr3:134880858 | ENST00000398015 | 5 | 16 | 564_984 | 474.0 | 985.0 | Topological domain | Cytoplasmic | |
| Tgene | EPHB1 | chr3:112277222 | chr3:134880858 | ENST00000398015 | 5 | 16 | 541_563 | 474.0 | 985.0 | Transmembrane | Helical |
| - 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 |
| Hgene | ATG3 | chr3:112277222 | chr3:134880858 | ENST00000283290 | - | 2 | 12 | 166_169 | 38.0 | 315.0 | Motif | Note=Caspase cleavage motif LETD |
| Hgene | ATG3 | chr3:112277222 | chr3:134880858 | ENST00000402314 | - | 2 | 11 | 166_169 | 38.0 | 312.0 | Motif | Note=Caspase cleavage motif LETD |
| Tgene | EPHB1 | chr3:112277222 | chr3:134880858 | ENST00000398015 | 5 | 16 | 183_319 | 474.0 | 985.0 | Compositional bias | Note=Cys-rich | |
| Tgene | EPHB1 | chr3:112277222 | chr3:134880858 | ENST00000398015 | 5 | 16 | 19_201 | 474.0 | 985.0 | Domain | Eph LBD | |
| Tgene | EPHB1 | chr3:112277222 | chr3:134880858 | ENST00000398015 | 5 | 16 | 322_432 | 474.0 | 985.0 | Domain | Fibronectin type-III 1 | |
| Tgene | EPHB1 | chr3:112277222 | chr3:134880858 | ENST00000398015 | 5 | 16 | 433_528 | 474.0 | 985.0 | Domain | Fibronectin type-III 2 | |
| Tgene | EPHB1 | chr3:112277222 | chr3:134880858 | ENST00000398015 | 5 | 16 | 18_540 | 474.0 | 985.0 | Topological domain | Extracellular |
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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 |
| ATG3 | |
| EPHB1 |
| - 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 ATG3-EPHB1 |
| 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 ATG3-EPHB1 |
| 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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