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Kinase Fusion Gene:RBPMS_NTRK3 |
Kinase Fusion Protein Summary |
 Kinase Fusion gene summary |
| Kinase Fusion partner gene information | Kinase Fusion gene name: RBPMS_NTRK3 | KinaseFusionDB ID: KFG5327 | FusionGDB2.0 ID: KFG5327 | Hgene | Tgene | Gene symbol | RBPMS | NTRK3 | Gene ID | 11030 | 4916 | |
| Gene name | RNA binding protein, mRNA processing factor | neurotrophic receptor tyrosine kinase 3 | ||||||||||
| Synonyms | HERMES | GP145-TrkC|TRKC|gp145(trkC) | ||||||||||
| Cytomap | 8p12 | 15q25.3 | ||||||||||
| Type of gene | protein-coding | protein-coding | ||||||||||
| Description | RNA-binding protein with multiple splicingRNA binding protein with multiple splicingheart and RRM expressed sequence | NT-3 growth factor receptorETS related protein-neurotrophic receptor tyrosine kinase fusion proteinETV6-NTRK3 fusionneurotrophic tyrosine kinase, receptor, type 3tyrosine kinase receptor C | ||||||||||
| Modification date | 20240407 | 20240411 | ||||||||||
| UniProtAcc | Q93062 | Q16288 | ||||||||||
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000287771, ENST00000320203, ENST00000339877, ENST00000397323, ENST00000517860, ENST00000519647, ENST00000520161, ENST00000520191, ENST00000538486, ENST00000520916, | ENST00000540489, ENST00000558306, ENST00000317501, ENST00000355254, ENST00000357724, ENST00000360948, ENST00000394480, ENST00000542733, ENST00000557856, ENST00000558676, | |||||||||
| Context (manual curation of fusion genes in KinaseFusionDB) | PubMed: RBPMS [Title/Abstract] AND NTRK3 [Title/Abstract] AND fusion [Title/Abstract] | |||||||||||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | NTRK3(88669502)-RBPMS(30402011), # samples:3 RBPMS(30361953)-NTRK3(88576276), # samples:4 | |||||||||||
| 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 | RBPMS | GO:0060395 | SMAD protein signal transduction | 17099224 |
| Tgene | NTRK3 | GO:0001933 | negative regulation of protein phosphorylation | 23027130 |
| Tgene | NTRK3 | GO:0007169 | cell surface receptor protein tyrosine kinase signaling pathway | 23027130 |
| Tgene | NTRK3 | GO:0008284 | positive regulation of cell population proliferation | 23027130 |
| Tgene | NTRK3 | GO:0010628 | positive regulation of gene expression | 23027130 |
| Tgene | NTRK3 | GO:0030335 | positive regulation of cell migration | 23027130 |
| Tgene | NTRK3 | GO:0032148 | activation of protein kinase B activity | 23027130 |
| Tgene | NTRK3 | GO:0033138 | positive regulation of peptidyl-serine phosphorylation | 23027130 |
| Tgene | NTRK3 | GO:0043406 | positive regulation of MAP kinase activity | 23027130 |
| Tgene | NTRK3 | GO:0050927 | positive regulation of positive chemotaxis | 23027130 |
| Tgene | NTRK3 | GO:0090630 | activation of GTPase activity | 23027130 |
| Kinase Fusion gene breakpoints across RBPMS (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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| Kinase Fusion gene breakpoints across NTRK3 (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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Kinase Fusion Gene Sample Information |
| Kinase Fusion gene information. |
| Kinase Fusion gene information from four resources (ChiTars 5.0, ChimerDB 4.0, COSMIC, and CCLE) * 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 | Sample | Hgene | Hchr | Hbp | Tgene | Tchr | Tbp |
| ChimerDB4 | TCGA-ET-A39L-01A | RBPMS | chr8 | 30361953 | NTRK3 | chr15 | 88576276 |
| ChimerDB4 | TCGA-ET-A39L-01A | RBPMS | chr8 | 30361953 | NTRK3 | chr15 | 88616138 |
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Kinase Fusion ORF Analysis |
| Kinase Fusion information from ORFfinder translation from full-length transcript sequence from KinaseFusionDB. |
| Henst | Tenst | Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Seq length (transcript) | Seq length (amino acids) |
| ENST00000538486 | ENST00000394480 | RBPMS | chr8 | 30361953 | NTRK3 | chr15 | 88576276 | 4080 | 597 |
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Kinase Fusion Amino Acid Sequences |
| For individual full-length fusion transcript sequence from KinaseFusionDB, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
| >Henst_Tenst_Hgene_Hchr_Hbp_Tgene_Tchr_Tbp_length(fusion AA)_AAseq >ENST00000538486_ENST00000394480_RBPMS_chr8_30361953_NTRK3_chr15_88576276_length(amino acids)=597 MAPALPLQVALPGPDCLGAPLPARALPRLSLALPESPAAAVADSPREPQPNPSPTATAPAPAPAPQPAAPARGSPGARGRLQWASAPSPS PAPQPCPARRGRTGKMNNGGKAEKENTPSEANLQEEEVRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAE AAKNALNGIRFDPEIPQTLRLEFAKANTKMAKNKLVGTPNPSTPLPNTVPQFIAREPCPVAVISGEEDSASPLHHINHGITTPSSLDAGP DTVVIGMTRIPVIENPQYFRQGHNCHKPDTYVQHIKRRDIVLKRELGEGAFGKVFLAECYNLSPTKDKMLVAVKALKDPTLAARKDFQRE AELLTNLQHEHIVKFYGVCGDGDPLIMVFEYMKHGDLNKFLRAHGPDAMILVDGQPRQAKGELGLSQMLHIASQIASGMVYLASQHFVHR DLATRNCLVGANLLVKIGDFGMSRDVYSTDYYRVGGHTMLPIRWMPPESIMYRKFTTESDVWSFGVILWEIFTYGKQPWFQLSNTEVIEC -------------------------------------------------------------- |
Multiple Sequence Alignment of All Fusion Protein Isoforms |
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Kinase 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/chr8:88669502/chr15:30402011) - 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 |
| RBPMS | NTRK3 |
| FUNCTION: Acts as a coactivator of transcriptional activity. Required to increase TGFB1/Smad-mediated transactivation. Acts through SMAD2, SMAD3 and SMAD4 to increase transcriptional activity. Increases phosphorylation of SMAD2 and SMAD3 on their C-terminal SSXS motif, possibly through recruitment of TGFBR1. Promotes the nuclear accumulation of SMAD2, SMAD3 and SMAD4 proteins (PubMed:26347403). Binds to poly(A) RNA (PubMed:17099224, PubMed:26347403). {ECO:0000269|PubMed:17099224, ECO:0000269|PubMed:26347403}. | FUNCTION: Receptor tyrosine kinase involved in nervous system and probably heart development. Upon binding of its ligand NTF3/neurotrophin-3, NTRK3 autophosphorylates and activates different signaling pathways, including the phosphatidylinositol 3-kinase/AKT and the MAPK pathways, that control cell survival and differentiation. {ECO:0000269|PubMed:25196463}. |
| 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 domain in the 5'-partner of fusion protein (protein functional feature from UniProt). |
| Partner | Hgeneene | Hbp | Tgeneene | Tbp | ENST | BPexon | TotalExon | Protein feature loci | BPloci | TotalLen | Feature | Note |
| - Retained domain in the 3'-partner of fusion protein (protein functional feature from UniProt). |
| Partner | Hgeneene | Hbp | Tgeneene | Tbp | ENST | BPexon | TotalExon | Protein feature loci | BPloci | TotalLen | Feature | Note |
| Tgene | RBPMS | 30361953 | NTRK3 | 88576276 | ENST00000538486 | 10 | 14 | 538_839 | 465 | 613 | Domain | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| Tgene | RBPMS | 30361953 | NTRK3 | 88576276 | ENST00000538486 | 11 | 15 | 538_839 | 465 | 613 | Domain | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| Tgene | RBPMS | 30361953 | NTRK3 | 88576276 | ENST00000538486 | 11 | 18 | 538_839 | 465 | 826 | Domain | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| Tgene | RBPMS | 30361953 | NTRK3 | 88576276 | ENST00000538486 | 11 | 19 | 538_839 | 465 | 840 | Domain | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| Tgene | RBPMS | 30361953 | NTRK3 | 88576276 | ENST00000538486 | 12 | 19 | 538_839 | 465 | 826 | Domain | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
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Kinase Fusion Protein Structures |
| CIF files of the predicted kinase fusion proteins * Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| Kinase Fusion protein CIF link (fusion AA seq ID in KinaseFusionDB) | Henst | Tenst | Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | AA seq | Len(AA seq) |
| PDB file >>>414_RBPMS_NTRK3 | ENST00000538486 | ENST00000394480 | RBPMS | chr8 | 30361953 | NTRK3 | chr15 | 88576276 | MAPALPLQVALPGPDCLGAPLPARALPRLSLALPESPAAAVADSPREPQPNPSPTATAPAPAPAPQPAAPARGSPGARGRLQWASAPSPS PAPQPCPARRGRTGKMNNGGKAEKENTPSEANLQEEEVRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAE AAKNALNGIRFDPEIPQTLRLEFAKANTKMAKNKLVGTPNPSTPLPNTVPQFIAREPCPVAVISGEEDSASPLHHINHGITTPSSLDAGP DTVVIGMTRIPVIENPQYFRQGHNCHKPDTYVQHIKRRDIVLKRELGEGAFGKVFLAECYNLSPTKDKMLVAVKALKDPTLAARKDFQRE AELLTNLQHEHIVKFYGVCGDGDPLIMVFEYMKHGDLNKFLRAHGPDAMILVDGQPRQAKGELGLSQMLHIASQIASGMVYLASQHFVHR DLATRNCLVGANLLVKIGDFGMSRDVYSTDYYRVGGHTMLPIRWMPPESIMYRKFTTESDVWSFGVILWEIFTYGKQPWFQLSNTEVIEC | 597 |
| 3D view using mol* of 414_RBPMS_NTRK3 | ||||||||||
| PDB file >>>TKFP_698_RBPMS_NTRK3 | ENST00000538486 | ENST00000394480 | RBPMS | chr8 | 30361953 | NTRK3 | chr15 | 88576276 | MAPALPLQVALPGPDCLGAPLPARALPRLSLALPESPAAAVADSPREPQPNPSPTATAPAPAPAPQPAAPARGSPGARGRLQWASAPSPS PAPQPCPARRGRTGKMNNGGKAEKENTPSEANLQEEEVRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAE AAKNALNGIRFDPEIPQTLRLEFAKANTKMAKNKLVGTPNPSTPLPNTVPQFIAREPCPVAVISGEEDSASPLHHINHGITTPSSLDAGP DTVVIGMTRIPVIENPQYFRQGHNCHKPDTYVQHIKRRDIVLKRELGEGAFGKVFLAECYNLSPTKDKMLVAVKALKDPTLAARKDFQRE AELLTNLQHEHIVKFYGVCGDGDPLIMVFEYMKHGDLNKFLRAHGPDAMILVDGQPRQAKGELGLSQMLHIASQIASGMVYLASQHFVHR DLATRNCLVGANLLVKIGDFGMSRDVYSTDYYRVGGHTMLPIRWMPPESIMYRKFTTESDVWSFGVILWEIFTYGKQPWFQLSNTEVIEC | 597_RBPMS_NTRK3 |
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Comparison of Fusion Protein Isoforms |
| Superimpose the 3D Structures Among All Fusion Protein Isoforms * Download the pdb file and open it from the molstar online viewer. |
| Comparison of the Secondary Structures of Fusion Protein Isoforms |
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Comparison of Fusion Protein Sequences/Structures with Known Sequences/Structures from PDB |
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pLDDT score distribution |
| pLDDT score distribution of the predicted fusion protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. * The blue color at the bottom marks the best active site residues. |
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Potential Active Site Information |
| The potential binding sites of these fusion proteins were identified using SiteMap, a module of the Schrodinger suite. |
| Kinase Fusion AA seq ID in KinaseFusionDB | Site score | Size | Dscore | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
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Ramachandran Plot of Kinase Fusion Protein Structure |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide. |
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Virtual Screening Results |
| Distribution of the average docking score across all approved kinase inhibitors. Distribution of the number of occurrence across all approved kinase inhibitors. |
| 5'-kinase fusion protein case |
| 3'-kinase fusion protein case |
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| Drug information from DrugBank of the top 20 interacting small molecules. * The detailed information of individual kinase inhibitors are available in the download page. |
| Fusion gene name info | Drug | Docking score | Glide g score | Glide energy |
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Kinase-Substrate Information of RBPMS_NTRK3 |
| Phosphorylation target of the kinase (phosphosite, 03-17-2024) |
| Kinase | Kinase UniProt Acc | Kinase species | Substrate | Substrate UniProt Acc | Substrate phosphorylated residues | Substrate phosphorylated sites (+/-7AA) | Domain |
| Biological Network Integration of This Kinase and Substrates (GeneMANIA website) |
| Enriched GO biological processes of the phosphorylation target genes of the kinase |
| Kinase | GOID | GO term | P.adjust |
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Related Drugs to RBPMS_NTRK3 |
| Drugs used for this fusion-positive patient. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Drug | Source | PMID |
| Distribution of the number of studies mentioning RBPMS-NTRK3 and kinase inhibitors the PubMed Abstract (04-01-2024) |
| Fusion gene - drug pair 1 | Fusion gene - drug pair 2 | PMID | Publication date | DOI | Study title |
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Related Diseases to RBPMS_NTRK3 |
| Diseases that have this fusion gene. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Disease | Source | PMID |
| Related diseases from the literature mentioned this fusion gene and drug. (PubMed, 04-01-2024) |
| MeSH ID | MeSH term |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | NTRK3 | C0036341 | Schizophrenia | 3 | PSYGENET |
| Tgene | NTRK3 | C0041696 | Unipolar Depression | 2 | PSYGENET |
| Tgene | NTRK3 | C1269683 | Major Depressive Disorder | 2 | PSYGENET |
| Tgene | NTRK3 | C1332965 | Congenital Mesoblastic Nephroma | 2 | ORPHANET |
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Clinical Trials of the Found Drugs/Small Molecules |
| Statistics of the Clinical Trials of the Found Kinase Inibitors from clinicaltrials.gov (06-17-2024) |
| Clinical Trials from clinicaltrials.gov (06-17-2024) |
| Fusion Gene | Kinase Inhibitor | NCT ID | Study Status | Phases | Disease | # Enrolment | Date |
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