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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:NTRK3-LOXL2 (FusionGDB2 ID:60338) |
Fusion Gene Summary for NTRK3-LOXL2 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: NTRK3-LOXL2 | Fusion gene ID: 60338 | Hgene | Tgene | Gene symbol | NTRK3 | LOXL2 | Gene ID | 4916 | 4017 |
| Gene name | neurotrophic receptor tyrosine kinase 3 | lysyl oxidase like 2 | |
| Synonyms | GP145-TrkC|TRKC|gp145(trkC) | LOR|LOR2|WS9-14 | |
| Cytomap | 15q25.3 | 8p21.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | NT-3 growth factor receptorETS related protein-neurotrophic receptor tyrosine kinase fusion proteinETV6-NTRK3 fusionneurotrophic tyrosine kinase, receptor, type 3tyrosine kinase receptor C | lysyl oxidase homolog 2lysyl oxidase related 2lysyl oxidase-like 2 delta e13lysyl oxidase-like 2 proteinlysyl oxidase-like protein 2lysyl oxidase-related protein 2lysyl oxidase-related protein WS9-14 | |
| Modification date | 20200313 | 20200329 | |
| UniProtAcc | . | Q9Y4K0 | |
| Ensembl transtripts involved in fusion gene | ENST00000394480, ENST00000557856, ENST00000357724, ENST00000355254, ENST00000360948, ENST00000542733, ENST00000558676, ENST00000317501, ENST00000558306, ENST00000540489, | ENST00000389131, ENST00000518472, | |
| Fusion gene scores | * DoF score | 12 X 15 X 5=900 | 8 X 4 X 7=224 |
| # samples | 17 | 8 | |
| ** MAII score | log2(17/900*10)=-2.40439025507934 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(8/224*10)=-1.48542682717024 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: NTRK3 [Title/Abstract] AND LOXL2 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | NTRK3(88799137)-LOXL2(23191136), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | NTRK3-LOXL2 seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF. NTRK3-LOXL2 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF. NTRK3-LOXL2 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF. NTRK3-LOXL2 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. NTRK3-LOXL2 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted 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 | NTRK3 | GO:0000187 | activation of MAPK activity | 23027130 |
| Hgene | NTRK3 | GO:0001933 | negative regulation of protein phosphorylation | 23027130 |
| Hgene | NTRK3 | GO:0007169 | transmembrane receptor protein tyrosine kinase signaling pathway | 23027130 |
| Hgene | NTRK3 | GO:0008284 | positive regulation of cell proliferation | 23027130 |
| Hgene | NTRK3 | GO:0010628 | positive regulation of gene expression | 23027130 |
| Hgene | NTRK3 | GO:0030335 | positive regulation of cell migration | 23027130 |
| Hgene | NTRK3 | GO:0032148 | activation of protein kinase B activity | 23027130 |
| Hgene | NTRK3 | GO:0033138 | positive regulation of peptidyl-serine phosphorylation | 23027130 |
| Hgene | NTRK3 | GO:0050927 | positive regulation of positive chemotaxis | 23027130 |
| Hgene | NTRK3 | GO:0090630 | activation of GTPase activity | 23027130 |
| Hgene | NTRK3 | GO:2000251 | positive regulation of actin cytoskeleton reorganization | 23027130 |
| Tgene | LOXL2 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 25959397 |
| Tgene | LOXL2 | GO:0001837 | epithelial to mesenchymal transition | 16096638 |
| Tgene | LOXL2 | GO:0006464 | cellular protein modification process | 23319596 |
| Tgene | LOXL2 | GO:0018057 | peptidyl-lysine oxidation | 25959397|27735137|29581294 |
| Tgene | LOXL2 | GO:0045892 | negative regulation of transcription, DNA-templated | 16096638 |
| Tgene | LOXL2 | GO:0046688 | response to copper ion | 23319596 |
| Fusion gene breakpoints across NTRK3 (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Fusion gene breakpoints across LOXL2 (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| 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 | LGG | TCGA-FG-6692-01A | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
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Fusion Gene ORF analysis for NTRK3-LOXL2 |
| 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 |
| Frame-shift | ENST00000394480 | ENST00000389131 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| 5CDS-intron | ENST00000394480 | ENST00000518472 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| Frame-shift | ENST00000557856 | ENST00000389131 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| 5CDS-intron | ENST00000557856 | ENST00000518472 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| Frame-shift | ENST00000357724 | ENST00000389131 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| 5CDS-intron | ENST00000357724 | ENST00000518472 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| Frame-shift | ENST00000355254 | ENST00000389131 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| 5CDS-intron | ENST00000355254 | ENST00000518472 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| Frame-shift | ENST00000360948 | ENST00000389131 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| 5CDS-intron | ENST00000360948 | ENST00000518472 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| intron-3CDS | ENST00000542733 | ENST00000389131 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| intron-intron | ENST00000542733 | ENST00000518472 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| Frame-shift | ENST00000558676 | ENST00000389131 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| 5CDS-intron | ENST00000558676 | ENST00000518472 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| Frame-shift | ENST00000317501 | ENST00000389131 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| 5CDS-intron | ENST00000317501 | ENST00000518472 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| intron-3CDS | ENST00000558306 | ENST00000389131 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| intron-intron | ENST00000558306 | ENST00000518472 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| Frame-shift | ENST00000540489 | ENST00000389131 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| 5CDS-intron | ENST00000540489 | ENST00000518472 | NTRK3 | chr15 | 88799137 | - | LOXL2 | chr8 | 23191136 | - |
| 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 NTRK3-LOXL2 |
| 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) |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page. |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page. |
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Fusion Protein Features for NTRK3-LOXL2 |
| Go to FGviewer for the breakpoints of :-: - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| . | LOXL2 |
| 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. | FUNCTION: Mediates the post-translational oxidative deamination of lysine residues on target proteins leading to the formation of deaminated lysine (allysine) (PubMed:27735137). Acts as a transcription corepressor and specifically mediates deamination of trimethylated 'Lys-4' of histone H3 (H3K4me3), a specific tag for epigenetic transcriptional activation (PubMed:27735137). Shows no activity against histone H3 when it is trimethylated on 'Lys-9' (H3K9me3) or 'Lys-27' (H3K27me3) or when 'Lys-4' is monomethylated (H3K4me1) or dimethylated (H3K4me2) (PubMed:27735137). Also mediates deamination of methylated TAF10, a member of the transcription factor IID (TFIID) complex, which induces release of TAF10 from promoters, leading to inhibition of TFIID-dependent transcription (PubMed:25959397). LOXL2-mediated deamination of TAF10 results in transcriptional repression of genes required for embryonic stem cell pluripotency including POU5F1/OCT4, NANOG, KLF4 and SOX2 (By similarity). Involved in epithelial to mesenchymal transition (EMT) via interaction with SNAI1 and participates in repression of E-cadherin CDH1, probably by mediating deamination of histone H3 (PubMed:16096638, PubMed:27735137, PubMed:24414204). During EMT, involved with SNAI1 in negatively regulating pericentromeric heterochromatin transcription (PubMed:24239292). SNAI1 recruits LOXL2 to pericentromeric regions to oxidize histone H3 and repress transcription which leads to release of heterochromatin component CBX5/HP1A, enabling chromatin reorganization and acquisition of mesenchymal traits (PubMed:24239292). Interacts with the endoplasmic reticulum protein HSPA5 which activates the IRE1-XBP1 pathway of the unfolded protein response, leading to expression of several transcription factors involved in EMT and subsequent EMT induction (PubMed:28332555). Involved in E-cadherin repression following hypoxia, a hallmark of EMT believed to amplify tumor aggressiveness, suggesting that it may play a role in tumor progression (PubMed:20026874). When secreted into the extracellular matrix, promotes cross-linking of extracellular matrix proteins by mediating oxidative deamination of peptidyl lysine residues in precursors to fibrous collagen and elastin (PubMed:20306300). Acts as a regulator of sprouting angiogenesis, probably via collagen IV scaffolding (PubMed:21835952). Acts as a regulator of chondrocyte differentiation, probably by regulating expression of factors that control chondrocyte differentiation (By similarity). {ECO:0000250|UniProtKB:P58022, ECO:0000269|PubMed:16096638, ECO:0000269|PubMed:20026874, ECO:0000269|PubMed:20306300, ECO:0000269|PubMed:21835952, ECO:0000269|PubMed:24239292, ECO:0000269|PubMed:24414204, ECO:0000269|PubMed:25959397, ECO:0000269|PubMed:27735137}. |
| 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 NTRK3-LOXL2 |
| 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 NTRK3-LOXL2 |
| 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 NTRK3-LOXL2 |
| 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 |
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Related Diseases for NTRK3-LOXL2 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | NTRK3 | C0036341 | Schizophrenia | 3 | PSYGENET |
| Hgene | NTRK3 | C0041696 | Unipolar Depression | 2 | PSYGENET |
| Hgene | NTRK3 | C1269683 | Major Depressive Disorder | 2 | PSYGENET |
| Hgene | NTRK3 | C1332965 | Congenital Mesoblastic Nephroma | 2 | ORPHANET |
| Hgene | NTRK3 | C0014175 | Endometriosis | 1 | CTD_human |
| Hgene | NTRK3 | C0017638 | Glioma | 1 | CTD_human |
| Hgene | NTRK3 | C0019569 | Hirschsprung Disease | 1 | GENOMICS_ENGLAND |
| Hgene | NTRK3 | C0023467 | Leukemia, Myelocytic, Acute | 1 | CTD_human |
| Hgene | NTRK3 | C0026998 | Acute Myeloid Leukemia, M1 | 1 | CTD_human |
| Hgene | NTRK3 | C0038220 | Status Epilepticus | 1 | CTD_human |
| Hgene | NTRK3 | C0238463 | Papillary thyroid carcinoma | 1 | ORPHANET |
| Hgene | NTRK3 | C0259783 | mixed gliomas | 1 | CTD_human |
| Hgene | NTRK3 | C0269102 | Endometrioma | 1 | CTD_human |
| Hgene | NTRK3 | C0270823 | Petit mal status | 1 | CTD_human |
| Hgene | NTRK3 | C0311335 | Grand Mal Status Epilepticus | 1 | CTD_human |
| Hgene | NTRK3 | C0393734 | Complex Partial Status Epilepticus | 1 | CTD_human |
| Hgene | NTRK3 | C0525045 | Mood Disorders | 1 | PSYGENET |
| Hgene | NTRK3 | C0555198 | Malignant Glioma | 1 | CTD_human |
| Hgene | NTRK3 | C0751522 | Status Epilepticus, Subclinical | 1 | CTD_human |
| Hgene | NTRK3 | C0751523 | Non-Convulsive Status Epilepticus | 1 | CTD_human |
| Hgene | NTRK3 | C0751524 | Simple Partial Status Epilepticus | 1 | CTD_human |
| Hgene | NTRK3 | C1879321 | Acute Myeloid Leukemia (AML-M2) | 1 | CTD_human |
| Tgene | LOXL2 | C0006142 | Malignant neoplasm of breast | 2 | CTD_human |
| Tgene | LOXL2 | C0678222 | Breast Carcinoma | 2 | CTD_human |
| Tgene | LOXL2 | C1257931 | Mammary Neoplasms, Human | 2 | CTD_human |
| Tgene | LOXL2 | C1458155 | Mammary Neoplasms | 2 | CTD_human |
| Tgene | LOXL2 | C4704874 | Mammary Carcinoma, Human | 2 | CTD_human |
| Tgene | LOXL2 | C0007621 | Neoplastic Cell Transformation | 1 | CTD_human |
| Tgene | LOXL2 | C0008312 | Primary biliary cirrhosis | 1 | CTD_human |
| Tgene | LOXL2 | C0019163 | Hepatitis B | 1 | CTD_human |
| Tgene | LOXL2 | C0019196 | Hepatitis C | 1 | CTD_human |
| Tgene | LOXL2 | C0019202 | Hepatolenticular Degeneration | 1 | CTD_human |
| Tgene | LOXL2 | C0023892 | Biliary cirrhosis | 1 | CTD_human |
| Tgene | LOXL2 | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
| Tgene | LOXL2 | C0027626 | Neoplasm Invasiveness | 1 | CTD_human |
| Tgene | LOXL2 | C0238065 | Secondary Biliary Cholangitis | 1 | CTD_human |
| Tgene | LOXL2 | C0279626 | Squamous cell carcinoma of esophagus | 1 | CTD_human |
| Tgene | LOXL2 | C1527352 | Hepatic Form of Wilson Disease | 1 | CTD_human |
| Tgene | LOXL2 | C4551595 | Biliary Cirrhosis, Primary, 1 | 1 | CTD_human |
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