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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:TPR-ALK (FusionGDB2 ID:HG7175TG238) |
Fusion Gene Summary for TPR-ALK |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: TPR-ALK | Fusion gene ID: hg7175tg238 | Hgene | Tgene | Gene symbol | TPR | ALK | Gene ID | 7175 | 238 |
| Gene name | translocated promoter region, nuclear basket protein | ALK receptor tyrosine kinase | |
| Synonyms | - | CD246|NBLST3 | |
| Cytomap | ('TPR')('ALK') 1q31.1 | 2p23.2-p23.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | nucleoprotein TPRNPC-associated intranuclear proteinmegatornuclear pore complex-associated protein TPRtranslocated promoter region (to activated MET oncogene)translocated promoter region proteintumor potentiating region | ALK tyrosine kinase receptorCD246 antigenanaplastic lymphoma receptor tyrosine kinasemutant anaplastic lymphoma kinase | |
| Modification date | 20200313 | 20200329 | |
| UniProtAcc | P12270 | Q9UM73 | |
| Ensembl transtripts involved in fusion gene | ENST00000367478, ENST00000474852, | ||
| Fusion gene scores | * DoF score | 8 X 11 X 4=352 | 56 X 74 X 20=82880 |
| # samples | 8 | 57 | |
| ** MAII score | log2(8/352*10)=-2.13750352374993 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(57/82880*10)=-7.18391827352181 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: TPR [Title/Abstract] AND ALK [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | |||
| 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 | TPR | GO:0006404 | RNA import into nucleus | 9864356 |
| Hgene | TPR | GO:0006606 | protein import into nucleus | 9864356 |
| Hgene | TPR | GO:0031990 | mRNA export from nucleus in response to heat stress | 17897941 |
| Hgene | TPR | GO:0034605 | cellular response to heat | 17897941 |
| Hgene | TPR | GO:0046832 | negative regulation of RNA export from nucleus | 22253824 |
| Hgene | TPR | GO:0070849 | response to epidermal growth factor | 18794356 |
| Tgene | ALK | GO:0016310 | phosphorylation | 9174053 |
| Tgene | ALK | GO:0046777 | protein autophosphorylation | 9174053 |
| 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 |
| ChimerKB4 | . | . | TPR | chr1 | 186325581 | - | ALK | chr2 | 186325581 | - |
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Fusion Gene ORF analysis for TPR-ALK |
| 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 |
| intron-intron | ENST00000367478 | ENST00000389048 | TPR | chr1 | 186325581 | - | ALK | chr2 | 186325581 | - |
| intron-intron | ENST00000367478 | ENST00000431873 | TPR | chr1 | 186325581 | - | ALK | chr2 | 186325581 | - |
| intron-intron | ENST00000367478 | ENST00000498037 | TPR | chr1 | 186325581 | - | ALK | chr2 | 186325581 | - |
| intron-intron | ENST00000474852 | ENST00000389048 | TPR | chr1 | 186325581 | - | ALK | chr2 | 186325581 | - |
| intron-intron | ENST00000474852 | ENST00000431873 | TPR | chr1 | 186325581 | - | ALK | chr2 | 186325581 | - |
| intron-intron | ENST00000474852 | ENST00000498037 | TPR | chr1 | 186325581 | - | ALK | chr2 | 186325581 | - |
| 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 TPR-ALK |
| 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 TPR-ALK |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:/:) - 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 |
| TPR | ALK |
| FUNCTION: Component of the nuclear pore complex (NPC), a complex required for the trafficking across the nuclear envelope. Functions as a scaffolding element in the nuclear phase of the NPC essential for normal nucleocytoplasmic transport of proteins and mRNAs, plays a role in the establishment of nuclear-peripheral chromatin compartmentalization in interphase, and in the mitotic spindle checkpoint signaling during mitosis. Involved in the quality control and retention of unspliced mRNAs in the nucleus; in association with NUP153, regulates the nuclear export of unspliced mRNA species bearing constitutive transport element (CTE) in a NXF1- and KHDRBS1-independent manner. Negatively regulates both the association of CTE-containing mRNA with large polyribosomes and translation initiation. Does not play any role in Rev response element (RRE)-mediated export of unspliced mRNAs. Implicated in nuclear export of mRNAs transcribed from heat shock gene promoters; associates both with chromatin in the HSP70 promoter and with mRNAs transcribed from this promoter under stress-induced conditions. Modulates the nucleocytoplasmic transport of activated MAPK1/ERK2 and huntingtin/HTT and may serve as a docking site for the XPO1/CRM1-mediated nuclear export complex. According to some authors, plays a limited role in the regulation of nuclear protein export (PubMed:22253824 and PubMed:11952838). Plays also a role as a structural and functional element of the perinuclear chromatin distribution; involved in the formation and/or maintenance of NPC-associated perinuclear heterochromatin exclusion zones (HEZs). Finally, acts as a spatial regulator of the spindle-assembly checkpoint (SAC) response ensuring a timely and effective recruitment of spindle checkpoint proteins like MAD1L1 and MAD2L1 to unattached kinetochore during the metaphase-anaphase transition before chromosome congression. Its N-terminus is involved in activation of oncogenic kinases. {ECO:0000269|PubMed:11952838, ECO:0000269|PubMed:15654337, ECO:0000269|PubMed:17897941, ECO:0000269|PubMed:18794356, ECO:0000269|PubMed:18981471, ECO:0000269|PubMed:19273613, ECO:0000269|PubMed:20133940, ECO:0000269|PubMed:20407419, ECO:0000269|PubMed:21613532, ECO:0000269|PubMed:22253824, ECO:0000269|PubMed:9864356}. | FUNCTION: Neuronal receptor tyrosine kinase that is essentially and transiently expressed in specific regions of the central and peripheral nervous systems and plays an important role in the genesis and differentiation of the nervous system. Transduces signals from ligands at the cell surface, through specific activation of the mitogen-activated protein kinase (MAPK) pathway. Phosphorylates almost exclusively at the first tyrosine of the Y-x-x-x-Y-Y motif. Following activation by ligand, ALK induces tyrosine phosphorylation of CBL, FRS2, IRS1 and SHC1, as well as of the MAP kinases MAPK1/ERK2 and MAPK3/ERK1. Acts as a receptor for ligands pleiotrophin (PTN), a secreted growth factor, and midkine (MDK), a PTN-related factor, thus participating in PTN and MDK signal transduction. PTN-binding induces MAPK pathway activation, which is important for the anti-apoptotic signaling of PTN and regulation of cell proliferation. MDK-binding induces phosphorylation of the ALK target insulin receptor substrate (IRS1), activates mitogen-activated protein kinases (MAPKs) and PI3-kinase, resulting also in cell proliferation induction. Drives NF-kappa-B activation, probably through IRS1 and the activation of the AKT serine/threonine kinase. Recruitment of IRS1 to activated ALK and the activation of NF-kappa-B are essential for the autocrine growth and survival signaling of MDK. Thinness gene involved in the resistance to weight gain: in hypothalamic neurons, controls energy expenditure acting as a negative regulator of white adipose tissue lipolysis and sympathetic tone to fine-tune energy homeostasis (By similarity). {ECO:0000250|UniProtKB:P97793, ECO:0000269|PubMed:11121404, ECO:0000269|PubMed:11278720, ECO:0000269|PubMed:11387242, ECO:0000269|PubMed:11809760, ECO:0000269|PubMed:12107166, ECO:0000269|PubMed:12122009, ECO:0000269|PubMed:15226403, ECO:0000269|PubMed:15908427, ECO:0000269|PubMed:16317043, ECO:0000269|PubMed:16878150, ECO:0000269|PubMed:17274988}. |
| 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 TPR-ALK |
| 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 TPR-ALK |
| 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 TPR-ALK |
| 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 | ALK | Q9UM73 | DB08865 | Crizotinib | Inhibitor | Small molecule | Approved |
| Tgene | ALK | Q9UM73 | DB09063 | Ceritinib | Antagonist | Small molecule | Approved |
| Tgene | ALK | Q9UM73 | DB11363 | Alectinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | ALK | Q9UM73 | DB12010 | Fostamatinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | ALK | Q9UM73 | DB12130 | Lorlatinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | ALK | Q9UM73 | DB12141 | Gilteritinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | ALK | Q9UM73 | DB12267 | Brigatinib | Inhibitor | Small molecule | Approved|Investigational |
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Related Diseases for TPR-ALK |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | TPR | C0238463 | Papillary thyroid carcinoma | 2 | ORPHANET |
| Hgene | TPR | C0040136 | Thyroid Neoplasm | 1 | CTD_human |
| Hgene | TPR | C0151468 | Thyroid Gland Follicular Adenoma | 1 | CTD_human |
| Hgene | TPR | C0549473 | Thyroid carcinoma | 1 | CTD_human |
| Tgene | C0007131 | Non-Small Cell Lung Carcinoma | 28 | CGI;CTD_human | |
| Tgene | C0027819 | Neuroblastoma | 13 | CGI;CTD_human;ORPHANET | |
| Tgene | C0152013 | Adenocarcinoma of lung (disorder) | 8 | CGI;CTD_human | |
| Tgene | C2751681 | NEUROBLASTOMA, SUSCEPTIBILITY TO, 3 | 8 | CLINGEN;UNIPROT | |
| Tgene | C0206180 | Ki-1+ Anaplastic Large Cell Lymphoma | 6 | CGI;CTD_human | |
| Tgene | C0334121 | Inflammatory Myofibroblastic Tumor | 4 | CGI;CTD_human;ORPHANET | |
| Tgene | C0018199 | Granuloma, Plasma Cell | 3 | CTD_human | |
| Tgene | C0007621 | Neoplastic Cell Transformation | 2 | CTD_human | |
| Tgene | C0027627 | Neoplasm Metastasis | 2 | CTD_human | |
| Tgene | C0238463 | Papillary thyroid carcinoma | 2 | ORPHANET | |
| Tgene | C0001973 | Alcoholic Intoxication, Chronic | 1 | PSYGENET | |
| Tgene | C0006118 | Brain Neoplasms | 1 | CGI;CTD_human | |
| Tgene | C0006142 | Malignant neoplasm of breast | 1 | CTD_human | |
| Tgene | C0007134 | Renal Cell Carcinoma | 1 | CTD_human | |
| Tgene | C0011570 | Mental Depression | 1 | PSYGENET | |
| Tgene | C0011581 | Depressive disorder | 1 | PSYGENET | |
| Tgene | C0027643 | Neoplasm Recurrence, Local | 1 | CTD_human | |
| Tgene | C0036341 | Schizophrenia | 1 | PSYGENET | |
| Tgene | C0079744 | Diffuse Large B-Cell Lymphoma | 1 | CTD_human | |
| Tgene | C0085269 | Plasma Cell Granuloma, Pulmonary | 1 | CTD_human | |
| Tgene | C0153633 | Malignant neoplasm of brain | 1 | CGI;CTD_human | |
| Tgene | C0278601 | Inflammatory Breast Carcinoma | 1 | CTD_human | |
| Tgene | C0279702 | Conventional (Clear Cell) Renal Cell Carcinoma | 1 | CTD_human | |
| Tgene | C0496899 | Benign neoplasm of brain, unspecified | 1 | CTD_human | |
| Tgene | C0678222 | Breast Carcinoma | 1 | CTD_human | |
| Tgene | C0750974 | Brain Tumor, Primary | 1 | CTD_human | |
| Tgene | C0750977 | Recurrent Brain Neoplasm | 1 | CTD_human | |
| Tgene | C0750979 | Primary malignant neoplasm of brain | 1 | CTD_human | |
| Tgene | C1257931 | Mammary Neoplasms, Human | 1 | CTD_human | |
| Tgene | C1266042 | Chromophobe Renal Cell Carcinoma | 1 | CTD_human | |
| Tgene | C1266043 | Sarcomatoid Renal Cell Carcinoma | 1 | CTD_human | |
| Tgene | C1266044 | Collecting Duct Carcinoma of the Kidney | 1 | CTD_human | |
| Tgene | C1306837 | Papillary Renal Cell Carcinoma | 1 | CTD_human | |
| Tgene | C1332079 | Anaplastic Large Cell Lymphoma, ALK-Positive | 1 | ORPHANET | |
| Tgene | C1458155 | Mammary Neoplasms | 1 | CTD_human | |
| Tgene | C1527390 | Neoplasms, Intracranial | 1 | CTD_human | |
| Tgene | C2931189 | Neural crest tumor | 1 | ORPHANET | |
| Tgene | C3899155 | hereditary neuroblastoma | 1 | GENOMICS_ENGLAND | |
| Tgene | C4704874 | Mammary Carcinoma, Human | 1 | CTD_human |
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