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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:NCOA1-ALK (FusionGDB2 ID:HG8648TG238) |
Fusion Gene Summary for NCOA1-ALK |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: NCOA1-ALK | Fusion gene ID: hg8648tg238 | Hgene | Tgene | Gene symbol | NCOA1 | ALK | Gene ID | 8648 | 238 |
| Gene name | nuclear receptor coactivator 1 | ALK receptor tyrosine kinase | |
| Synonyms | F-SRC-1|KAT13A|RIP160|SRC1|bHLHe42|bHLHe74 | CD246|NBLST3 | |
| Cytomap | ('NCOA1')('ALK') 2p23.3 | 2p23.2-p23.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | nuclear receptor coactivator 1Hin-2 proteinclass E basic helix-loop-helix protein 74renal carcinoma antigen NY-REN-52steroid receptor coactivator-1 | ALK tyrosine kinase receptorCD246 antigenanaplastic lymphoma receptor tyrosine kinasemutant anaplastic lymphoma kinase | |
| Modification date | 20200313 | 20200329 | |
| UniProtAcc | Q15788 | Q9UM73 | |
| Ensembl transtripts involved in fusion gene | ENST00000288599, ENST00000348332, ENST00000395856, ENST00000405141, ENST00000406961, ENST00000407230, ENST00000538539, ENST00000469850, | ||
| Fusion gene scores | * DoF score | 16 X 13 X 8=1664 | 56 X 74 X 20=82880 |
| # samples | 17 | 57 | |
| ** MAII score | log2(17/1664*10)=-3.29104878200339 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: NCOA1 [Title/Abstract] AND ALK [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | NCOA1(24985645)-ALK(29940563), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | NCOA1-ALK seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF. NCOA1-ALK seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF. NCOA1-ALK seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF. NCOA1-ALK seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. NCOA1-ALK seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF. NCOA1-ALK seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF. NCOA1-ALK seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. NCOA1-ALK seems lost the major protein functional domain in Tgene partner, which is a kinase 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 | NCOA1 | GO:0000435 | positive regulation of transcription from RNA polymerase II promoter by galactose | 10207113 |
| Hgene | NCOA1 | GO:0006351 | transcription, DNA-templated | 9223431 |
| Hgene | NCOA1 | GO:0045893 | positive regulation of transcription, DNA-templated | 11891224|15367689 |
| Hgene | NCOA1 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 15919756 |
| 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 |
| ChimerDB4 | SKCM | TCGA-D3-A3CF-06A | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
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Fusion Gene ORF analysis for NCOA1-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 |
| 5CDS-intron | ENST00000288599 | ENST00000498037 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| 5CDS-intron | ENST00000348332 | ENST00000498037 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| 5CDS-intron | ENST00000395856 | ENST00000498037 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| 5CDS-intron | ENST00000405141 | ENST00000498037 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| 5CDS-intron | ENST00000406961 | ENST00000498037 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| 5CDS-intron | ENST00000407230 | ENST00000498037 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| 5CDS-intron | ENST00000538539 | ENST00000498037 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| Frame-shift | ENST00000288599 | ENST00000389048 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| Frame-shift | ENST00000288599 | ENST00000431873 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| Frame-shift | ENST00000348332 | ENST00000389048 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| Frame-shift | ENST00000348332 | ENST00000431873 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| Frame-shift | ENST00000395856 | ENST00000389048 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| Frame-shift | ENST00000395856 | ENST00000431873 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| Frame-shift | ENST00000405141 | ENST00000389048 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| Frame-shift | ENST00000405141 | ENST00000431873 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| Frame-shift | ENST00000406961 | ENST00000389048 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| Frame-shift | ENST00000406961 | ENST00000431873 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| Frame-shift | ENST00000407230 | ENST00000389048 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| Frame-shift | ENST00000407230 | ENST00000431873 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| Frame-shift | ENST00000538539 | ENST00000389048 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| Frame-shift | ENST00000538539 | ENST00000431873 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| intron-3CDS | ENST00000469850 | ENST00000389048 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| intron-3CDS | ENST00000469850 | ENST00000431873 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| intron-intron | ENST00000469850 | ENST00000498037 | NCOA1 | chr2 | 24985645 | - | ALK | chr2 | 29940563 | - |
| 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 NCOA1-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 NCOA1-ALK |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:24985645/:29940563) - 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 |
| NCOA1 | ALK |
| FUNCTION: Nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. Involved in the coactivation of different nuclear receptors, such as for steroids (PGR, GR and ER), retinoids (RXRs), thyroid hormone (TRs) and prostanoids (PPARs). Also involved in coactivation mediated by STAT3, STAT5A, STAT5B and STAT6 transcription factors. Displays histone acetyltransferase activity toward H3 and H4; the relevance of such activity remains however unclear. Plays a central role in creating multisubunit coactivator complexes that act via remodeling of chromatin, and possibly acts by participating in both chromatin remodeling and recruitment of general transcription factors. Required with NCOA2 to control energy balance between white and brown adipose tissues. Required for mediating steroid hormone response. Isoform 2 has a higher thyroid hormone-dependent transactivation activity than isoform 1 and isoform 3. {ECO:0000269|PubMed:10449719, ECO:0000269|PubMed:12954634, ECO:0000269|PubMed:7481822, ECO:0000269|PubMed:9223281, ECO:0000269|PubMed:9223431, ECO:0000269|PubMed:9296499, ECO:0000269|PubMed:9427757}. | 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 NCOA1-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 NCOA1-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 NCOA1-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 NCOA1-ALK |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | NCOA1 | C0006142 | Malignant neoplasm of breast | 1 | CTD_human |
| Hgene | NCOA1 | C0014175 | Endometriosis | 1 | CTD_human |
| Hgene | NCOA1 | C0024668 | Mammary Neoplasms, Experimental | 1 | CTD_human |
| Hgene | NCOA1 | C0027627 | Neoplasm Metastasis | 1 | CTD_human |
| Hgene | NCOA1 | C0033578 | Prostatic Neoplasms | 1 | CTD_human |
| Hgene | NCOA1 | C0269102 | Endometrioma | 1 | CTD_human |
| Hgene | NCOA1 | C0376358 | Malignant neoplasm of prostate | 1 | CTD_human |
| Hgene | NCOA1 | C0678222 | Breast Carcinoma | 1 | CTD_human |
| Hgene | NCOA1 | C1257931 | Mammary Neoplasms, Human | 1 | CTD_human |
| Hgene | NCOA1 | C1458155 | Mammary Neoplasms | 1 | CTD_human |
| Hgene | NCOA1 | C4704874 | Mammary Carcinoma, Human | 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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