|
||||||
|
 | 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:CADM1-COL1A2 (FusionGDB2 ID:12441) |
Fusion Gene Summary for CADM1-COL1A2 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CADM1-COL1A2 | Fusion gene ID: 12441 | Hgene | Tgene | Gene symbol | CADM1 | COL1A2 | Gene ID | 23705 | 1278 |
| Gene name | cell adhesion molecule 1 | collagen type I alpha 2 chain | |
| Synonyms | BL2|IGSF4|IGSF4A|NECL2|Necl-2|RA175|ST17|SYNCAM|TSLC1|sTSLC-1|sgIGSF|synCAM1 | EDSARTH2|EDSCV|OI4 | |
| Cytomap | 11q23.3 | 7q21.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | cell adhesion molecule 1TSLC-1TSLC1/Nectin-like 2/IGSF4immunoglobulin superfamily member 4immunoglobulin superfamily, member 4D variant 1immunoglobulin superfamily, member 4D variant 2nectin-like 2nectin-like protein 2spermatogenic immunoglobulin | collagen alpha-2(I) chainalpha 2 type I procollagenalpha 2(I) procollagenalpha 2(I)-collagenalpha-2 type I collagencollagen I, alpha-2 polypeptidecollagen of skin, tendon and bone, alpha-2 chaincollagen, type I, alpha 2epididymis secretory sperm b | |
| Modification date | 20200313 | 20200322 | |
| UniProtAcc | Q9BY67 | P08123 | |
| Ensembl transtripts involved in fusion gene | ENST00000331581, ENST00000452722, ENST00000536727, ENST00000537058, ENST00000537140, ENST00000542447, | ENST00000297268, | |
| Fusion gene scores | * DoF score | 7 X 5 X 4=140 | 43 X 46 X 7=13846 |
| # samples | 8 | 54 | |
| ** MAII score | log2(8/140*10)=-0.807354922057604 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(54/13846*10)=-4.68036603576588 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: CADM1 [Title/Abstract] AND COL1A2 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | CADM1(115044413)-COL1A2(94038920), # samples:1 | ||
| 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 | CADM1 | GO:0001913 | T cell mediated cytotoxicity | 15811952 |
| Hgene | CADM1 | GO:0008037 | cell recognition | 15811952 |
| Hgene | CADM1 | GO:0042271 | susceptibility to natural killer cell mediated cytotoxicity | 15811952 |
| Hgene | CADM1 | GO:0045954 | positive regulation of natural killer cell mediated cytotoxicity | 15811952 |
| Hgene | CADM1 | GO:0050715 | positive regulation of cytokine secretion | 15811952 |
| Hgene | CADM1 | GO:0050798 | activated T cell proliferation | 15811952 |
| Hgene | CADM1 | GO:0051606 | detection of stimulus | 15811952 |
| Tgene | COL1A2 | GO:0007179 | transforming growth factor beta receptor signaling pathway | 17217948 |
| Tgene | COL1A2 | GO:0007266 | Rho protein signal transduction | 17217948 |
| Fusion gene breakpoints across CADM1 (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 COL1A2 (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 |
| ChiTaRS5.0 | N/A | BU625674 | CADM1 | chr11 | 115044413 | + | COL1A2 | chr7 | 94038920 | - |
Top |
Fusion Gene ORF analysis for CADM1-COL1A2 |
| 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 | ENST00000331581 | ENST00000297268 | CADM1 | chr11 | 115044413 | + | COL1A2 | chr7 | 94038920 | - |
| intron-intron | ENST00000452722 | ENST00000297268 | CADM1 | chr11 | 115044413 | + | COL1A2 | chr7 | 94038920 | - |
| intron-intron | ENST00000536727 | ENST00000297268 | CADM1 | chr11 | 115044413 | + | COL1A2 | chr7 | 94038920 | - |
| intron-intron | ENST00000537058 | ENST00000297268 | CADM1 | chr11 | 115044413 | + | COL1A2 | chr7 | 94038920 | - |
| intron-intron | ENST00000537140 | ENST00000297268 | CADM1 | chr11 | 115044413 | + | COL1A2 | chr7 | 94038920 | - |
| intron-intron | ENST00000542447 | ENST00000297268 | CADM1 | chr11 | 115044413 | + | COL1A2 | chr7 | 94038920 | - |
| 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 |
Top |
Fusion Genomic Features for CADM1-COL1A2 |
| 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. |
Top |
Fusion Protein Features for CADM1-COL1A2 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:115044413/:94038920) - 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. |
 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| CADM1 | COL1A2 |
| FUNCTION: Mediates homophilic cell-cell adhesion in a Ca(2+)-independent manner (PubMed:22438059, PubMed:12050160). Also mediates heterophilic cell-cell adhesion with CADM3 and NECTIN3 in a Ca(2+)-independent manner (By similarity). Interaction with CRTAM promotes natural killer (NK) cell cytotoxicity and interferon-gamma (IFN-gamma) secretion by CD8+ cells in vitro as well as NK cell-mediated rejection of tumors expressing CADM1 in vivo (PubMed:15811952). In mast cells, may mediate attachment to and promote communication with nerves (PubMed:15905536). CADM1, together with MITF, is essential for development and survival of mast cells in vivo (PubMed:22438059). By interacting with CRTAM and thus promoting the adhesion between CD8+ T-cells and CD8+ dendritic cells, regulates the retention of activated CD8+ T-cell within the draining lymph node (By similarity). Required for the intestinal retention of intraepithelial CD4+ CD8+ T-cells and, to a lesser extent, intraepithelial and lamina propria CD8+ T-cells and CD4+ T-cells (By similarity). Interaction with CRTAM promotes the adhesion to gut-associated CD103+ dendritic cells, which may facilitate the expression of gut-homing and adhesion molecules on T-cells and the conversion of CD4+ T-cells into CD4+ CD8+ T-cells (By similarity). Acts as a synaptic cell adhesion molecule and plays a role in the formation of dendritic spines and in synapse assembly (By similarity). May be involved in neuronal migration, axon growth, pathfinding, and fasciculation on the axons of differentiating neurons (By similarity). May play diverse roles in the spermatogenesis including in the adhesion of spermatocytes and spermatids to Sertoli cells and for their normal differentiation into mature spermatozoa (By similarity). Acts as a tumor suppressor in non-small-cell lung cancer (NSCLC) cells (PubMed:11279526, PubMed:12234973). May contribute to the less invasive phenotypes of lepidic growth tumor cells (PubMed:12920246). {ECO:0000250|UniProtKB:Q8R5M8, ECO:0000269|PubMed:11279526, ECO:0000269|PubMed:12050160, ECO:0000269|PubMed:12234973, ECO:0000269|PubMed:12920246, ECO:0000269|PubMed:15811952, ECO:0000269|PubMed:15905536, ECO:0000269|PubMed:22438059}. | FUNCTION: Type I collagen is a member of group I collagen (fibrillar forming collagen). |
| 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 |
Top |
Fusion Gene Sequence for CADM1-COL1A2 |
| 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. |
Top |
Fusion Gene PPI Analysis for CADM1-COL1A2 |
| 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 |
Top |
Related Drugs for CADM1-COL1A2 |
| 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 |
Top |
Related Diseases for CADM1-COL1A2 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2021-Present -The University of Texas Health Science Center at Houston (UTHealth)
Web File Viewing | Emergency Information |Campus Carry|Site Policies