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Fusion gene ID: 20313 |
FusionGeneSummary for LSAMP_COL4A5 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: LSAMP_COL4A5 | Fusion gene ID: 20313 | Hgene | Tgene | Gene symbol | LSAMP | COL4A5 | Gene ID | 4045 | 1287 |
| Gene name | limbic system associated membrane protein | collagen type IV alpha 5 chain | |
| Synonyms | IGLON3|LAMP | ASLN|ATS|CA54 | |
| Cytomap | 3q13.31 | Xq22.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | limbic system-associated membrane proteinIgLON family member 3 | collagen alpha-5(IV) chaincollagen IV, alpha-5 polypeptidecollagen of basement membrane, alpha-5 chaincollagen, type IV, alpha 5dA149D17.3dA24A23.1 | |
| Modification date | 20180522 | 20180523 | |
| UniProtAcc | Q13449 | P29400 | |
| Ensembl transtripts involved in fusion gene | ENST00000539563, ENST00000490035, ENST00000498645, | ENST00000328300, ENST00000361603, ENST00000477429, | |
| Fusion gene scores | * DoF score | 6 X 7 X 4=168 | 2 X 2 X 2=8 |
| # samples | 8 | 2 | |
| ** MAII score | log2(8/168*10)=-1.0703893278914 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(2/8*10)=1.32192809488736 | |
| Context | PubMed: LSAMP [Title/Abstract] AND COL4A5 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | Tumor suppressor gene involved fusion gene, retained protein feature but frameshift. DDR (DNA damage repair) gene involved fusion gene, in-frame but not retained their domain. | ||
| * 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 |
| Fusion gene information from three resources (ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018)) * 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. |
| Data type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| TCGA | RV | SKCM | TCGA-FS-A1ZJ-06A | LSAMP | chr3 | 115738362 | - | COL4A5 | chrX | 107811989 | + |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| 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 | ENST00000539563 | ENST00000328300 | LSAMP | chr3 | 115738362 | - | COL4A5 | chrX | 107811989 | + |
| Frame-shift | ENST00000539563 | ENST00000361603 | LSAMP | chr3 | 115738362 | - | COL4A5 | chrX | 107811989 | + |
| 5CDS-intron | ENST00000539563 | ENST00000477429 | LSAMP | chr3 | 115738362 | - | COL4A5 | chrX | 107811989 | + |
| Frame-shift | ENST00000490035 | ENST00000328300 | LSAMP | chr3 | 115738362 | - | COL4A5 | chrX | 107811989 | + |
| Frame-shift | ENST00000490035 | ENST00000361603 | LSAMP | chr3 | 115738362 | - | COL4A5 | chrX | 107811989 | + |
| 5CDS-intron | ENST00000490035 | ENST00000477429 | LSAMP | chr3 | 115738362 | - | COL4A5 | chrX | 107811989 | + |
| 5UTR-3CDS | ENST00000498645 | ENST00000328300 | LSAMP | chr3 | 115738362 | - | COL4A5 | chrX | 107811989 | + |
| 5UTR-3CDS | ENST00000498645 | ENST00000361603 | LSAMP | chr3 | 115738362 | - | COL4A5 | chrX | 107811989 | + |
| 5UTR-intron | ENST00000498645 | ENST00000477429 | LSAMP | chr3 | 115738362 | - | COL4A5 | chrX | 107811989 | + |
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FusionProtFeatures for LSAMP_COL4A5 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| LSAMP | COL4A5 |
| Mediates selective neuronal growth and axon targeting.Contributes to the guidance of developing axons and remodeling ofmature circuits in the limbic system. Essential for normal growthof the hyppocampal mossy fiber projection (By similarity).{ECO:0000250}. | Type IV collagen is the major structural component ofglomerular basement membranes (GBM), forming a 'chicken-wire'meshwork together with laminins, proteoglycans andentactin/nidogen. |
| 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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FusionGeneSequence for LSAMP_COL4A5 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. (nt: nucleotides, aa: amino acids) |
| * Fusion amino acid sequences. |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| * Fusion transcript sequences (Full-length transcript). |
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FusionGenePPI for LSAMP_COL4A5 |
| 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 |
| LSAMP | NTM, LSAMP, NEGR1, DNAAF2 | COL4A5 | DAZAP2, TK1, CDKN1A, SMN1, NR1H2, ANXA7, VHL, ELAVL1, ANTXR2, STRN3, PDK1, DAP3, KIF21B, CASC5, VPS26B, CEP170P1, PLOD1, COL8A2, COLGALT2 |
| - 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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RelatedDrugs for LSAMP_COL4A5 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for LSAMP_COL4A5 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | LSAMP | C0036341 | Schizophrenia | 1 | PSYGENET |
| Hgene | LSAMP | C0041696 | Unipolar Depression | 1 | PSYGENET |
| Hgene | LSAMP | C1269683 | Major Depressive Disorder | 1 | PSYGENET |
| Tgene | COL4A5 | C1567742 | Alport Syndrome, X-Linked | 17 | CTD_human;ORPHANET;UNIPROT |
| Tgene | COL4A5 | C0086533 | Leiomyoma, Epithelioid | 1 | CTD_human |
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