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Fusion gene ID: 3644 |
FusionGeneSummary for AVL9_LRAT |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: AVL9_LRAT | Fusion gene ID: 3644 | Hgene | Tgene | Gene symbol | AVL9 | LRAT | Gene ID | 23080 | 9227 |
| Gene name | AVL9 cell migration associated | lecithin retinol acyltransferase | |
| Synonyms | KIAA0241 | LCA14 | |
| Cytomap | 7p14.3 | 4q32.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | late secretory pathway protein AVL9 homologAVL9 homolog (S. cerevisiase) | lecithin retinol acyltransferaselecithin retinol acyltransferase (phosphatidylcholine--retinol O-acyltransferase) | |
| Modification date | 20180523 | 20180519 | |
| UniProtAcc | Q8NBF6 | O95237 | |
| Ensembl transtripts involved in fusion gene | ENST00000404479, ENST00000318709, ENST00000459629, ENST00000409301, | ENST00000500890, ENST00000507827, ENST00000336356, | |
| Fusion gene scores | * DoF score | 6 X 6 X 3=108 | 3 X 2 X 3=18 |
| # samples | 7 | 3 | |
| ** MAII score | log2(7/108*10)=-0.625604485218502 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: AVL9 [Title/Abstract] AND LRAT [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | |||
| * 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 | AVL9 | GO:0016477 | cell migration | 22595670 |
| Tgene | LRAT | GO:0042572 | retinol metabolic process | 10819989 |
| 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 |
| ChiTaRS3.1 | BX093249 | AVL9 | chr7 | 32800442 | + | LRAT | chr4 | 155672877 | + |
| * 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 |
| intron-intron | ENST00000404479 | ENST00000500890 | AVL9 | chr7 | 32800442 | + | LRAT | chr4 | 155672877 | + |
| intron-intron | ENST00000404479 | ENST00000507827 | AVL9 | chr7 | 32800442 | + | LRAT | chr4 | 155672877 | + |
| intron-3UTR | ENST00000404479 | ENST00000336356 | AVL9 | chr7 | 32800442 | + | LRAT | chr4 | 155672877 | + |
| intron-intron | ENST00000318709 | ENST00000500890 | AVL9 | chr7 | 32800442 | + | LRAT | chr4 | 155672877 | + |
| intron-intron | ENST00000318709 | ENST00000507827 | AVL9 | chr7 | 32800442 | + | LRAT | chr4 | 155672877 | + |
| intron-3UTR | ENST00000318709 | ENST00000336356 | AVL9 | chr7 | 32800442 | + | LRAT | chr4 | 155672877 | + |
| intron-intron | ENST00000459629 | ENST00000500890 | AVL9 | chr7 | 32800442 | + | LRAT | chr4 | 155672877 | + |
| intron-intron | ENST00000459629 | ENST00000507827 | AVL9 | chr7 | 32800442 | + | LRAT | chr4 | 155672877 | + |
| intron-3UTR | ENST00000459629 | ENST00000336356 | AVL9 | chr7 | 32800442 | + | LRAT | chr4 | 155672877 | + |
| intron-intron | ENST00000409301 | ENST00000500890 | AVL9 | chr7 | 32800442 | + | LRAT | chr4 | 155672877 | + |
| intron-intron | ENST00000409301 | ENST00000507827 | AVL9 | chr7 | 32800442 | + | LRAT | chr4 | 155672877 | + |
| intron-3UTR | ENST00000409301 | ENST00000336356 | AVL9 | chr7 | 32800442 | + | LRAT | chr4 | 155672877 | + |
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FusionProtFeatures for AVL9_LRAT |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| AVL9 | LRAT |
| Functions in cell migration.{ECO:0000269|PubMed:22595670}. | Transfers the acyl group from the sn-1 position ofphosphatidylcholine to all-trans retinol, producing all-transretinyl esters. Retinyl esters are storage forms of vitamin A.LRAT plays a critical role in vision. It provides the all-transretinyl ester substrates for the isomerohydrolase which processesthe esters into 11-cis-retinol in the retinal pigment epithelium;due to a membrane-associated alcohol dehydrogenase, 11 cis-retinolis oxidized and converted into 11-cis-retinaldehyde which is thechromophore for rhodopsin and the cone photopigments.{ECO:0000269|PubMed:9920938}. |
| 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 AVL9_LRAT |
| 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 AVL9_LRAT |
| 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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RelatedDrugs for AVL9_LRAT |
| 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 |
| Tgene | LRAT | O95237 | DB00162 | Vitamin A | Lecithin retinol acyltransferase | small molecule | approved|nutraceutical|vet_approved |
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RelatedDiseases for AVL9_LRAT |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | AVL9 | C3495559 | Juvenile arthritis | 1 | CTD_human |
| Tgene | LRAT | C0917796 | Optic Atrophy, Hereditary, Leber | 2 | CTD_human |
| Tgene | LRAT | C0015398 | Eye Diseases, Hereditary | 1 | CTD_human |
| Tgene | LRAT | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
| Tgene | LRAT | C0042842 | Vitamin A Deficiency | 1 | CTD_human |
| Tgene | LRAT | C0339527 | Leber Congenital Amaurosis | 1 | CTD_human;ORPHANET |
| Tgene | LRAT | C2750063 | Leber Congenital Amaurosis 14 | 1 | CTD_human;UNIPROT |
| Tgene | LRAT | C4277682 | Chemical and Drug Induced Liver Injury | 1 | CTD_human |
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