|
||||||
|
 | |
| |
| |
| |
| |
|
Fusion gene ID: 20054 |
FusionGeneSummary for LRAT_VTI1A |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: LRAT_VTI1A | Fusion gene ID: 20054 | Hgene | Tgene | Gene symbol | LRAT | VTI1A | Gene ID | 9227 | 143187 |
| Gene name | lecithin retinol acyltransferase | vesicle transport through interaction with t-SNAREs 1A | |
| Synonyms | LCA14 | MMDS3|MVti1|VTI1RP2|Vti1-rp2 | |
| Cytomap | 4q32.1 | 10q25.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | lecithin retinol acyltransferaselecithin retinol acyltransferase (phosphatidylcholine--retinol O-acyltransferase) | vesicle transport through interaction with t-SNAREs homolog 1ASNARE Vti1a-beta proteinvesicle transport v-SNARE protein Vti1-like 2 | |
| Modification date | 20180519 | 20180523 | |
| UniProtAcc | O95237 | Q96AJ9 | |
| Ensembl transtripts involved in fusion gene | ENST00000500890, ENST00000507827, ENST00000336356, | ENST00000432306, ENST00000393077, ENST00000483122, | |
| Fusion gene scores | * DoF score | 2 X 1 X 2=4 | 8 X 5 X 8=320 |
| # samples | 2 | 13 | |
| ** MAII score | log2(2/4*10)=2.32192809488736 | log2(13/320*10)=-1.29956028185891 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: LRAT [Title/Abstract] AND VTI1A [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 | LRAT | GO:0042572 | retinol metabolic process | 10819989 |
| Tgene | VTI1A | GO:0042147 | retrograde transport, endosome to Golgi | 15215310|18195106 |
| 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 | LIHC | TCGA-GJ-A6C0-01A | LRAT | chr4 | 155557548 | + | VTI1A | chr10 | 114575049 | + |
| * 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 |
| 3UTR-intron | ENST00000500890 | ENST00000432306 | LRAT | chr4 | 155557548 | + | VTI1A | chr10 | 114575049 | + |
| 3UTR-intron | ENST00000500890 | ENST00000393077 | LRAT | chr4 | 155557548 | + | VTI1A | chr10 | 114575049 | + |
| 3UTR-intron | ENST00000500890 | ENST00000483122 | LRAT | chr4 | 155557548 | + | VTI1A | chr10 | 114575049 | + |
| intron-intron | ENST00000507827 | ENST00000432306 | LRAT | chr4 | 155557548 | + | VTI1A | chr10 | 114575049 | + |
| intron-intron | ENST00000507827 | ENST00000393077 | LRAT | chr4 | 155557548 | + | VTI1A | chr10 | 114575049 | + |
| intron-intron | ENST00000507827 | ENST00000483122 | LRAT | chr4 | 155557548 | + | VTI1A | chr10 | 114575049 | + |
| intron-intron | ENST00000336356 | ENST00000432306 | LRAT | chr4 | 155557548 | + | VTI1A | chr10 | 114575049 | + |
| intron-intron | ENST00000336356 | ENST00000393077 | LRAT | chr4 | 155557548 | + | VTI1A | chr10 | 114575049 | + |
| intron-intron | ENST00000336356 | ENST00000483122 | LRAT | chr4 | 155557548 | + | VTI1A | chr10 | 114575049 | + |
Top |
FusionProtFeatures for LRAT_VTI1A |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| LRAT | VTI1A |
| 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}. | V-SNARE that mediates vesicle transport pathways throughinteractions with t-SNAREs on the target membrane. Theseinteractions are proposed to mediate aspects of the specificity ofvesicle trafficking and to promote fusion of the lipid bilayers.Involved in vesicular transport from the late endosomes to thetrans-Golgi network. Along with VAMP7, involved in an non-conventional RAB1-dependent traffic route to the cell surface usedby KCNIP1 and KCND2. May be involved in increased cytokinesecretion associated with cellular senescence.{ECO:0000269|PubMed:18195106, ECO:0000269|PubMed:19138172}. |
| 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 |
FusionGeneSequence for LRAT_VTI1A |
| 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). |
Top |
FusionGenePPI for LRAT_VTI1A |
| 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 |
| LRAT | LRAT, NME2P1 | VTI1A | VAMP4, VAMP3, STX7, STX8, VAMP8, TMBIM6, STX6, STX12, CLEC12A, HAUS1 |
| - 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 |
RelatedDrugs for LRAT_VTI1A |
| 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 |
| Hgene | LRAT | O95237 | DB00162 | Vitamin A | Lecithin retinol acyltransferase | small molecule | approved|nutraceutical|vet_approved |
Top |
RelatedDiseases for LRAT_VTI1A |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | LRAT | C0917796 | Optic Atrophy, Hereditary, Leber | 2 | CTD_human |
| Hgene | LRAT | C0015398 | Eye Diseases, Hereditary | 1 | CTD_human |
| Hgene | LRAT | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
| Hgene | LRAT | C0042842 | Vitamin A Deficiency | 1 | CTD_human |
| Hgene | LRAT | C0339527 | Leber Congenital Amaurosis | 1 | CTD_human;ORPHANET |
| Hgene | LRAT | C2750063 | Leber Congenital Amaurosis 14 | 1 | CTD_human;UNIPROT |
| Hgene | LRAT | C4277682 | Chemical and Drug Induced Liver Injury | 1 | CTD_human |
| Tgene | VTI1A | C0001418 | Adenocarcinoma | 1 | CTD_human |
| Tgene | VTI1A | C0009404 | Colorectal Neoplasms | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|