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Fusion gene ID: 2210 |
FusionGeneSummary for APOC1_SLC38A4 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: APOC1_SLC38A4 | Fusion gene ID: 2210 | Hgene | Tgene | Gene symbol | APOC1 | SLC38A4 | Gene ID | 341 | 55089 |
| Gene name | apolipoprotein C1 | solute carrier family 38 member 4 | |
| Synonyms | Apo-CI|ApoC-I|apo-CIB|apoC-IB | ATA3|NAT3|PAAT|SNAT4 | |
| Cytomap | 19q13.32 | 12q13.11 | |
| Type of gene | protein-coding | protein-coding | |
| Description | apolipoprotein C-I | sodium-coupled neutral amino acid transporter 4N amino acid transporter 3Na(+)-coupled neutral amino acid transporter 4amino acid transporter A3amino acid transporter system A3system A amino acid transporter 3system N amino acid transporter 3 | |
| Modification date | 20180519 | 20180527 | |
| UniProtAcc | P02654 | Q969I6 | |
| Ensembl transtripts involved in fusion gene | ENST00000588750, ENST00000588802, ENST00000252491, ENST00000592885, ENST00000589781, ENST00000586638, | ENST00000447411, ENST00000266579, | |
| Fusion gene scores | * DoF score | 4 X 2 X 4=32 | 1 X 1 X 1=1 |
| # samples | 4 | 1 | |
| ** MAII score | log2(4/32*10)=0.321928094887362 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(1/1*10)=3.32192809488736 | |
| Context | PubMed: APOC1 [Title/Abstract] AND SLC38A4 [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 | APOC1 | GO:0010900 | negative regulation of phosphatidylcholine catabolic process | 2302419 |
| Hgene | APOC1 | GO:0010916 | negative regulation of very-low-density lipoprotein particle clearance | 1917954 |
| Hgene | APOC1 | GO:0032375 | negative regulation of cholesterol transport | 10978346 |
| Hgene | APOC1 | GO:0033344 | cholesterol efflux | 11162594 |
| Hgene | APOC1 | GO:0033700 | phospholipid efflux | 11162594 |
| Hgene | APOC1 | GO:0034369 | plasma lipoprotein particle remodeling | 10978346 |
| Hgene | APOC1 | GO:0034382 | chylomicron remnant clearance | 4020294 |
| Hgene | APOC1 | GO:0045717 | negative regulation of fatty acid biosynthetic process | 15576844 |
| Hgene | APOC1 | GO:0045833 | negative regulation of lipid metabolic process | 182536 |
| Hgene | APOC1 | GO:0048261 | negative regulation of receptor-mediated endocytosis | 1917954 |
| Hgene | APOC1 | GO:0050995 | negative regulation of lipid catabolic process | 15576844 |
| Hgene | APOC1 | GO:0051005 | negative regulation of lipoprotein lipase activity | 15576844 |
| 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-2Y-A9HB-01A | APOC1 | chr19 | 45422606 | + | SLC38A4 | chr12 | 47226191 | - |
| * 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 | ENST00000588750 | ENST00000447411 | APOC1 | chr19 | 45422606 | + | SLC38A4 | chr12 | 47226191 | - |
| intron-intron | ENST00000588750 | ENST00000266579 | APOC1 | chr19 | 45422606 | + | SLC38A4 | chr12 | 47226191 | - |
| 5CDS-intron | ENST00000588802 | ENST00000447411 | APOC1 | chr19 | 45422606 | + | SLC38A4 | chr12 | 47226191 | - |
| 5CDS-intron | ENST00000588802 | ENST00000266579 | APOC1 | chr19 | 45422606 | + | SLC38A4 | chr12 | 47226191 | - |
| 5CDS-intron | ENST00000252491 | ENST00000447411 | APOC1 | chr19 | 45422606 | + | SLC38A4 | chr12 | 47226191 | - |
| 5CDS-intron | ENST00000252491 | ENST00000266579 | APOC1 | chr19 | 45422606 | + | SLC38A4 | chr12 | 47226191 | - |
| 5CDS-intron | ENST00000592885 | ENST00000447411 | APOC1 | chr19 | 45422606 | + | SLC38A4 | chr12 | 47226191 | - |
| 5CDS-intron | ENST00000592885 | ENST00000266579 | APOC1 | chr19 | 45422606 | + | SLC38A4 | chr12 | 47226191 | - |
| 5CDS-intron | ENST00000589781 | ENST00000447411 | APOC1 | chr19 | 45422606 | + | SLC38A4 | chr12 | 47226191 | - |
| 5CDS-intron | ENST00000589781 | ENST00000266579 | APOC1 | chr19 | 45422606 | + | SLC38A4 | chr12 | 47226191 | - |
| 5CDS-intron | ENST00000586638 | ENST00000447411 | APOC1 | chr19 | 45422606 | + | SLC38A4 | chr12 | 47226191 | - |
| 5CDS-intron | ENST00000586638 | ENST00000266579 | APOC1 | chr19 | 45422606 | + | SLC38A4 | chr12 | 47226191 | - |
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FusionProtFeatures for APOC1_SLC38A4 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| APOC1 | SLC38A4 |
| Inhibitor of lipoprotein binding to the low densitylipoprotein (LDL) receptor, LDL receptor-related protein, and verylow density lipoprotein (VLDL) receptor. Associates with highdensity lipoproteins (HDL) and the triacylglycerol-richlipoproteins in the plasma and makes up about 10% of the proteinof the VLDL and 2% of that of HDL. Appears to interfere directlywith fatty acid uptake and is also the major plasma inhibitor ofcholesteryl ester transfer protein (CETP). Binds free fatty acidsand reduces their intracellular esterification. Modulates theinteraction of APOE with beta-migrating VLDL and inhibits bindingof beta-VLDL to the LDL receptor-related protein.{ECO:0000269|PubMed:17339654, ECO:0000303|PubMed:25160599}. | Sodium-dependent amino acid transporter. Mediateselectrogenic symport of neutral amino acids and sodium ions. Has abroad specificity, with a preference for Ala, followed by His,Cys, Asn, Ser, Gly, Val, Thr, Gln and Met. May mediate sodium-independent transport of cationic amino acids, such as Arg andLys. Amino acid uptake is pH-dependent, with low transportactivities at pH 6.5, intermediate at pH 7.0 and highest betweenpH 7.5 and 8.5. {ECO:0000269|PubMed:11342143,ECO:0000269|PubMed:11414754}. |
| 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 APOC1_SLC38A4 |
| 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 APOC1_SLC38A4 |
| 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 |
| APOC1 | APOA1, HMP19, VKORC1, ALB | SLC38A4 |
| - 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 APOC1_SLC38A4 |
| 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 APOC1_SLC38A4 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | APOC1 | C0018801 | Heart failure | 1 | CTD_human |
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