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Fusion Protein:XRCC5-ABCB4 |
Fusion Gene and Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: XRCC5-ABCB4 | FusionPDB ID: 99760 | FusionGDB2.0 ID: 99760 | Hgene | Tgene | Gene symbol | XRCC5 | ABCB4 | Gene ID | 7520 | 5244 |
| Gene name | X-ray repair cross complementing 5 | ATP binding cassette subfamily B member 4 | |
| Synonyms | KARP-1|KARP1|KU80|KUB2|Ku86|NFIV | ABC21|GBD1|ICP3|MDR2|MDR2/3|MDR3|PFIC-3|PGY3 | |
| Cytomap | 2q35 | 7q21.12 | |
| Type of gene | protein-coding | protein-coding | |
| Description | X-ray repair cross-complementing protein 586 kDa subunit of Ku antigenATP-dependent DNA helicase 2 subunit 2ATP-dependent DNA helicase II 80 kDa subunitCTC box-binding factor 85 kDa subunitCTC85CTCBFDNA repair protein XRCC5Ku autoantigen, 80kDaKu | phosphatidylcholine translocator ABCB4ATP-binding cassette sub-family B member 4ATP-binding cassette, sub-family B (MDR/TAP), member 4P-glycoprotein 3P-glycoprotein-3/multiple drug resistance-3multidrug resistance protein 3multiple drug resistance 3 | |
| Modification date | 20200313 | 20200315 | |
| UniProtAcc | . | P21439 Main function of 5'-partner protein: FUNCTION: Energy-dependent phospholipid efflux translocator that acts as a positive regulator of biliary lipid secretion. Functions as a floppase that translocates specifically phosphatidylcholine (PC) from the inner to the outer leaflet of the canalicular membrane bilayer into the canaliculi of hepatocytes. Translocation of PC makes the biliary phospholipids available for extraction into the canaliculi lumen by bile salt mixed micelles and therefore protects the biliary tree from the detergent activity of bile salts (PubMed:7957936, PubMed:8898203, PubMed:9366571, PubMed:17523162, PubMed:23468132, PubMed:24806754, PubMed:24723470, PubMed:24594635, PubMed:21820390). Plays a role in the recruitment of phosphatidylcholine (PC), phosphatidylethanolamine (PE) and sphingomyelin (SM) molecules to nonraft membranes and to further enrichment of SM and cholesterol in raft membranes in hepatocytes (PubMed:23468132). Required for proper phospholipid bile formation (By similarity). Indirectly involved in cholesterol efflux activity from hepatocytes into the canalicular lumen in the presence of bile salts in an ATP-dependent manner (PubMed:24045840). Promotes biliary phospholipid secretion as canaliculi-containing vesicles from the canalicular plasma membrane (PubMed:9366571, PubMed:28012258). In cooperation with ATP8B1, functions to protect hepatocytes from the deleterious detergent activity of bile salts (PubMed:21820390). Does not confer multidrug resistance (By similarity). {ECO:0000250|UniProtKB:P21440, ECO:0000269|PubMed:17523162, ECO:0000269|PubMed:21820390, ECO:0000269|PubMed:23468132, ECO:0000269|PubMed:24045840, ECO:0000269|PubMed:24594635, ECO:0000269|PubMed:24723470, ECO:0000269|PubMed:24806754, ECO:0000269|PubMed:28012258, ECO:0000269|PubMed:7957936, ECO:0000269|PubMed:8898203, ECO:0000269|PubMed:9366571}. | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000471649, ENST00000392132, ENST00000392133, | ENST00000265723, ENST00000358400, ENST00000359206, ENST00000453593, ENST00000545634, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 13 X 10 X 7=910 | 4 X 5 X 4=80 |
| # samples | 12 | 4 | |
| ** MAII score | log2(12/910*10)=-2.92283213947754 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(4/80*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Fusion gene context | PubMed: XRCC5 [Title/Abstract] AND ABCB4 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Fusion neoantigen context | PubMed: XRCC5 [Title/Abstract] AND ABCB4 [Title/Abstract] AND neoantigen [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | XRCC5(216997110)-ABCB4(87031618), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | XRCC5-ABCB4 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. XRCC5-ABCB4 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. XRCC5-ABCB4 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. XRCC5-ABCB4 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. XRCC5-ABCB4 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF. XRCC5-ABCB4 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF. XRCC5-ABCB4 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. | ||
| * 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 | XRCC5 | GO:0002218 | activation of innate immune response | 28712728 |
| Hgene | XRCC5 | GO:0006303 | double-strand break repair via nonhomologous end joining | 26359349 |
| Hgene | XRCC5 | GO:0045860 | positive regulation of protein kinase activity | 22504299 |
| Hgene | XRCC5 | GO:0071480 | cellular response to gamma radiation | 26359349 |
| Tgene | ABCB4 | GO:0032376 | positive regulation of cholesterol transport | 17523162 |
| Tgene | ABCB4 | GO:0045332 | phospholipid translocation | 8898203 |
| Tgene | ABCB4 | GO:0055088 | lipid homeostasis | 17523162 |
| Tgene | ABCB4 | GO:0061092 | positive regulation of phospholipid translocation | 17523162 |
| Tgene | ABCB4 | GO:0099040 | ceramide translocation | 8898203 |
| Tgene | ABCB4 | GO:1903413 | cellular response to bile acid | 17523162 |
| Tgene | ABCB4 | GO:2001140 | positive regulation of phospholipid transport | 8898203 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:216997110/chr7:87031618) - 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. |
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| Retention analysis results 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, are available here. |
| Fusion gene breakpoints across XRCC5 (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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| Fusion gene breakpoints across ABCB4 (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Fusion Amino Acid Sequences |
| Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB. |
| 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) |
| ENST00000392133 | XRCC5 | chr2 | 216997110 | + | ENST00000358400 | ABCB4 | chr7 | 87031618 | - | 1832 | 1574 | 71 | 1780 | 569 |
| ENST00000392133 | XRCC5 | chr2 | 216997110 | + | ENST00000265723 | ABCB4 | chr7 | 87031618 | - | 1828 | 1574 | 71 | 1780 | 569 |
| ENST00000392132 | XRCC5 | chr2 | 216997110 | + | ENST00000358400 | ABCB4 | chr7 | 87031618 | - | 1511 | 1253 | 56 | 1459 | 467 |
| ENST00000392132 | XRCC5 | chr2 | 216997110 | + | ENST00000265723 | ABCB4 | chr7 | 87031618 | - | 1507 | 1253 | 56 | 1459 | 467 |
| 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 |
| ENST00000392133 | ENST00000358400 | XRCC5 | chr2 | 216997110 | + | ABCB4 | chr7 | 87031618 | - | 0.002278749 | 0.99772125 |
| ENST00000392133 | ENST00000265723 | XRCC5 | chr2 | 216997110 | + | ABCB4 | chr7 | 87031618 | - | 0.002342912 | 0.99765706 |
| ENST00000392132 | ENST00000358400 | XRCC5 | chr2 | 216997110 | + | ABCB4 | chr7 | 87031618 | - | 0.000551236 | 0.9994487 |
| ENST00000392132 | ENST00000265723 | XRCC5 | chr2 | 216997110 | + | ABCB4 | chr7 | 87031618 | - | 0.00056796 | 0.999432 |
| Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones. |
Get the fusion protein sequences from here. |
| Fusion protein sequence information is available in the fasta format. >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP |
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Fusion Protein Breakpoint Sequences for XRCC5-ABCB4 |
| +/-13 AA sequence from the breakpoints of the fusion protein sequences. |
| Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
| XRCC5 | chr2 | 216997110 | ABCB4 | chr7 | 87031618 | 1253 | 399 | NQVLKVFAARDDEVVQEALDKAREGR |
| XRCC5 | chr2 | 216997110 | ABCB4 | chr7 | 87031618 | 1574 | 501 | NQVLKVFAARDDEVVQEALDKAREGR |
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Potential FusionNeoAntigen Information of XRCC5-ABCB4 in HLA I |
| Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific. |
| XRCC5-ABCB4_216997110_87031618.msa |
| Potential FusionNeoAntigen Information * We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5) |
| Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA I | FusionNeoAntigen peptide | Binding score | Immunogenic score | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-B18:01 | DEVVQEAL | 0.9977 | 0.9428 | 11 | 19 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-B41:01 | RDDEVVQEA | 0.6004 | 0.8901 | 9 | 18 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-B27:07 | ARDDEVVQEAL | 0.9999 | 0.7861 | 8 | 19 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-B39:01 | ARDDEVVQEAL | 0.9996 | 0.9191 | 8 | 19 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-B38:02 | ARDDEVVQEAL | 0.9995 | 0.9501 | 8 | 19 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-A68:05 | EVVQEALDKAR | 0.9979 | 0.5183 | 12 | 23 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-B39:08 | RDDEVVQEAL | 0.9207 | 0.8495 | 9 | 19 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-C07:13 | ARDDEVVQEAL | 0.9996 | 0.9477 | 8 | 19 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-B39:05 | ARDDEVVQEAL | 0.9993 | 0.9112 | 8 | 19 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-B18:04 | DEVVQEAL | 0.9982 | 0.9489 | 11 | 19 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-B18:07 | DEVVQEAL | 0.9981 | 0.9178 | 11 | 19 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-B18:08 | DEVVQEAL | 0.9978 | 0.9301 | 11 | 19 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-B18:05 | DEVVQEAL | 0.9977 | 0.9428 | 11 | 19 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-B18:06 | DEVVQEAL | 0.9977 | 0.9485 | 11 | 19 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-B18:03 | DEVVQEAL | 0.9964 | 0.9389 | 11 | 19 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-B18:11 | DEVVQEAL | 0.9761 | 0.868 | 11 | 19 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-C03:06 | FAARDDEVV | 0.9836 | 0.9919 | 6 | 15 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-B27:09 | ARDDEVVQEAL | 0.9999 | 0.8365 | 8 | 19 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-C07:04 | ARDDEVVQEAL | 0.9985 | 0.8723 | 8 | 19 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | HLA-B39:11 | ARDDEVVQEAL | 0.9976 | 0.7824 | 8 | 19 |
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Potential FusionNeoAntigen Information of XRCC5-ABCB4 in HLA II |
| Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific. |
| XRCC5-ABCB4_216997110_87031618.msa |
| Potential FusionNeoAntigen Information * We used NetMHCIIpan v4.1 (%rank<0.5). |
| Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA II | FusionNeoAntigen peptide | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB1-1457 | NQVLKVFAARDDEVV | 0 | 15 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0101 | DDEVVQEALDKAREG | 10 | 25 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0101 | RDDEVVQEALDKARE | 9 | 24 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0101 | DEVVQEALDKAREGR | 11 | 26 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0101 | ARDDEVVQEALDKAR | 8 | 23 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0101 | AARDDEVVQEALDKA | 7 | 22 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0103 | DDEVVQEALDKAREG | 10 | 25 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0103 | RDDEVVQEALDKARE | 9 | 24 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0103 | DEVVQEALDKAREGR | 11 | 26 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0103 | ARDDEVVQEALDKAR | 8 | 23 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0103 | AARDDEVVQEALDKA | 7 | 22 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0104 | DDEVVQEALDKAREG | 10 | 25 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0104 | RDDEVVQEALDKARE | 9 | 24 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0104 | DEVVQEALDKAREGR | 11 | 26 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0104 | ARDDEVVQEALDKAR | 8 | 23 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0104 | AARDDEVVQEALDKA | 7 | 22 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0106 | DDEVVQEALDKAREG | 10 | 25 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0106 | RDDEVVQEALDKARE | 9 | 24 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0106 | DEVVQEALDKAREGR | 11 | 26 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0106 | ARDDEVVQEALDKAR | 8 | 23 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0106 | AARDDEVVQEALDKA | 7 | 22 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0107 | DDEVVQEALDKAREG | 10 | 25 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0107 | RDDEVVQEALDKARE | 9 | 24 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0107 | DEVVQEALDKAREGR | 11 | 26 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0107 | ARDDEVVQEALDKAR | 8 | 23 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0107 | AARDDEVVQEALDKA | 7 | 22 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0108 | DDEVVQEALDKAREG | 10 | 25 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0108 | RDDEVVQEALDKARE | 9 | 24 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0108 | DEVVQEALDKAREGR | 11 | 26 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0108 | ARDDEVVQEALDKAR | 8 | 23 |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 | DRB4-0108 | AARDDEVVQEALDKA | 7 | 22 |
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Fusion breakpoint peptide structures of XRCC5-ABCB4 |
| 3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens * The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA. |
| File name | BPseq | Hgene | Tgene | Hchr | Hbp | Tchr | Tbp | AAlen |
| 2282 | FAARDDEVVQEALD | XRCC5 | ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 1253 |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of XRCC5-ABCB4 |
| Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens * We used Glide to predict the interaction between HLAs and neoantigens. |
| HLA allele | PDB ID | File name | BPseq | Docking score | Glide score |
| HLA-B14:02 | 3BVN | 2282 | FAARDDEVVQEALD | -7.9962 | -8.1096 |
| HLA-B14:02 | 3BVN | 2282 | FAARDDEVVQEALD | -5.70842 | -6.74372 |
| HLA-B52:01 | 3W39 | 2282 | FAARDDEVVQEALD | -6.83737 | -6.95077 |
| HLA-B52:01 | 3W39 | 2282 | FAARDDEVVQEALD | -4.4836 | -5.5189 |
| HLA-A11:01 | 4UQ2 | 2282 | FAARDDEVVQEALD | -10.0067 | -10.1201 |
| HLA-A11:01 | 4UQ2 | 2282 | FAARDDEVVQEALD | -9.03915 | -10.0745 |
| HLA-A24:02 | 5HGA | 2282 | FAARDDEVVQEALD | -6.56204 | -6.67544 |
| HLA-A24:02 | 5HGA | 2282 | FAARDDEVVQEALD | -5.42271 | -6.45801 |
| HLA-B44:05 | 3DX8 | 2282 | FAARDDEVVQEALD | -7.85648 | -8.89178 |
| HLA-B44:05 | 3DX8 | 2282 | FAARDDEVVQEALD | -5.3978 | -5.5112 |
| HLA-A02:01 | 6TDR | 2282 | FAARDDEVVQEALD | -3.37154 | -4.40684 |
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Vaccine Design for the FusionNeoAntigens of XRCC5-ABCB4 |
| mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is. |
| Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 11 | 19 | DEVVQEAL | GATGAGGTTGTCCAAGAAGCCCTG |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 12 | 23 | EVVQEALDKAR | GAGGTTGTCCAAGAAGCCCTGGACAAAGCCAGA |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 6 | 15 | FAARDDEVV | TTTGCAGCAAGAGATGATGAGGTTGTC |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 8 | 19 | ARDDEVVQEAL | GCAAGAGATGATGAGGTTGTCCAAGAAGCCCTG |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 9 | 18 | RDDEVVQEA | AGAGATGATGAGGTTGTCCAAGAAGCC |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 9 | 19 | RDDEVVQEAL | AGAGATGATGAGGTTGTCCAAGAAGCCCTG |
| mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs. |
| Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide | FusionNEoAntigen RNA sequence |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 0 | 15 | NQVLKVFAARDDEVV | AATCAAGTTCTAAAGGTCTTTGCAGCAAGAGATGATGAGGTTGTC |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 10 | 25 | DDEVVQEALDKAREG | GATGATGAGGTTGTCCAAGAAGCCCTGGACAAAGCCAGAGAAGGC |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 11 | 26 | DEVVQEALDKAREGR | GATGAGGTTGTCCAAGAAGCCCTGGACAAAGCCAGAGAAGGCCGC |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 7 | 22 | AARDDEVVQEALDKA | GCAGCAAGAGATGATGAGGTTGTCCAAGAAGCCCTGGACAAAGCC |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 8 | 23 | ARDDEVVQEALDKAR | GCAAGAGATGATGAGGTTGTCCAAGAAGCCCTGGACAAAGCCAGA |
| XRCC5-ABCB4 | chr2 | 216997110 | chr7 | 87031618 | 9 | 24 | RDDEVVQEALDKARE | AGAGATGATGAGGTTGTCCAAGAAGCCCTGGACAAAGCCAGAGAA |
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Information of the samples that have these potential fusion neoantigens of XRCC5-ABCB4 |
| These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens. |
| Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
| LIHC | XRCC5-ABCB4 | chr2 | 216997110 | ENST00000392132 | chr7 | 87031618 | ENST00000265723 | TCGA-BC-A10T-01A |
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Potential target of CAR-T therapy development for XRCC5-ABCB4 |
| Predicted 3D structure. We used RoseTTAFold. |
| 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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features * Minus value of BPloci means that the break point is located before the CDS. |
| - In-frame and retained 'Transmembrane'. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| Subcellular localization prediction of the transmembrane domain retained fusion proteins * We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image. |
| Hgene | Hchr | Hbp | Henst | Tgene | Tchr | Tbp | Tenst | DeepLoc result |
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Related Drugs to XRCC5-ABCB4 |
| Drugs used for this fusion-positive patient. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to XRCC5-ABCB4 |
| Diseases that have this fusion gene. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Disease | Source | PMID |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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