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Center for Computational Systems Medicine
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Fusion Gene and Fusion Protein Summary

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Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

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Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

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Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

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Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

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Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

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Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

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Potential target of CAR-T therapy development

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Information on the samples that have these potential fusion neoantigens

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Fusion Protein Targeting Drugs - (Manual Curation)

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Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:CASK-ABCB4

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CASK-ABCB4
FusionPDB ID: 13186
FusionGDB2.0 ID: 13186
HgeneTgene
Gene symbol

CASK

ABCB4

Gene ID

8573

5244

Gene namecalcium/calmodulin dependent serine protein kinaseATP binding cassette subfamily B member 4
SynonymsCAGH39|CAMGUK|CMG|FGS4|LIN2|MICPCH|MRXSNA|TNRC8|hCASKABC21|GBD1|ICP3|MDR2|MDR2/3|MDR3|PFIC-3|PGY3
Cytomap

Xp11.4

7q21.12

Type of geneprotein-codingprotein-coding
Descriptionperipheral plasma membrane protein CASKcalcium/calmodulin-dependent serin protein kinasecalcium/calmodulin-dependent serine protein kinase (MAGUK family)calcium/calmodulin-dependent serine protein kinase membrane-associated guanylate kinaseprotein linphosphatidylcholine 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 date2020032720200315
UniProtAcc

Q8WXE0

Main function of 5'-partner protein:

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 geneENST idsENST00000318588, ENST00000361962, 
ENST00000378154, ENST00000378158, 
ENST00000378163, ENST00000378166, 
ENST00000421587, ENST00000442742, 
ENST00000472704, 		ENST00000265723, 
ENST00000358400, ENST00000359206, 
ENST00000453593, ENST00000545634, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score13 X 12 X 5=7804 X 5 X 4=80
# samples 144
** MAII scorelog2(14/780*10)=-2.47804729680464
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: CASK [Title/Abstract] AND ABCB4 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: CASK [Title/Abstract] AND ABCB4 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CASK(41782183)-ABCB4(87104787), # samples:1
CASK(41782183)-ABCB4(87092224), # samples:1
Anticipated loss of major functional domain due to fusion event.CASK-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.
CASK-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.
CASK-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.
CASK-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.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneCASK

GO:0010839

negative regulation of keratinocyte proliferation

18664494

TgeneABCB4

GO:0032376

positive regulation of cholesterol transport

17523162

TgeneABCB4

GO:0045332

phospholipid translocation

8898203

TgeneABCB4

GO:0055088

lipid homeostasis

17523162

TgeneABCB4

GO:0061092

positive regulation of phospholipid translocation

17523162

TgeneABCB4

GO:0099040

ceramide translocation

8898203

TgeneABCB4

GO:1903413

cellular response to bile acid

17523162

TgeneABCB4

GO:2001140

positive regulation of phospholipid transport

8898203



check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chrX:41782183/chr7:87104787)
- 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.
FGviewer

check buttonRetention 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.

check buttonFusion gene breakpoints across CASK (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion 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.
all structure


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Fusion Amino Acid Sequences


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000421587CASKchrX41782183-ENST00000359206ABCB4chr787092224-38398311037871225
ENST00000421587CASKchrX41782183-ENST00000358400ABCB4chr787092224-36988311036461178
ENST00000421587CASKchrX41782183-ENST00000265723ABCB4chr787092224-38568311038081232
ENST00000421587CASKchrX41782183-ENST00000545634ABCB4chr787092224-37888311037871226
ENST00000421587CASKchrX41782183-ENST00000453593ABCB4chr787092224-36478311036461179
ENST00000318588CASKchrX41782183-ENST00000359206ABCB4chr787092224-38611052138091262
ENST00000318588CASKchrX41782183-ENST00000358400ABCB4chr787092224-37201052136681215
ENST00000318588CASKchrX41782183-ENST00000265723ABCB4chr787092224-38781052138301269
ENST00000318588CASKchrX41782183-ENST00000545634ABCB4chr787092224-38101052138091262
ENST00000318588CASKchrX41782183-ENST00000453593ABCB4chr787092224-36691052136681215
ENST00000361962CASKchrX41782183-ENST00000359206ABCB4chr787092224-38611052138091262
ENST00000361962CASKchrX41782183-ENST00000358400ABCB4chr787092224-37201052136681215
ENST00000361962CASKchrX41782183-ENST00000265723ABCB4chr787092224-38781052138301269
ENST00000361962CASKchrX41782183-ENST00000545634ABCB4chr787092224-38101052138091262
ENST00000361962CASKchrX41782183-ENST00000453593ABCB4chr787092224-36691052136681215
ENST00000378163CASKchrX41782183-ENST00000359206ABCB4chr787092224-429053429742381313
ENST00000378163CASKchrX41782183-ENST00000358400ABCB4chr787092224-414953429740971266
ENST00000378163CASKchrX41782183-ENST00000265723ABCB4chr787092224-430753429742591320
ENST00000378163CASKchrX41782183-ENST00000545634ABCB4chr787092224-423953429742381313
ENST00000378163CASKchrX41782183-ENST00000453593ABCB4chr787092224-409853429740971266
ENST00000378158CASKchrX41782183-ENST00000359206ABCB4chr787092224-416641017341141313
ENST00000378158CASKchrX41782183-ENST00000358400ABCB4chr787092224-402541017339731266
ENST00000378158CASKchrX41782183-ENST00000265723ABCB4chr787092224-418341017341351320
ENST00000378158CASKchrX41782183-ENST00000545634ABCB4chr787092224-411541017341141314
ENST00000378158CASKchrX41782183-ENST00000453593ABCB4chr787092224-397441017339731267
ENST00000378166CASKchrX41782183-ENST00000359206ABCB4chr787092224-384286237901262
ENST00000378166CASKchrX41782183-ENST00000358400ABCB4chr787092224-370186236491215
ENST00000378166CASKchrX41782183-ENST00000265723ABCB4chr787092224-385986238111269
ENST00000378166CASKchrX41782183-ENST00000545634ABCB4chr787092224-379186237901263
ENST00000378166CASKchrX41782183-ENST00000453593ABCB4chr787092224-365086236491216
ENST00000442742CASKchrX41782183-ENST00000359206ABCB4chr787092224-38347810537821225
ENST00000442742CASKchrX41782183-ENST00000358400ABCB4chr787092224-36937810536411178
ENST00000442742CASKchrX41782183-ENST00000265723ABCB4chr787092224-38517810538031232
ENST00000442742CASKchrX41782183-ENST00000545634ABCB4chr787092224-37837810537821225
ENST00000442742CASKchrX41782183-ENST00000453593ABCB4chr787092224-36427810536411178
ENST00000378154CASKchrX41782183-ENST00000359206ABCB4chr787092224-429053429742381313
ENST00000378154CASKchrX41782183-ENST00000358400ABCB4chr787092224-414953429740971266
ENST00000378154CASKchrX41782183-ENST00000265723ABCB4chr787092224-430753429742591320
ENST00000378154CASKchrX41782183-ENST00000545634ABCB4chr787092224-423953429742381313
ENST00000378154CASKchrX41782183-ENST00000453593ABCB4chr787092224-409853429740971266

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000421587ENST00000359206CASKchrX41782183-ABCB4chr787092224-0.0030792560.9969208
ENST00000421587ENST00000358400CASKchrX41782183-ABCB4chr787092224-0.0018449190.99815506
ENST00000421587ENST00000265723CASKchrX41782183-ABCB4chr787092224-0.003167660.9968323
ENST00000421587ENST00000545634CASKchrX41782183-ABCB4chr787092224-0.0034044090.99659556
ENST00000421587ENST00000453593CASKchrX41782183-ABCB4chr787092224-0.0020856820.99791425
ENST00000318588ENST00000359206CASKchrX41782183-ABCB4chr787092224-0.0031086520.9968913
ENST00000318588ENST00000358400CASKchrX41782183-ABCB4chr787092224-0.001865320.9981346
ENST00000318588ENST00000265723CASKchrX41782183-ABCB4chr787092224-0.0032013270.99679863
ENST00000318588ENST00000545634CASKchrX41782183-ABCB4chr787092224-0.0034347350.9965653
ENST00000318588ENST00000453593CASKchrX41782183-ABCB4chr787092224-0.0021053050.9978947
ENST00000361962ENST00000359206CASKchrX41782183-ABCB4chr787092224-0.0031086520.9968913
ENST00000361962ENST00000358400CASKchrX41782183-ABCB4chr787092224-0.001865320.9981346
ENST00000361962ENST00000265723CASKchrX41782183-ABCB4chr787092224-0.0032013270.99679863
ENST00000361962ENST00000545634CASKchrX41782183-ABCB4chr787092224-0.0034347350.9965653
ENST00000361962ENST00000453593CASKchrX41782183-ABCB4chr787092224-0.0021053050.9978947
ENST00000378163ENST00000359206CASKchrX41782183-ABCB4chr787092224-0.0048370790.99516284
ENST00000378163ENST00000358400CASKchrX41782183-ABCB4chr787092224-0.0030923250.99690765
ENST00000378163ENST00000265723CASKchrX41782183-ABCB4chr787092224-0.0048823980.99511766
ENST00000378163ENST00000545634CASKchrX41782183-ABCB4chr787092224-0.0051903780.9948096
ENST00000378163ENST00000453593CASKchrX41782183-ABCB4chr787092224-0.0034355270.99656445
ENST00000378158ENST00000359206CASKchrX41782183-ABCB4chr787092224-0.004156680.99584335
ENST00000378158ENST00000358400CASKchrX41782183-ABCB4chr787092224-0.0025475710.99745244
ENST00000378158ENST00000265723CASKchrX41782183-ABCB4chr787092224-0.0041881340.99581194
ENST00000378158ENST00000545634CASKchrX41782183-ABCB4chr787092224-0.004525220.99547476
ENST00000378158ENST00000453593CASKchrX41782183-ABCB4chr787092224-0.0028269730.99717295
ENST00000378166ENST00000359206CASKchrX41782183-ABCB4chr787092224-0.0030668290.9969331
ENST00000378166ENST00000358400CASKchrX41782183-ABCB4chr787092224-0.0018356820.99816436
ENST00000378166ENST00000265723CASKchrX41782183-ABCB4chr787092224-0.0031534410.9968465
ENST00000378166ENST00000545634CASKchrX41782183-ABCB4chr787092224-0.0033922640.9966078
ENST00000378166ENST00000453593CASKchrX41782183-ABCB4chr787092224-0.0020748470.99792516
ENST00000442742ENST00000359206CASKchrX41782183-ABCB4chr787092224-0.0030353750.99696463
ENST00000442742ENST00000358400CASKchrX41782183-ABCB4chr787092224-0.0018116520.9981883
ENST00000442742ENST00000265723CASKchrX41782183-ABCB4chr787092224-0.003119070.9968809
ENST00000442742ENST00000545634CASKchrX41782183-ABCB4chr787092224-0.0033508070.9966492
ENST00000442742ENST00000453593CASKchrX41782183-ABCB4chr787092224-0.0020487670.9979512
ENST00000378154ENST00000359206CASKchrX41782183-ABCB4chr787092224-0.0048370790.99516284
ENST00000378154ENST00000358400CASKchrX41782183-ABCB4chr787092224-0.0030923250.99690765
ENST00000378154ENST00000265723CASKchrX41782183-ABCB4chr787092224-0.0048823980.99511766
ENST00000378154ENST00000545634CASKchrX41782183-ABCB4chr787092224-0.0051903780.9948096
ENST00000378154ENST00000453593CASKchrX41782183-ABCB4chr787092224-0.0034355270.99656445

check button 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 CASK-ABCB4

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide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Potential FusionNeoAntigen Information of CASK-ABCB4 in HLA I

check button 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.
CASK-ABCB4_41782183_87092224.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)
Fusion geneHchrHbpTgeneTchrTbpHLA IFusionNeoAntigen peptideBinding scoreImmunogenic scoreNeoantigen start (at BP 13)Neoantigen end (at BP 13)
CASK-ABCB4chrX41782183chr787092224105HLA-B35:08DSIKGNLEF0.99060.8818918
CASK-ABCB4chrX41782183chr787092224105HLA-B35:01DSIKGNLEF0.98130.8232918
CASK-ABCB4chrX41782183chr787092224105HLA-B15:02DSIKGNLEF0.97260.8826918
CASK-ABCB4chrX41782183chr787092224105HLA-B35:05DSIKGNLEF0.9220.5188918
CASK-ABCB4chrX41782183chr787092224105HLA-B35:03KPDSIKGNL0.61980.6966716
CASK-ABCB4chrX41782183chr787092224105HLA-B35:04KPDSIKGNL0.30820.7668716
CASK-ABCB4chrX41782183chr787092224105HLA-B35:02KPDSIKGNL0.30820.7668716
CASK-ABCB4chrX41782183chr787092224105HLA-B57:01KPDSIKGNLEF0.99870.9509718
CASK-ABCB4chrX41782183chr787092224105HLA-B35:08KPDSIKGNLEF0.99680.7915718
CASK-ABCB4chrX41782183chr787092224105HLA-B58:02KPDSIKGNLEF0.99630.8832718
CASK-ABCB4chrX41782183chr787092224105HLA-B57:03KPDSIKGNLEF0.99440.955718
CASK-ABCB4chrX41782183chr787092224105HLA-B15:17KPDSIKGNLEF0.98780.8625718
CASK-ABCB4chrX41782183chr787092224105HLA-B58:01KPDSIKGNLEF0.98040.8636718
CASK-ABCB4chrX41782183chr787092224105HLA-C04:10KPDSIKGNL0.99610.5948716
CASK-ABCB4chrX41782183chr787092224105HLA-C04:07KPDSIKGNL0.99580.6302716
CASK-ABCB4chrX41782183chr787092224105HLA-C08:15KPDSIKGNL0.98710.8999716
CASK-ABCB4chrX41782183chr787092224105HLA-B15:31DSIKGNLEF0.98010.7701918
CASK-ABCB4chrX41782183chr787092224105HLA-B15:21DSIKGNLEF0.97850.8699918
CASK-ABCB4chrX41782183chr787092224105HLA-B39:10KPDSIKGNL0.39370.6063716
CASK-ABCB4chrX41782183chr787092224105HLA-C04:14KPDSIKGNL0.38560.6328716
CASK-ABCB4chrX41782183chr787092224105HLA-B35:12KPDSIKGNL0.30820.7668716
CASK-ABCB4chrX41782183chr787092224105HLA-B39:10HKPDSIKGNL0.97240.7579616
CASK-ABCB4chrX41782183chr787092224105HLA-C04:10KPDSIKGNLEF0.99980.8519718
CASK-ABCB4chrX41782183chr787092224105HLA-A25:01DSIKGNLEF0.99870.9484918
CASK-ABCB4chrX41782183chr787092224105HLA-C04:01KPDSIKGNL0.99580.6302716
CASK-ABCB4chrX41782183chr787092224105HLA-C18:01KPDSIKGNL0.99420.6311716
CASK-ABCB4chrX41782183chr787092224105HLA-C08:02KPDSIKGNL0.98710.8999716
CASK-ABCB4chrX41782183chr787092224105HLA-B35:24DSIKGNLEF0.9870.8225918
CASK-ABCB4chrX41782183chr787092224105HLA-B35:77DSIKGNLEF0.98130.8232918
CASK-ABCB4chrX41782183chr787092224105HLA-B35:23DSIKGNLEF0.98060.8275918
CASK-ABCB4chrX41782183chr787092224105HLA-B35:11DSIKGNLEF0.97960.868918
CASK-ABCB4chrX41782183chr787092224105HLA-B35:20DSIKGNLEF0.97840.8408918
CASK-ABCB4chrX41782183chr787092224105HLA-B15:13DSIKGNLEF0.95190.6807918
CASK-ABCB4chrX41782183chr787092224105HLA-B35:30DSIKGNLEF0.92880.6562918
CASK-ABCB4chrX41782183chr787092224105HLA-B35:17DSIKGNLEF0.92880.6562918
CASK-ABCB4chrX41782183chr787092224105HLA-B15:08DSIKGNLEF0.86860.8145918
CASK-ABCB4chrX41782183chr787092224105HLA-B35:43DSIKGNLEF0.85640.8059918
CASK-ABCB4chrX41782183chr787092224105HLA-B18:04DSIKGNLEF0.85430.9196918
CASK-ABCB4chrX41782183chr787092224105HLA-B15:11DSIKGNLEF0.84880.7837918
CASK-ABCB4chrX41782183chr787092224105HLA-B18:07DSIKGNLEF0.74240.8864918
CASK-ABCB4chrX41782183chr787092224105HLA-B35:13KPDSIKGNL0.55020.6982716
CASK-ABCB4chrX41782183chr787092224105HLA-B35:09KPDSIKGNL0.30820.7668716
CASK-ABCB4chrX41782183chr787092224105HLA-B67:01HKPDSIKGNL0.97120.5002616
CASK-ABCB4chrX41782183chr787092224105HLA-B57:10KPDSIKGNLEF0.99870.9509718
CASK-ABCB4chrX41782183chr787092224105HLA-B57:04KPDSIKGNLEF0.99780.6763718
CASK-ABCB4chrX41782183chr787092224105HLA-B58:06KPDSIKGNLEF0.99660.7389718
CASK-ABCB4chrX41782183chr787092224105HLA-B57:02KPDSIKGNLEF0.99650.8605718

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Potential FusionNeoAntigen Information of CASK-ABCB4 in HLA II

check button 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.
CASK-ABCB4_41782183_87092224.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).
Fusion geneHchrHbpTgeneTchrTbpHLA IIFusionNeoAntigen peptideNeoantigen start (at BP 13)Neoantigen end (at BP 13)
CASK-ABCB4chrX41782183chr787092224105DRB3-0201IKGNLEFNDVHFSYP1126
CASK-ABCB4chrX41782183chr787092224105DRB3-0204IKGNLEFNDVHFSYP1126
CASK-ABCB4chrX41782183chr787092224105DRB3-0214IKGNLEFNDVHFSYP1126
CASK-ABCB4chrX41782183chr787092224105DRB3-0224IKGNLEFNDVHFSYP1126

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Fusion breakpoint peptide structures of CASK-ABCB4

check button3D 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 nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
3386HKPDSIKGNLEFNDCASKABCB4chrX41782183chr787092224105

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CASK-ABCB4

check buttonVirtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.
HLA allelePDB IDFile nameBPseqDocking scoreGlide score
HLA-B14:023BVN3386HKPDSIKGNLEFND-7.9962-8.1096
HLA-B14:023BVN3386HKPDSIKGNLEFND-5.70842-6.74372
HLA-B52:013W393386HKPDSIKGNLEFND-6.83737-6.95077
HLA-B52:013W393386HKPDSIKGNLEFND-4.4836-5.5189
HLA-A11:014UQ23386HKPDSIKGNLEFND-10.0067-10.1201
HLA-A11:014UQ23386HKPDSIKGNLEFND-9.03915-10.0745
HLA-A24:025HGA3386HKPDSIKGNLEFND-6.56204-6.67544
HLA-A24:025HGA3386HKPDSIKGNLEFND-5.42271-6.45801
HLA-B44:053DX83386HKPDSIKGNLEFND-7.85648-8.89178
HLA-B44:053DX83386HKPDSIKGNLEFND-5.3978-5.5112
HLA-A02:016TDR3386HKPDSIKGNLEFND-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of CASK-ABCB4

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptide sequenceFusionNeoAntigen RNA sequence
CASK-ABCB4chrX41782183chr787092224616HKPDSIKGNLGCTGTGCGAGGTGATCGGAAATTTCGATAC
CASK-ABCB4chrX41782183chr787092224716KPDSIKGNLGTGCGAGGTGATCGGAAATTTCGATAC
CASK-ABCB4chrX41782183chr787092224718KPDSIKGNLEFGTGCGAGGTGATCGGAAATTTCGATACTCCGAT
CASK-ABCB4chrX41782183chr787092224918DSIKGNLEFGGTGATCGGAAATTTCGATACTCCGAT

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
CASK-ABCB4chrX41782183chr7870922241126IKGNLEFNDVHFSYPCGGAAATTTCGATACTCCGATTGGCAGGATAAATTGTTTATGTCG

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Information of the samples that have these potential fusion neoantigens of CASK-ABCB4

check button 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 typeFusion geneHchrHbpHenstTchrTbpTenstSample
STADCASK-ABCB4chrX41782183ENST00000318588chr787092224ENST00000265723TCGA-CD-5799-01A

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Potential target of CAR-T therapy development for CASK-ABCB4

check button Predicted 3D structure. We used RoseTTAFold.

check buttonRetention 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'.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneABCB4chrX:41782183chr7:87092224ENST00000265723228119_13901287.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000265723228189_21001287.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000265723228218_23801287.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000265723228297_31801287.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000265723228333_35401287.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST0000026572322851_7301287.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000265723228712_73201287.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000265723228756_77601287.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000265723228832_85201287.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000265723228854_87301287.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000265723228934_95601287.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000265723228973_99401287.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000358400227119_13901233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000358400227189_21001233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000358400227218_23801233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000358400227297_31801233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000358400227333_35401233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST0000035840022751_7301233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000358400227712_73201233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000358400227756_77601233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000358400227832_85201233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000358400227854_87301233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000358400227934_95601233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000358400227973_99401233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000359206228119_13901280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000359206228189_21001280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000359206228218_23801280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000359206228297_31801280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000359206228333_35401280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST0000035920622851_7301280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000359206228712_73201280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000359206228756_77601280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000359206228832_85201280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000359206228854_87301280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000359206228934_95601280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000359206228973_99401280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000453593126119_13901233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000453593126189_21001233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000453593126218_23801233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000453593126297_31801233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000453593126333_35401233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST0000045359312651_7301233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000453593126712_73201233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000453593126756_77601233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000453593126832_85201233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000453593126854_87301233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000453593126934_95601233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000453593126973_99401233.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000545634127119_13901280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000545634127189_21001280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000545634127218_23801280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000545634127297_31801280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000545634127333_35401280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST0000054563412751_7301280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000545634127712_73201280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000545634127756_77601280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000545634127832_85201280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000545634127854_87301280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000545634127934_95601280.0TransmembraneHelical
TgeneABCB4chrX:41782183chr7:87092224ENST00000545634127973_99401280.0TransmembraneHelical

check button 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.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result

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Related Drugs to CASK-ABCB4

check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to CASK-ABCB4

check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource