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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:SKAP1-ABCC11

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SKAP1-ABCC11
FusionPDB ID: 82045
FusionGDB2.0 ID: 82045
HgeneTgene
Gene symbol

SKAP1

ABCC11

Gene ID

8631

85320

Gene namesrc kinase associated phosphoprotein 1ATP binding cassette subfamily C member 11
SynonymsHEL-S-81p|SCAP1|SKAP55EWWD|MRP8|WW
Cytomap

17q21.32

16q12.1

Type of geneprotein-codingprotein-coding
Descriptionsrc kinase-associated phosphoprotein 1SKAP-55epididymis secretory sperm binding protein Li 81ppp55src family-associated phosphoprotein 1src kinase-associated phosphoprotein of 55 kDaATP-binding cassette sub-family C member 11ATP-binding cassette protein C11ATP-binding cassette transporter MRP8ATP-binding cassette transporter sub-family C member 11ATP-binding cassette, sub-family C (CFTR/MRP), member 11multi-resistance protein 8
Modification date2020031320200313
UniProtAcc.

Q96J66

Main function of 5'-partner protein: FUNCTION: ATP-dependent transporter of the ATP-binding cassette (ABC) family that actively extrudes physiological compounds, and xenobiotics from cells. Participates in physiological processes involving bile acids, conjugated steroids and cyclic nucleotides (PubMed:12764137, PubMed:15537867). Stimulates the ATP-dependent uptake of a range of physiological lipophilic anions, including the glutathione S-conjugates leukotriene C4 and dinitrophenyl S-glutathione, steroid sulfates such as dehydroepiandrosterone 3-sulfate (DHEAS) and estrone 3-sulfate, glucuronides such as estradiol 17-beta-D-glucuronide (E(2)17betaG), the monoanionic bile acids glycocholate and taurocholate, and methotrexate (PubMed:15537867, PubMed:25896536). Enhances also the cellular extrusion of cAMP and cGMP (PubMed:12764137, PubMed:15537867). Confers resistance to anticancer drugs, such as 5-fluorouracil (5-FU) and methotrexate (PubMed:25896536, PubMed:15537867, PubMed:12764137). Probably functions to secrete earwax (PubMed:16444273, PubMed:19383836). Required for the secretion of components contributing to axillary odor formation (PubMed:19710689, PubMed:12764137, PubMed:15537867, PubMed:16444273, PubMed:19383836, PubMed:25896536). {ECO:0000269|PubMed:12764137, ECO:0000269|PubMed:15537867, ECO:0000269|PubMed:16444273, ECO:0000269|PubMed:19383836, ECO:0000269|PubMed:19710689, ECO:0000269|PubMed:25896536}.
Ensembl transtripts involved in fusion geneENST idsENST00000336915, ENST00000584924, 
ENST00000565329, ENST00000537808, 
ENST00000353782, ENST00000356608, 
ENST00000394747, ENST00000394748, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score26 X 10 X 10=26006 X 5 X 3=90
# samples 357
** MAII scorelog2(35/2600*10)=-2.89308479608349
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/90*10)=-0.362570079384708
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: SKAP1 [Title/Abstract] AND ABCC11 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: SKAP1 [Title/Abstract] AND ABCC11 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SKAP1(46423267)-ABCC11(48211024), # samples:3
Anticipated loss of major functional domain due to fusion event.SKAP1-ABCC11 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.
SKAP1-ABCC11 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.
SKAP1-ABCC11 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
SKAP1-ABCC11 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneSKAP1

GO:0002821

positive regulation of adaptive immune response

12652296

HgeneSKAP1

GO:0033625

positive regulation of integrin activation

12652296

HgeneSKAP1

GO:0034116

positive regulation of heterotypic cell-cell adhesion

12652296

HgeneSKAP1

GO:0045944

positive regulation of transcription by RNA polymerase II

11909961

HgeneSKAP1

GO:1903039

positive regulation of leukocyte cell-cell adhesion

12652296

TgeneABCC11

GO:0015711

organic anion transport

15537867|16359813

TgeneABCC11

GO:0015865

purine nucleotide transport

12764137



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/chr17:46423267/chr16:48211024)
- 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 SKAP1 (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 ABCC11 (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)
ENST00000336915SKAP1chr1746423266-ENST00000353782ABCC11chr1648209328-121135070846258
ENST00000336915SKAP1chr1746423266-ENST00000356608ABCC11chr1648209328-132535070960296
ENST00000336915SKAP1chr1746423266-ENST00000394747ABCC11chr1648209328-132435070960296
ENST00000336915SKAP1chr1746423266-ENST00000394748ABCC11chr1648209328-132435070960296
ENST00000584924SKAP1chr1746423266-ENST00000353782ABCC11chr1648209328-124037999875258
ENST00000584924SKAP1chr1746423266-ENST00000356608ABCC11chr1648209328-135437999989296
ENST00000584924SKAP1chr1746423266-ENST00000394747ABCC11chr1648209328-135337999989296
ENST00000584924SKAP1chr1746423266-ENST00000394748ABCC11chr1648209328-135337999989296
ENST00000336915SKAP1chr1746423267-ENST00000353782ABCC11chr1648209328-121135070846258
ENST00000336915SKAP1chr1746423267-ENST00000356608ABCC11chr1648209328-132535070960296
ENST00000336915SKAP1chr1746423267-ENST00000394747ABCC11chr1648209328-132435070960296
ENST00000336915SKAP1chr1746423267-ENST00000394748ABCC11chr1648209328-132435070960296
ENST00000584924SKAP1chr1746423267-ENST00000353782ABCC11chr1648209328-124037999875258
ENST00000584924SKAP1chr1746423267-ENST00000356608ABCC11chr1648209328-135437999989296
ENST00000584924SKAP1chr1746423267-ENST00000394747ABCC11chr1648209328-135337999989296
ENST00000584924SKAP1chr1746423267-ENST00000394748ABCC11chr1648209328-135337999989296

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
ENST00000336915ENST00000353782SKAP1chr1746423266-ABCC11chr1648209328-0.0035861640.9964139
ENST00000336915ENST00000356608SKAP1chr1746423266-ABCC11chr1648209328-0.0042743850.99572563
ENST00000336915ENST00000394747SKAP1chr1746423266-ABCC11chr1648209328-0.0042869010.9957131
ENST00000336915ENST00000394748SKAP1chr1746423266-ABCC11chr1648209328-0.0042869010.9957131
ENST00000584924ENST00000353782SKAP1chr1746423266-ABCC11chr1648209328-0.003750960.996249
ENST00000584924ENST00000356608SKAP1chr1746423266-ABCC11chr1648209328-0.0045262810.9954737
ENST00000584924ENST00000394747SKAP1chr1746423266-ABCC11chr1648209328-0.0045055780.99549437
ENST00000584924ENST00000394748SKAP1chr1746423266-ABCC11chr1648209328-0.0045055780.99549437
ENST00000336915ENST00000353782SKAP1chr1746423267-ABCC11chr1648209328-0.0035861640.9964139
ENST00000336915ENST00000356608SKAP1chr1746423267-ABCC11chr1648209328-0.0042743850.99572563
ENST00000336915ENST00000394747SKAP1chr1746423267-ABCC11chr1648209328-0.0042869010.9957131
ENST00000336915ENST00000394748SKAP1chr1746423267-ABCC11chr1648209328-0.0042869010.9957131
ENST00000584924ENST00000353782SKAP1chr1746423267-ABCC11chr1648209328-0.003750960.996249
ENST00000584924ENST00000356608SKAP1chr1746423267-ABCC11chr1648209328-0.0045262810.9954737
ENST00000584924ENST00000394747SKAP1chr1746423267-ABCC11chr1648209328-0.0045055780.99549437
ENST00000584924ENST00000394748SKAP1chr1746423267-ABCC11chr1648209328-0.0045055780.99549437

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 SKAP1-ABCC11

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
SKAP1chr1746423266ABCC11chr164820932835093TSDAPFLSDYQDEGKSSLGMALFRLV
SKAP1chr1746423266ABCC11chr164820932837993TSDAPFLSDYQDEGKSSLGMALFRLV
SKAP1chr1746423267ABCC11chr164820932835093TSDAPFLSDYQDEGKSSLGMALFRLV
SKAP1chr1746423267ABCC11chr164820932837993TSDAPFLSDYQDEGKSSLGMALFRLV

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Potential FusionNeoAntigen Information of SKAP1-ABCC11 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.
SKAP1-ABCC11_46423266_48209328.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)
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:24YQDEGKSSL0.99670.5937918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:01YQDEGKSSL0.99610.9237918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:13YQDEGKSSL0.99240.941918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B48:01YQDEGKSSL0.99230.6378918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:06YQDEGKSSL0.9910.7952918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B38:02YQDEGKSSL0.98970.9617918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B38:01YQDEGKSSL0.98750.9563918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B14:02YQDEGKSSL0.98680.8342918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B14:01YQDEGKSSL0.98680.8342918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B15:10YQDEGKSSL0.98340.7416918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B18:01DEGKSSLGM0.94560.90241120
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B15:18YQDEGKSSL0.92630.8461918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:60YQDEGKSSL0.89330.5786918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:24YQDEGKSSL0.89170.6124918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:67YQDEGKSSL0.89170.6124918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:30YQDEGKSSL0.89170.6124918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B15:03YQDEGKSSL0.86750.8761918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B15:37YQDEGKSSL0.86420.8075918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:11YQDEGKSSL0.86330.6526918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:21YQDEGKSSL0.84860.7457918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:04YQDEGKSSL0.77940.7055918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B35:03YQDEGKSSL0.73530.9398918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:35YQDEGKSSL0.71220.6349918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B15:02YQDEGKSSL0.70940.9647918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B13:02YQDEGKSSL0.68770.7678918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B13:01YQDEGKSSL0.67940.9808918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:29YQDEGKSSL0.67170.6203918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:20YQDEGKSSL0.64190.6195918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:27YQDEGKSSL0.630.6044918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:38YQDEGKSSL0.62260.7135918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B35:02YQDEGKSSL0.61060.9731918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B35:04YQDEGKSSL0.61060.9731918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:16YQDEGKSSL0.59840.5927918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B08:01YQDEGKSSL0.54940.7724918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B07:10YQDEGKSSL0.54530.5658918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B08:09YQDEGKSSL0.54520.7671918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B47:01YQDEGKSSL0.54440.7161918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:13YQDEGKSSL0.43830.7469918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B52:01YQDEGKSSL0.1410.9839918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:01DYQDEGKSSL0.83330.9331818
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B48:01SDYQDEGKSSL0.99820.5111718
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:01YQDEGKSSLGM0.99290.9503920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:13YQDEGKSSLGM0.98670.966920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:13SDYQDEGKSSL0.98190.8304718
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:08QDEGKSSL0.96910.95181018
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C04:07YQDEGKSSL0.99990.86918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C05:09YQDEGKSSL0.99990.925918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C04:10YQDEGKSSL0.99990.8247918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C08:15YQDEGKSSL0.99990.9778918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C01:17YQDEGKSSL0.99970.9617918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C03:07YQDEGKSSL0.99870.9754918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C03:19YQDEGKSSL0.99830.9882918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C04:06YQDEGKSSL0.99780.9222918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:09YQDEGKSSL0.99750.7247918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C08:04YQDEGKSSL0.99650.9505918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C08:13YQDEGKSSL0.99650.9505918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:10YQDEGKSSL0.99610.9324918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C04:14YQDEGKSSL0.99560.8455918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:12YQDEGKSSL0.99440.9255918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C01:30YQDEGKSSL0.99440.9651918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C15:06YQDEGKSSL0.99340.9463918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C08:03YQDEGKSSL0.99330.9793918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C12:12YQDEGKSSL0.99170.9529918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:05YQDEGKSSL0.99140.9131918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C03:14YQDEGKSSL0.98870.9728918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:08YQDEGKSSL0.98560.945918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C07:13YQDEGKSSL0.98490.9507918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C07:29YQDEGKSSL0.97710.9424918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C03:08YQDEGKSSL0.97620.9588918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C07:80YQDEGKSSL0.97370.9467918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C07:67YQDEGKSSL0.97370.9467918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C07:10YQDEGKSSL0.97160.9746918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C07:05YQDEGKSSL0.97160.9766918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C07:27YQDEGKSSL0.9670.9543918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C02:06YQDEGKSSL0.96540.9546918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C07:19YQDEGKSSL0.95340.8261918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C07:95YQDEGKSSL0.94610.8263918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C07:46YQDEGKSSL0.93880.9097918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:01YQDEGKSSL0.89170.6124918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:07YQDEGKSSL0.88750.6495918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C12:16YQDEGKSSL0.87680.9571918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B14:03YQDEGKSSL0.87270.8757918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B15:04YQDEGKSSL0.74280.9375918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B42:02YQDEGKSSL0.73920.7633918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B15:21YQDEGKSSL0.70320.9172918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B07:12YQDEGKSSL0.65570.721918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B35:12YQDEGKSSL0.61060.9731918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B15:05YQDEGKSSL0.59710.9299918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B15:31YQDEGKSSL0.58880.9358918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C04:10DYQDEGKSSL0.99910.9039818
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C04:07DYQDEGKSSL0.99890.9198818
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C08:15YQDEGKSSLG0.99780.975919
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C08:15DYQDEGKSSL0.99760.9801818
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B14:03DYQDEGKSSL0.95130.884818
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C04:14DYQDEGKSSL0.91010.9197818
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:08DYQDEGKSSL0.87320.9575818
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:09DYQDEGKSSL0.85490.819818
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:08YQDEGKSSLG0.83810.9117919
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:05DYQDEGKSSL0.63860.9256818
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C08:15SDYQDEGKSSL10.9009718
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C04:10YQDEGKSSLGM10.922920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C08:15YQDEGKSSLGM10.9888920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C05:09YQDEGKSSLGM10.9441920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C05:09SDYQDEGKSSL10.9223718
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C08:13YQDEGKSSLGM0.99820.9862920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C08:04YQDEGKSSLGM0.99820.9862920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:08SDYQDEGKSSL0.99810.815718
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C08:03YQDEGKSSLGM0.99640.9935920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:08YQDEGKSSLGM0.99540.947920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:09YQDEGKSSLGM0.99270.8706920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:05YQDEGKSSLGM0.98370.9399920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C18:01YQDEGKSSL0.99990.8531918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C05:01YQDEGKSSL0.99990.925918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C01:03YQDEGKSSL0.99990.959918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C04:03YQDEGKSSL0.99990.8758918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C04:01YQDEGKSSL0.99990.86918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C08:02YQDEGKSSL0.99990.9778918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C01:02YQDEGKSSL0.99970.9602918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C03:03YQDEGKSSL0.99870.9877918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C03:04YQDEGKSSL0.99870.9877918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C14:03YQDEGKSSL0.99830.9696918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C14:02YQDEGKSSL0.99830.9696918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C04:04YQDEGKSSL0.99680.9197918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:02YQDEGKSSL0.99670.944918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C03:17YQDEGKSSL0.99660.9692918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:31YQDEGKSSL0.99610.9224918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C06:06YQDEGKSSL0.99610.9871918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C03:05YQDEGKSSL0.99590.9524918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B67:01YQDEGKSSL0.99550.8914918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C03:67YQDEGKSSL0.99410.9843918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C08:01YQDEGKSSL0.99330.9793918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C17:01YQDEGKSSL0.99320.9473918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C15:05YQDEGKSSL0.99270.9383918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B27:06YQDEGKSSL0.98860.8739918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B38:05YQDEGKSSL0.98750.9563918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C03:06YQDEGKSSL0.98410.9892918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:11YQDEGKSSL0.98290.9061918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B27:09YQDEGKSSL0.97830.8941918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C07:02YQDEGKSSL0.97370.9467918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C07:04YQDEGKSSL0.97360.9585918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C03:02YQDEGKSSL0.97290.9709918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C07:17YQDEGKSSL0.97030.9641918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C12:02YQDEGKSSL0.96760.9557918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C02:10YQDEGKSSL0.96510.9701918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C02:02YQDEGKSSL0.96510.9701918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B18:05DEGKSSLGM0.94560.90241120
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C07:01YQDEGKSSL0.94020.8154918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B18:06DEGKSSLGM0.93880.90831120
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B15:09YQDEGKSSL0.93860.84918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B18:08DEGKSSLGM0.93670.74541120
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C07:22YQDEGKSSL0.92540.8343918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B15:54YQDEGKSSL0.87130.8863918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B18:03DEGKSSLGM0.86990.89341120
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B15:73YQDEGKSSL0.85220.9152918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:14YQDEGKSSL0.84870.6264918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:06YQDEGKSSL0.84860.7457918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B15:53YQDEGKSSL0.82040.8934918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B15:30YQDEGKSSL0.81020.8412918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B08:12YQDEGKSSL0.80280.8241918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B48:02YQDEGKSSL0.79980.9704918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B40:21YQDEGKSSL0.79270.506918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B35:13YQDEGKSSL0.74590.9453918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:03YQDEGKSSL0.74410.7107918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B07:13YQDEGKSSL0.690.8602918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B41:03YQDEGKSSL0.68110.7671918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B35:09YQDEGKSSL0.61060.9731918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B35:28YQDEGKSSL0.59820.9767918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B15:20YQDEGKSSL0.59330.9656918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B35:20YQDEGKSSL0.58590.9805918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B08:18YQDEGKSSL0.54940.7724918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B18:11DEGKSSLGM0.47430.7871120
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B18:04YQDEGKSSL0.17260.9461918
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C04:01DYQDEGKSSL0.99890.9198818
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C18:01DYQDEGKSSL0.99810.9099818
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C08:02YQDEGKSSLG0.99780.975919
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C08:02DYQDEGKSSL0.99760.9801818
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:11DYQDEGKSSL0.86510.8898818
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:11YQDEGKSSLG0.80110.8571919
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B15:09DYQDEGKSSL0.76660.8194818
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C08:02YQDEGKSSLGM10.9888920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C05:01SDYQDEGKSSL10.9223718
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C08:02SDYQDEGKSSL10.9009718
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C04:03YQDEGKSSLGM10.9139920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C05:01YQDEGKSSLGM10.9441920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:11SDYQDEGKSSL0.99790.7076718
SKAP1-ABCC11chr1746423266chr1648209328350HLA-C08:01YQDEGKSSLGM0.99640.9935920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B15:73YQDEGKSSLGM0.99630.8856920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:11YQDEGKSSLGM0.99570.9048920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B15:30YQDEGKSSLGM0.99570.8944920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:02YQDEGKSSLGM0.9930.9677920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B39:02SDYQDEGKSSL0.99260.8217718
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B40:21YQDEGKSSLGM0.98760.5196920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-A02:14YQDEGKSSLGM0.98450.5461920
SKAP1-ABCC11chr1746423266chr1648209328350HLA-B15:09YQDEGKSSLGM0.96410.7725920

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Potential FusionNeoAntigen Information of SKAP1-ABCC11 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.

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)

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Fusion breakpoint peptide structures of SKAP1-ABCC11

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
5607LSDYQDEGKSSLGMSKAP1ABCC11chr1746423266chr1648209328350

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SKAP1-ABCC11

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-B14:023BVN5607LSDYQDEGKSSLGM-7.2642-7.2642
HLA-A11:014UQ25607LSDYQDEGKSSLGM-10.292-10.292
HLA-A24:025HGA5607LSDYQDEGKSSLGM-6.21134-6.21134

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Vaccine Design for the FusionNeoAntigens of SKAP1-ABCC11

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
SKAP1-ABCC11chr1746423266chr16482093281018QDEGKSSLAGGATGAGGGGAAGTCCTCCTTGG
SKAP1-ABCC11chr1746423266chr16482093281120DEGKSSLGMATGAGGGGAAGTCCTCCTTGGGCATGG
SKAP1-ABCC11chr1746423266chr1648209328718SDYQDEGKSSLCAGATTATCAGGATGAGGGGAAGTCCTCCTTGG
SKAP1-ABCC11chr1746423266chr1648209328818DYQDEGKSSLATTATCAGGATGAGGGGAAGTCCTCCTTGG
SKAP1-ABCC11chr1746423266chr1648209328918YQDEGKSSLATCAGGATGAGGGGAAGTCCTCCTTGG
SKAP1-ABCC11chr1746423266chr1648209328919YQDEGKSSLGATCAGGATGAGGGGAAGTCCTCCTTGGGCA
SKAP1-ABCC11chr1746423266chr1648209328920YQDEGKSSLGMATCAGGATGAGGGGAAGTCCTCCTTGGGCATGG

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

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Information of the samples that have these potential fusion neoantigens of SKAP1-ABCC11

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
BRCASKAP1-ABCC11chr1746423266ENST00000336915chr1648209328ENST00000353782TCGA-BH-A0C3

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Potential target of CAR-T therapy development for SKAP1-ABCC11

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

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 SKAP1-ABCC11

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 SKAP1-ABCC11

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