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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:ATP11A-EXOC6B

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ATP11A-EXOC6B
FusionPDB ID: 7713
FusionGDB2.0 ID: 7713
HgeneTgene
Gene symbol

ATP11A

EXOC6B

Gene ID

23250

23233

Gene nameATPase phospholipid transporting 11Aexocyst complex component 6B
SynonymsATPIH|ATPISSEC15B|SEC15L2|SEMDJL3
Cytomap

13q34

2p13.2

Type of geneprotein-codingprotein-coding
Descriptionprobable phospholipid-transporting ATPase IHATPase, class VI, type 11AP4-ATPase flippase complex alpha subunit ATP11Aphospholipid-translocating ATPasepotential phospholipid-transporting ATPase IHexocyst complex component 6BSEC15 homolog BSEC15-like protein 2exocyst complex component Sec15B
Modification date2020031320200313
UniProtAcc

Q6ZP68

Main function of 5'-partner protein:

Q9Y2D4

Main function of 5'-partner protein: FUNCTION: Component of the exocyst complex involved in the docking of exocytic vesicles with fusion sites on the plasma membrane.
Ensembl transtripts involved in fusion geneENST idsENST00000283558, ENST00000375630, 
ENST00000375645, ENST00000487903, 
ENST00000419448, 
ENST00000410104, 
ENST00000490919, ENST00000272427, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score20 X 11 X 16=352010 X 8 X 6=480
# samples 3111
** MAII scorelog2(31/3520*10)=-3.50523530825042
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(11/480*10)=-2.12553088208386
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: ATP11A [Title/Abstract] AND EXOC6B [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ATP11A [Title/Abstract] AND EXOC6B [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ATP11A(113439571)-EXOC6B(72606999), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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


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/chr13:113439571/chr2:72606999)
- 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 ATP11A (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 EXOC6B (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)
ENST00000283558ATP11Achr13113439571+ENST00000272427EXOC6Bchr272606999-405725055705216
ENST00000375630ATP11Achr13113439571+ENST00000272427EXOC6Bchr272606999-405725055705216
ENST00000487903ATP11Achr13113439571+ENST00000272427EXOC6Bchr272606999-405725055705216
ENST00000375645ATP11Achr13113439571+ENST00000272427EXOC6Bchr272606999-405725055705216

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
ENST00000283558ENST00000272427ATP11Achr13113439571+EXOC6Bchr272606999-0.0049120440.9950879
ENST00000375630ENST00000272427ATP11Achr13113439571+EXOC6Bchr272606999-0.0049120440.9950879
ENST00000487903ENST00000272427ATP11Achr13113439571+EXOC6Bchr272606999-0.0049120440.9950879
ENST00000375645ENST00000272427ATP11Achr13113439571+EXOC6Bchr272606999-0.0049120440.9950879

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 ATP11A-EXOC6B

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ATP11Achr13113439571EXOC6Bchr27260699925065PQRYPDNRIVSSKGKVAQTACMSACK

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Potential FusionNeoAntigen Information of ATP11A-EXOC6B 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.
ATP11A-EXOC6B_113439571_72606999.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)
ATP11A-EXOC6Bchr13113439571chr272606999250HLA-B73:01NRIVSSKGKVA0.99550.8174617

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Potential FusionNeoAntigen Information of ATP11A-EXOC6B 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.
ATP11A-EXOC6B_113439571_72606999.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)
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0102DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0102PDNRIVSSKGKVAQT419
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0103DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0103PDNRIVSSKGKVAQT419
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0109DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0115DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0123DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0123PDNRIVSSKGKVAQT419
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0123NRIVSSKGKVAQTAC621
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0901DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0902DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0902PDNRIVSSKGKVAQT419
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0903DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0903PDNRIVSSKGKVAQT419
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0905DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0905PDNRIVSSKGKVAQT419
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0906DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0906PDNRIVSSKGKVAQT419
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0906YPDNRIVSSKGKVAQ318
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0907DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-0909DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1103DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1121DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1136DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1141DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1148DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1155DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1159DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1163DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1170DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1176DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1185DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1186DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1308DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1316DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1320DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1324DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1331DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1354DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1367DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1367PDNRIVSSKGKVAQT419
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1370DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1372DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1376DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1378DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1384DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1398DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1615DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB1-1615PDNRIVSSKGKVAQT419
ATP11A-EXOC6Bchr13113439571chr272606999250DRB5-0112DNRIVSSKGKVAQTA520
ATP11A-EXOC6Bchr13113439571chr272606999250DRB5-0112PDNRIVSSKGKVAQT419
ATP11A-EXOC6Bchr13113439571chr272606999250DRB5-0204DNRIVSSKGKVAQTA520

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Fusion breakpoint peptide structures of ATP11A-EXOC6B

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
6353NRIVSSKGKVAQTAATP11AEXOC6Bchr13113439571chr272606999250

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ATP11A-EXOC6B

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-B14:023BVN6353NRIVSSKGKVAQTA-7.9962-8.1096
HLA-B14:023BVN6353NRIVSSKGKVAQTA-5.70842-6.74372
HLA-B52:013W396353NRIVSSKGKVAQTA-6.83737-6.95077
HLA-B52:013W396353NRIVSSKGKVAQTA-4.4836-5.5189
HLA-A11:014UQ26353NRIVSSKGKVAQTA-10.0067-10.1201
HLA-A11:014UQ26353NRIVSSKGKVAQTA-9.03915-10.0745
HLA-A24:025HGA6353NRIVSSKGKVAQTA-6.56204-6.67544
HLA-A24:025HGA6353NRIVSSKGKVAQTA-5.42271-6.45801
HLA-B44:053DX86353NRIVSSKGKVAQTA-7.85648-8.89178
HLA-B44:053DX86353NRIVSSKGKVAQTA-5.3978-5.5112
HLA-A02:016TDR6353NRIVSSKGKVAQTA-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of ATP11A-EXOC6B

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
ATP11A-EXOC6Bchr13113439571chr272606999617NRIVSSKGKVAAACAGGATCGTCTCGTCCAAGGGAAAGGTGGCC

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
ATP11A-EXOC6Bchr13113439571chr272606999318YPDNRIVSSKGKVAQTACCCAGACAACAGGATCGTCTCGTCCAAGGGAAAGGTGGCCCAG
ATP11A-EXOC6Bchr13113439571chr272606999419PDNRIVSSKGKVAQTCCAGACAACAGGATCGTCTCGTCCAAGGGAAAGGTGGCCCAGACA
ATP11A-EXOC6Bchr13113439571chr272606999520DNRIVSSKGKVAQTAGACAACAGGATCGTCTCGTCCAAGGGAAAGGTGGCCCAGACAGCG
ATP11A-EXOC6Bchr13113439571chr272606999621NRIVSSKGKVAQTACAACAGGATCGTCTCGTCCAAGGGAAAGGTGGCCCAGACAGCGTGT

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Information of the samples that have these potential fusion neoantigens of ATP11A-EXOC6B

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
Non-CancerATP11A-EXOC6Bchr13113439571ENST00000283558chr272606999ENST00000272427TCGA-HU-A4GP-11A

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Potential target of CAR-T therapy development for ATP11A-EXOC6B

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 ATP11A-EXOC6B

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 ATP11A-EXOC6B

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