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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:APP-PRKAA1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: APP-PRKAA1
FusionPDB ID: 5701
FusionGDB2.0 ID: 5701
HgeneTgene
Gene symbol

APP

PRKAA1

Gene ID

351

5562

Gene nameamyloid beta precursor proteinprotein kinase AMP-activated catalytic subunit alpha 1
SynonymsAAA|ABETA|ABPP|AD1|APPI|CTFgamma|CVAP|PN-II|PN2|preA4AMPK|AMPKa1
Cytomap

21q21.3

5p13.1

Type of geneprotein-codingprotein-coding
Descriptionamyloid-beta precursor proteinalzheimer disease amyloid proteinamyloid beta (A4) precursor proteinamyloid beta A4 proteinamyloid precursor proteinbeta-amyloid peptidebeta-amyloid peptide(1-40)beta-amyloid peptide(1-42)beta-amyloid precursor protei5'-AMP-activated protein kinase catalytic subunit alpha-15'-AMP-activated protein kinase, catalytic alpha-1 chainACACA kinaseAMP -activate kinase alpha 1 subunitAMP-activated protein kinase, catalytic, alpha-1AMPK alpha 1AMPK subunit alpha-1HMGCR k
Modification date2020032920200327
UniProtAcc

Q8NEU8

Main function of 5'-partner protein: FUNCTION: Multifunctional adapter protein that binds to various membrane receptors, nuclear factors and signaling proteins to regulate many processes, such as cell proliferation, immune response, endosomal trafficking and cell metabolism (PubMed:26583432, PubMed:15016378, PubMed:24879834). Regulates signaling pathway leading to cell proliferation through interaction with RAB5A and subunits of the NuRD/MeCP1 complex (PubMed:15016378). Plays a role in immune response by modulating phagocytosis, inflammatory and innate immune responses. In macrophages, enhances Fc-gamma receptor-mediated phagocytosis through interaction with RAB31 leading to activation of PI3K/Akt signaling. In response to LPS, modulates inflammatory responses by playing a key role on the regulation of TLR4 signaling and in the nuclear translocation of RELA/NF-kappa-B p65 and the secretion of pro- and anti-inflammatory cytokines. Also functions as a negative regulator of innate immune response via inhibition of AKT1 signaling pathway by forming a complex with APPL1 and PIK3R1 (By similarity). Plays a role in endosomal trafficking of TGFBR1 from the endosomes to the nucleus (PubMed:26583432). Plays a role in cell metabolism by regulating adiponecting ans insulin signaling pathways and adaptative thermogenesis (PubMed:24879834) (By similarity). In muscle, negatively regulates adiponectin-simulated glucose uptake and fatty acid oxidation by inhibiting adiponectin signaling pathway through APPL1 sequestration thereby antagonizing APPL1 action (By similarity). In muscles, negativeliy regulates insulin-induced plasma membrane recruitment of GLUT4 and glucose uptake through interaction with TBC1D1 (PubMed:24879834). Plays a role in cold and diet-induced adaptive thermogenesis by activating ventromedial hypothalamus (VMH) neurons throught AMPK inhibition which enhances sympathetic outflow to subcutaneous white adipose tissue (sWAT), sWAT beiging and cold tolerance (By similarity). Also plays a role in other signaling pathways namely Wnt/beta-catenin, HGF and glucocorticoid receptor signaling (PubMed:19433865) (By similarity). Positive regulator of beta-catenin/TCF-dependent transcription through direct interaction with RUVBL2/reptin resulting in the relief of RUVBL2-mediated repression of beta-catenin/TCF target genes by modulating the interactions within the beta-catenin-reptin-HDAC complex (PubMed:19433865). May affect adult neurogenesis in hippocampus and olfactory system via regulating the sensitivity of glucocorticoid receptor. Required for fibroblast migration through HGF cell signaling (By similarity). {ECO:0000250|UniProtKB:Q8K3G9, ECO:0000269|PubMed:15016378, ECO:0000269|PubMed:19433865, ECO:0000269|PubMed:24879834, ECO:0000269|PubMed:26583432}.
.
Ensembl transtripts involved in fusion geneENST idsENST00000474136, ENST00000346798, 
ENST00000348990, ENST00000354192, 
ENST00000357903, ENST00000358918, 
ENST00000359726, ENST00000439274, 
ENST00000440126, ENST00000448388, 
ENST00000296800, ENST00000354209, 
ENST00000397128, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score31 X 25 X 12=93009 X 8 X 4=288
# samples 3310
** MAII scorelog2(33/9300*10)=-4.81669278663694
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/288*10)=-1.52606881166759
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: APP [Title/Abstract] AND PRKAA1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: APP [Title/Abstract] AND PRKAA1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)APP(27423315)-PRKAA1(40775605), # samples:1
Anticipated loss of major functional domain due to fusion event.APP-PRKAA1 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.
APP-PRKAA1 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.
APP-PRKAA1 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.
APP-PRKAA1 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
HgeneAPP

GO:0001934

positive regulation of protein phosphorylation

11404397

HgeneAPP

GO:0008285

negative regulation of cell proliferation

22944668

HgeneAPP

GO:1905606

regulation of presynapse assembly

19726636

TgenePRKAA1

GO:0006468

protein phosphorylation

17028174

TgenePRKAA1

GO:0010508

positive regulation of autophagy

22012985

TgenePRKAA1

GO:0010628

positive regulation of gene expression

17028174



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/chr21:27423315/chr5:40775605)
- 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 APP (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 PRKAA1 (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)
ENST00000346798APPchr2127423315-ENST00000397128PRKAA1chr540775605-5506696342106690
ENST00000346798APPchr2127423315-ENST00000354209PRKAA1chr540775605-2160696342151705
ENST00000346798APPchr2127423315-ENST00000296800PRKAA1chr540775605-1576696341077347
ENST00000354192APPchr2127423315-ENST00000397128PRKAA1chr540775605-54316211272031634
ENST00000354192APPchr2127423315-ENST00000354209PRKAA1chr540775605-20856211272076649
ENST00000354192APPchr2127423315-ENST00000296800PRKAA1chr540775605-15016211271002291
ENST00000348990APPchr2127423315-ENST00000397128PRKAA1chr540775605-56198091472219690
ENST00000348990APPchr2127423315-ENST00000354209PRKAA1chr540775605-22738091472264705
ENST00000348990APPchr2127423315-ENST00000296800PRKAA1chr540775605-16898091471190347
ENST00000357903APPchr2127423315-ENST00000397128PRKAA1chr540775605-56398291672239690
ENST00000357903APPchr2127423315-ENST00000354209PRKAA1chr540775605-22938291672284705
ENST00000357903APPchr2127423315-ENST00000296800PRKAA1chr540775605-17098291671210347
ENST00000358918APPchr2127423315-ENST00000397128PRKAA1chr540775605-56728622002272690
ENST00000358918APPchr2127423315-ENST00000354209PRKAA1chr540775605-23268622002317705
ENST00000358918APPchr2127423315-ENST00000296800PRKAA1chr540775605-17428622001243347
ENST00000359726APPchr2127423315-ENST00000397128PRKAA1chr540775605-56728622002272690
ENST00000359726APPchr2127423315-ENST00000354209PRKAA1chr540775605-23268622002317705
ENST00000359726APPchr2127423315-ENST00000296800PRKAA1chr540775605-17428622001243347
ENST00000448388APPchr2127423315-ENST00000397128PRKAA1chr540775605-55597491682159663
ENST00000448388APPchr2127423315-ENST00000354209PRKAA1chr540775605-22137491682204678
ENST00000448388APPchr2127423315-ENST00000296800PRKAA1chr540775605-16297491681130320
ENST00000440126APPchr2127423315-ENST00000397128PRKAA1chr540775605-57239132392323694
ENST00000440126APPchr2127423315-ENST00000354209PRKAA1chr540775605-23779132392368709
ENST00000440126APPchr2127423315-ENST00000296800PRKAA1chr540775605-17939132391294351
ENST00000439274APPchr2127423315-ENST00000397128PRKAA1chr540775605-5338528341938634
ENST00000439274APPchr2127423315-ENST00000354209PRKAA1chr540775605-1992528341983649
ENST00000439274APPchr2127423315-ENST00000296800PRKAA1chr540775605-140852834909291

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
ENST00000346798ENST00000397128APPchr2127423315-PRKAA1chr540775605-0.0001890690.999811
ENST00000346798ENST00000354209APPchr2127423315-PRKAA1chr540775605-0.0022005270.99779946
ENST00000346798ENST00000296800APPchr2127423315-PRKAA1chr540775605-0.0003023910.9996977
ENST00000354192ENST00000397128APPchr2127423315-PRKAA1chr540775605-0.0001787480.99982125
ENST00000354192ENST00000354209APPchr2127423315-PRKAA1chr540775605-0.0015893060.9984107
ENST00000354192ENST00000296800APPchr2127423315-PRKAA1chr540775605-0.0003892580.9996107
ENST00000348990ENST00000397128APPchr2127423315-PRKAA1chr540775605-0.0001986360.99980134
ENST00000348990ENST00000354209APPchr2127423315-PRKAA1chr540775605-0.002896420.9971035
ENST00000348990ENST00000296800APPchr2127423315-PRKAA1chr540775605-0.0004154560.9995845
ENST00000357903ENST00000397128APPchr2127423315-PRKAA1chr540775605-0.0001998770.99980015
ENST00000357903ENST00000354209APPchr2127423315-PRKAA1chr540775605-0.0031124320.9968876
ENST00000357903ENST00000296800APPchr2127423315-PRKAA1chr540775605-0.0004375780.99956244
ENST00000358918ENST00000397128APPchr2127423315-PRKAA1chr540775605-0.0002074470.9997925
ENST00000358918ENST00000354209APPchr2127423315-PRKAA1chr540775605-0.0034168880.99658316
ENST00000358918ENST00000296800APPchr2127423315-PRKAA1chr540775605-0.0005270110.99947304
ENST00000359726ENST00000397128APPchr2127423315-PRKAA1chr540775605-0.0002074470.9997925
ENST00000359726ENST00000354209APPchr2127423315-PRKAA1chr540775605-0.0034168880.99658316
ENST00000359726ENST00000296800APPchr2127423315-PRKAA1chr540775605-0.0005270110.99947304
ENST00000448388ENST00000397128APPchr2127423315-PRKAA1chr540775605-0.0002124530.9997875
ENST00000448388ENST00000354209APPchr2127423315-PRKAA1chr540775605-0.0025368250.9974631
ENST00000448388ENST00000296800APPchr2127423315-PRKAA1chr540775605-0.000253570.9997464
ENST00000440126ENST00000397128APPchr2127423315-PRKAA1chr540775605-0.0002208240.99977916
ENST00000440126ENST00000354209APPchr2127423315-PRKAA1chr540775605-0.0011477070.99885225
ENST00000440126ENST00000296800APPchr2127423315-PRKAA1chr540775605-0.0002342750.9997657
ENST00000439274ENST00000397128APPchr2127423315-PRKAA1chr540775605-0.0001738410.99982613
ENST00000439274ENST00000354209APPchr2127423315-PRKAA1chr540775605-0.0013153670.9986846
ENST00000439274ENST00000296800APPchr2127423315-PRKAA1chr540775605-0.0003212780.99967873

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 APP-PRKAA1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
APPchr2127423315PRKAA1chr540775605528164VWWGGADTDYADGRYQVISTPSDIFM
APPchr2127423315PRKAA1chr540775605621164VWWGGADTDYADGRYQVISTPSDIFM
APPchr2127423315PRKAA1chr540775605696220VWWGGADTDYADGRYQVISTPSDIFM
APPchr2127423315PRKAA1chr540775605749193VWWGGADTDYADGRYQVISTPSDIFM
APPchr2127423315PRKAA1chr540775605809220VWWGGADTDYADGRYQVISTPSDIFM
APPchr2127423315PRKAA1chr540775605829220VWWGGADTDYADGRYQVISTPSDIFM
APPchr2127423315PRKAA1chr540775605862220VWWGGADTDYADGRYQVISTPSDIFM
APPchr2127423315PRKAA1chr540775605913224VWWGGADTDYADGRYQVISTPSDIFM

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Potential FusionNeoAntigen Information of APP-PRKAA1 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.
APP-PRKAA1_27423315_40775605.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)
APP-PRKAA1chr2127423315chr540775605696HLA-B27:04GRYQVISTP0.99760.79041221
APP-PRKAA1chr2127423315chr540775605696HLA-B35:04YADGRYQVI0.91590.916918
APP-PRKAA1chr2127423315chr540775605696HLA-B35:02YADGRYQVI0.91590.916918
APP-PRKAA1chr2127423315chr540775605696HLA-B52:01YADGRYQVI0.86780.9696918
APP-PRKAA1chr2127423315chr540775605696HLA-C05:09YADGRYQV10.95917
APP-PRKAA1chr2127423315chr540775605696HLA-C04:10YADGRYQV10.9195917
APP-PRKAA1chr2127423315chr540775605696HLA-C04:07YADGRYQV10.9273917
APP-PRKAA1chr2127423315chr540775605696HLA-C08:15YADGRYQV0.99990.9761917
APP-PRKAA1chr2127423315chr540775605696HLA-C04:06YADGRYQV0.99980.9097917
APP-PRKAA1chr2127423315chr540775605696HLA-C04:14YADGRYQV0.99930.9217917
APP-PRKAA1chr2127423315chr540775605696HLA-C08:04YADGRYQV0.99690.9818917
APP-PRKAA1chr2127423315chr540775605696HLA-C08:13YADGRYQV0.99690.9818917
APP-PRKAA1chr2127423315chr540775605696HLA-C08:03YADGRYQV0.9940.9781917
APP-PRKAA1chr2127423315chr540775605696HLA-C04:10YADGRYQVI0.99990.9372918
APP-PRKAA1chr2127423315chr540775605696HLA-C08:15YADGRYQVI0.99990.9798918
APP-PRKAA1chr2127423315chr540775605696HLA-C05:09YADGRYQVI0.99990.9682918
APP-PRKAA1chr2127423315chr540775605696HLA-C04:07YADGRYQVI0.99990.9383918
APP-PRKAA1chr2127423315chr540775605696HLA-C01:17YADGRYQVI0.99980.9023918
APP-PRKAA1chr2127423315chr540775605696HLA-C03:07YADGRYQVI0.99930.9725918
APP-PRKAA1chr2127423315chr540775605696HLA-C15:04YADGRYQVI0.99870.906918
APP-PRKAA1chr2127423315chr540775605696HLA-C15:06YADGRYQVI0.99860.9114918
APP-PRKAA1chr2127423315chr540775605696HLA-C01:30YADGRYQVI0.9980.9153918
APP-PRKAA1chr2127423315chr540775605696HLA-C03:19YADGRYQVI0.99770.9744918
APP-PRKAA1chr2127423315chr540775605696HLA-B27:14GRYQVISTP0.99770.66021221
APP-PRKAA1chr2127423315chr540775605696HLA-C04:06YADGRYQVI0.99540.9477918
APP-PRKAA1chr2127423315chr540775605696HLA-C03:08YADGRYQVI0.99180.857918
APP-PRKAA1chr2127423315chr540775605696HLA-C08:13YADGRYQVI0.99090.9672918
APP-PRKAA1chr2127423315chr540775605696HLA-C08:04YADGRYQVI0.99090.9672918
APP-PRKAA1chr2127423315chr540775605696HLA-B73:01GRYQVISTP0.98130.76521221
APP-PRKAA1chr2127423315chr540775605696HLA-C04:14YADGRYQVI0.96710.9396918
APP-PRKAA1chr2127423315chr540775605696HLA-C12:04YADGRYQVI0.95240.9856918
APP-PRKAA1chr2127423315chr540775605696HLA-C06:03YADGRYQVI0.95230.9806918
APP-PRKAA1chr2127423315chr540775605696HLA-C08:03YADGRYQVI0.93850.977918
APP-PRKAA1chr2127423315chr540775605696HLA-C12:12YADGRYQVI0.93350.8458918
APP-PRKAA1chr2127423315chr540775605696HLA-B14:03YADGRYQVI0.93080.6776918
APP-PRKAA1chr2127423315chr540775605696HLA-B35:12YADGRYQVI0.91590.916918
APP-PRKAA1chr2127423315chr540775605696HLA-C03:14YADGRYQVI0.87810.9602918
APP-PRKAA1chr2127423315chr540775605696HLA-B51:07YADGRYQVI0.87630.8892918
APP-PRKAA1chr2127423315chr540775605696HLA-C02:06YADGRYQVI0.85970.9645918
APP-PRKAA1chr2127423315chr540775605696HLA-C07:13YADGRYQVI0.84670.8381918
APP-PRKAA1chr2127423315chr540775605696HLA-B39:10YADGRYQVI0.81940.735918
APP-PRKAA1chr2127423315chr540775605696HLA-C07:29YADGRYQVI0.80650.8465918
APP-PRKAA1chr2127423315chr540775605696HLA-B78:01YADGRYQVI0.76560.6107918
APP-PRKAA1chr2127423315chr540775605696HLA-B27:14GRYQVISTPS0.99910.62661222
APP-PRKAA1chr2127423315chr540775605696HLA-B73:01DGRYQVISTP0.92220.84161121
APP-PRKAA1chr2127423315chr540775605696HLA-C04:03YADGRYQV10.9429917
APP-PRKAA1chr2127423315chr540775605696HLA-C04:01YADGRYQV10.9273917
APP-PRKAA1chr2127423315chr540775605696HLA-C18:01YADGRYQV10.9367917
APP-PRKAA1chr2127423315chr540775605696HLA-C05:01YADGRYQV10.95917
APP-PRKAA1chr2127423315chr540775605696HLA-C08:02YADGRYQV0.99990.9761917
APP-PRKAA1chr2127423315chr540775605696HLA-C03:06YADGRYQV0.99910.9818917
APP-PRKAA1chr2127423315chr540775605696HLA-C08:01YADGRYQV0.9940.9781917
APP-PRKAA1chr2127423315chr540775605696HLA-B07:13YADGRYQV0.96770.7454917
APP-PRKAA1chr2127423315chr540775605696HLA-C08:02YADGRYQVI0.99990.9798918
APP-PRKAA1chr2127423315chr540775605696HLA-C18:01YADGRYQVI0.99990.9351918
APP-PRKAA1chr2127423315chr540775605696HLA-C05:01YADGRYQVI0.99990.9682918
APP-PRKAA1chr2127423315chr540775605696HLA-C04:01YADGRYQVI0.99990.9383918
APP-PRKAA1chr2127423315chr540775605696HLA-C01:03YADGRYQVI0.99990.9049918
APP-PRKAA1chr2127423315chr540775605696HLA-C04:03YADGRYQVI0.99990.9439918
APP-PRKAA1chr2127423315chr540775605696HLA-C01:02YADGRYQVI0.99980.9036918
APP-PRKAA1chr2127423315chr540775605696HLA-C03:03YADGRYQVI0.99870.9719918
APP-PRKAA1chr2127423315chr540775605696HLA-C15:09YADGRYQVI0.99870.906918
APP-PRKAA1chr2127423315chr540775605696HLA-C03:04YADGRYQVI0.99870.9719918
APP-PRKAA1chr2127423315chr540775605696HLA-C03:05YADGRYQVI0.99830.8714918
APP-PRKAA1chr2127423315chr540775605696HLA-C15:05YADGRYQVI0.99830.916918
APP-PRKAA1chr2127423315chr540775605696HLA-C03:17YADGRYQVI0.99810.9397918
APP-PRKAA1chr2127423315chr540775605696HLA-C15:02YADGRYQVI0.99780.8913918
APP-PRKAA1chr2127423315chr540775605696HLA-B27:10GRYQVISTP0.99770.86531221
APP-PRKAA1chr2127423315chr540775605696HLA-B27:08GRYQVISTP0.99750.57671221
APP-PRKAA1chr2127423315chr540775605696HLA-B27:09GRYQVISTP0.99730.66661221
APP-PRKAA1chr2127423315chr540775605696HLA-C03:02YADGRYQVI0.99610.9467918
APP-PRKAA1chr2127423315chr540775605696HLA-C03:67YADGRYQVI0.99550.9595918
APP-PRKAA1chr2127423315chr540775605696HLA-C06:06YADGRYQVI0.99520.9843918
APP-PRKAA1chr2127423315chr540775605696HLA-C04:04YADGRYQVI0.99340.9388918
APP-PRKAA1chr2127423315chr540775605696HLA-C03:06YADGRYQVI0.98770.9738918
APP-PRKAA1chr2127423315chr540775605696HLA-C16:02YADGRYQVI0.98090.9845918
APP-PRKAA1chr2127423315chr540775605696HLA-C16:04YADGRYQVI0.97240.9333918
APP-PRKAA1chr2127423315chr540775605696HLA-C16:01YADGRYQVI0.96990.9572918
APP-PRKAA1chr2127423315chr540775605696HLA-C07:04YADGRYQVI0.94860.9287918
APP-PRKAA1chr2127423315chr540775605696HLA-C08:01YADGRYQVI0.93850.977918
APP-PRKAA1chr2127423315chr540775605696HLA-C12:03YADGRYQVI0.9250.9528918
APP-PRKAA1chr2127423315chr540775605696HLA-B35:09YADGRYQVI0.91590.916918
APP-PRKAA1chr2127423315chr540775605696HLA-B78:02YADGRYQVI0.870.7409918
APP-PRKAA1chr2127423315chr540775605696HLA-B35:13YADGRYQVI0.8250.83918
APP-PRKAA1chr2127423315chr540775605696HLA-C17:01YADGRYQVI0.80490.9291918
APP-PRKAA1chr2127423315chr540775605696HLA-C02:02YADGRYQVI0.8030.9769918
APP-PRKAA1chr2127423315chr540775605696HLA-C02:10YADGRYQVI0.8030.9769918
APP-PRKAA1chr2127423315chr540775605696HLA-C12:02YADGRYQVI0.67360.9346918
APP-PRKAA1chr2127423315chr540775605696HLA-B07:13YADGRYQVI0.67120.8171918

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Potential FusionNeoAntigen Information of APP-PRKAA1 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.
APP-PRKAA1_27423315_40775605.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)
APP-PRKAA1chr2127423315chr540775605696DRB1-0401ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0401DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0401YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0403ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0403DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0403YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0405ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0405YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0405DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0405DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0407DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0407ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0407YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0407DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0409ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0409DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0409YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0409DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0411ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0411DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0411YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0411DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0417ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0417DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0417YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0417DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0419ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0419DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0419YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0424ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0424DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0424YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0424DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0427DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0427ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0427YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0429ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0429YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0429DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0429DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0430ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0430YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0430DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0430DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0431DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0431ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0431YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0433ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0433DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0433YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0434ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0434DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0434YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0435ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0435DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0435YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0438ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0438DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0438YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0439ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0439DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0439YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0441ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0441DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0441YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0443ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0443DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0443YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0445ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0445YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0445DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0445DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0446ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0446DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0446YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0447ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0447DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0447YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0448ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0448YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0448DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0448DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0449ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0449DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0449YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0450ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0450DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0450YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0451ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0451DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0451YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0452ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0452DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0452YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0454DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0454ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0454YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0457ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0457YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0457DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0457DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0459ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0459DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0459YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0460ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0460DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0460YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0461ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0461DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0461YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0462ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0462DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0462YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0462DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0463ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0463DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0463YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0464ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0464DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0464YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0465ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0465DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0465YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0467ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0467DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0467YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0469ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0469DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0469YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0469DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0471ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0471DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0471YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0472ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0472DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0474DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0474ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0474YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0475ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0475DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0475YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0476ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0476DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0476YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0477ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0477YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0477DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0477DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0478DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0478ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0478YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0480ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0480DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0480YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0480DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0482ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0482DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0482YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0482DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0483ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0483YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0483DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0483DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0484ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0484YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0484DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0484DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0485ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0485DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0485YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0486ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0486DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0486YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0486DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0487ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0487YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0487DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0487DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0488ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0488DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0488YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0489ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0489YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0489DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0489DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0491ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0491DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0491YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0491DYADGRYQVISTPSD823
APP-PRKAA1chr2127423315chr540775605696DRB1-0801ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0801DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0801YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0803ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0803DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0803YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0805ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0805DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0805YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0807ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0807DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0807YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0808ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0808DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0808YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0811ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0811DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0811YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0814ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0814DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0814YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0816ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0816DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0816YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0818ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0818DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0818YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0823ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0823DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0823YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0825ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0825DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0825YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0826ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0826DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0826YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0827ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0827DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0827YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0829ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0829DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0829YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0832DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0832ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0832YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0833ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0833DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0833YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0834DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0834ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0835ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0835DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0835YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0836ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0836DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0836YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0837ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0837DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0837YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0838ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0838DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0838YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0839ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0839DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0839YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0840ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-0840DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-0840YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-0908ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-1303ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-1303DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-1303YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-13101ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-13101DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-1310ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-1310DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-1312ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-1312DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-1312YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-1313ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-1313DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-1313YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-1330ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-1330DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-1330YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-1349ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-1349DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-1349YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-1355ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-1355DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-1366ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-1366DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-1388ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-1388DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-1390ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-1390DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-1390YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-1395ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-1395DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-1395YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-1410DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-1410ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-1410YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-1413ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-1413DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-1413YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-1422ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-1422DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-1425ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-1425DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-1446DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-1446ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-1469ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-1469DGRYQVISTPSDIFM1126
APP-PRKAA1chr2127423315chr540775605696DRB1-1469YADGRYQVISTPSDI924
APP-PRKAA1chr2127423315chr540775605696DRB1-1485ADGRYQVISTPSDIF1025
APP-PRKAA1chr2127423315chr540775605696DRB1-1485DGRYQVISTPSDIFM1126

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Fusion breakpoint peptide structures of APP-PRKAA1

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
1432DTDYADGRYQVISTAPPPRKAA1chr2127423315chr540775605696

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of APP-PRKAA1

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-B14:023BVN1432DTDYADGRYQVIST-7.9962-8.1096
HLA-B14:023BVN1432DTDYADGRYQVIST-5.70842-6.74372
HLA-B52:013W391432DTDYADGRYQVIST-6.83737-6.95077
HLA-B52:013W391432DTDYADGRYQVIST-4.4836-5.5189
HLA-A11:014UQ21432DTDYADGRYQVIST-10.0067-10.1201
HLA-A11:014UQ21432DTDYADGRYQVIST-9.03915-10.0745
HLA-A24:025HGA1432DTDYADGRYQVIST-6.56204-6.67544
HLA-A24:025HGA1432DTDYADGRYQVIST-5.42271-6.45801
HLA-B44:053DX81432DTDYADGRYQVIST-7.85648-8.89178
HLA-B44:053DX81432DTDYADGRYQVIST-5.3978-5.5112
HLA-A02:016TDR1432DTDYADGRYQVIST-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of APP-PRKAA1

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
APP-PRKAA1chr2127423315chr5407756051121DGRYQVISTPTGGGAGGTACCAGGTCATCAGTACACCATC
APP-PRKAA1chr2127423315chr5407756051221GRYQVISTPGAGGTACCAGGTCATCAGTACACCATC
APP-PRKAA1chr2127423315chr5407756051222GRYQVISTPSGAGGTACCAGGTCATCAGTACACCATCTGA
APP-PRKAA1chr2127423315chr540775605917YADGRYQVTGCAGATGGGAGGTACCAGGTCAT
APP-PRKAA1chr2127423315chr540775605918YADGRYQVITGCAGATGGGAGGTACCAGGTCATCAG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
APP-PRKAA1chr2127423315chr5407756051025ADGRYQVISTPSDIFAGATGGGAGGTACCAGGTCATCAGTACACCATCTGATATTTTCAT
APP-PRKAA1chr2127423315chr5407756051126DGRYQVISTPSDIFMTGGGAGGTACCAGGTCATCAGTACACCATCTGATATTTTCATGGT
APP-PRKAA1chr2127423315chr540775605823DYADGRYQVISTPSDCTATGCAGATGGGAGGTACCAGGTCATCAGTACACCATCTGATAT
APP-PRKAA1chr2127423315chr540775605924YADGRYQVISTPSDITGCAGATGGGAGGTACCAGGTCATCAGTACACCATCTGATATTTT

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Information of the samples that have these potential fusion neoantigens of APP-PRKAA1

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
STADAPP-PRKAA1chr2127423315ENST00000346798chr540775605ENST00000296800TCGA-CG-5718

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Potential target of CAR-T therapy development for APP-PRKAA1

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 APP-PRKAA1

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 APP-PRKAA1

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