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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:AFF1-PTPN13

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: AFF1-PTPN13
FusionPDB ID: 2666
FusionGDB2.0 ID: 2666
HgeneTgene
Gene symbol

AFF1

PTPN13

Gene ID

4299

5783

Gene nameAF4/FMR2 family member 1protein tyrosine phosphatase non-receptor type 13
SynonymsAF4|MLLT2|PBM1FAP-1|PNP1|PTP-BAS|PTP-BL|PTP1E|PTPL1|PTPLE|hPTP1E
Cytomap

4q21.3-q22.1

4q21.3

Type of geneprotein-codingprotein-coding
DescriptionAF4/FMR2 family member 1ALL1-fused gene from chromosome 4 proteinmyeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 2pre-B-cell monocytic leukemia partner 1proto-oncogene AF4tyrosine-protein phosphatase non-receptor type 13fas-associated protein-tyrosine phosphatase 1hPTPE1protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)protein-tyrosine phosphatase 1Eprotein-tyrosine phosphatas
Modification date2020031320200313
UniProtAcc

P51825

Main function of 5'-partner protein:

PRY,PRY2

Main function of 5'-partner protein: 147
Ensembl transtripts involved in fusion geneENST idsENST00000511996, ENST00000395146, 
ENST00000307808, ENST00000544085, 
ENST00000427191, ENST00000436978, 
ENST00000316707, ENST00000411767, 
ENST00000502971, ENST00000511467, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score27 X 51 X 13=179018 X 13 X 6=624
# samples 6815
** MAII scorelog2(68/17901*10)=-4.71836162613835
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/624*10)=-2.05658352836637
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: AFF1 [Title/Abstract] AND PTPN13 [Title/Abstract] AND fusion [Title/Abstract]

The landscape and therapeutic relevance of cancer-associated transcript fusions (pmid: 25500544)
Fusion neoantigen context

PubMed: AFF1 [Title/Abstract] AND PTPN13 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)AFF1(87869723)-PTPN13(87556405), # samples:3
PTPN13(87610343)-AFF1(88005272), # samples:2
PTPN13(87556524)-AFF1(87869649), # samples:2
Anticipated loss of major functional domain due to fusion event.AFF1-PTPN13 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.
AFF1-PTPN13 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.
AFF1-PTPN13 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.
AFF1-PTPN13 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.
PTPN13-AFF1 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.
PTPN13-AFF1 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.
AFF1-PTPN13 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
AFF1-PTPN13 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
AFF1-PTPN13 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
AFF1-PTPN13 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
TgenePTPN13

GO:0006470

protein dephosphorylation

17657516|19307596

TgenePTPN13

GO:0014066

regulation of phosphatidylinositol 3-kinase signaling

23604317



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/chr4:87869723/chr4:87556405)
- 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 AFF1 (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 PTPN13 (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)
ENST00000395146AFF1chr488046295+ENST00000427191PTPN13chr487720254+4511284826639041212
ENST00000395146AFF1chr488046295+ENST00000436978PTPN13chr487720254+4525284826639041212
ENST00000307808AFF1chr488046295+ENST00000427191PTPN13chr487720254+4635297242040281202
ENST00000307808AFF1chr488046295+ENST00000436978PTPN13chr487720254+4649297242040281202
ENST00000544085AFF1chr488046295+ENST00000427191PTPN13chr487720254+333316701322726864
ENST00000544085AFF1chr488046295+ENST00000436978PTPN13chr487720254+334716701322726864
ENST00000395146AFF1chr488048855+ENST00000427191PTPN13chr487718027+4958323926643511361
ENST00000395146AFF1chr488048855+ENST00000436978PTPN13chr487718027+4972323926643511361
ENST00000307808AFF1chr488048855+ENST00000427191PTPN13chr487718027+5082336342044751351
ENST00000307808AFF1chr488048855+ENST00000436978PTPN13chr487718027+5096336342044751351
ENST00000544085AFF1chr488048855+ENST00000427191PTPN13chr487718027+3780206113231731013
ENST00000544085AFF1chr488048855+ENST00000436978PTPN13chr487718027+3794206113231731013
ENST00000395146AFF1chr488048855-ENST00000427191PTPN13chr487666119+8759323926681522628
ENST00000395146AFF1chr488048855-ENST00000436978PTPN13chr487666119+8845323926682242652
ENST00000307808AFF1chr488048855-ENST00000427191PTPN13chr487666119+8883336342082762618
ENST00000307808AFF1chr488048855-ENST00000436978PTPN13chr487666119+8969336342083482642
ENST00000544085AFF1chr488048855-ENST00000427191PTPN13chr487666119+7581206113269742280
ENST00000544085AFF1chr488048855-ENST00000436978PTPN13chr487666119+7667206113270462304

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
ENST00000395146ENST00000427191AFF1chr488046295+PTPN13chr487720254+0.0033439490.99665606
ENST00000395146ENST00000436978AFF1chr488046295+PTPN13chr487720254+0.0033015470.99669844
ENST00000307808ENST00000427191AFF1chr488046295+PTPN13chr487720254+0.0034815640.9965184
ENST00000307808ENST00000436978AFF1chr488046295+PTPN13chr487720254+0.0034532410.9965468
ENST00000544085ENST00000427191AFF1chr488046295+PTPN13chr487720254+0.0031104690.99688953
ENST00000544085ENST00000436978AFF1chr488046295+PTPN13chr487720254+0.0030516660.9969483
ENST00000395146ENST00000427191AFF1chr488048855+PTPN13chr487718027+0.0037046810.9962953
ENST00000395146ENST00000436978AFF1chr488048855+PTPN13chr487718027+0.0036598690.99634016
ENST00000307808ENST00000427191AFF1chr488048855+PTPN13chr487718027+0.003952290.9960477
ENST00000307808ENST00000436978AFF1chr488048855+PTPN13chr487718027+0.0039048360.9960951
ENST00000544085ENST00000427191AFF1chr488048855+PTPN13chr487718027+0.001544450.9984555
ENST00000544085ENST00000436978AFF1chr488048855+PTPN13chr487718027+0.0015130060.998487
ENST00000395146ENST00000427191AFF1chr488048855-PTPN13chr487666119+0.0008027730.9991972
ENST00000395146ENST00000436978AFF1chr488048855-PTPN13chr487666119+0.0007621540.9992379
ENST00000307808ENST00000427191AFF1chr488048855-PTPN13chr487666119+0.0008749890.99912506
ENST00000307808ENST00000436978AFF1chr488048855-PTPN13chr487666119+0.0008365030.9991635
ENST00000544085ENST00000427191AFF1chr488048855-PTPN13chr487666119+0.0005799430.99942005
ENST00000544085ENST00000436978AFF1chr488048855-PTPN13chr487666119+0.0005508420.9994492

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 AFF1-PTPN13

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
AFF1chr488046295PTPN13chr4877202541670513SSSSSHKESSKTNLIQKPQEKKTDDD
AFF1chr488046295PTPN13chr4877202542848861SSSSSHKESSKTNLIQKPQEKKTDDD
AFF1chr488046295PTPN13chr4877202542972851SSSSSHKESSKTNLIQKPQEKKTDDD
AFF1chr488048855PTPN13chr4876661192061641HMREAKKMKQKAELMKKKITLQNTSD
AFF1chr488048855PTPN13chr4876661193239989HMREAKKMKQKAELMKKKITLQNTSD
AFF1chr488048855PTPN13chr4876661193363979HMREAKKMKQKAELMKKKITLQNTSD
AFF1chr488048855PTPN13chr4877180272061641HMREAKKMKQKAELMATKMNGCEEYC
AFF1chr488048855PTPN13chr4877180273239989HMREAKKMKQKAELMATKMNGCEEYC
AFF1chr488048855PTPN13chr4877180273363979HMREAKKMKQKAELMATKMNGCEEYC

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Potential FusionNeoAntigen Information of AFF1-PTPN13 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.
AFF1-PTPN13_88046295_87720254.msa
AFF1-PTPN13_88048855_87666119.msa
AFF1-PTPN13_88048855_87718027.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)
AFF1-PTPN13chr488046295chr4877202542972HLA-B39:13KESSKTNL0.970.8105614
AFF1-PTPN13chr488046295chr4877202542972HLA-A30:08SSKTNLIQK0.99830.6077817
AFF1-PTPN13chr488046295chr4877202542972HLA-B13:01KESSKTNLI0.98880.8048615
AFF1-PTPN13chr488046295chr4877202542972HLA-B44:03KESSKTNLI0.96240.9209615
AFF1-PTPN13chr488046295chr4877202542972HLA-B39:01HKESSKTNL0.95930.9189514
AFF1-PTPN13chr488046295chr4877202542972HLA-B45:01KESSKTNLI0.93210.6615
AFF1-PTPN13chr488046295chr4877202542972HLA-B39:13HKESSKTNL0.9290.8874514
AFF1-PTPN13chr488046295chr4877202542972HLA-B47:01KESSKTNLI0.78640.529615
AFF1-PTPN13chr488046295chr4877202542972HLA-B15:10HKESSKTNL0.59180.5993514
AFF1-PTPN13chr488046295chr4877202542972HLA-B41:01KESSKTNLI0.41460.6991615
AFF1-PTPN13chr488046295chr4877202542972HLA-B39:13KESSKTNLI0.11640.7707615
AFF1-PTPN13chr488046295chr4877202542972HLA-B39:01SHKESSKTNL0.98270.9374414
AFF1-PTPN13chr488046295chr4877202542972HLA-B38:02SHKESSKTNL0.94520.975414
AFF1-PTPN13chr488046295chr4877202542972HLA-B38:01SHKESSKTNL0.94090.9673414
AFF1-PTPN13chr488046295chr4877202542972HLA-B15:10SHKESSKTNL0.93190.6602414
AFF1-PTPN13chr488046295chr4877202542972HLA-B14:01SHKESSKTNL0.71660.6938414
AFF1-PTPN13chr488046295chr4877202542972HLA-B14:02SHKESSKTNL0.71660.6938414
AFF1-PTPN13chr488046295chr4877202542972HLA-B15:37SHKESSKTNL0.71230.7626414
AFF1-PTPN13chr488046295chr4877202542972HLA-A30:08KTNLIQKPQEK0.99880.67881021
AFF1-PTPN13chr488046295chr4877202542972HLA-A30:08KESSKTNLIQK0.99620.7131617
AFF1-PTPN13chr488046295chr4877202542972HLA-B38:01SHKESSKTNLI0.97810.9003415
AFF1-PTPN13chr488046295chr4877202542972HLA-B39:08KESSKTNL0.97380.7527614
AFF1-PTPN13chr488046295chr4877202542972HLA-B40:06KESSKTNLI0.99910.5483615
AFF1-PTPN13chr488046295chr4877202542972HLA-B39:05HKESSKTNL0.93840.9098514
AFF1-PTPN13chr488046295chr4877202542972HLA-B14:03HKESSKTNL0.33460.8393514
AFF1-PTPN13chr488046295chr4877202542972HLA-B39:08KESSKTNLI0.33290.5984615
AFF1-PTPN13chr488046295chr4877202542972HLA-B39:09SHKESSKTNL0.9840.6131414
AFF1-PTPN13chr488046295chr4877202542972HLA-B39:12SHKESSKTNL0.97680.9394414
AFF1-PTPN13chr488046295chr4877202542972HLA-B39:05SHKESSKTNL0.94120.9281414
AFF1-PTPN13chr488046295chr4877202542972HLA-B14:03SHKESSKTNL0.8810.8638414
AFF1-PTPN13chr488046295chr4877202542972HLA-A30:01SSKTNLIQK0.99820.7436817
AFF1-PTPN13chr488046295chr4877202542972HLA-B40:04KESSKTNLI0.9950.665615
AFF1-PTPN13chr488046295chr4877202542972HLA-B44:07KESSKTNLI0.96240.9209615
AFF1-PTPN13chr488046295chr4877202542972HLA-B44:26KESSKTNLI0.96240.9209615
AFF1-PTPN13chr488046295chr4877202542972HLA-B44:13KESSKTNLI0.96240.9209615
AFF1-PTPN13chr488046295chr4877202542972HLA-B39:02HKESSKTNL0.96060.8942514
AFF1-PTPN13chr488046295chr4877202542972HLA-B15:09HKESSKTNL0.57130.5803514
AFF1-PTPN13chr488046295chr4877202542972HLA-B39:11HKESSKTNL0.50720.7516514
AFF1-PTPN13chr488046295chr4877202542972HLA-B39:02KESSKTNLI0.0920.7718615
AFF1-PTPN13chr488046295chr4877202542972HLA-B39:31SHKESSKTNL0.98290.9378414
AFF1-PTPN13chr488046295chr4877202542972HLA-B38:05SHKESSKTNL0.94090.9673414
AFF1-PTPN13chr488046295chr4877202542972HLA-B15:09SHKESSKTNL0.86310.6108414
AFF1-PTPN13chr488046295chr4877202542972HLA-B39:11SHKESSKTNL0.79910.7705414
AFF1-PTPN13chr488046295chr4877202542972HLA-A30:01KTNLIQKPQEK0.99890.84161021
AFF1-PTPN13chr488046295chr4877202542972HLA-A30:01KESSKTNLIQK0.99610.7958617
AFF1-PTPN13chr488046295chr4877202542972HLA-B38:05SHKESSKTNLI0.97810.9003415
AFF1-PTPN13chr488048855chr4876661193363HLA-B08:01ELMKKKITL0.99890.79611221
AFF1-PTPN13chr488048855chr4876661193363HLA-B08:09ELMKKKITL0.99830.7331221
AFF1-PTPN13chr488048855chr4876661193363HLA-A30:08KQKAELMKK0.99720.5214817
AFF1-PTPN13chr488048855chr4876661193363HLA-B13:01ELMKKKITL0.02810.74751221
AFF1-PTPN13chr488048855chr4876661193363HLA-B08:01ELMKKKITLQ0.98320.73431222
AFF1-PTPN13chr488048855chr4876661193363HLA-B08:01AELMKKKITL0.95220.90021121
AFF1-PTPN13chr488048855chr4876661193363HLA-B39:13AELMKKKITL0.76120.92081121
AFF1-PTPN13chr488048855chr4876661193363HLA-B42:02ELMKKKITL0.99950.77821221
AFF1-PTPN13chr488048855chr4876661193363HLA-B14:03ELMKKKITL0.79870.621221
AFF1-PTPN13chr488048855chr4876661193363HLA-B39:12ELMKKKITL0.31730.84251221
AFF1-PTPN13chr488048855chr4876661193363HLA-B08:18ELMKKKITL0.99890.79611221
AFF1-PTPN13chr488048855chr4876661193363HLA-A30:01KQKAELMKK0.99680.7432817
AFF1-PTPN13chr488048855chr4876661193363HLA-B08:12ELMKKKITL0.92380.89121221
AFF1-PTPN13chr488048855chr4876661193363HLA-C07:04ELMKKKITL0.73930.91921221
AFF1-PTPN13chr488048855chr4876661193363HLA-A30:01KMKQKAELMK0.9960.7583616
AFF1-PTPN13chr488048855chr4876661193363HLA-A30:01KQKAELMKKK0.98670.7321818
AFF1-PTPN13chr488048855chr4876661193363HLA-B40:04AELMKKKITL0.9850.57551121
AFF1-PTPN13chr488048855chr4876661193363HLA-B08:18ELMKKKITLQ0.98320.73431222
AFF1-PTPN13chr488048855chr4876661193363HLA-B08:18AELMKKKITL0.95220.90021121
AFF1-PTPN13chr488048855chr4876661193363HLA-B39:02AELMKKKITL0.85120.9241121
AFF1-PTPN13chr488048855chr4876661193363HLA-B41:03AELMKKKITL0.77890.7291121
AFF1-PTPN13chr488048855chr4876661193363HLA-A30:01KMKQKAELMKK0.99620.7551617
AFF1-PTPN13chr488048855chr4877180273363HLA-B47:01AELMATKM0.9980.59161119
AFF1-PTPN13chr488048855chr4877180273363HLA-B15:01KMKQKAELM0.99180.8109615
AFF1-PTPN13chr488048855chr4877180273363HLA-B15:03KKMKQKAEL0.32930.6811514
AFF1-PTPN13chr488048855chr4877180273363HLA-A30:08KQKAELMATK0.99480.6288818
AFF1-PTPN13chr488048855chr4877180273363HLA-C05:09KAELMATKM0.99950.91321019
AFF1-PTPN13chr488048855chr4877180273363HLA-C08:15KAELMATKM0.99910.98021019
AFF1-PTPN13chr488048855chr4877180273363HLA-B15:04KMKQKAELM0.95760.8071615
AFF1-PTPN13chr488048855chr4877180273363HLA-B15:07KMKQKAELM0.95330.5178615
AFF1-PTPN13chr488048855chr4877180273363HLA-B15:04KQKAELMAT0.82510.9436817
AFF1-PTPN13chr488048855chr4877180273363HLA-C08:13KAELMATKM0.49940.94311019
AFF1-PTPN13chr488048855chr4877180273363HLA-C08:04KAELMATKM0.49940.94311019
AFF1-PTPN13chr488048855chr4877180273363HLA-B40:04AELMATKM0.99940.76361119
AFF1-PTPN13chr488048855chr4877180273363HLA-B18:11AELMATKM0.99120.75211119
AFF1-PTPN13chr488048855chr4877180273363HLA-B41:03AELMATKM0.81530.77011119
AFF1-PTPN13chr488048855chr4877180273363HLA-C05:01KAELMATKM0.99950.91321019
AFF1-PTPN13chr488048855chr4877180273363HLA-C08:02KAELMATKM0.99910.98021019
AFF1-PTPN13chr488048855chr4877180273363HLA-B15:27KMKQKAELM0.99230.8746615
AFF1-PTPN13chr488048855chr4877180273363HLA-B15:34KMKQKAELM0.99180.8109615
AFF1-PTPN13chr488048855chr4877180273363HLA-B15:125KMKQKAELM0.99180.8109615
AFF1-PTPN13chr488048855chr4877180273363HLA-B15:33KMKQKAELM0.99180.8109615
AFF1-PTPN13chr488048855chr4877180273363HLA-B15:135KMKQKAELM0.9910.8137615
AFF1-PTPN13chr488048855chr4877180273363HLA-B15:50KMKQKAELM0.98640.8141615
AFF1-PTPN13chr488048855chr4877180273363HLA-B15:24KMKQKAELM0.98620.8572615
AFF1-PTPN13chr488048855chr4877180273363HLA-B15:35KMKQKAELM0.92820.7881615
AFF1-PTPN13chr488048855chr4877180273363HLA-B15:12KMKQKAELM0.91840.7778615
AFF1-PTPN13chr488048855chr4877180273363HLA-B39:02KKMKQKAEL0.89920.8141514
AFF1-PTPN13chr488048855chr4877180273363HLA-B15:73KMKQKAELM0.83940.8581615
AFF1-PTPN13chr488048855chr4877180273363HLA-B15:30KMKQKAELM0.60450.8321615
AFF1-PTPN13chr488048855chr4877180273363HLA-B07:13KAELMATKM0.02410.70971019
AFF1-PTPN13chr488048855chr4877180273363HLA-A30:01KQKAELMATK0.99490.7769818

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Potential FusionNeoAntigen Information of AFF1-PTPN13 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 AFF1-PTPN13

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
4221KESSKTNLIQKPQEAFF1PTPN13chr488046295chr4877202542972
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
4434KMKQKAELMATKMNAFF1PTPN13chr488048855chr4877180273363
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
4435KMKQKAELMKKKITAFF1PTPN13chr488048855chr4876661193363

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of AFF1-PTPN13

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-B14:023BVN4221KESSKTNLIQKPQE-5.49577-5.60917
HLA-B14:023BVN4221KESSKTNLIQKPQE-4.37152-5.40682
HLA-B52:013W394221KESSKTNLIQKPQE-6.90336-7.01676
HLA-B52:013W394221KESSKTNLIQKPQE-4.80833-5.84363
HLA-A11:014UQ24221KESSKTNLIQKPQE-9.82261-9.93601
HLA-A24:025HGA4221KESSKTNLIQKPQE-9.78612-9.89952
HLA-A24:025HGA4221KESSKTNLIQKPQE-4.98992-6.02522
HLA-B27:056PYJ4221KESSKTNLIQKPQE-5.31553-6.35083
HLA-B44:053DX84221KESSKTNLIQKPQE-5.70582-5.81922
HLA-B44:053DX84221KESSKTNLIQKPQE-4.32241-5.35771
HLA-B14:023BVN4434KMKQKAELMATKMN-7.9962-8.1096
HLA-B14:023BVN4434KMKQKAELMATKMN-5.70842-6.74372
HLA-B52:013W394434KMKQKAELMATKMN-6.83737-6.95077
HLA-B52:013W394434KMKQKAELMATKMN-4.4836-5.5189
HLA-A11:014UQ24434KMKQKAELMATKMN-10.0067-10.1201
HLA-A11:014UQ24434KMKQKAELMATKMN-9.03915-10.0745
HLA-A24:025HGA4434KMKQKAELMATKMN-6.56204-6.67544
HLA-A24:025HGA4434KMKQKAELMATKMN-5.42271-6.45801
HLA-B44:053DX84434KMKQKAELMATKMN-7.85648-8.89178
HLA-B44:053DX84434KMKQKAELMATKMN-5.3978-5.5112
HLA-A02:016TDR4434KMKQKAELMATKMN-3.37154-4.40684
HLA-B53:011A1O4435KMKQKAELMKKKIT-3.20963-4.24493
HLA-B51:011E284435KMKQKAELMKKKIT-4.71049-4.82389
HLA-B51:011E284435KMKQKAELMKKKIT-2.41218-3.44748
HLA-B57:032BVO4435KMKQKAELMKKKIT-1.15793-2.19323
HLA-A03:012XPG4435KMKQKAELMKKKIT-2.82905-3.86435
HLA-B14:023BVN4435KMKQKAELMKKKIT-6.01624-6.12964
HLA-B14:023BVN4435KMKQKAELMKKKIT-3.0101-4.0454
HLA-B44:033DX74435KMKQKAELMKKKIT0.0456146-0.989685
HLA-B52:013W394435KMKQKAELMKKKIT-5.58746-5.70086
HLA-B52:013W394435KMKQKAELMKKKIT-3.59213-4.62743
HLA-B18:014JQV4435KMKQKAELMKKKIT-3.3293-3.4427
HLA-B18:014JQV4435KMKQKAELMKKKIT-0.305763-1.34106
HLA-A11:014UQ24435KMKQKAELMKKKIT-8.33749-8.45089
HLA-A11:014UQ24435KMKQKAELMKKKIT-6.15985-7.19515
HLA-A24:025HGA4435KMKQKAELMKKKIT-5.17069-6.20599
HLA-A24:025HGA4435KMKQKAELMKKKIT-4.18377-4.29717
HLA-B57:015VUD4435KMKQKAELMKKKIT-1.89423-2.92953
HLA-B27:056PYJ4435KMKQKAELMKKKIT-2.66447-3.69977
HLA-B27:056PYJ4435KMKQKAELMKKKIT-2.44586-2.55926
HLA-B27:036PZ54435KMKQKAELMKKKIT-5.44487-5.55827
HLA-B27:036PZ54435KMKQKAELMKKKIT-3.87227-4.90757
HLA-B44:053DX84435KMKQKAELMKKKIT-5.01764-5.13104
HLA-B44:053DX84435KMKQKAELMKKKIT-2.6392-3.6745
HLA-B44:021M6O4435KMKQKAELMKKKIT-6.36013-6.47353
HLA-B44:021M6O4435KMKQKAELMKKKIT-4.88756-5.92286
HLA-B07:025EO04435KMKQKAELMKKKIT-4.6629-4.7763
HLA-B07:025EO04435KMKQKAELMKKKIT-4.00587-5.04117
HLA-A02:016TDR4435KMKQKAELMKKKIT-4.04667-4.16007
HLA-A02:016TDR4435KMKQKAELMKKKIT-1.46854-2.50384

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Vaccine Design for the FusionNeoAntigens of AFF1-PTPN13

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
AFF1-PTPN13chr488046295chr4877202541021KTNLIQKPQEKTAAAACAAACTTAATTCAGAAGCCACAAGAAAA
AFF1-PTPN13chr488046295chr487720254414SHKESSKTNLCTCCCACAAAGAATCTTCTAAAACAAACTT
AFF1-PTPN13chr488046295chr487720254415SHKESSKTNLICTCCCACAAAGAATCTTCTAAAACAAACTTAAT
AFF1-PTPN13chr488046295chr487720254514HKESSKTNLCCACAAAGAATCTTCTAAAACAAACTT
AFF1-PTPN13chr488046295chr487720254614KESSKTNLCAAAGAATCTTCTAAAACAAACTT
AFF1-PTPN13chr488046295chr487720254615KESSKTNLICAAAGAATCTTCTAAAACAAACTTAAT
AFF1-PTPN13chr488046295chr487720254617KESSKTNLIQKCAAAGAATCTTCTAAAACAAACTTAATTCAGAA
AFF1-PTPN13chr488046295chr487720254817SSKTNLIQKATCTTCTAAAACAAACTTAATTCAGAA
AFF1-PTPN13chr488048855chr4876661191121AELMKKKITLTTAATGAAAAAGAAAATCACATTGCAAAAT
AFF1-PTPN13chr488048855chr4876661191221ELMKKKITLATGAAAAAGAAAATCACATTGCAAAAT
AFF1-PTPN13chr488048855chr4876661191222ELMKKKITLQATGAAAAAGAAAATCACATTGCAAAATACA
AFF1-PTPN13chr488048855chr487666119616KMKQKAELMKAAGCAGAAAGCAGAGTTAATGAAAAAGAAA
AFF1-PTPN13chr488048855chr487666119617KMKQKAELMKKAAGCAGAAAGCAGAGTTAATGAAAAAGAAAATC
AFF1-PTPN13chr488048855chr487666119817KQKAELMKKAAAGCAGAGTTAATGAAAAAGAAAATC
AFF1-PTPN13chr488048855chr487666119818KQKAELMKKKAAAGCAGAGTTAATGAAAAAGAAAATCACA
AFF1-PTPN13chr488048855chr4877180271019KAELMATKMGAGTTAATGGCCACCAAAATGAATGGC
AFF1-PTPN13chr488048855chr4877180271119AELMATKMTTAATGGCCACCAAAATGAATGGC
AFF1-PTPN13chr488048855chr487718027514KKMKQKAELATGAAGCAGAAAGCAGAGTTAATGGCC
AFF1-PTPN13chr488048855chr487718027615KMKQKAELMAAGCAGAAAGCAGAGTTAATGGCCACC
AFF1-PTPN13chr488048855chr487718027817KQKAELMATAAAGCAGAGTTAATGGCCACCAAAATG
AFF1-PTPN13chr488048855chr487718027818KQKAELMATKAAAGCAGAGTTAATGGCCACCAAAATGAAT

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 AFF1-PTPN13

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
BLCAAFF1-PTPN13chr488046295ENST00000307808chr487720254ENST00000427191TCGA-E7-A6MD-01A
BLCAAFF1-PTPN13chr488048855ENST00000307808chr487666119ENST00000427191TCGA-GC-A3BM-01A
CESCAFF1-PTPN13chr488048855ENST00000307808chr487718027ENST00000427191TCGA-EA-A5ZD

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Potential target of CAR-T therapy development for AFF1-PTPN13

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 AFF1-PTPN13

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 AFF1-PTPN13

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