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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:PTPRK-EPB41L2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PTPRK-EPB41L2
FusionPDB ID: 70438
FusionGDB2.0 ID: 70438
HgeneTgene
Gene symbol

PTPRK

EPB41L2

Gene ID

5796

2037

Gene nameprotein tyrosine phosphatase receptor type Kerythrocyte membrane protein band 4.1 like 2
SynonymsR-PTP-kappa4.1-G|4.1G
Cytomap

6q22.33

6q23.1-q23.2

Type of geneprotein-codingprotein-coding
Descriptionreceptor-type tyrosine-protein phosphatase kappadJ480J14.2.1 (protein tyrosine phosphatase, receptor type, K (R-PTP-KAPPA, protein tyrosine phosphatase kappa , protein tyrosine phosphatase kappaprotein-tyrosine phosphatase kappaprotein-tyrosine phosphaband 4.1-like protein 2erythrocyte membrane protein band 4.1 like-protein 2generally expressed protein 4.1
Modification date2020032220200313
UniProtAcc.

O43491

Main function of 5'-partner protein: FUNCTION: Required for dynein-dynactin complex and NUMA1 recruitment at the mitotic cell cortex during anaphase (PubMed:23870127). {ECO:0000269|PubMed:23870127}.
Ensembl transtripts involved in fusion geneENST idsENST00000368207, ENST00000368210, 
ENST00000368213, ENST00000368215, 
ENST00000368226, ENST00000368227, 
ENST00000525459, ENST00000532331, 
ENST00000524481, 		ENST00000337057, 
ENST00000368128, ENST00000392427, 
ENST00000445890, ENST00000524581, 
ENST00000525193, ENST00000525271, 
ENST00000527411, ENST00000527659, 
ENST00000528282, ENST00000529208, 
ENST00000530148, ENST00000530481, 
ENST00000530757, ENST00000531410, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score36 X 18 X 16=1036810 X 9 X 8=720
# samples 4810
** MAII scorelog2(48/10368*10)=-4.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/720*10)=-2.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PTPRK [Title/Abstract] AND EPB41L2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PTPRK [Title/Abstract] AND EPB41L2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)EPB41L2(131276245)-PTPRK(128330413), # samples:2
PTPRK(128841404)-EPB41L2(131184858), # samples:2
Anticipated loss of major functional domain due to fusion event.EPB41L2-PTPRK 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.
EPB41L2-PTPRK 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.
PTPRK-EPB41L2 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.
PTPRK-EPB41L2 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.
PTPRK-EPB41L2 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.
PTPRK-EPB41L2 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.
EPB41L2-PTPRK seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
EPB41L2-PTPRK seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
EPB41L2-PTPRK seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
EPB41L2-PTPRK seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
EPB41L2-PTPRK 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
HgenePTPRK

GO:0006470

protein dephosphorylation

16263724

HgenePTPRK

GO:0007165

signal transduction

16849327

HgenePTPRK

GO:0007179

transforming growth factor beta receptor signaling pathway

15899872

HgenePTPRK

GO:0008285

negative regulation of cell proliferation

15899872|18276111

HgenePTPRK

GO:0010839

negative regulation of keratinocyte proliferation

16263724

HgenePTPRK

GO:0030336

negative regulation of cell migration

18276111

HgenePTPRK

GO:0034394

protein localization to cell surface

18276111

HgenePTPRK

GO:0034614

cellular response to reactive oxygen species

16849327

HgenePTPRK

GO:0034644

cellular response to UV

16849327

HgenePTPRK

GO:0045786

negative regulation of cell cycle

15899872

HgenePTPRK

GO:0045892

negative regulation of transcription, DNA-templated

18276111



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/chr6:131276245/chr6:128330413)
- 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 PTPRK (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 EPB41L2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


Top

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)
ENST00000368226PTPRKchr6128841404-ENST00000528282EPB41L2chr6131184858-18624165322177
ENST00000368226PTPRKchr6128841404-ENST00000530481EPB41L2chr6131184858-18624165322177
ENST00000368226PTPRKchr6128841404-ENST00000445890EPB41L2chr6131184858-18624165322177
ENST00000368226PTPRKchr6128841404-ENST00000337057EPB41L2chr6131184858-18624165322177
ENST00000368226PTPRKchr6128841404-ENST00000530757EPB41L2chr6131184858-18594165322177
ENST00000368226PTPRKchr6128841404-ENST00000392427EPB41L2chr6131184858-18594165322177
ENST00000368226PTPRKchr6128841404-ENST00000368128EPB41L2chr6131184858-18524164430148
ENST00000368226PTPRKchr6128841404-ENST00000527411EPB41L2chr6131184858-18524164430148
ENST00000368226PTPRKchr6128841404-ENST00000524581EPB41L2chr6131184858-10744165322177
ENST00000368226PTPRKchr6128841404-ENST00000525271EPB41L2chr6131184858-10274164430148
ENST00000368226PTPRKchr6128841404-ENST00000525193EPB41L2chr6131184858-6054165322177
ENST00000368226PTPRKchr6128841404-ENST00000527659EPB41L2chr6131184858-6054165322177
ENST00000368226PTPRKchr6128841404-ENST00000529208EPB41L2chr6131184858-6054165322177
ENST00000368226PTPRKchr6128841404-ENST00000531410EPB41L2chr6131184858-18624165322177
ENST00000368227PTPRKchr6128841404-ENST00000528282EPB41L2chr6131184858-19134675832194
ENST00000368227PTPRKchr6128841404-ENST00000530481EPB41L2chr6131184858-19134675832194
ENST00000368227PTPRKchr6128841404-ENST00000445890EPB41L2chr6131184858-19134675832194
ENST00000368227PTPRKchr6128841404-ENST00000337057EPB41L2chr6131184858-19134675832194
ENST00000368227PTPRKchr6128841404-ENST00000530757EPB41L2chr6131184858-19104675832194
ENST00000368227PTPRKchr6128841404-ENST00000392427EPB41L2chr6131184858-19104675832194
ENST00000368227PTPRKchr6128841404-ENST00000368128EPB41L2chr6131184858-19034674940165
ENST00000368227PTPRKchr6128841404-ENST00000527411EPB41L2chr6131184858-19034674940165
ENST00000368227PTPRKchr6128841404-ENST00000524581EPB41L2chr6131184858-11254675832194
ENST00000368227PTPRKchr6128841404-ENST00000525271EPB41L2chr6131184858-10784674940165
ENST00000368227PTPRKchr6128841404-ENST00000525193EPB41L2chr6131184858-6564675832194
ENST00000368227PTPRKchr6128841404-ENST00000527659EPB41L2chr6131184858-6564675832194
ENST00000368227PTPRKchr6128841404-ENST00000529208EPB41L2chr6131184858-6564675832194
ENST00000368227PTPRKchr6128841404-ENST00000531410EPB41L2chr6131184858-19134675832194
ENST00000532331PTPRKchr6128841404-ENST00000528282EPB41L2chr6131184858-16642182406134
ENST00000532331PTPRKchr6128841404-ENST00000530481EPB41L2chr6131184858-16642182406134
ENST00000532331PTPRKchr6128841404-ENST00000445890EPB41L2chr6131184858-16642182406134
ENST00000532331PTPRKchr6128841404-ENST00000337057EPB41L2chr6131184858-16642182406134
ENST00000532331PTPRKchr6128841404-ENST00000530757EPB41L2chr6131184858-16612182406134
ENST00000532331PTPRKchr6128841404-ENST00000392427EPB41L2chr6131184858-16612182406134
ENST00000532331PTPRKchr6128841404-ENST00000368128EPB41L2chr6131184858-16542182406134
ENST00000532331PTPRKchr6128841404-ENST00000527411EPB41L2chr6131184858-16542182406134
ENST00000532331PTPRKchr6128841404-ENST00000524581EPB41L2chr6131184858-8762182406134
ENST00000532331PTPRKchr6128841404-ENST00000525271EPB41L2chr6131184858-8292182406134
ENST00000532331PTPRKchr6128841404-ENST00000525193EPB41L2chr6131184858-4072182406135
ENST00000532331PTPRKchr6128841404-ENST00000527659EPB41L2chr6131184858-4072182406135
ENST00000532331PTPRKchr6128841404-ENST00000529208EPB41L2chr6131184858-4072182406135
ENST00000532331PTPRKchr6128841404-ENST00000531410EPB41L2chr6131184858-16642182406134
ENST00000368213PTPRKchr6128841404-ENST00000528282EPB41L2chr6131184858-17713254411147
ENST00000368213PTPRKchr6128841404-ENST00000530481EPB41L2chr6131184858-17713254411147
ENST00000368213PTPRKchr6128841404-ENST00000445890EPB41L2chr6131184858-17713254411147
ENST00000368213PTPRKchr6128841404-ENST00000337057EPB41L2chr6131184858-17713254411147
ENST00000368213PTPRKchr6128841404-ENST00000530757EPB41L2chr6131184858-17683254411147
ENST00000368213PTPRKchr6128841404-ENST00000392427EPB41L2chr6131184858-17683254411147
ENST00000368213PTPRKchr6128841404-ENST00000368128EPB41L2chr6131184858-1761325109513134
ENST00000368213PTPRKchr6128841404-ENST00000527411EPB41L2chr6131184858-1761325109513134
ENST00000368213PTPRKchr6128841404-ENST00000524581EPB41L2chr6131184858-9833254411147
ENST00000368213PTPRKchr6128841404-ENST00000525271EPB41L2chr6131184858-936325109513134
ENST00000368213PTPRKchr6128841404-ENST00000525193EPB41L2chr6131184858-5143254411147
ENST00000368213PTPRKchr6128841404-ENST00000527659EPB41L2chr6131184858-5143254411147
ENST00000368213PTPRKchr6128841404-ENST00000529208EPB41L2chr6131184858-5143254411147
ENST00000368213PTPRKchr6128841404-ENST00000531410EPB41L2chr6131184858-17713254411147
ENST00000368210PTPRKchr6128841404-ENST00000528282EPB41L2chr6131184858-18043584741158
ENST00000368210PTPRKchr6128841404-ENST00000530481EPB41L2chr6131184858-18043584741158
ENST00000368210PTPRKchr6128841404-ENST00000445890EPB41L2chr6131184858-18043584741158
ENST00000368210PTPRKchr6128841404-ENST00000337057EPB41L2chr6131184858-18043584741158
ENST00000368210PTPRKchr6128841404-ENST00000530757EPB41L2chr6131184858-18013584741158
ENST00000368210PTPRKchr6128841404-ENST00000392427EPB41L2chr6131184858-18013584741158
ENST00000368210PTPRKchr6128841404-ENST00000368128EPB41L2chr6131184858-1794358142546134
ENST00000368210PTPRKchr6128841404-ENST00000527411EPB41L2chr6131184858-1794358142546134
ENST00000368210PTPRKchr6128841404-ENST00000524581EPB41L2chr6131184858-10163584741158
ENST00000368210PTPRKchr6128841404-ENST00000525271EPB41L2chr6131184858-969358142546134
ENST00000368210PTPRKchr6128841404-ENST00000525193EPB41L2chr6131184858-5473584741158
ENST00000368210PTPRKchr6128841404-ENST00000527659EPB41L2chr6131184858-5473584741158
ENST00000368210PTPRKchr6128841404-ENST00000529208EPB41L2chr6131184858-5473584741158
ENST00000368210PTPRKchr6128841404-ENST00000531410EPB41L2chr6131184858-18043584741158
ENST00000368215PTPRKchr6128841404-ENST00000528282EPB41L2chr6131184858-15461001028892
ENST00000368215PTPRKchr6128841404-ENST00000530481EPB41L2chr6131184858-15461001028892
ENST00000368215PTPRKchr6128841404-ENST00000445890EPB41L2chr6131184858-15461001028892
ENST00000368215PTPRKchr6128841404-ENST00000337057EPB41L2chr6131184858-15461001028892
ENST00000368215PTPRKchr6128841404-ENST00000530757EPB41L2chr6131184858-15431001028892
ENST00000368215PTPRKchr6128841404-ENST00000392427EPB41L2chr6131184858-15431001028892
ENST00000368215PTPRKchr6128841404-ENST00000368128EPB41L2chr6131184858-15361001028892
ENST00000368215PTPRKchr6128841404-ENST00000527411EPB41L2chr6131184858-15361001028892
ENST00000368215PTPRKchr6128841404-ENST00000524581EPB41L2chr6131184858-7581001028892
ENST00000368215PTPRKchr6128841404-ENST00000525271EPB41L2chr6131184858-7111001028892
ENST00000368215PTPRKchr6128841404-ENST00000525193EPB41L2chr6131184858-2891001028893
ENST00000368215PTPRKchr6128841404-ENST00000527659EPB41L2chr6131184858-2891001028893
ENST00000368215PTPRKchr6128841404-ENST00000529208EPB41L2chr6131184858-2891001028893
ENST00000368215PTPRKchr6128841404-ENST00000531410EPB41L2chr6131184858-15461001028892
ENST00000368207PTPRKchr6128841404-ENST00000528282EPB41L2chr6131184858-17713254411147
ENST00000368207PTPRKchr6128841404-ENST00000530481EPB41L2chr6131184858-17713254411147
ENST00000368207PTPRKchr6128841404-ENST00000445890EPB41L2chr6131184858-17713254411147
ENST00000368207PTPRKchr6128841404-ENST00000337057EPB41L2chr6131184858-17713254411147
ENST00000368207PTPRKchr6128841404-ENST00000530757EPB41L2chr6131184858-17683254411147
ENST00000368207PTPRKchr6128841404-ENST00000392427EPB41L2chr6131184858-17683254411147
ENST00000368207PTPRKchr6128841404-ENST00000368128EPB41L2chr6131184858-1761325109513134
ENST00000368207PTPRKchr6128841404-ENST00000527411EPB41L2chr6131184858-1761325109513134
ENST00000368207PTPRKchr6128841404-ENST00000524581EPB41L2chr6131184858-9833254411147
ENST00000368207PTPRKchr6128841404-ENST00000525271EPB41L2chr6131184858-936325109513134
ENST00000368207PTPRKchr6128841404-ENST00000525193EPB41L2chr6131184858-5143254411147
ENST00000368207PTPRKchr6128841404-ENST00000527659EPB41L2chr6131184858-5143254411147
ENST00000368207PTPRKchr6128841404-ENST00000529208EPB41L2chr6131184858-5143254411147
ENST00000368207PTPRKchr6128841404-ENST00000531410EPB41L2chr6131184858-17713254411147
ENST00000525459PTPRKchr6128841404-ENST00000528282EPB41L2chr6131184858-17753294452148
ENST00000525459PTPRKchr6128841404-ENST00000530481EPB41L2chr6131184858-17753294452148
ENST00000525459PTPRKchr6128841404-ENST00000445890EPB41L2chr6131184858-17753294452148
ENST00000525459PTPRKchr6128841404-ENST00000337057EPB41L2chr6131184858-17753294452148
ENST00000525459PTPRKchr6128841404-ENST00000530757EPB41L2chr6131184858-17723294452148
ENST00000525459PTPRKchr6128841404-ENST00000392427EPB41L2chr6131184858-17723294452148
ENST00000525459PTPRKchr6128841404-ENST00000368128EPB41L2chr6131184858-1765329113517134
ENST00000525459PTPRKchr6128841404-ENST00000527411EPB41L2chr6131184858-1765329113517134
ENST00000525459PTPRKchr6128841404-ENST00000524581EPB41L2chr6131184858-9873294452148
ENST00000525459PTPRKchr6128841404-ENST00000525271EPB41L2chr6131184858-940329113517134
ENST00000525459PTPRKchr6128841404-ENST00000525193EPB41L2chr6131184858-5183294452148
ENST00000525459PTPRKchr6128841404-ENST00000527659EPB41L2chr6131184858-5183294452148
ENST00000525459PTPRKchr6128841404-ENST00000529208EPB41L2chr6131184858-5183294452148
ENST00000525459PTPRKchr6128841404-ENST00000531410EPB41L2chr6131184858-17753294452148

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
ENST00000368226ENST00000528282PTPRKchr6128841404-EPB41L2chr6131184858-0.811639550.18836042
ENST00000368226ENST00000530481PTPRKchr6128841404-EPB41L2chr6131184858-0.811639550.18836042
ENST00000368226ENST00000445890PTPRKchr6128841404-EPB41L2chr6131184858-0.811639550.18836042
ENST00000368226ENST00000337057PTPRKchr6128841404-EPB41L2chr6131184858-0.811639550.18836042
ENST00000368226ENST00000530757PTPRKchr6128841404-EPB41L2chr6131184858-0.812935650.18706441
ENST00000368226ENST00000392427PTPRKchr6128841404-EPB41L2chr6131184858-0.812935650.18706441
ENST00000368226ENST00000368128PTPRKchr6128841404-EPB41L2chr6131184858-0.77023050.22976956
ENST00000368226ENST00000527411PTPRKchr6128841404-EPB41L2chr6131184858-0.68367380.31632617
ENST00000368226ENST00000524581PTPRKchr6128841404-EPB41L2chr6131184858-0.75799670.24200332
ENST00000368226ENST00000525271PTPRKchr6128841404-EPB41L2chr6131184858-0.714659040.28534096
ENST00000368226ENST00000525193PTPRKchr6128841404-EPB41L2chr6131184858-0.162939220.8370608
ENST00000368226ENST00000527659PTPRKchr6128841404-EPB41L2chr6131184858-0.162939220.8370608
ENST00000368226ENST00000529208PTPRKchr6128841404-EPB41L2chr6131184858-0.162939220.8370608
ENST00000368226ENST00000531410PTPRKchr6128841404-EPB41L2chr6131184858-0.811639550.18836042
ENST00000368227ENST00000528282PTPRKchr6128841404-EPB41L2chr6131184858-0.918423950.08157608
ENST00000368227ENST00000530481PTPRKchr6128841404-EPB41L2chr6131184858-0.918423950.08157608
ENST00000368227ENST00000445890PTPRKchr6128841404-EPB41L2chr6131184858-0.918423950.08157608
ENST00000368227ENST00000337057PTPRKchr6128841404-EPB41L2chr6131184858-0.918423950.08157608
ENST00000368227ENST00000530757PTPRKchr6128841404-EPB41L2chr6131184858-0.91208540.08791456
ENST00000368227ENST00000392427PTPRKchr6128841404-EPB41L2chr6131184858-0.91208540.08791456
ENST00000368227ENST00000368128PTPRKchr6128841404-EPB41L2chr6131184858-0.906967160.093032904
ENST00000368227ENST00000527411PTPRKchr6128841404-EPB41L2chr6131184858-0.88998490.110015094
ENST00000368227ENST00000524581PTPRKchr6128841404-EPB41L2chr6131184858-0.835698540.16430144
ENST00000368227ENST00000525271PTPRKchr6128841404-EPB41L2chr6131184858-0.791472260.20852771
ENST00000368227ENST00000525193PTPRKchr6128841404-EPB41L2chr6131184858-0.280928020.71907204
ENST00000368227ENST00000527659PTPRKchr6128841404-EPB41L2chr6131184858-0.280928020.71907204
ENST00000368227ENST00000529208PTPRKchr6128841404-EPB41L2chr6131184858-0.280928020.71907204
ENST00000368227ENST00000531410PTPRKchr6128841404-EPB41L2chr6131184858-0.918423950.08157608
ENST00000532331ENST00000528282PTPRKchr6128841404-EPB41L2chr6131184858-0.78492340.21507667
ENST00000532331ENST00000530481PTPRKchr6128841404-EPB41L2chr6131184858-0.78492340.21507667
ENST00000532331ENST00000445890PTPRKchr6128841404-EPB41L2chr6131184858-0.78492340.21507667
ENST00000532331ENST00000337057PTPRKchr6128841404-EPB41L2chr6131184858-0.78492340.21507667
ENST00000532331ENST00000530757PTPRKchr6128841404-EPB41L2chr6131184858-0.78629340.21370658
ENST00000532331ENST00000392427PTPRKchr6128841404-EPB41L2chr6131184858-0.78629340.21370658
ENST00000532331ENST00000368128PTPRKchr6128841404-EPB41L2chr6131184858-0.744256730.25574327
ENST00000532331ENST00000527411PTPRKchr6128841404-EPB41L2chr6131184858-0.71591590.28408408
ENST00000532331ENST00000524581PTPRKchr6128841404-EPB41L2chr6131184858-0.860699950.13930008
ENST00000532331ENST00000525271PTPRKchr6128841404-EPB41L2chr6131184858-0.85575390.14424612
ENST00000532331ENST00000525193PTPRKchr6128841404-EPB41L2chr6131184858-0.313227150.6867728
ENST00000532331ENST00000527659PTPRKchr6128841404-EPB41L2chr6131184858-0.313227150.6867728
ENST00000532331ENST00000529208PTPRKchr6128841404-EPB41L2chr6131184858-0.313227150.6867728
ENST00000532331ENST00000531410PTPRKchr6128841404-EPB41L2chr6131184858-0.78492340.21507667
ENST00000368213ENST00000528282PTPRKchr6128841404-EPB41L2chr6131184858-0.787201050.21279895
ENST00000368213ENST00000530481PTPRKchr6128841404-EPB41L2chr6131184858-0.787201050.21279895
ENST00000368213ENST00000445890PTPRKchr6128841404-EPB41L2chr6131184858-0.787201050.21279895
ENST00000368213ENST00000337057PTPRKchr6128841404-EPB41L2chr6131184858-0.787201050.21279895
ENST00000368213ENST00000530757PTPRKchr6128841404-EPB41L2chr6131184858-0.780189750.21981029
ENST00000368213ENST00000392427PTPRKchr6128841404-EPB41L2chr6131184858-0.780189750.21981029
ENST00000368213ENST00000368128PTPRKchr6128841404-EPB41L2chr6131184858-0.715903460.28409654
ENST00000368213ENST00000527411PTPRKchr6128841404-EPB41L2chr6131184858-0.6373430.36265704
ENST00000368213ENST00000524581PTPRKchr6128841404-EPB41L2chr6131184858-0.82602210.1739779
ENST00000368213ENST00000525271PTPRKchr6128841404-EPB41L2chr6131184858-0.80412980.1958702
ENST00000368213ENST00000525193PTPRKchr6128841404-EPB41L2chr6131184858-0.26314850.7368515
ENST00000368213ENST00000527659PTPRKchr6128841404-EPB41L2chr6131184858-0.26314850.7368515
ENST00000368213ENST00000529208PTPRKchr6128841404-EPB41L2chr6131184858-0.26314850.7368515
ENST00000368213ENST00000531410PTPRKchr6128841404-EPB41L2chr6131184858-0.787201050.21279895
ENST00000368210ENST00000528282PTPRKchr6128841404-EPB41L2chr6131184858-0.899121640.100878365
ENST00000368210ENST00000530481PTPRKchr6128841404-EPB41L2chr6131184858-0.899121640.100878365
ENST00000368210ENST00000445890PTPRKchr6128841404-EPB41L2chr6131184858-0.899121640.100878365
ENST00000368210ENST00000337057PTPRKchr6128841404-EPB41L2chr6131184858-0.899121640.100878365
ENST00000368210ENST00000530757PTPRKchr6128841404-EPB41L2chr6131184858-0.89672180.10327828
ENST00000368210ENST00000392427PTPRKchr6128841404-EPB41L2chr6131184858-0.89672180.10327828
ENST00000368210ENST00000368128PTPRKchr6128841404-EPB41L2chr6131184858-0.89279570.10720439
ENST00000368210ENST00000527411PTPRKchr6128841404-EPB41L2chr6131184858-0.874228240.12577179
ENST00000368210ENST00000524581PTPRKchr6128841404-EPB41L2chr6131184858-0.811332460.18866757
ENST00000368210ENST00000525271PTPRKchr6128841404-EPB41L2chr6131184858-0.785685840.2143142
ENST00000368210ENST00000525193PTPRKchr6128841404-EPB41L2chr6131184858-0.216224970.78377503
ENST00000368210ENST00000527659PTPRKchr6128841404-EPB41L2chr6131184858-0.216224970.78377503
ENST00000368210ENST00000529208PTPRKchr6128841404-EPB41L2chr6131184858-0.216224970.78377503
ENST00000368210ENST00000531410PTPRKchr6128841404-EPB41L2chr6131184858-0.899121640.100878365
ENST00000368215ENST00000528282PTPRKchr6128841404-EPB41L2chr6131184858-0.928454340.0715457
ENST00000368215ENST00000530481PTPRKchr6128841404-EPB41L2chr6131184858-0.928454340.0715457
ENST00000368215ENST00000445890PTPRKchr6128841404-EPB41L2chr6131184858-0.928454340.0715457
ENST00000368215ENST00000337057PTPRKchr6128841404-EPB41L2chr6131184858-0.928454340.0715457
ENST00000368215ENST00000530757PTPRKchr6128841404-EPB41L2chr6131184858-0.925483050.074517004
ENST00000368215ENST00000392427PTPRKchr6128841404-EPB41L2chr6131184858-0.925483050.074517004
ENST00000368215ENST00000368128PTPRKchr6128841404-EPB41L2chr6131184858-0.89353510.10646493
ENST00000368215ENST00000527411PTPRKchr6128841404-EPB41L2chr6131184858-0.89765460.102345444
ENST00000368215ENST00000524581PTPRKchr6128841404-EPB41L2chr6131184858-0.9013820.09861798
ENST00000368215ENST00000525271PTPRKchr6128841404-EPB41L2chr6131184858-0.87516560.124834485
ENST00000368215ENST00000525193PTPRKchr6128841404-EPB41L2chr6131184858-0.42034930.5796507
ENST00000368215ENST00000527659PTPRKchr6128841404-EPB41L2chr6131184858-0.42034930.5796507
ENST00000368215ENST00000529208PTPRKchr6128841404-EPB41L2chr6131184858-0.42034930.5796507
ENST00000368215ENST00000531410PTPRKchr6128841404-EPB41L2chr6131184858-0.928454340.0715457
ENST00000368207ENST00000528282PTPRKchr6128841404-EPB41L2chr6131184858-0.787201050.21279895
ENST00000368207ENST00000530481PTPRKchr6128841404-EPB41L2chr6131184858-0.787201050.21279895
ENST00000368207ENST00000445890PTPRKchr6128841404-EPB41L2chr6131184858-0.787201050.21279895
ENST00000368207ENST00000337057PTPRKchr6128841404-EPB41L2chr6131184858-0.787201050.21279895
ENST00000368207ENST00000530757PTPRKchr6128841404-EPB41L2chr6131184858-0.780189750.21981029
ENST00000368207ENST00000392427PTPRKchr6128841404-EPB41L2chr6131184858-0.780189750.21981029
ENST00000368207ENST00000368128PTPRKchr6128841404-EPB41L2chr6131184858-0.715903460.28409654
ENST00000368207ENST00000527411PTPRKchr6128841404-EPB41L2chr6131184858-0.6373430.36265704
ENST00000368207ENST00000524581PTPRKchr6128841404-EPB41L2chr6131184858-0.82602210.1739779
ENST00000368207ENST00000525271PTPRKchr6128841404-EPB41L2chr6131184858-0.80412980.1958702
ENST00000368207ENST00000525193PTPRKchr6128841404-EPB41L2chr6131184858-0.26314850.7368515
ENST00000368207ENST00000527659PTPRKchr6128841404-EPB41L2chr6131184858-0.26314850.7368515
ENST00000368207ENST00000529208PTPRKchr6128841404-EPB41L2chr6131184858-0.26314850.7368515
ENST00000368207ENST00000531410PTPRKchr6128841404-EPB41L2chr6131184858-0.787201050.21279895
ENST00000525459ENST00000528282PTPRKchr6128841404-EPB41L2chr6131184858-0.86299680.1370032
ENST00000525459ENST00000530481PTPRKchr6128841404-EPB41L2chr6131184858-0.86299680.1370032
ENST00000525459ENST00000445890PTPRKchr6128841404-EPB41L2chr6131184858-0.86299680.1370032
ENST00000525459ENST00000337057PTPRKchr6128841404-EPB41L2chr6131184858-0.86299680.1370032
ENST00000525459ENST00000530757PTPRKchr6128841404-EPB41L2chr6131184858-0.862483260.13751675
ENST00000525459ENST00000392427PTPRKchr6128841404-EPB41L2chr6131184858-0.862483260.13751675
ENST00000525459ENST00000368128PTPRKchr6128841404-EPB41L2chr6131184858-0.74916780.2508322
ENST00000525459ENST00000527411PTPRKchr6128841404-EPB41L2chr6131184858-0.7474430.25255704
ENST00000525459ENST00000524581PTPRKchr6128841404-EPB41L2chr6131184858-0.77427680.22572313
ENST00000525459ENST00000525271PTPRKchr6128841404-EPB41L2chr6131184858-0.740875840.25912422
ENST00000525459ENST00000525193PTPRKchr6128841404-EPB41L2chr6131184858-0.229596420.77040356
ENST00000525459ENST00000527659PTPRKchr6128841404-EPB41L2chr6131184858-0.229596420.77040356
ENST00000525459ENST00000529208PTPRKchr6128841404-EPB41L2chr6131184858-0.229596420.77040356
ENST00000525459ENST00000531410PTPRKchr6128841404-EPB41L2chr6131184858-0.86299680.1370032

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 PTPRK-EPB41L2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PTPRKchr6128841404EPB41L2chr613118485810030GLSWDRPKASSPQTVKGGISETRIEK
PTPRKchr6128841404EPB41L2chr613118485821872GLSWDRPKASSPQTVKGGISETRIEK
PTPRKchr6128841404EPB41L2chr613118485832572GLSWDRPKASSPQTVKGGISETRIEK
PTPRKchr6128841404EPB41L2chr613118485832972GLSWDRPKASSPQTVKGGISETRIEK
PTPRKchr6128841404EPB41L2chr613118485835872GLSWDRPKASSPQTVKGGISETRIEK

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Potential FusionNeoAntigen Information of PTPRK-EPB41L2 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.
PTPRK-EPB41L2_128841404_131184858.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)
PTPRK-EPB41L2chr6128841404chr6131184858325HLA-A30:08KASSPQTVK0.99630.6868716
PTPRK-EPB41L2chr6128841404chr6131184858325HLA-B07:02RPKASSPQTV0.99830.5745515
PTPRK-EPB41L2chr6128841404chr6131184858325HLA-B82:01RPKASSPQTV0.56170.5707515
PTPRK-EPB41L2chr6128841404chr6131184858325HLA-B07:12RPKASSPQTV0.99270.6723515
PTPRK-EPB41L2chr6128841404chr6131184858325HLA-A30:01KASSPQTVK0.99580.7664716
PTPRK-EPB41L2chr6128841404chr6131184858325HLA-B07:22RPKASSPQTV0.99830.5745515
PTPRK-EPB41L2chr6128841404chr6131184858325HLA-B07:09RPKASSPQTV0.99790.5578515
PTPRK-EPB41L2chr6128841404chr6131184858325HLA-B82:02RPKASSPQTV0.56170.5707515
PTPRK-EPB41L2chr6128841404chr6131184858325HLA-B67:01RPKASSPQTV0.36380.6286515
PTPRK-EPB41L2chr6128841404chr6131184858325HLA-A30:01RPKASSPQTVK0.99040.6946516

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Potential FusionNeoAntigen Information of PTPRK-EPB41L2 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 PTPRK-EPB41L2

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
6712PKASSPQTVKGGISPTPRKEPB41L2chr6128841404chr6131184858325

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PTPRK-EPB41L2

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-B14:023BVN6712PKASSPQTVKGGIS-7.9962-8.1096
HLA-B14:023BVN6712PKASSPQTVKGGIS-5.70842-6.74372
HLA-B52:013W396712PKASSPQTVKGGIS-6.83737-6.95077
HLA-B52:013W396712PKASSPQTVKGGIS-4.4836-5.5189
HLA-A11:014UQ26712PKASSPQTVKGGIS-10.0067-10.1201
HLA-A11:014UQ26712PKASSPQTVKGGIS-9.03915-10.0745
HLA-A24:025HGA6712PKASSPQTVKGGIS-6.56204-6.67544
HLA-A24:025HGA6712PKASSPQTVKGGIS-5.42271-6.45801
HLA-B44:053DX86712PKASSPQTVKGGIS-7.85648-8.89178
HLA-B44:053DX86712PKASSPQTVKGGIS-5.3978-5.5112
HLA-A02:016TDR6712PKASSPQTVKGGIS-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of PTPRK-EPB41L2

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
PTPRK-EPB41L2chr6128841404chr6131184858515RPKASSPQTVCGGCCCAAGGCCAGTTCTCCGCAGACTGTA
PTPRK-EPB41L2chr6128841404chr6131184858516RPKASSPQTVKCGGCCCAAGGCCAGTTCTCCGCAGACTGTAAAA
PTPRK-EPB41L2chr6128841404chr6131184858716KASSPQTVKAAGGCCAGTTCTCCGCAGACTGTAAAA

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 PTPRK-EPB41L2

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
COADPTPRK-EPB41L2chr6128841404ENST00000368207chr6131184858ENST00000368128TCGA-CM-6164-01A

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Potential target of CAR-T therapy development for PTPRK-EPB41L2

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 PTPRK-EPB41L2

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 PTPRK-EPB41L2

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