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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:PPFIA1-MARK2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PPFIA1-MARK2
FusionPDB ID: 67404
FusionGDB2.0 ID: 67404
HgeneTgene
Gene symbol

PPFIA1

MARK2

Gene ID

8500

2011

Gene namePTPRF interacting protein alpha 1microtubule affinity regulating kinase 2
SynonymsLIP.1|LIP1|LIPRINEMK-1|EMK1|PAR-1|Par-1b|Par1b
Cytomap

11q13.3

11q13.1

Type of geneprotein-codingprotein-coding
Descriptionliprin-alpha-1LAR-interacting protein 1LIP-1Liprin-alpha1protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-1protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1serine/threonine-protein kinase MARK2ELKL motif kinase 1MAP/microtubule affinity-regulating kinase 2PAR1 homolog bSer/Thr protein kinase PAR-1Bserine/threonine protein kinase EMKtesticular tissue protein Li 117
Modification date2020032720200329
UniProtAcc.

Q7KZI7

Main function of 5'-partner protein: FUNCTION: Serine/threonine-protein kinase (PubMed:23666762). Involved in cell polarity and microtubule dynamics regulation. Phosphorylates CRTC2/TORC2, DCX, HDAC7, KIF13B, MAP2, MAP4 and RAB11FIP2. Phosphorylates the microtubule-associated protein MAPT/TAU (PubMed:23666762). Plays a key role in cell polarity by phosphorylating the microtubule-associated proteins MAP2, MAP4 and MAPT/TAU at KXGS motifs, causing detachment from microtubules, and their disassembly. Regulates epithelial cell polarity by phosphorylating RAB11FIP2. Involved in the regulation of neuronal migration through its dual activities in regulating cellular polarity and microtubule dynamics, possibly by phosphorylating and regulating DCX. Regulates axogenesis by phosphorylating KIF13B, promoting interaction between KIF13B and 14-3-3 and inhibiting microtubule-dependent accumulation of KIF13B. Also required for neurite outgrowth and establishment of neuronal polarity. Regulates localization and activity of some histone deacetylases by mediating phosphorylation of HDAC7, promoting subsequent interaction between HDAC7 and 14-3-3 and export from the nucleus. Also acts as a positive regulator of the Wnt signaling pathway, probably by mediating phosphorylation of dishevelled proteins (DVL1, DVL2 and/or DVL3). Modulates the developmental decision to build a columnar versus a hepatic epithelial cell apparently by promoting a switch from a direct to a transcytotic mode of apical protein delivery. Essential for the asymmetric development of membrane domains of polarized epithelial cells. {ECO:0000269|PubMed:11433294, ECO:0000269|PubMed:12429843, ECO:0000269|PubMed:14976552, ECO:0000269|PubMed:15158914, ECO:0000269|PubMed:15324659, ECO:0000269|PubMed:15365179, ECO:0000269|PubMed:16775013, ECO:0000269|PubMed:16980613, ECO:0000269|PubMed:18626018, ECO:0000269|PubMed:20194617, ECO:0000269|PubMed:23666762}.
Ensembl transtripts involved in fusion geneENST idsENST00000253925, ENST00000389547, 
ENST00000530548, 
ENST00000315032, 
ENST00000350490, ENST00000361128, 
ENST00000377810, ENST00000502399, 
ENST00000508192, ENST00000509502, 
ENST00000513765, ENST00000408948, 
ENST00000425897, ENST00000377809, 
ENST00000402010, ENST00000413835, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score44 X 20 X 15=132007 X 6 X 3=126
# samples 6010
** MAII scorelog2(60/13200*10)=-4.4594316186373
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/126*10)=-0.333423733725192
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PPFIA1 [Title/Abstract] AND MARK2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PPFIA1 [Title/Abstract] AND MARK2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PPFIA1(70118542)-MARK2(63662631), # samples:3
Anticipated loss of major functional domain due to fusion event.PPFIA1-MARK2 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.
PPFIA1-MARK2 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.
PPFIA1-MARK2 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.
PPFIA1-MARK2 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
TgeneMARK2

GO:0006468

protein phosphorylation

14976552

TgeneMARK2

GO:0010976

positive regulation of neuron projection development

12429843

TgeneMARK2

GO:0018105

peptidyl-serine phosphorylation

10542369|16717194

TgeneMARK2

GO:0030010

establishment of cell polarity

12429843

TgeneMARK2

GO:0035556

intracellular signal transduction

14976552

TgeneMARK2

GO:0045197

establishment or maintenance of epithelial cell apical/basal polarity

15324659

TgeneMARK2

GO:0070507

regulation of microtubule cytoskeleton organization

10542369



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/chr11:70118542/chr11:63662631)
- 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 PPFIA1 (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 MARK2 (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)
ENST00000253925PPFIA1chr1170118542+ENST00000377809MARK2chr1163662631+4529479652746893
ENST00000253925PPFIA1chr1170118542+ENST00000402010MARK2chr1163662631+4574479652791908
ENST00000253925PPFIA1chr1170118542+ENST00000413835MARK2chr1163662631+4412479652629854
ENST00000389547PPFIA1chr1170118542+ENST00000377809MARK2chr1163662631+4512462482729893
ENST00000389547PPFIA1chr1170118542+ENST00000402010MARK2chr1163662631+4557462482774908
ENST00000389547PPFIA1chr1170118542+ENST00000413835MARK2chr1163662631+4395462482612854
ENST00000253925PPFIA1chr1170118542+ENST00000377809MARK2chr1163662630+4529479652746893
ENST00000253925PPFIA1chr1170118542+ENST00000402010MARK2chr1163662630+4574479652791908
ENST00000253925PPFIA1chr1170118542+ENST00000413835MARK2chr1163662630+4412479652629854
ENST00000389547PPFIA1chr1170118542+ENST00000377809MARK2chr1163662630+4512462482729893
ENST00000389547PPFIA1chr1170118542+ENST00000402010MARK2chr1163662630+4557462482774908
ENST00000389547PPFIA1chr1170118542+ENST00000413835MARK2chr1163662630+4395462482612854

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
ENST00000253925ENST00000377809PPFIA1chr1170118542+MARK2chr1163662631+0.003715910.99628407
ENST00000253925ENST00000402010PPFIA1chr1170118542+MARK2chr1163662631+0.0038336690.99616635
ENST00000253925ENST00000413835PPFIA1chr1170118542+MARK2chr1163662631+0.0051007480.9948992
ENST00000389547ENST00000377809PPFIA1chr1170118542+MARK2chr1163662631+0.0037117120.9962883
ENST00000389547ENST00000402010PPFIA1chr1170118542+MARK2chr1163662631+0.0038280930.9961719
ENST00000389547ENST00000413835PPFIA1chr1170118542+MARK2chr1163662631+0.0050798010.9949202
ENST00000253925ENST00000377809PPFIA1chr1170118542+MARK2chr1163662630+0.003715910.99628407
ENST00000253925ENST00000402010PPFIA1chr1170118542+MARK2chr1163662630+0.0038336690.99616635
ENST00000253925ENST00000413835PPFIA1chr1170118542+MARK2chr1163662630+0.0051007480.9948992
ENST00000389547ENST00000377809PPFIA1chr1170118542+MARK2chr1163662630+0.0037117120.9962883
ENST00000389547ENST00000402010PPFIA1chr1170118542+MARK2chr1163662630+0.0038280930.9961719
ENST00000389547ENST00000413835PPFIA1chr1170118542+MARK2chr1163662630+0.0050798010.9949202

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 PPFIA1-MARK2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PPFIA1chr1170118542MARK2chr1163662630462136ERDSLQRQLNTALPQPTLGHLDSKPS
PPFIA1chr1170118542MARK2chr1163662630479136ERDSLQRQLNTALPQPTLGHLDSKPS
PPFIA1chr1170118542MARK2chr1163662631462136ERDSLQRQLNTALPQPTLGHLDSKPS
PPFIA1chr1170118542MARK2chr1163662631479136ERDSLQRQLNTALPQPTLGHLDSKPS

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Potential FusionNeoAntigen Information of PPFIA1-MARK2 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.
PPFIA1-MARK2_70118542_63662630.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)
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B51:02TALPQPTL0.99890.97941018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B51:01TALPQPTL0.99850.97921018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B52:01TALPQPTL0.99840.99811018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:03LPQPTLGHL0.98210.84241221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:08LPQPTLGHL0.96060.70711221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B53:01LPQPTLGHL0.9280.51781221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:05LPQPTLGHL0.91160.71961221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:03NTALPQPTL0.89710.9574918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:02LPQPTLGHL0.88840.9711221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:04LPQPTLGHL0.88840.9711221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:04NTALPQPTL0.77530.9799918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:02NTALPQPTL0.77530.9799918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B81:01LPQPTLGHL0.22320.59981221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B82:01LPQPTLGHL0.18330.68491221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B07:02ALPQPTLGHL0.54080.61351121
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B07:05ALPQPTLGHL0.53970.67391121
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B81:01ALPQPTLGHL0.5250.7651121
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B82:01ALPQPTLGHL0.36620.84331121
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C03:19TALPQPTL0.99980.99711018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C03:07TALPQPTL0.99970.99411018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C03:08TALPQPTL0.99940.97631018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B51:07TALPQPTL0.99860.99581018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C08:04TALPQPTL0.98110.99861018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C08:13TALPQPTL0.98110.99861018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B51:08TALPQPTL0.9770.90881018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C08:03TALPQPTL0.86170.99911018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C03:08NTALPQPTL0.99810.9395918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C03:07NTALPQPTL0.9980.9811918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C03:19NTALPQPTL0.99690.9928918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C15:06NTALPQPTL0.99450.9473918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C04:06NTALPQPTL0.98150.9662918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C08:13NTALPQPTL0.9510.9899918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C08:04NTALPQPTL0.9510.9899918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C01:17NTALPQPTL0.92820.9805918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:12LPQPTLGHL0.88840.9711221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B51:07LPQPTLGHL0.8760.98021221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B78:01LPQPTLGHL0.860.53521221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B07:12LPQPTLGHL0.84110.51911221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C08:03NTALPQPTL0.79030.9961918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C01:30NTALPQPTL0.79020.9841918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:12NTALPQPTL0.77530.9799918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B39:10LPQPTLGHL0.76570.97741221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B42:02LPQPTLGHL0.72110.92991221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C02:06NTALPQPTL0.71950.9876918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C03:14NTALPQPTL0.70650.9927918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B42:01LPQPTLGHL0.63510.92581221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C01:30ALPQPTLGHL0.93190.97551121
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C01:17ALPQPTLGHL0.88710.97451121
PPFIA1-MARK2chr1170118542chr1163662630479HLA-A02:07ALPQPTLGHL0.75820.74931121
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B07:04ALPQPTLGHL0.67130.62041121
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B07:12ALPQPTLGHL0.62890.76261121
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B42:01ALPQPTLGHL0.44180.92831121
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C03:05TALPQPTL0.99970.98331018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C03:17TALPQPTL0.99930.99371018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C03:04TALPQPTL0.99920.99631018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C03:03TALPQPTL0.99920.99631018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B51:13TALPQPTL0.99850.86361018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B51:14TALPQPTL0.99740.96721018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:22TALPQPTL0.99680.90231018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B51:06TALPQPTL0.99330.98091018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B51:21TALPQPTL0.9930.97431018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B51:09TALPQPTL0.9920.97381018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:13TALPQPTL0.98580.97811018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B51:29TALPQPTL0.98420.91018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C03:06TALPQPTL0.98060.99691018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C16:01TALPQPTL0.96350.99561018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C16:02TALPQPTL0.95240.99751018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C08:01TALPQPTL0.86170.99911018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B07:13TALPQPTL0.69160.92711018
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C03:03NTALPQPTL0.99820.9922918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C03:04NTALPQPTL0.99820.9922918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C03:67NTALPQPTL0.99730.988918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C03:17NTALPQPTL0.99590.9824918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C03:05NTALPQPTL0.99570.9406918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C15:05NTALPQPTL0.99370.9587918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C15:02NTALPQPTL0.99090.9137918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C01:03NTALPQPTL0.99060.9758918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:23LPQPTLGHL0.98060.88021221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:13LPQPTLGHL0.97740.85161221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-A68:02NTALPQPTL0.96650.7874918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C03:06NTALPQPTL0.95850.9936918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B55:04LPQPTLGHL0.95430.53081221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:11LPQPTLGHL0.94680.92361221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C01:02NTALPQPTL0.93870.9797918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-A69:01NTALPQPTL0.92550.8601918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:30LPQPTLGHL0.92320.80071221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:17LPQPTLGHL0.92320.80071221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-A25:01NTALPQPTL0.92080.946918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:09LPQPTLGHL0.88840.9711221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:13NTALPQPTL0.88350.9594918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B78:02LPQPTLGHL0.88090.63631221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B53:02LPQPTLGHL0.82070.51151221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B67:01LPQPTLGHL0.80860.95541221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C08:01NTALPQPTL0.79030.9961918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:09NTALPQPTL0.77530.9799918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C16:01NTALPQPTL0.72610.9893918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C16:02NTALPQPTL0.71560.9941918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C17:01NTALPQPTL0.55690.9659918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B51:06NTALPQPTL0.41230.764918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B82:02LPQPTLGHL0.18330.68491221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B07:13NTALPQPTL0.16610.8615918
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B35:43LPQPTLGHL0.03040.86081221
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C01:03ALPQPTLGHL0.9570.9571121
PPFIA1-MARK2chr1170118542chr1163662630479HLA-C01:02ALPQPTLGHL0.91650.97451121
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B07:26ALPQPTLGHL0.65910.64681121
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B07:22ALPQPTLGHL0.54080.61351121
PPFIA1-MARK2chr1170118542chr1163662630479HLA-B82:02ALPQPTLGHL0.36620.84331121

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Potential FusionNeoAntigen Information of PPFIA1-MARK2 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 PPFIA1-MARK2

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
8131RQLNTALPQPTLGHPPFIA1MARK2chr1170118542chr1163662630479

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PPFIA1-MARK2

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-B14:023BVN8131RQLNTALPQPTLGH-6.61234-6.72414
HLA-B14:023BVN8131RQLNTALPQPTLGH-4.84535-5.88845
HLA-B52:013W398131RQLNTALPQPTLGH-6.69006-6.80186
HLA-B52:013W398131RQLNTALPQPTLGH-4.30971-5.35281
HLA-A24:025HGA8131RQLNTALPQPTLGH-5.87505-5.98685
HLA-A24:025HGA8131RQLNTALPQPTLGH-5.27746-6.32056
HLA-B44:053DX88131RQLNTALPQPTLGH-8.48373-8.59553
HLA-B44:053DX88131RQLNTALPQPTLGH-5.07395-6.11705

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Vaccine Design for the FusionNeoAntigens of PPFIA1-MARK2

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
PPFIA1-MARK2chr1170118542chr11636626301018TALPQPTLCTTCCACAGCCCACCTTGGGACAC
PPFIA1-MARK2chr1170118542chr11636626301121ALPQPTLGHLCCACAGCCCACCTTGGGACACCTTGACTCC
PPFIA1-MARK2chr1170118542chr11636626301221LPQPTLGHLCAGCCCACCTTGGGACACCTTGACTCC
PPFIA1-MARK2chr1170118542chr1163662630918NTALPQPTLGCACTTCCACAGCCCACCTTGGGACAC

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 PPFIA1-MARK2

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
BRCAPPFIA1-MARK2chr1170118542ENST00000253925chr1163662630ENST00000377809TCGA-A2-A1G4

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Potential target of CAR-T therapy development for PPFIA1-MARK2

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 PPFIA1-MARK2

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 PPFIA1-MARK2

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