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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:PARD3-IL2RA

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PARD3-IL2RA
FusionPDB ID: 62709
FusionGDB2.0 ID: 62709
HgeneTgene
Gene symbol

PARD3

IL2RA

Gene ID

56288

3559

Gene namepar-3 family cell polarity regulatorinterleukin 2 receptor subunit alpha
SynonymsASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2CD25|IDDM10|IL2R|IMD41|TCGFR|p55
Cytomap

10p11.22-p11.21

10p15.1

Type of geneprotein-codingprotein-coding
Descriptionpartitioning defective 3 homologCTCL tumor antigen se2-5PAR3-alphaatypical PKC isotype-specific interacting proteinbazookapar-3 family cell polarity regulator alphapar-3 partitioning defective 3 homologprotein phosphatase 1, regulatory subunit 118interleukin-2 receptor subunit alphaIL-2 receptor subunit alphaIL-2R subunit alphaTAC antigeninterleukin 2 receptor, alpha
Modification date2020032720200322
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000340077, ENST00000346874, 
ENST00000350537, ENST00000374773, 
ENST00000374776, ENST00000374788, 
ENST00000374789, ENST00000374790, 
ENST00000374794, ENST00000545260, 
ENST00000545693, ENST00000374768, 
ENST00000466092, ENST00000544292, 
ENST00000256876, ENST00000379954, 
ENST00000379959, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score33 X 20 X 14=92404 X 4 X 4=64
# samples 495
** MAII scorelog2(49/9240*10)=-4.23703919730085
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/64*10)=-0.356143810225275
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PARD3 [Title/Abstract] AND IL2RA [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PARD3 [Title/Abstract] AND IL2RA [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PARD3(34805907)-IL2RA(6067988), # samples:3
Anticipated loss of major functional domain due to fusion event.PARD3-IL2RA 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.
PARD3-IL2RA 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.
PARD3-IL2RA 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.
PARD3-IL2RA 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


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/chr10:34805907/chr10:6067988)
- 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 PARD3 (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 IL2RA (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)
ENST00000545260PARD3chr1034805907-ENST00000379959IL2RAchr106067988-36717331981487429
ENST00000545260PARD3chr1034805907-ENST00000379954IL2RAchr106067988-20737331981271357
ENST00000545260PARD3chr1034805907-ENST00000256876IL2RAchr106067988-15367331981460420
ENST00000545693PARD3chr1034805907-ENST00000379959IL2RAchr106067988-36717331981487429
ENST00000545693PARD3chr1034805907-ENST00000379954IL2RAchr106067988-20737331981271357
ENST00000545693PARD3chr1034805907-ENST00000256876IL2RAchr106067988-15367331981460420
ENST00000350537PARD3chr1034805907-ENST00000379959IL2RAchr106067988-36677291941483429
ENST00000350537PARD3chr1034805907-ENST00000379954IL2RAchr106067988-20697291941267357
ENST00000350537PARD3chr1034805907-ENST00000256876IL2RAchr106067988-15327291941456420
ENST00000346874PARD3chr1034805907-ENST00000379959IL2RAchr106067988-36677291941483429
ENST00000346874PARD3chr1034805907-ENST00000379954IL2RAchr106067988-20697291941267357
ENST00000346874PARD3chr1034805907-ENST00000256876IL2RAchr106067988-15327291941456420
ENST00000374789PARD3chr1034805907-ENST00000379959IL2RAchr106067988-36677291941483429
ENST00000374789PARD3chr1034805907-ENST00000379954IL2RAchr106067988-20697291941267357
ENST00000374789PARD3chr1034805907-ENST00000256876IL2RAchr106067988-15327291941456420
ENST00000374790PARD3chr1034805907-ENST00000379959IL2RAchr106067988-36677291941483429
ENST00000374790PARD3chr1034805907-ENST00000379954IL2RAchr106067988-20697291941267357
ENST00000374790PARD3chr1034805907-ENST00000256876IL2RAchr106067988-15327291941456420
ENST00000374794PARD3chr1034805907-ENST00000379959IL2RAchr106067988-36677291941483429
ENST00000374794PARD3chr1034805907-ENST00000379954IL2RAchr106067988-20697291941267357
ENST00000374794PARD3chr1034805907-ENST00000256876IL2RAchr106067988-15327291941456420
ENST00000374788PARD3chr1034805907-ENST00000379959IL2RAchr106067988-36677291941483429
ENST00000374788PARD3chr1034805907-ENST00000379954IL2RAchr106067988-20697291941267357
ENST00000374788PARD3chr1034805907-ENST00000256876IL2RAchr106067988-15327291941456420
ENST00000374776PARD3chr1034805907-ENST00000379959IL2RAchr106067988-36677291941483429
ENST00000374776PARD3chr1034805907-ENST00000379954IL2RAchr106067988-20697291941267357
ENST00000374776PARD3chr1034805907-ENST00000256876IL2RAchr106067988-15327291941456420
ENST00000340077PARD3chr1034805907-ENST00000379959IL2RAchr106067988-36717331981487429
ENST00000340077PARD3chr1034805907-ENST00000379954IL2RAchr106067988-20737331981271357
ENST00000340077PARD3chr1034805907-ENST00000256876IL2RAchr106067988-15367331981460420
ENST00000374773PARD3chr1034805907-ENST00000379959IL2RAchr106067988-36677291941483429
ENST00000374773PARD3chr1034805907-ENST00000379954IL2RAchr106067988-20697291941267357
ENST00000374773PARD3chr1034805907-ENST00000256876IL2RAchr106067988-15327291941456420

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
ENST00000545260ENST00000379959PARD3chr1034805907-IL2RAchr106067988-0.0061009820.993899
ENST00000545260ENST00000379954PARD3chr1034805907-IL2RAchr106067988-0.0076708380.9923292
ENST00000545260ENST00000256876PARD3chr1034805907-IL2RAchr106067988-0.0261533480.9738467
ENST00000545693ENST00000379959PARD3chr1034805907-IL2RAchr106067988-0.0061009820.993899
ENST00000545693ENST00000379954PARD3chr1034805907-IL2RAchr106067988-0.0076708380.9923292
ENST00000545693ENST00000256876PARD3chr1034805907-IL2RAchr106067988-0.0261533480.9738467
ENST00000350537ENST00000379959PARD3chr1034805907-IL2RAchr106067988-0.0061373110.99386275
ENST00000350537ENST00000379954PARD3chr1034805907-IL2RAchr106067988-0.0074048570.99259514
ENST00000350537ENST00000256876PARD3chr1034805907-IL2RAchr106067988-0.0254054680.97459453
ENST00000346874ENST00000379959PARD3chr1034805907-IL2RAchr106067988-0.0061373110.99386275
ENST00000346874ENST00000379954PARD3chr1034805907-IL2RAchr106067988-0.0074048570.99259514
ENST00000346874ENST00000256876PARD3chr1034805907-IL2RAchr106067988-0.0254054680.97459453
ENST00000374789ENST00000379959PARD3chr1034805907-IL2RAchr106067988-0.0061373110.99386275
ENST00000374789ENST00000379954PARD3chr1034805907-IL2RAchr106067988-0.0074048570.99259514
ENST00000374789ENST00000256876PARD3chr1034805907-IL2RAchr106067988-0.0254054680.97459453
ENST00000374790ENST00000379959PARD3chr1034805907-IL2RAchr106067988-0.0061373110.99386275
ENST00000374790ENST00000379954PARD3chr1034805907-IL2RAchr106067988-0.0074048570.99259514
ENST00000374790ENST00000256876PARD3chr1034805907-IL2RAchr106067988-0.0254054680.97459453
ENST00000374794ENST00000379959PARD3chr1034805907-IL2RAchr106067988-0.0061373110.99386275
ENST00000374794ENST00000379954PARD3chr1034805907-IL2RAchr106067988-0.0074048570.99259514
ENST00000374794ENST00000256876PARD3chr1034805907-IL2RAchr106067988-0.0254054680.97459453
ENST00000374788ENST00000379959PARD3chr1034805907-IL2RAchr106067988-0.0061373110.99386275
ENST00000374788ENST00000379954PARD3chr1034805907-IL2RAchr106067988-0.0074048570.99259514
ENST00000374788ENST00000256876PARD3chr1034805907-IL2RAchr106067988-0.0254054680.97459453
ENST00000374776ENST00000379959PARD3chr1034805907-IL2RAchr106067988-0.0061373110.99386275
ENST00000374776ENST00000379954PARD3chr1034805907-IL2RAchr106067988-0.0074048570.99259514
ENST00000374776ENST00000256876PARD3chr1034805907-IL2RAchr106067988-0.0254054680.97459453
ENST00000340077ENST00000379959PARD3chr1034805907-IL2RAchr106067988-0.0061009820.993899
ENST00000340077ENST00000379954PARD3chr1034805907-IL2RAchr106067988-0.0076708380.9923292
ENST00000340077ENST00000256876PARD3chr1034805907-IL2RAchr106067988-0.0261533480.9738467
ENST00000374773ENST00000379959PARD3chr1034805907-IL2RAchr106067988-0.0061373110.99386275
ENST00000374773ENST00000379954PARD3chr1034805907-IL2RAchr106067988-0.0074048570.99259514
ENST00000374773ENST00000256876PARD3chr1034805907-IL2RAchr106067988-0.0254054680.97459453

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 PARD3-IL2RA

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PARD3chr1034805907IL2RAchr106067988729172FQPYQATSEIEVTPSVLRAKLCDDDP
PARD3chr1034805907IL2RAchr106067988733172FQPYQATSEIEVTPSVLRAKLCDDDP

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Potential FusionNeoAntigen Information of PARD3-IL2RA 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.
PARD3-IL2RA_34805907_6067988.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)
PARD3-IL2RAchr1034805907chr106067988733HLA-B07:02TPSVLRAKL0.9990.52281221
PARD3-IL2RAchr1034805907chr106067988733HLA-B07:10TPSVLRAKL0.99890.58051221
PARD3-IL2RAchr1034805907chr106067988733HLA-A30:08VTPSVLRAK0.94730.75851120
PARD3-IL2RAchr1034805907chr106067988733HLA-B08:01TPSVLRAKL0.91290.51281221
PARD3-IL2RAchr1034805907chr106067988733HLA-B08:09TPSVLRAKL0.81550.65581221
PARD3-IL2RAchr1034805907chr106067988733HLA-B35:03TPSVLRAKL0.69860.92461221
PARD3-IL2RAchr1034805907chr106067988733HLA-B35:05TPSVLRAKL0.48420.62641221
PARD3-IL2RAchr1034805907chr106067988733HLA-B35:02TPSVLRAKL0.47780.97631221
PARD3-IL2RAchr1034805907chr106067988733HLA-B35:04TPSVLRAKL0.47780.97631221
PARD3-IL2RAchr1034805907chr106067988733HLA-B81:01TPSVLRAKL0.04240.50091221
PARD3-IL2RAchr1034805907chr106067988733HLA-A66:01EVTPSVLRAK0.99070.65961020
PARD3-IL2RAchr1034805907chr106067988733HLA-A26:03EVTPSVLRAK0.87280.65711020
PARD3-IL2RAchr1034805907chr106067988733HLA-B81:01VTPSVLRAKL0.68720.53351121
PARD3-IL2RAchr1034805907chr106067988733HLA-B07:02VTPSVLRAKL0.39960.57681121
PARD3-IL2RAchr1034805907chr106067988733HLA-A02:21ATSEIEVTPSV0.99380.6827516
PARD3-IL2RAchr1034805907chr106067988733HLA-B42:02TPSVLRAKL0.93890.52071221
PARD3-IL2RAchr1034805907chr106067988733HLA-B42:01TPSVLRAKL0.92760.51831221
PARD3-IL2RAchr1034805907chr106067988733HLA-B07:12TPSVLRAKL0.90350.71571221
PARD3-IL2RAchr1034805907chr106067988733HLA-B14:03TPSVLRAKL0.73530.90981221
PARD3-IL2RAchr1034805907chr106067988733HLA-B35:12TPSVLRAKL0.47780.97631221
PARD3-IL2RAchr1034805907chr106067988733HLA-B39:10TPSVLRAKL0.33650.96211221
PARD3-IL2RAchr1034805907chr106067988733HLA-B40:06TSEIEVTPSV0.96630.9002616
PARD3-IL2RAchr1034805907chr106067988733HLA-C01:17VTPSVLRAKL0.78490.97771121
PARD3-IL2RAchr1034805907chr106067988733HLA-C01:30VTPSVLRAKL0.67850.97821121
PARD3-IL2RAchr1034805907chr106067988733HLA-B07:04VTPSVLRAKL0.67390.51271121
PARD3-IL2RAchr1034805907chr106067988733HLA-B42:01VTPSVLRAKL0.64110.57451121
PARD3-IL2RAchr1034805907chr106067988733HLA-B40:06ATSEIEVTPSV0.99280.9132516
PARD3-IL2RAchr1034805907chr106067988733HLA-B07:22TPSVLRAKL0.9990.52281221
PARD3-IL2RAchr1034805907chr106067988733HLA-B07:09TPSVLRAKL0.99870.56581221
PARD3-IL2RAchr1034805907chr106067988733HLA-A30:01VTPSVLRAK0.94850.87151120
PARD3-IL2RAchr1034805907chr106067988733HLA-B08:18TPSVLRAKL0.91290.51281221
PARD3-IL2RAchr1034805907chr106067988733HLA-B08:12TPSVLRAKL0.59660.7531221
PARD3-IL2RAchr1034805907chr106067988733HLA-B35:09TPSVLRAKL0.47780.97631221
PARD3-IL2RAchr1034805907chr106067988733HLA-B35:17TPSVLRAKL0.47420.77231221
PARD3-IL2RAchr1034805907chr106067988733HLA-B35:30TPSVLRAKL0.47420.77231221
PARD3-IL2RAchr1034805907chr106067988733HLA-B67:01TPSVLRAKL0.37960.91811221
PARD3-IL2RAchr1034805907chr106067988733HLA-A68:02TSEIEVTPSV0.90260.7804616
PARD3-IL2RAchr1034805907chr106067988733HLA-A69:01TSEIEVTPSV0.83990.8995616
PARD3-IL2RAchr1034805907chr106067988733HLA-C01:02VTPSVLRAKL0.75790.97631121
PARD3-IL2RAchr1034805907chr106067988733HLA-B07:22VTPSVLRAKL0.39960.57681121
PARD3-IL2RAchr1034805907chr106067988733HLA-A68:02ATSEIEVTPSV0.99780.6735516
PARD3-IL2RAchr1034805907chr106067988733HLA-A68:02EVTPSVLRAKL0.99460.52081021
PARD3-IL2RAchr1034805907chr106067988733HLA-A02:06ATSEIEVTPSV0.99380.6827516
PARD3-IL2RAchr1034805907chr106067988733HLA-A69:01ATSEIEVTPSV0.99180.763516
PARD3-IL2RAchr1034805907chr106067988733HLA-B40:04ATSEIEVTPSV0.91690.8246516

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Potential FusionNeoAntigen Information of PARD3-IL2RA 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.
PARD3-IL2RA_34805907_6067988.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).
Fusion geneHchrHbpTgeneTchrTbpHLA IIFusionNeoAntigen peptideNeoantigen start (at BP 13)Neoantigen end (at BP 13)
PARD3-IL2RAchr1034805907chr106067988733DRB1-0303ATSEIEVTPSVLRAK520
PARD3-IL2RAchr1034805907chr106067988733DRB1-0303TSEIEVTPSVLRAKL621
PARD3-IL2RAchr1034805907chr106067988733DRB1-0701FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0701QPYQATSEIEVTPSV116
PARD3-IL2RAchr1034805907chr106067988733DRB1-0703FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0703QPYQATSEIEVTPSV116
PARD3-IL2RAchr1034805907chr106067988733DRB1-0704FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0705FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0705QPYQATSEIEVTPSV116
PARD3-IL2RAchr1034805907chr106067988733DRB1-0706FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0706QPYQATSEIEVTPSV116
PARD3-IL2RAchr1034805907chr106067988733DRB1-0707FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0707QPYQATSEIEVTPSV116
PARD3-IL2RAchr1034805907chr106067988733DRB1-0708FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0708QPYQATSEIEVTPSV116
PARD3-IL2RAchr1034805907chr106067988733DRB1-0709FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0709QPYQATSEIEVTPSV116
PARD3-IL2RAchr1034805907chr106067988733DRB1-0711FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0712FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0712QPYQATSEIEVTPSV116
PARD3-IL2RAchr1034805907chr106067988733DRB1-0713FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0713QPYQATSEIEVTPSV116
PARD3-IL2RAchr1034805907chr106067988733DRB1-0714FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0714QPYQATSEIEVTPSV116
PARD3-IL2RAchr1034805907chr106067988733DRB1-0715FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0715QPYQATSEIEVTPSV116
PARD3-IL2RAchr1034805907chr106067988733DRB1-0716FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0716QPYQATSEIEVTPSV116
PARD3-IL2RAchr1034805907chr106067988733DRB1-0717FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0717QPYQATSEIEVTPSV116
PARD3-IL2RAchr1034805907chr106067988733DRB1-0719FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0719QPYQATSEIEVTPSV116
PARD3-IL2RAchr1034805907chr106067988733DRB1-0901FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0901QPYQATSEIEVTPSV116
PARD3-IL2RAchr1034805907chr106067988733DRB1-0903FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0904FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0904QPYQATSEIEVTPSV116
PARD3-IL2RAchr1034805907chr106067988733DRB1-0905FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0905QPYQATSEIEVTPSV116
PARD3-IL2RAchr1034805907chr106067988733DRB1-0907FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0907QPYQATSEIEVTPSV116
PARD3-IL2RAchr1034805907chr106067988733DRB1-0908FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0909FQPYQATSEIEVTPS015
PARD3-IL2RAchr1034805907chr106067988733DRB1-0909QPYQATSEIEVTPSV116
PARD3-IL2RAchr1034805907chr106067988733DRB1-1406ATSEIEVTPSVLRAK520
PARD3-IL2RAchr1034805907chr106067988733DRB1-1420ATSEIEVTPSVLRAK520
PARD3-IL2RAchr1034805907chr106067988733DRB1-1421ATSEIEVTPSVLRAK520
PARD3-IL2RAchr1034805907chr106067988733DRB1-1429ATSEIEVTPSVLRAK520
PARD3-IL2RAchr1034805907chr106067988733DRB1-1429TSEIEVTPSVLRAKL621
PARD3-IL2RAchr1034805907chr106067988733DRB1-1447ATSEIEVTPSVLRAK520
PARD3-IL2RAchr1034805907chr106067988733DRB1-1447TSEIEVTPSVLRAKL621
PARD3-IL2RAchr1034805907chr106067988733DRB1-1452ATSEIEVTPSVLRAK520
PARD3-IL2RAchr1034805907chr106067988733DRB1-1452TSEIEVTPSVLRAKL621
PARD3-IL2RAchr1034805907chr106067988733DRB1-1483ATSEIEVTPSVLRAK520
PARD3-IL2RAchr1034805907chr106067988733DRB1-1525ATSEIEVTPSVLRAK520
PARD3-IL2RAchr1034805907chr106067988733DRB1-1525TSEIEVTPSVLRAKL621
PARD3-IL2RAchr1034805907chr106067988733DRB5-0101ATSEIEVTPSVLRAK520
PARD3-IL2RAchr1034805907chr106067988733DRB5-0101TSEIEVTPSVLRAKL621
PARD3-IL2RAchr1034805907chr106067988733DRB5-0105ATSEIEVTPSVLRAK520
PARD3-IL2RAchr1034805907chr106067988733DRB5-0105TSEIEVTPSVLRAKL621
PARD3-IL2RAchr1034805907chr106067988733DRB5-0106ATSEIEVTPSVLRAK520
PARD3-IL2RAchr1034805907chr106067988733DRB5-0106TSEIEVTPSVLRAKL621
PARD3-IL2RAchr1034805907chr106067988733DRB5-0106QATSEIEVTPSVLRA419
PARD3-IL2RAchr1034805907chr106067988733DRB5-0106SEIEVTPSVLRAKLC722
PARD3-IL2RAchr1034805907chr106067988733DRB5-0111ATSEIEVTPSVLRAK520
PARD3-IL2RAchr1034805907chr106067988733DRB5-0111TSEIEVTPSVLRAKL621
PARD3-IL2RAchr1034805907chr106067988733DRB5-0113ATSEIEVTPSVLRAK520
PARD3-IL2RAchr1034805907chr106067988733DRB5-0113TSEIEVTPSVLRAKL621
PARD3-IL2RAchr1034805907chr106067988733DRB5-0114ATSEIEVTPSVLRAK520
PARD3-IL2RAchr1034805907chr106067988733DRB5-0114TSEIEVTPSVLRAKL621
PARD3-IL2RAchr1034805907chr106067988733DRB5-0202ATSEIEVTPSVLRAK520
PARD3-IL2RAchr1034805907chr106067988733DRB5-0202TSEIEVTPSVLRAKL621
PARD3-IL2RAchr1034805907chr106067988733DRB5-0203ATSEIEVTPSVLRAK520
PARD3-IL2RAchr1034805907chr106067988733DRB5-0203TSEIEVTPSVLRAKL621
PARD3-IL2RAchr1034805907chr106067988733DRB5-0204ATSEIEVTPSVLRAK520
PARD3-IL2RAchr1034805907chr106067988733DRB5-0204TSEIEVTPSVLRAKL621
PARD3-IL2RAchr1034805907chr106067988733DRB5-0205ATSEIEVTPSVLRAK520
PARD3-IL2RAchr1034805907chr106067988733DRB5-0205TSEIEVTPSVLRAKL621
PARD3-IL2RAchr1034805907chr106067988733DRB5-0205QATSEIEVTPSVLRA419
PARD3-IL2RAchr1034805907chr106067988733DRB5-0205SEIEVTPSVLRAKLC722

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Fusion breakpoint peptide structures of PARD3-IL2RA

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
9637TSEIEVTPSVLRAKPARD3IL2RAchr1034805907chr106067988733

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PARD3-IL2RA

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-B14:023BVN9637TSEIEVTPSVLRAK-7.15543-7.26883
HLA-B14:023BVN9637TSEIEVTPSVLRAK-4.77435-5.80965
HLA-B52:013W399637TSEIEVTPSVLRAK-6.80875-6.92215
HLA-B52:013W399637TSEIEVTPSVLRAK-4.20386-5.23916
HLA-A11:014UQ29637TSEIEVTPSVLRAK-7.5194-8.5547
HLA-A11:014UQ29637TSEIEVTPSVLRAK-6.9601-7.0735
HLA-A24:025HGA9637TSEIEVTPSVLRAK-7.52403-7.63743
HLA-A24:025HGA9637TSEIEVTPSVLRAK-5.82433-6.85963
HLA-B27:056PYJ9637TSEIEVTPSVLRAK-3.28285-4.31815
HLA-B44:053DX89637TSEIEVTPSVLRAK-5.91172-6.94702
HLA-B44:053DX89637TSEIEVTPSVLRAK-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of PARD3-IL2RA

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
PARD3-IL2RAchr1034805907chr1060679881020EVTPSVLRAKTTCGAGCAAAGCTCTGTGACGATGACCCGC
PARD3-IL2RAchr1034805907chr1060679881021EVTPSVLRAKLTTCGAGCAAAGCTCTGTGACGATGACCCGCCAG
PARD3-IL2RAchr1034805907chr1060679881120VTPSVLRAKGAGCAAAGCTCTGTGACGATGACCCGC
PARD3-IL2RAchr1034805907chr1060679881121VTPSVLRAKLGAGCAAAGCTCTGTGACGATGACCCGCCAG
PARD3-IL2RAchr1034805907chr1060679881221TPSVLRAKLCAAAGCTCTGTGACGATGACCCGCCAG
PARD3-IL2RAchr1034805907chr106067988516ATSEIEVTPSVTCACACCTTCAGTCCTTCGAGCAAAGCTCTGTG
PARD3-IL2RAchr1034805907chr106067988616TSEIEVTPSVCACCTTCAGTCCTTCGAGCAAAGCTCTGTG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
PARD3-IL2RAchr1034805907chr106067988015FQPYQATSEIEVTPSCAAGTGAAATTGAGGTCACACCTTCAGTCCTTCGAGCAAAGCTCT
PARD3-IL2RAchr1034805907chr106067988116QPYQATSEIEVTPSVGTGAAATTGAGGTCACACCTTCAGTCCTTCGAGCAAAGCTCTGTG
PARD3-IL2RAchr1034805907chr106067988419QATSEIEVTPSVLRAAGGTCACACCTTCAGTCCTTCGAGCAAAGCTCTGTGACGATGACC
PARD3-IL2RAchr1034805907chr106067988520ATSEIEVTPSVLRAKTCACACCTTCAGTCCTTCGAGCAAAGCTCTGTGACGATGACCCGC
PARD3-IL2RAchr1034805907chr106067988621TSEIEVTPSVLRAKLCACCTTCAGTCCTTCGAGCAAAGCTCTGTGACGATGACCCGCCAG
PARD3-IL2RAchr1034805907chr106067988722SEIEVTPSVLRAKLCCTTCAGTCCTTCGAGCAAAGCTCTGTGACGATGACCCGCCAGAGA

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Information of the samples that have these potential fusion neoantigens of PARD3-IL2RA

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
UCECPARD3-IL2RAchr1034805907ENST00000340077chr106067988ENST00000256876TCGA-AJ-A3TW-01A

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Potential target of CAR-T therapy development for PARD3-IL2RA

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
TgeneIL2RAchr10:34805907chr10:6067988ENST0000037995908241_2590273.0TransmembraneHelical

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 PARD3-IL2RA

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 PARD3-IL2RA

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