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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:PPP1R1B-IKZF3

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PPP1R1B-IKZF3
FusionPDB ID: 67868
FusionGDB2.0 ID: 67868
HgeneTgene
Gene symbol

PPP1R1B

IKZF3

Gene ID

84152

22806

Gene nameprotein phosphatase 1 regulatory inhibitor subunit 1BIKAROS family zinc finger 3
SynonymsDARPP-32|DARPP32AIO|AIOLOS|ZNFN1A3
Cytomap

17q12

17q12-q21.1

Type of geneprotein-codingprotein-coding
Descriptionprotein phosphatase 1 regulatory subunit 1Bdopamine and cAMP-regulated neuronal phosphoprotein 32zinc finger protein Aioloszinc finger DNA binding protein Aioloszinc finger protein, subfamily 1A, 3 (Aiolos)
Modification date2020031320200327
UniProtAcc.

Q9UKT9

Main function of 5'-partner protein: FUNCTION: Transcription factor that plays an important role in the regulation of lymphocyte differentiation. Plays an essential role in regulation of B-cell differentiation, proliferation and maturation to an effector state. Involved in regulating BCL2 expression and controlling apoptosis in T-cells in an IL2-dependent manner. {ECO:0000269|PubMed:10369681}.
Ensembl transtripts involved in fusion geneENST idsENST00000254079, ENST00000394265, 
ENST00000394267, ENST00000579000, 
ENST00000580825, 		ENST00000583368, 
ENST00000346243, ENST00000346872, 
ENST00000350532, ENST00000351680, 
ENST00000377944, ENST00000377945, 
ENST00000377952, ENST00000377958, 
ENST00000394189, ENST00000439016, 
ENST00000439167, ENST00000467757, 
ENST00000535189, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score11 X 11 X 6=72634 X 12 X 14=5712
# samples 1149
** MAII scorelog2(11/726*10)=-2.72246602447109
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(49/5712*10)=-3.54314232502653
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PPP1R1B [Title/Abstract] AND IKZF3 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PPP1R1B [Title/Abstract] AND IKZF3 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PPP1R1B(37791979)-IKZF3(37988404), # samples:1
Anticipated loss of major functional domain due to fusion event.PPP1R1B-IKZF3 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.
PPP1R1B-IKZF3 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
HgenePPP1R1B

GO:0032515

negative regulation of phosphoprotein phosphatase activity

10807923



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/chr17:37791979/chr17:37988404)
- 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 PPP1R1B (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 IKZF3 (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)
ENST00000580825PPP1R1Bchr1737791979+ENST00000346872IKZF3chr1737988404-32218532882375695
ENST00000580825PPP1R1Bchr1737791979+ENST00000394189IKZF3chr1737988404-23368532881829513
ENST00000580825PPP1R1Bchr1737791979+ENST00000439167IKZF3chr1737988404-26638532882156622
ENST00000580825PPP1R1Bchr1737791979+ENST00000535189IKZF3chr1737988404-27808532882273661
ENST00000580825PPP1R1Bchr1737791979+ENST00000377944IKZF3chr1737988404-24538532881946552
ENST00000580825PPP1R1Bchr1737791979+ENST00000377945IKZF3chr1737988404-24808532881973561
ENST00000580825PPP1R1Bchr1737791979+ENST00000377952IKZF3chr1737988404-22198532881712474
ENST00000580825PPP1R1Bchr1737791979+ENST00000377958IKZF3chr1737988404-26218532882114608
ENST00000580825PPP1R1Bchr1737791979+ENST00000346243IKZF3chr1737988404-21428532882141617
ENST00000580825PPP1R1Bchr1737791979+ENST00000350532IKZF3chr1737988404-22598532882258656
ENST00000580825PPP1R1Bchr1737791979+ENST00000351680IKZF3chr1737988404-22598532882258656
ENST00000580825PPP1R1Bchr1737791979+ENST00000467757IKZF3chr1737988404-22088532882207639
ENST00000580825PPP1R1Bchr1737791979+ENST00000439016IKZF3chr1737988404-20918532882090600
ENST00000254079PPP1R1Bchr1737791979+ENST00000346872IKZF3chr1737988404-3402103442556850
ENST00000254079PPP1R1Bchr1737791979+ENST00000394189IKZF3chr1737988404-2517103442010668
ENST00000254079PPP1R1Bchr1737791979+ENST00000439167IKZF3chr1737988404-2844103442337777
ENST00000254079PPP1R1Bchr1737791979+ENST00000535189IKZF3chr1737988404-2961103442454816
ENST00000254079PPP1R1Bchr1737791979+ENST00000377944IKZF3chr1737988404-2634103442127707
ENST00000254079PPP1R1Bchr1737791979+ENST00000377945IKZF3chr1737988404-2661103442154716
ENST00000254079PPP1R1Bchr1737791979+ENST00000377952IKZF3chr1737988404-2400103441893629
ENST00000254079PPP1R1Bchr1737791979+ENST00000377958IKZF3chr1737988404-2802103442295763
ENST00000254079PPP1R1Bchr1737791979+ENST00000346243IKZF3chr1737988404-2323103442322773
ENST00000254079PPP1R1Bchr1737791979+ENST00000350532IKZF3chr1737988404-2440103442439812
ENST00000254079PPP1R1Bchr1737791979+ENST00000351680IKZF3chr1737988404-2440103442439812
ENST00000254079PPP1R1Bchr1737791979+ENST00000467757IKZF3chr1737988404-2389103442388795
ENST00000254079PPP1R1Bchr1737791979+ENST00000439016IKZF3chr1737988404-2272103442271756
ENST00000579000PPP1R1Bchr1737791979+ENST00000346872IKZF3chr1737988404-30276591932181662
ENST00000579000PPP1R1Bchr1737791979+ENST00000394189IKZF3chr1737988404-21426591931635480
ENST00000579000PPP1R1Bchr1737791979+ENST00000439167IKZF3chr1737988404-24696591931962589
ENST00000579000PPP1R1Bchr1737791979+ENST00000535189IKZF3chr1737988404-25866591932079628
ENST00000579000PPP1R1Bchr1737791979+ENST00000377944IKZF3chr1737988404-22596591931752519
ENST00000579000PPP1R1Bchr1737791979+ENST00000377945IKZF3chr1737988404-22866591931779528
ENST00000579000PPP1R1Bchr1737791979+ENST00000377952IKZF3chr1737988404-20256591931518441
ENST00000579000PPP1R1Bchr1737791979+ENST00000377958IKZF3chr1737988404-24276591931920575
ENST00000579000PPP1R1Bchr1737791979+ENST00000346243IKZF3chr1737988404-19486591931947585
ENST00000579000PPP1R1Bchr1737791979+ENST00000350532IKZF3chr1737988404-20656591932064624
ENST00000579000PPP1R1Bchr1737791979+ENST00000351680IKZF3chr1737988404-20656591932064624
ENST00000579000PPP1R1Bchr1737791979+ENST00000467757IKZF3chr1737988404-20146591932013607
ENST00000579000PPP1R1Bchr1737791979+ENST00000439016IKZF3chr1737988404-18976591931896568
ENST00000394265PPP1R1Bchr1737791979+ENST00000346872IKZF3chr1737988404-2977609502131693
ENST00000394265PPP1R1Bchr1737791979+ENST00000394189IKZF3chr1737988404-2092609501585511
ENST00000394265PPP1R1Bchr1737791979+ENST00000439167IKZF3chr1737988404-2419609501912620
ENST00000394265PPP1R1Bchr1737791979+ENST00000535189IKZF3chr1737988404-2536609502029659
ENST00000394265PPP1R1Bchr1737791979+ENST00000377944IKZF3chr1737988404-2209609501702550
ENST00000394265PPP1R1Bchr1737791979+ENST00000377945IKZF3chr1737988404-2236609501729559
ENST00000394265PPP1R1Bchr1737791979+ENST00000377952IKZF3chr1737988404-1975609501468472
ENST00000394265PPP1R1Bchr1737791979+ENST00000377958IKZF3chr1737988404-2377609501870606
ENST00000394265PPP1R1Bchr1737791979+ENST00000346243IKZF3chr1737988404-1898609501897616
ENST00000394265PPP1R1Bchr1737791979+ENST00000350532IKZF3chr1737988404-2015609502014655
ENST00000394265PPP1R1Bchr1737791979+ENST00000351680IKZF3chr1737988404-2015609502014655
ENST00000394265PPP1R1Bchr1737791979+ENST00000467757IKZF3chr1737988404-1964609501963638
ENST00000394265PPP1R1Bchr1737791979+ENST00000439016IKZF3chr1737988404-1847609501846599
ENST00000394267PPP1R1Bchr1737791979+ENST00000346872IKZF3chr1737988404-30616932362215659
ENST00000394267PPP1R1Bchr1737791979+ENST00000394189IKZF3chr1737988404-21766932361669477
ENST00000394267PPP1R1Bchr1737791979+ENST00000439167IKZF3chr1737988404-25036932361996586
ENST00000394267PPP1R1Bchr1737791979+ENST00000535189IKZF3chr1737988404-26206932362113625
ENST00000394267PPP1R1Bchr1737791979+ENST00000377944IKZF3chr1737988404-22936932361786516
ENST00000394267PPP1R1Bchr1737791979+ENST00000377945IKZF3chr1737988404-23206932361813525
ENST00000394267PPP1R1Bchr1737791979+ENST00000377952IKZF3chr1737988404-20596932361552438
ENST00000394267PPP1R1Bchr1737791979+ENST00000377958IKZF3chr1737988404-24616932361954572
ENST00000394267PPP1R1Bchr1737791979+ENST00000346243IKZF3chr1737988404-19826932361981582
ENST00000394267PPP1R1Bchr1737791979+ENST00000350532IKZF3chr1737988404-20996932362098621
ENST00000394267PPP1R1Bchr1737791979+ENST00000351680IKZF3chr1737988404-20996932362098621
ENST00000394267PPP1R1Bchr1737791979+ENST00000467757IKZF3chr1737988404-20486932362047604
ENST00000394267PPP1R1Bchr1737791979+ENST00000439016IKZF3chr1737988404-19316932361930565

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
ENST00000580825ENST00000346872PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0034795960.9965204
ENST00000580825ENST00000394189PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0044121720.9955878
ENST00000580825ENST00000439167PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0036659510.9963341
ENST00000580825ENST00000535189PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0035931880.99640673
ENST00000580825ENST00000377944PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0039841090.99601585
ENST00000580825ENST00000377945PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0041349690.995865
ENST00000580825ENST00000377952PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0039673740.99603266
ENST00000580825ENST00000377958PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0038012210.9961987
ENST00000580825ENST00000346243PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0069154170.99308455
ENST00000580825ENST00000350532PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0055458890.9944541
ENST00000580825ENST00000351680PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0068414670.9931585
ENST00000580825ENST00000467757PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0070067410.9929932
ENST00000580825ENST00000439016PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0072424220.99275756
ENST00000254079ENST00000346872PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0038702140.99612975
ENST00000254079ENST00000394189PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0045364480.99546355
ENST00000254079ENST00000439167PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0037015260.9962985
ENST00000254079ENST00000535189PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0037607770.9962392
ENST00000254079ENST00000377944PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0040234490.9959766
ENST00000254079ENST00000377945PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0045218240.9954782
ENST00000254079ENST00000377952PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0042093570.99579066
ENST00000254079ENST00000377958PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0038990430.9961009
ENST00000254079ENST00000346243PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0065810650.9934189
ENST00000254079ENST00000350532PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0055577570.9944423
ENST00000254079ENST00000351680PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0066324920.9933675
ENST00000254079ENST00000467757PPP1R1Bchr1737791979+IKZF3chr1737988404-0.00737120.9926288
ENST00000254079ENST00000439016PPP1R1Bchr1737791979+IKZF3chr1737988404-0.007097170.9929028
ENST00000579000ENST00000346872PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0019130870.9980869
ENST00000579000ENST00000394189PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0046217550.99537826
ENST00000579000ENST00000439167PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0041802250.9958198
ENST00000579000ENST00000535189PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0031654320.9968346
ENST00000579000ENST00000377944PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0042934940.9957065
ENST00000579000ENST00000377945PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0030807410.9969193
ENST00000579000ENST00000377952PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0029390380.99706095
ENST00000579000ENST00000377958PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0033342830.99666566
ENST00000579000ENST00000346243PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0053411050.9946589
ENST00000579000ENST00000350532PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0042865260.9957135
ENST00000579000ENST00000351680PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0055066120.99449337
ENST00000579000ENST00000467757PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0052026240.99479735
ENST00000579000ENST00000439016PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0071109970.9928889
ENST00000394265ENST00000346872PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0007168970.99928313
ENST00000394265ENST00000394189PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0024831780.9975169
ENST00000394265ENST00000439167PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0009251230.9990748
ENST00000394265ENST00000535189PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0008745370.9991254
ENST00000394265ENST00000377944PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0017162280.99828374
ENST00000394265ENST00000377945PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0010850640.99891496
ENST00000394265ENST00000377952PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0015821870.99841785
ENST00000394265ENST00000377958PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0014176570.99858236
ENST00000394265ENST00000346243PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0017276250.9982724
ENST00000394265ENST00000350532PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0014280620.9985719
ENST00000394265ENST00000351680PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0020366890.9979633
ENST00000394265ENST00000467757PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0022626860.9977373
ENST00000394265ENST00000439016PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0025680870.99743193
ENST00000394267ENST00000346872PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0007658440.9992342
ENST00000394267ENST00000394189PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0025139830.997486
ENST00000394267ENST00000439167PPP1R1Bchr1737791979+IKZF3chr1737988404-0.000981260.9990188
ENST00000394267ENST00000535189PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0009465560.9990534
ENST00000394267ENST00000377944PPP1R1Bchr1737791979+IKZF3chr1737988404-0.001807570.9981925
ENST00000394267ENST00000377945PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0011581810.9988418
ENST00000394267ENST00000377952PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0016178080.9983822
ENST00000394267ENST00000377958PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0015521240.9984479
ENST00000394267ENST00000346243PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0018318260.9981681
ENST00000394267ENST00000350532PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0015467640.99845326
ENST00000394267ENST00000351680PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0021370680.997863
ENST00000394267ENST00000467757PPP1R1Bchr1737791979+IKZF3chr1737988404-0.002417830.9975822
ENST00000394267ENST00000439016PPP1R1Bchr1737791979+IKZF3chr1737988404-0.0026452370.99735475

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 PPP1R1B-IKZF3

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PPP1R1Bchr1737791979IKZF3chr17379884041034342DGGSEDQVEDPALSDIQTNAELKSTQ
PPP1R1Bchr1737791979IKZF3chr1737988404103446ETRRDTQEGRDTETQRHSGGERHRDA
PPP1R1Bchr1737791979IKZF3chr1737988404659154DGGSEDQVEDPALSDIQTNAELKSTQ
PPP1R1Bchr1737791979IKZF3chr1737988404693151DGGSEDQVEDPALSDIQTNAELKSTQ
PPP1R1Bchr1737791979IKZF3chr1737988404853187DGGSEDQVEDPALSDIQTNAELKSTQ

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Potential FusionNeoAntigen Information of PPP1R1B-IKZF3 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.
PPP1R1B-IKZF3_37791979_37988404.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)
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:27ALSDIQTNA0.99360.55031120
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:24ALSDIQTNA0.99290.52391120
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:67ALSDIQTNA0.99290.52391120
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:30ALSDIQTNA0.99290.52391120
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:11ALSDIQTNA0.99270.56591120
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:13ALSDIQTNA0.99250.6821120
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:16ALSDIQTNA0.99160.53921120
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:21ALSDIQTNA0.99080.66161120
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:38ALSDIQTNA0.98760.70751120
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:29ALSDIQTNA0.95130.52071120
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:35ALSDIQTNA0.90240.54711120
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:20ALSDIQTNA0.9020.53131120
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-B41:01VEDPALSDI0.2740.6162716
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-B39:13VEDPALSDI0.0350.7033716
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:27ALSDIQTNAEL0.99770.50391122
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:13ALSDIQTNAEL0.99710.66431122
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:16ALSDIQTNAEL0.9940.54391122
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:67ALSDIQTNAEL0.99290.55021122
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:30ALSDIQTNAEL0.99290.55021122
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:24ALSDIQTNAEL0.99290.55021122
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:11ALSDIQTNAEL0.99210.57991122
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:38ALSDIQTNAEL0.99080.64331122
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:04ALSDIQTNAEL0.98990.581122
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:29ALSDIQTNAEL0.95060.54511122
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:20ALSDIQTNAEL0.93780.55431122
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:35ALSDIQTNAEL0.9320.56721122
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:01ALSDIQTNA0.99290.52391120
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-B39:08VEDPALSDI0.29130.5442716
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-C05:09LSDIQTNAEL10.93071222
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-C08:15LSDIQTNAEL0.99990.96941222
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:01ALSDIQTNAEL0.99290.55021122
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:03ALSDIQTNA0.99630.6321120
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:14ALSDIQTNA0.99090.5581120
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:06ALSDIQTNA0.99080.66161120
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-C05:01LSDIQTNAEL10.93071222
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-C08:02LSDIQTNAEL0.99990.96941222
PPP1R1B-IKZF3chr1737791979chr17379884041034HLA-A02:03ALSDIQTNAEL0.99820.56921122

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Potential FusionNeoAntigen Information of PPP1R1B-IKZF3 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.
PPP1R1B-IKZF3_37791979_37988404.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)
PPP1R1B-IKZF3chr1737791979chr17379884041034DRB1-0405DPALSDIQTNAELKS924
PPP1R1B-IKZF3chr1737791979chr17379884041034DRB1-0411DPALSDIQTNAELKS924
PPP1R1B-IKZF3chr1737791979chr17379884041034DRB1-0411EDPALSDIQTNAELK823
PPP1R1B-IKZF3chr1737791979chr17379884041034DRB1-0417DPALSDIQTNAELKS924
PPP1R1B-IKZF3chr1737791979chr17379884041034DRB1-0429DPALSDIQTNAELKS924
PPP1R1B-IKZF3chr1737791979chr17379884041034DRB1-0430DPALSDIQTNAELKS924
PPP1R1B-IKZF3chr1737791979chr17379884041034DRB1-0445DPALSDIQTNAELKS924
PPP1R1B-IKZF3chr1737791979chr17379884041034DRB1-0448DPALSDIQTNAELKS924
PPP1R1B-IKZF3chr1737791979chr17379884041034DRB1-0457DPALSDIQTNAELKS924
PPP1R1B-IKZF3chr1737791979chr17379884041034DRB1-0467DPALSDIQTNAELKS924
PPP1R1B-IKZF3chr1737791979chr17379884041034DRB1-0467EDPALSDIQTNAELK823
PPP1R1B-IKZF3chr1737791979chr17379884041034DRB1-0477DPALSDIQTNAELKS924
PPP1R1B-IKZF3chr1737791979chr17379884041034DRB1-0483DPALSDIQTNAELKS924
PPP1R1B-IKZF3chr1737791979chr17379884041034DRB1-0484DPALSDIQTNAELKS924
PPP1R1B-IKZF3chr1737791979chr17379884041034DRB1-0487DPALSDIQTNAELKS924
PPP1R1B-IKZF3chr1737791979chr17379884041034DRB1-0489DPALSDIQTNAELKS924
PPP1R1B-IKZF3chr1737791979chr17379884041034DRB1-0491DPALSDIQTNAELKS924
PPP1R1B-IKZF3chr1737791979chr17379884041034DRB1-0491EDPALSDIQTNAELK823
PPP1R1B-IKZF3chr1737791979chr17379884041034DRB3-0204ALSDIQTNAELKSTQ1126

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Fusion breakpoint peptide structures of PPP1R1B-IKZF3

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
7611QVEDPALSDIQTNAPPP1R1BIKZF3chr1737791979chr17379884041034

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PPP1R1B-IKZF3

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-B14:023BVN7611QVEDPALSDIQTNA-7.9962-8.1096
HLA-B14:023BVN7611QVEDPALSDIQTNA-5.70842-6.74372
HLA-B52:013W397611QVEDPALSDIQTNA-6.83737-6.95077
HLA-B52:013W397611QVEDPALSDIQTNA-4.4836-5.5189
HLA-A11:014UQ27611QVEDPALSDIQTNA-10.0067-10.1201
HLA-A11:014UQ27611QVEDPALSDIQTNA-9.03915-10.0745
HLA-A24:025HGA7611QVEDPALSDIQTNA-6.56204-6.67544
HLA-A24:025HGA7611QVEDPALSDIQTNA-5.42271-6.45801
HLA-B44:053DX87611QVEDPALSDIQTNA-7.85648-8.89178
HLA-B44:053DX87611QVEDPALSDIQTNA-5.3978-5.5112
HLA-A02:016TDR7611QVEDPALSDIQTNA-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of PPP1R1B-IKZF3

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
PPP1R1B-IKZF3chr1737791979chr17379884041120ALSDIQTNATAAGTGATATACAAACAAATGCGGAAC
PPP1R1B-IKZF3chr1737791979chr17379884041122ALSDIQTNAELTAAGTGATATACAAACAAATGCGGAACTGAAAA
PPP1R1B-IKZF3chr1737791979chr17379884041222LSDIQTNAELGTGATATACAAACAAATGCGGAACTGAAAA
PPP1R1B-IKZF3chr1737791979chr1737988404716VEDPALSDIAAGACCCAGCACTAAGTGATATACAAA

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
PPP1R1B-IKZF3chr1737791979chr17379884041126ALSDIQTNAELKSTQTAAGTGATATACAAACAAATGCGGAACTGAAAAGCACTCAGGAGC
PPP1R1B-IKZF3chr1737791979chr1737988404823EDPALSDIQTNAELKACCCAGCACTAAGTGATATACAAACAAATGCGGAACTGAAAAGCA
PPP1R1B-IKZF3chr1737791979chr1737988404924DPALSDIQTNAELKSCAGCACTAAGTGATATACAAACAAATGCGGAACTGAAAAGCACTC

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Information of the samples that have these potential fusion neoantigens of PPP1R1B-IKZF3

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
ESCAPPP1R1B-IKZF3chr1737791979ENST00000254079chr1737988404ENST00000346243TCGA-2H-A9GF

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Potential target of CAR-T therapy development for PPP1R1B-IKZF3

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 PPP1R1B-IKZF3

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 PPP1R1B-IKZF3

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