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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:IKZF3-SMARCE1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: IKZF3-SMARCE1
FusionPDB ID: 39409
FusionGDB2.0 ID: 39409
HgeneTgene
Gene symbol

IKZF3

SMARCE1

Gene ID

22806

6605

Gene nameIKAROS family zinc finger 3SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1
SynonymsAIO|AIOLOS|ZNFN1A3BAF57|CSS5
Cytomap

17q12-q21.1

17q21.2

Type of geneprotein-codingprotein-coding
Descriptionzinc finger protein Aioloszinc finger DNA binding protein Aioloszinc finger protein, subfamily 1A, 3 (Aiolos)SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1BRG1-associated factor 57SWI/SNF-related matrix-associated actin-dependent regulator of chromatin e1chromatin remodeling complex BRG1-associated factor 57
Modification date2020032720200313
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 idsENST00000346243, ENST00000346872, 
ENST00000350532, ENST00000351680, 
ENST00000377944, ENST00000377945, 
ENST00000377952, ENST00000377958, 
ENST00000394189, ENST00000439016, 
ENST00000467757, ENST00000439167, 
ENST00000535189, ENST00000583368, 
ENST00000474246, ENST00000348513, 
ENST00000377808, ENST00000400122, 
ENST00000431889, ENST00000544009, 
ENST00000578044, ENST00000580419, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score10 X 9 X 7=63010 X 11 X 5=550
# samples 1112
** MAII scorelog2(11/630*10)=-2.51784830486262
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/550*10)=-2.1963972128035
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: IKZF3 [Title/Abstract] AND SMARCE1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: IKZF3 [Title/Abstract] AND SMARCE1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)IKZF3(37985639)-SMARCE1(38788619), # samples:1
Anticipated loss of major functional domain due to fusion event.IKZF3-SMARCE1 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.
IKZF3-SMARCE1 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.
IKZF3-SMARCE1 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.
IKZF3-SMARCE1 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
TgeneSMARCE1

GO:0006337

nucleosome disassembly

8895581

TgeneSMARCE1

GO:0006338

chromatin remodeling

11726552

TgeneSMARCE1

GO:0045892

negative regulation of transcription, DNA-templated

12192000



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/chr17:37985639/chr17:38788619)
- 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 IKZF3 (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 SMARCE1 (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)
ENST00000346872IKZF3chr1737985639-ENST00000348513SMARCE1chr1738788619-474322562919285
ENST00000346872IKZF3chr1737985639-ENST00000544009SMARCE1chr1738788619-143122562919285
ENST00000346872IKZF3chr1737985639-ENST00000431889SMARCE1chr1738788619-123722562919285
ENST00000346872IKZF3chr1737985639-ENST00000580419SMARCE1chr1738788619-92622562919285
ENST00000346872IKZF3chr1737985639-ENST00000377808SMARCE1chr1738788619-100522562775237
ENST00000346872IKZF3chr1737985639-ENST00000400122SMARCE1chr1738788619-100522562775237
ENST00000346872IKZF3chr1737985639-ENST00000578044SMARCE1chr1738788619-92622562919285
ENST00000394189IKZF3chr1737985639-ENST00000348513SMARCE1chr1738788619-474322562919285
ENST00000394189IKZF3chr1737985639-ENST00000544009SMARCE1chr1738788619-143122562919285
ENST00000394189IKZF3chr1737985639-ENST00000431889SMARCE1chr1738788619-123722562919285
ENST00000394189IKZF3chr1737985639-ENST00000580419SMARCE1chr1738788619-92622562919285
ENST00000394189IKZF3chr1737985639-ENST00000377808SMARCE1chr1738788619-100522562775237
ENST00000394189IKZF3chr1737985639-ENST00000400122SMARCE1chr1738788619-100522562775237
ENST00000394189IKZF3chr1737985639-ENST00000578044SMARCE1chr1738788619-92622562919285
ENST00000377944IKZF3chr1737985639-ENST00000348513SMARCE1chr1738788619-474322562919285
ENST00000377944IKZF3chr1737985639-ENST00000544009SMARCE1chr1738788619-143122562919285
ENST00000377944IKZF3chr1737985639-ENST00000431889SMARCE1chr1738788619-123722562919285
ENST00000377944IKZF3chr1737985639-ENST00000580419SMARCE1chr1738788619-92622562919285
ENST00000377944IKZF3chr1737985639-ENST00000377808SMARCE1chr1738788619-100522562775237
ENST00000377944IKZF3chr1737985639-ENST00000400122SMARCE1chr1738788619-100522562775237
ENST00000377944IKZF3chr1737985639-ENST00000578044SMARCE1chr1738788619-92622562919285
ENST00000377945IKZF3chr1737985639-ENST00000348513SMARCE1chr1738788619-474322562919285
ENST00000377945IKZF3chr1737985639-ENST00000544009SMARCE1chr1738788619-143122562919285
ENST00000377945IKZF3chr1737985639-ENST00000431889SMARCE1chr1738788619-123722562919285
ENST00000377945IKZF3chr1737985639-ENST00000580419SMARCE1chr1738788619-92622562919285
ENST00000377945IKZF3chr1737985639-ENST00000377808SMARCE1chr1738788619-100522562775237
ENST00000377945IKZF3chr1737985639-ENST00000400122SMARCE1chr1738788619-100522562775237
ENST00000377945IKZF3chr1737985639-ENST00000578044SMARCE1chr1738788619-92622562919285
ENST00000377952IKZF3chr1737985639-ENST00000348513SMARCE1chr1738788619-474322562919285
ENST00000377952IKZF3chr1737985639-ENST00000544009SMARCE1chr1738788619-143122562919285
ENST00000377952IKZF3chr1737985639-ENST00000431889SMARCE1chr1738788619-123722562919285
ENST00000377952IKZF3chr1737985639-ENST00000580419SMARCE1chr1738788619-92622562919285
ENST00000377952IKZF3chr1737985639-ENST00000377808SMARCE1chr1738788619-100522562775237
ENST00000377952IKZF3chr1737985639-ENST00000400122SMARCE1chr1738788619-100522562775237
ENST00000377952IKZF3chr1737985639-ENST00000578044SMARCE1chr1738788619-92622562919285
ENST00000377958IKZF3chr1737985639-ENST00000348513SMARCE1chr1738788619-474322562919285
ENST00000377958IKZF3chr1737985639-ENST00000544009SMARCE1chr1738788619-143122562919285
ENST00000377958IKZF3chr1737985639-ENST00000431889SMARCE1chr1738788619-123722562919285
ENST00000377958IKZF3chr1737985639-ENST00000580419SMARCE1chr1738788619-92622562919285
ENST00000377958IKZF3chr1737985639-ENST00000377808SMARCE1chr1738788619-100522562775237
ENST00000377958IKZF3chr1737985639-ENST00000400122SMARCE1chr1738788619-100522562775237
ENST00000377958IKZF3chr1737985639-ENST00000578044SMARCE1chr1738788619-92622562919285
ENST00000346243IKZF3chr1737985639-ENST00000348513SMARCE1chr1738788619-46811630857285
ENST00000346243IKZF3chr1737985639-ENST00000544009SMARCE1chr1738788619-13691630857285
ENST00000346243IKZF3chr1737985639-ENST00000431889SMARCE1chr1738788619-11751630857285
ENST00000346243IKZF3chr1737985639-ENST00000580419SMARCE1chr1738788619-8641630857285
ENST00000346243IKZF3chr1737985639-ENST00000377808SMARCE1chr1738788619-9431630713237
ENST00000346243IKZF3chr1737985639-ENST00000400122SMARCE1chr1738788619-9431630713237
ENST00000346243IKZF3chr1737985639-ENST00000578044SMARCE1chr1738788619-8641630857285
ENST00000350532IKZF3chr1737985639-ENST00000348513SMARCE1chr1738788619-46811630857285
ENST00000350532IKZF3chr1737985639-ENST00000544009SMARCE1chr1738788619-13691630857285
ENST00000350532IKZF3chr1737985639-ENST00000431889SMARCE1chr1738788619-11751630857285
ENST00000350532IKZF3chr1737985639-ENST00000580419SMARCE1chr1738788619-8641630857285
ENST00000350532IKZF3chr1737985639-ENST00000377808SMARCE1chr1738788619-9431630713237
ENST00000350532IKZF3chr1737985639-ENST00000400122SMARCE1chr1738788619-9431630713237
ENST00000350532IKZF3chr1737985639-ENST00000578044SMARCE1chr1738788619-8641630857285
ENST00000351680IKZF3chr1737985639-ENST00000348513SMARCE1chr1738788619-46811630857285
ENST00000351680IKZF3chr1737985639-ENST00000544009SMARCE1chr1738788619-13691630857285
ENST00000351680IKZF3chr1737985639-ENST00000431889SMARCE1chr1738788619-11751630857285
ENST00000351680IKZF3chr1737985639-ENST00000580419SMARCE1chr1738788619-8641630857285
ENST00000351680IKZF3chr1737985639-ENST00000377808SMARCE1chr1738788619-9431630713237
ENST00000351680IKZF3chr1737985639-ENST00000400122SMARCE1chr1738788619-9431630713237
ENST00000351680IKZF3chr1737985639-ENST00000578044SMARCE1chr1738788619-8641630857285
ENST00000467757IKZF3chr1737985639-ENST00000348513SMARCE1chr1738788619-46811630857285
ENST00000467757IKZF3chr1737985639-ENST00000544009SMARCE1chr1738788619-13691630857285
ENST00000467757IKZF3chr1737985639-ENST00000431889SMARCE1chr1738788619-11751630857285
ENST00000467757IKZF3chr1737985639-ENST00000580419SMARCE1chr1738788619-8641630857285
ENST00000467757IKZF3chr1737985639-ENST00000377808SMARCE1chr1738788619-9431630713237
ENST00000467757IKZF3chr1737985639-ENST00000400122SMARCE1chr1738788619-9431630713237
ENST00000467757IKZF3chr1737985639-ENST00000578044SMARCE1chr1738788619-8641630857285
ENST00000439016IKZF3chr1737985639-ENST00000348513SMARCE1chr1738788619-46821641858285
ENST00000439016IKZF3chr1737985639-ENST00000544009SMARCE1chr1738788619-13701641858285
ENST00000439016IKZF3chr1737985639-ENST00000431889SMARCE1chr1738788619-11761641858285
ENST00000439016IKZF3chr1737985639-ENST00000580419SMARCE1chr1738788619-8651641858285
ENST00000439016IKZF3chr1737985639-ENST00000377808SMARCE1chr1738788619-9441641714237
ENST00000439016IKZF3chr1737985639-ENST00000400122SMARCE1chr1738788619-9441641714237
ENST00000439016IKZF3chr1737985639-ENST00000578044SMARCE1chr1738788619-8651641858285

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
ENST00000346872ENST00000348513IKZF3chr1737985639-SMARCE1chr1738788619-0.0003259990.99967396
ENST00000346872ENST00000544009IKZF3chr1737985639-SMARCE1chr1738788619-0.0010169760.99898297
ENST00000346872ENST00000431889IKZF3chr1737985639-SMARCE1chr1738788619-0.0019620340.998038
ENST00000346872ENST00000580419IKZF3chr1737985639-SMARCE1chr1738788619-0.0041033090.9958967
ENST00000346872ENST00000377808IKZF3chr1737985639-SMARCE1chr1738788619-0.0051342110.99486583
ENST00000346872ENST00000400122IKZF3chr1737985639-SMARCE1chr1738788619-0.0051342110.99486583
ENST00000346872ENST00000578044IKZF3chr1737985639-SMARCE1chr1738788619-0.0041033090.9958967
ENST00000394189ENST00000348513IKZF3chr1737985639-SMARCE1chr1738788619-0.0003259990.99967396
ENST00000394189ENST00000544009IKZF3chr1737985639-SMARCE1chr1738788619-0.0010169760.99898297
ENST00000394189ENST00000431889IKZF3chr1737985639-SMARCE1chr1738788619-0.0019620340.998038
ENST00000394189ENST00000580419IKZF3chr1737985639-SMARCE1chr1738788619-0.0041033090.9958967
ENST00000394189ENST00000377808IKZF3chr1737985639-SMARCE1chr1738788619-0.0051342110.99486583
ENST00000394189ENST00000400122IKZF3chr1737985639-SMARCE1chr1738788619-0.0051342110.99486583
ENST00000394189ENST00000578044IKZF3chr1737985639-SMARCE1chr1738788619-0.0041033090.9958967
ENST00000377944ENST00000348513IKZF3chr1737985639-SMARCE1chr1738788619-0.0003259990.99967396
ENST00000377944ENST00000544009IKZF3chr1737985639-SMARCE1chr1738788619-0.0010169760.99898297
ENST00000377944ENST00000431889IKZF3chr1737985639-SMARCE1chr1738788619-0.0019620340.998038
ENST00000377944ENST00000580419IKZF3chr1737985639-SMARCE1chr1738788619-0.0041033090.9958967
ENST00000377944ENST00000377808IKZF3chr1737985639-SMARCE1chr1738788619-0.0051342110.99486583
ENST00000377944ENST00000400122IKZF3chr1737985639-SMARCE1chr1738788619-0.0051342110.99486583
ENST00000377944ENST00000578044IKZF3chr1737985639-SMARCE1chr1738788619-0.0041033090.9958967
ENST00000377945ENST00000348513IKZF3chr1737985639-SMARCE1chr1738788619-0.0003259990.99967396
ENST00000377945ENST00000544009IKZF3chr1737985639-SMARCE1chr1738788619-0.0010169760.99898297
ENST00000377945ENST00000431889IKZF3chr1737985639-SMARCE1chr1738788619-0.0019620340.998038
ENST00000377945ENST00000580419IKZF3chr1737985639-SMARCE1chr1738788619-0.0041033090.9958967
ENST00000377945ENST00000377808IKZF3chr1737985639-SMARCE1chr1738788619-0.0051342110.99486583
ENST00000377945ENST00000400122IKZF3chr1737985639-SMARCE1chr1738788619-0.0051342110.99486583
ENST00000377945ENST00000578044IKZF3chr1737985639-SMARCE1chr1738788619-0.0041033090.9958967
ENST00000377952ENST00000348513IKZF3chr1737985639-SMARCE1chr1738788619-0.0003259990.99967396
ENST00000377952ENST00000544009IKZF3chr1737985639-SMARCE1chr1738788619-0.0010169760.99898297
ENST00000377952ENST00000431889IKZF3chr1737985639-SMARCE1chr1738788619-0.0019620340.998038
ENST00000377952ENST00000580419IKZF3chr1737985639-SMARCE1chr1738788619-0.0041033090.9958967
ENST00000377952ENST00000377808IKZF3chr1737985639-SMARCE1chr1738788619-0.0051342110.99486583
ENST00000377952ENST00000400122IKZF3chr1737985639-SMARCE1chr1738788619-0.0051342110.99486583
ENST00000377952ENST00000578044IKZF3chr1737985639-SMARCE1chr1738788619-0.0041033090.9958967
ENST00000377958ENST00000348513IKZF3chr1737985639-SMARCE1chr1738788619-0.0003259990.99967396
ENST00000377958ENST00000544009IKZF3chr1737985639-SMARCE1chr1738788619-0.0010169760.99898297
ENST00000377958ENST00000431889IKZF3chr1737985639-SMARCE1chr1738788619-0.0019620340.998038
ENST00000377958ENST00000580419IKZF3chr1737985639-SMARCE1chr1738788619-0.0041033090.9958967
ENST00000377958ENST00000377808IKZF3chr1737985639-SMARCE1chr1738788619-0.0051342110.99486583
ENST00000377958ENST00000400122IKZF3chr1737985639-SMARCE1chr1738788619-0.0051342110.99486583
ENST00000377958ENST00000578044IKZF3chr1737985639-SMARCE1chr1738788619-0.0041033090.9958967
ENST00000346243ENST00000348513IKZF3chr1737985639-SMARCE1chr1738788619-0.0003157830.9996842
ENST00000346243ENST00000544009IKZF3chr1737985639-SMARCE1chr1738788619-0.0008747580.9991253
ENST00000346243ENST00000431889IKZF3chr1737985639-SMARCE1chr1738788619-0.0017823040.99821764
ENST00000346243ENST00000580419IKZF3chr1737985639-SMARCE1chr1738788619-0.006195860.9938041
ENST00000346243ENST00000377808IKZF3chr1737985639-SMARCE1chr1738788619-0.007263490.9927366
ENST00000346243ENST00000400122IKZF3chr1737985639-SMARCE1chr1738788619-0.007263490.9927366
ENST00000346243ENST00000578044IKZF3chr1737985639-SMARCE1chr1738788619-0.006195860.9938041
ENST00000350532ENST00000348513IKZF3chr1737985639-SMARCE1chr1738788619-0.0003157830.9996842
ENST00000350532ENST00000544009IKZF3chr1737985639-SMARCE1chr1738788619-0.0008747580.9991253
ENST00000350532ENST00000431889IKZF3chr1737985639-SMARCE1chr1738788619-0.0017823040.99821764
ENST00000350532ENST00000580419IKZF3chr1737985639-SMARCE1chr1738788619-0.006195860.9938041
ENST00000350532ENST00000377808IKZF3chr1737985639-SMARCE1chr1738788619-0.007263490.9927366
ENST00000350532ENST00000400122IKZF3chr1737985639-SMARCE1chr1738788619-0.007263490.9927366
ENST00000350532ENST00000578044IKZF3chr1737985639-SMARCE1chr1738788619-0.006195860.9938041
ENST00000351680ENST00000348513IKZF3chr1737985639-SMARCE1chr1738788619-0.0003157830.9996842
ENST00000351680ENST00000544009IKZF3chr1737985639-SMARCE1chr1738788619-0.0008747580.9991253
ENST00000351680ENST00000431889IKZF3chr1737985639-SMARCE1chr1738788619-0.0017823040.99821764
ENST00000351680ENST00000580419IKZF3chr1737985639-SMARCE1chr1738788619-0.006195860.9938041
ENST00000351680ENST00000377808IKZF3chr1737985639-SMARCE1chr1738788619-0.007263490.9927366
ENST00000351680ENST00000400122IKZF3chr1737985639-SMARCE1chr1738788619-0.007263490.9927366
ENST00000351680ENST00000578044IKZF3chr1737985639-SMARCE1chr1738788619-0.006195860.9938041
ENST00000467757ENST00000348513IKZF3chr1737985639-SMARCE1chr1738788619-0.0003157830.9996842
ENST00000467757ENST00000544009IKZF3chr1737985639-SMARCE1chr1738788619-0.0008747580.9991253
ENST00000467757ENST00000431889IKZF3chr1737985639-SMARCE1chr1738788619-0.0017823040.99821764
ENST00000467757ENST00000580419IKZF3chr1737985639-SMARCE1chr1738788619-0.006195860.9938041
ENST00000467757ENST00000377808IKZF3chr1737985639-SMARCE1chr1738788619-0.007263490.9927366
ENST00000467757ENST00000400122IKZF3chr1737985639-SMARCE1chr1738788619-0.007263490.9927366
ENST00000467757ENST00000578044IKZF3chr1737985639-SMARCE1chr1738788619-0.006195860.9938041
ENST00000439016ENST00000348513IKZF3chr1737985639-SMARCE1chr1738788619-0.0003144650.9996855
ENST00000439016ENST00000544009IKZF3chr1737985639-SMARCE1chr1738788619-0.0008663210.99913365
ENST00000439016ENST00000431889IKZF3chr1737985639-SMARCE1chr1738788619-0.0017723040.99822766
ENST00000439016ENST00000580419IKZF3chr1737985639-SMARCE1chr1738788619-0.0060124010.99398756
ENST00000439016ENST00000377808IKZF3chr1737985639-SMARCE1chr1738788619-0.0070566550.99294335
ENST00000439016ENST00000400122IKZF3chr1737985639-SMARCE1chr1738788619-0.0070566550.99294335
ENST00000439016ENST00000578044IKZF3chr1737985639-SMARCE1chr1738788619-0.0060124010.99398756

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 IKZF3-SMARCE1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
IKZF3chr1737985639SMARCE1chr173878861916354SGEGPANEDEDIGDYDDGFSMKHTAT
IKZF3chr1737985639SMARCE1chr173878861916454SGEGPANEDEDIGDYDDGFSMKHTAT
IKZF3chr1737985639SMARCE1chr173878861922554SGEGPANEDEDIGDYDDGFSMKHTAT

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Potential FusionNeoAntigen Information of IKZF3-SMARCE1 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.
IKZF3-SMARCE1_37985639_38788619.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)
IKZF3-SMARCE1chr1737985639chr1738788619163HLA-B18:01NEDEDIGDY0.8190.8816615
IKZF3-SMARCE1chr1737985639chr1738788619163HLA-B47:01GDYDDGFSM0.53970.60381221
IKZF3-SMARCE1chr1737985639chr1738788619163HLA-B39:13GDYDDGFSM0.11290.85461221
IKZF3-SMARCE1chr1737985639chr1738788619163HLA-B39:08GDYDDGFSM0.4730.80091221
IKZF3-SMARCE1chr1737985639chr1738788619163HLA-C08:15IGDYDDGFSM0.99990.94541121
IKZF3-SMARCE1chr1737985639chr1738788619163HLA-B18:04NEDEDIGDY0.87980.8996615
IKZF3-SMARCE1chr1737985639chr1738788619163HLA-B18:05NEDEDIGDY0.8190.8816615
IKZF3-SMARCE1chr1737985639chr1738788619163HLA-B40:04GDYDDGFSM0.74920.7231221
IKZF3-SMARCE1chr1737985639chr1738788619163HLA-B18:06NEDEDIGDY0.71790.8753615
IKZF3-SMARCE1chr1737985639chr1738788619163HLA-B18:11NEDEDIGDY0.59820.7041615
IKZF3-SMARCE1chr1737985639chr1738788619163HLA-C08:02IGDYDDGFSM0.99990.94541121

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Potential FusionNeoAntigen Information of IKZF3-SMARCE1 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 IKZF3-SMARCE1

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
6128NEDEDIGDYDDGFSIKZF3SMARCE1chr1737985639chr1738788619163

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of IKZF3-SMARCE1

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-B14:023BVN6128NEDEDIGDYDDGFS-7.15543-7.26883
HLA-B14:023BVN6128NEDEDIGDYDDGFS-4.77435-5.80965
HLA-B52:013W396128NEDEDIGDYDDGFS-6.80875-6.92215
HLA-B52:013W396128NEDEDIGDYDDGFS-4.20386-5.23916
HLA-A11:014UQ26128NEDEDIGDYDDGFS-7.5194-8.5547
HLA-A11:014UQ26128NEDEDIGDYDDGFS-6.9601-7.0735
HLA-A24:025HGA6128NEDEDIGDYDDGFS-7.52403-7.63743
HLA-A24:025HGA6128NEDEDIGDYDDGFS-5.82433-6.85963
HLA-B27:056PYJ6128NEDEDIGDYDDGFS-3.28285-4.31815
HLA-B44:053DX86128NEDEDIGDYDDGFS-5.91172-6.94702
HLA-B44:053DX86128NEDEDIGDYDDGFS-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of IKZF3-SMARCE1

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
IKZF3-SMARCE1chr1737985639chr17387886191121IGDYDDGFSMTAGGAGATTATGATGATGGCTTTTCAATGA
IKZF3-SMARCE1chr1737985639chr17387886191221GDYDDGFSMGAGATTATGATGATGGCTTTTCAATGA
IKZF3-SMARCE1chr1737985639chr1738788619615NEDEDIGDYATGAAGATGAAGACATAGGAGATTATG

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 IKZF3-SMARCE1

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
READIKZF3-SMARCE1chr1737985639ENST00000346243chr1738788619ENST00000348513TCGA-EI-6509

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Potential target of CAR-T therapy development for IKZF3-SMARCE1

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 IKZF3-SMARCE1

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 IKZF3-SMARCE1

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