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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-MED24

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: IKZF3-MED24
FusionPDB ID: 39403
FusionGDB2.0 ID: 39403
HgeneTgene
Gene symbol

IKZF3

MED24

Gene ID

22806

9862

Gene nameIKAROS family zinc finger 3mediator complex subunit 24
SynonymsAIO|AIOLOS|ZNFN1A3ARC100|CRSP100|CRSP4|DRIP100|MED5|THRAP4|TRAP100
Cytomap

17q12-q21.1

17q21.1

Type of geneprotein-codingprotein-coding
Descriptionzinc finger protein Aioloszinc finger DNA binding protein Aioloszinc finger protein, subfamily 1A, 3 (Aiolos)mediator of RNA polymerase II transcription subunit 24CRSP complex subunit 4activator-recruited cofactor 100 kDa componentcofactor required for Sp1 transcriptional activation subunit 4cofactor required for Sp1 transcriptional activation, subunit 4, 10
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}.

O75448

Main function of 5'-partner protein: FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. {ECO:0000269|PubMed:12218053, ECO:0000269|PubMed:16595664}.
Ensembl transtripts involved in fusion geneENST idsENST00000346243, ENST00000346872, 
ENST00000350532, ENST00000351680, 
ENST00000377944, ENST00000377945, 
ENST00000377952, ENST00000377958, 
ENST00000394189, ENST00000439016, 
ENST00000467757, ENST00000439167, 
ENST00000535189, ENST00000583368, 
ENST00000479829, ENST00000356271, 
ENST00000394126, ENST00000394127, 
ENST00000394128, ENST00000501516, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score10 X 9 X 7=63016 X 15 X 7=1680
# samples 1123
** MAII scorelog2(11/630*10)=-2.51784830486262
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(23/1680*10)=-2.86875546672175
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: IKZF3 [Title/Abstract] AND MED24 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: IKZF3 [Title/Abstract] AND MED24 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)IKZF3(37985640)-MED24(38176186), # samples:2
MED24(38176526)-IKZF3(37949186), # samples:2
Anticipated loss of major functional domain due to fusion event.IKZF3-MED24 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-MED24 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.
MED24-IKZF3 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
MED24-IKZF3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
MED24-IKZF3 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
MED24-IKZF3 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
MED24-IKZF3 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
MED24-IKZF3 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneMED24

GO:0006367

transcription initiation from RNA polymerase II promoter

12218053

TgeneMED24

GO:0045893

positive regulation of transcription, DNA-templated

10198638



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/chr17:37985640/chr17:38176186)
- 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 MED24 (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)
ENST00000346872IKZF3chr1737985640-ENST00000394126MED24chr1738176186-923225888163241
ENST00000346872IKZF3chr1737985640-ENST00000356271MED24chr1738176186-922225888163241
ENST00000346872IKZF3chr1737985640-ENST00000394128MED24chr1738176186-91822562490142
ENST00000346872IKZF3chr1737985640-ENST00000394127MED24chr1738176186-91222562490142
ENST00000346872IKZF3chr1737985640-ENST00000501516MED24chr1738176186-49122562490143
ENST00000394189IKZF3chr1737985640-ENST00000394126MED24chr1738176186-923225888163241
ENST00000394189IKZF3chr1737985640-ENST00000356271MED24chr1738176186-922225888163241
ENST00000394189IKZF3chr1737985640-ENST00000394128MED24chr1738176186-91822562490142
ENST00000394189IKZF3chr1737985640-ENST00000394127MED24chr1738176186-91222562490142
ENST00000394189IKZF3chr1737985640-ENST00000501516MED24chr1738176186-49122562490143
ENST00000377944IKZF3chr1737985640-ENST00000394126MED24chr1738176186-923225888163241
ENST00000377944IKZF3chr1737985640-ENST00000356271MED24chr1738176186-922225888163241
ENST00000377944IKZF3chr1737985640-ENST00000394128MED24chr1738176186-91822562490142
ENST00000377944IKZF3chr1737985640-ENST00000394127MED24chr1738176186-91222562490142
ENST00000377944IKZF3chr1737985640-ENST00000501516MED24chr1738176186-49122562490143
ENST00000377945IKZF3chr1737985640-ENST00000394126MED24chr1738176186-923225888163241
ENST00000377945IKZF3chr1737985640-ENST00000356271MED24chr1738176186-922225888163241
ENST00000377945IKZF3chr1737985640-ENST00000394128MED24chr1738176186-91822562490142
ENST00000377945IKZF3chr1737985640-ENST00000394127MED24chr1738176186-91222562490142
ENST00000377945IKZF3chr1737985640-ENST00000501516MED24chr1738176186-49122562490143
ENST00000377952IKZF3chr1737985640-ENST00000394126MED24chr1738176186-923225888163241
ENST00000377952IKZF3chr1737985640-ENST00000356271MED24chr1738176186-922225888163241
ENST00000377952IKZF3chr1737985640-ENST00000394128MED24chr1738176186-91822562490142
ENST00000377952IKZF3chr1737985640-ENST00000394127MED24chr1738176186-91222562490142
ENST00000377952IKZF3chr1737985640-ENST00000501516MED24chr1738176186-49122562490143
ENST00000377958IKZF3chr1737985640-ENST00000394126MED24chr1738176186-923225888163241
ENST00000377958IKZF3chr1737985640-ENST00000356271MED24chr1738176186-922225888163241
ENST00000377958IKZF3chr1737985640-ENST00000394128MED24chr1738176186-91822562490142
ENST00000377958IKZF3chr1737985640-ENST00000394127MED24chr1738176186-91222562490142
ENST00000377958IKZF3chr1737985640-ENST00000501516MED24chr1738176186-49122562490143
ENST00000346243IKZF3chr1737985640-ENST00000394126MED24chr1738176186-861163826101241
ENST00000346243IKZF3chr1737985640-ENST00000356271MED24chr1738176186-860163826101241
ENST00000346243IKZF3chr1737985640-ENST00000394128MED24chr1738176186-8561630428142
ENST00000346243IKZF3chr1737985640-ENST00000394127MED24chr1738176186-8501630428142
ENST00000346243IKZF3chr1737985640-ENST00000501516MED24chr1738176186-4291630428142
ENST00000350532IKZF3chr1737985640-ENST00000394126MED24chr1738176186-861163826101241
ENST00000350532IKZF3chr1737985640-ENST00000356271MED24chr1738176186-860163826101241
ENST00000350532IKZF3chr1737985640-ENST00000394128MED24chr1738176186-8561630428142
ENST00000350532IKZF3chr1737985640-ENST00000394127MED24chr1738176186-8501630428142
ENST00000350532IKZF3chr1737985640-ENST00000501516MED24chr1738176186-4291630428142
ENST00000351680IKZF3chr1737985640-ENST00000394126MED24chr1738176186-861163826101241
ENST00000351680IKZF3chr1737985640-ENST00000356271MED24chr1738176186-860163826101241
ENST00000351680IKZF3chr1737985640-ENST00000394128MED24chr1738176186-8561630428142
ENST00000351680IKZF3chr1737985640-ENST00000394127MED24chr1738176186-8501630428142
ENST00000351680IKZF3chr1737985640-ENST00000501516MED24chr1738176186-4291630428142
ENST00000467757IKZF3chr1737985640-ENST00000394126MED24chr1738176186-861163826101241
ENST00000467757IKZF3chr1737985640-ENST00000356271MED24chr1738176186-860163826101241
ENST00000467757IKZF3chr1737985640-ENST00000394128MED24chr1738176186-8561630428142
ENST00000467757IKZF3chr1737985640-ENST00000394127MED24chr1738176186-8501630428142
ENST00000467757IKZF3chr1737985640-ENST00000501516MED24chr1738176186-4291630428142
ENST00000439016IKZF3chr1737985640-ENST00000394126MED24chr1738176186-862164827102241
ENST00000439016IKZF3chr1737985640-ENST00000356271MED24chr1738176186-861164827102241
ENST00000439016IKZF3chr1737985640-ENST00000394128MED24chr1738176186-8571641429142
ENST00000439016IKZF3chr1737985640-ENST00000394127MED24chr1738176186-8511641429142
ENST00000439016IKZF3chr1737985640-ENST00000501516MED24chr1738176186-4301641429143
ENST00000346872IKZF3chr1737985639-ENST00000394126MED24chr1738176186-923225888163241
ENST00000346872IKZF3chr1737985639-ENST00000356271MED24chr1738176186-922225888163241
ENST00000346872IKZF3chr1737985639-ENST00000394128MED24chr1738176186-91822562490142
ENST00000346872IKZF3chr1737985639-ENST00000394127MED24chr1738176186-91222562490142
ENST00000346872IKZF3chr1737985639-ENST00000501516MED24chr1738176186-49122562490143
ENST00000394189IKZF3chr1737985639-ENST00000394126MED24chr1738176186-923225888163241
ENST00000394189IKZF3chr1737985639-ENST00000356271MED24chr1738176186-922225888163241
ENST00000394189IKZF3chr1737985639-ENST00000394128MED24chr1738176186-91822562490142
ENST00000394189IKZF3chr1737985639-ENST00000394127MED24chr1738176186-91222562490142
ENST00000394189IKZF3chr1737985639-ENST00000501516MED24chr1738176186-49122562490143
ENST00000377944IKZF3chr1737985639-ENST00000394126MED24chr1738176186-923225888163241
ENST00000377944IKZF3chr1737985639-ENST00000356271MED24chr1738176186-922225888163241
ENST00000377944IKZF3chr1737985639-ENST00000394128MED24chr1738176186-91822562490142
ENST00000377944IKZF3chr1737985639-ENST00000394127MED24chr1738176186-91222562490142
ENST00000377944IKZF3chr1737985639-ENST00000501516MED24chr1738176186-49122562490143
ENST00000377945IKZF3chr1737985639-ENST00000394126MED24chr1738176186-923225888163241
ENST00000377945IKZF3chr1737985639-ENST00000356271MED24chr1738176186-922225888163241
ENST00000377945IKZF3chr1737985639-ENST00000394128MED24chr1738176186-91822562490142
ENST00000377945IKZF3chr1737985639-ENST00000394127MED24chr1738176186-91222562490142
ENST00000377945IKZF3chr1737985639-ENST00000501516MED24chr1738176186-49122562490143
ENST00000377952IKZF3chr1737985639-ENST00000394126MED24chr1738176186-923225888163241
ENST00000377952IKZF3chr1737985639-ENST00000356271MED24chr1738176186-922225888163241
ENST00000377952IKZF3chr1737985639-ENST00000394128MED24chr1738176186-91822562490142
ENST00000377952IKZF3chr1737985639-ENST00000394127MED24chr1738176186-91222562490142
ENST00000377952IKZF3chr1737985639-ENST00000501516MED24chr1738176186-49122562490143
ENST00000377958IKZF3chr1737985639-ENST00000394126MED24chr1738176186-923225888163241
ENST00000377958IKZF3chr1737985639-ENST00000356271MED24chr1738176186-922225888163241
ENST00000377958IKZF3chr1737985639-ENST00000394128MED24chr1738176186-91822562490142
ENST00000377958IKZF3chr1737985639-ENST00000394127MED24chr1738176186-91222562490142
ENST00000377958IKZF3chr1737985639-ENST00000501516MED24chr1738176186-49122562490143
ENST00000346243IKZF3chr1737985639-ENST00000394126MED24chr1738176186-861163826101241
ENST00000346243IKZF3chr1737985639-ENST00000356271MED24chr1738176186-860163826101241
ENST00000346243IKZF3chr1737985639-ENST00000394128MED24chr1738176186-8561630428142
ENST00000346243IKZF3chr1737985639-ENST00000394127MED24chr1738176186-8501630428142
ENST00000346243IKZF3chr1737985639-ENST00000501516MED24chr1738176186-4291630428142
ENST00000350532IKZF3chr1737985639-ENST00000394126MED24chr1738176186-861163826101241
ENST00000350532IKZF3chr1737985639-ENST00000356271MED24chr1738176186-860163826101241
ENST00000350532IKZF3chr1737985639-ENST00000394128MED24chr1738176186-8561630428142
ENST00000350532IKZF3chr1737985639-ENST00000394127MED24chr1738176186-8501630428142
ENST00000350532IKZF3chr1737985639-ENST00000501516MED24chr1738176186-4291630428142
ENST00000351680IKZF3chr1737985639-ENST00000394126MED24chr1738176186-861163826101241
ENST00000351680IKZF3chr1737985639-ENST00000356271MED24chr1738176186-860163826101241
ENST00000351680IKZF3chr1737985639-ENST00000394128MED24chr1738176186-8561630428142
ENST00000351680IKZF3chr1737985639-ENST00000394127MED24chr1738176186-8501630428142
ENST00000351680IKZF3chr1737985639-ENST00000501516MED24chr1738176186-4291630428142
ENST00000467757IKZF3chr1737985639-ENST00000394126MED24chr1738176186-861163826101241
ENST00000467757IKZF3chr1737985639-ENST00000356271MED24chr1738176186-860163826101241
ENST00000467757IKZF3chr1737985639-ENST00000394128MED24chr1738176186-8561630428142
ENST00000467757IKZF3chr1737985639-ENST00000394127MED24chr1738176186-8501630428142
ENST00000467757IKZF3chr1737985639-ENST00000501516MED24chr1738176186-4291630428142
ENST00000439016IKZF3chr1737985639-ENST00000394126MED24chr1738176186-862164827102241
ENST00000439016IKZF3chr1737985639-ENST00000356271MED24chr1738176186-861164827102241
ENST00000439016IKZF3chr1737985639-ENST00000394128MED24chr1738176186-8571641429142
ENST00000439016IKZF3chr1737985639-ENST00000394127MED24chr1738176186-8511641429142
ENST00000439016IKZF3chr1737985639-ENST00000501516MED24chr1738176186-4301641429143

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
ENST00000346872ENST00000394126IKZF3chr1737985640-MED24chr1738176186-0.0099014910.99009854
ENST00000346872ENST00000356271IKZF3chr1737985640-MED24chr1738176186-0.0100612940.98993874
ENST00000346872ENST00000394128IKZF3chr1737985640-MED24chr1738176186-0.0095692160.9904308
ENST00000346872ENST00000394127IKZF3chr1737985640-MED24chr1738176186-0.0087288030.99127126
ENST00000346872ENST00000501516IKZF3chr1737985640-MED24chr1738176186-0.004244140.99575585
ENST00000394189ENST00000394126IKZF3chr1737985640-MED24chr1738176186-0.0099014910.99009854
ENST00000394189ENST00000356271IKZF3chr1737985640-MED24chr1738176186-0.0100612940.98993874
ENST00000394189ENST00000394128IKZF3chr1737985640-MED24chr1738176186-0.0095692160.9904308
ENST00000394189ENST00000394127IKZF3chr1737985640-MED24chr1738176186-0.0087288030.99127126
ENST00000394189ENST00000501516IKZF3chr1737985640-MED24chr1738176186-0.004244140.99575585
ENST00000377944ENST00000394126IKZF3chr1737985640-MED24chr1738176186-0.0099014910.99009854
ENST00000377944ENST00000356271IKZF3chr1737985640-MED24chr1738176186-0.0100612940.98993874
ENST00000377944ENST00000394128IKZF3chr1737985640-MED24chr1738176186-0.0095692160.9904308
ENST00000377944ENST00000394127IKZF3chr1737985640-MED24chr1738176186-0.0087288030.99127126
ENST00000377944ENST00000501516IKZF3chr1737985640-MED24chr1738176186-0.004244140.99575585
ENST00000377945ENST00000394126IKZF3chr1737985640-MED24chr1738176186-0.0099014910.99009854
ENST00000377945ENST00000356271IKZF3chr1737985640-MED24chr1738176186-0.0100612940.98993874
ENST00000377945ENST00000394128IKZF3chr1737985640-MED24chr1738176186-0.0095692160.9904308
ENST00000377945ENST00000394127IKZF3chr1737985640-MED24chr1738176186-0.0087288030.99127126
ENST00000377945ENST00000501516IKZF3chr1737985640-MED24chr1738176186-0.004244140.99575585
ENST00000377952ENST00000394126IKZF3chr1737985640-MED24chr1738176186-0.0099014910.99009854
ENST00000377952ENST00000356271IKZF3chr1737985640-MED24chr1738176186-0.0100612940.98993874
ENST00000377952ENST00000394128IKZF3chr1737985640-MED24chr1738176186-0.0095692160.9904308
ENST00000377952ENST00000394127IKZF3chr1737985640-MED24chr1738176186-0.0087288030.99127126
ENST00000377952ENST00000501516IKZF3chr1737985640-MED24chr1738176186-0.004244140.99575585
ENST00000377958ENST00000394126IKZF3chr1737985640-MED24chr1738176186-0.0099014910.99009854
ENST00000377958ENST00000356271IKZF3chr1737985640-MED24chr1738176186-0.0100612940.98993874
ENST00000377958ENST00000394128IKZF3chr1737985640-MED24chr1738176186-0.0095692160.9904308
ENST00000377958ENST00000394127IKZF3chr1737985640-MED24chr1738176186-0.0087288030.99127126
ENST00000377958ENST00000501516IKZF3chr1737985640-MED24chr1738176186-0.004244140.99575585
ENST00000346243ENST00000394126IKZF3chr1737985640-MED24chr1738176186-0.0124575180.9875425
ENST00000346243ENST00000356271IKZF3chr1737985640-MED24chr1738176186-0.0124750470.987525
ENST00000346243ENST00000394128IKZF3chr1737985640-MED24chr1738176186-0.0123309320.98766905
ENST00000346243ENST00000394127IKZF3chr1737985640-MED24chr1738176186-0.0113707660.9886292
ENST00000346243ENST00000501516IKZF3chr1737985640-MED24chr1738176186-0.0077605220.9922395
ENST00000350532ENST00000394126IKZF3chr1737985640-MED24chr1738176186-0.0124575180.9875425
ENST00000350532ENST00000356271IKZF3chr1737985640-MED24chr1738176186-0.0124750470.987525
ENST00000350532ENST00000394128IKZF3chr1737985640-MED24chr1738176186-0.0123309320.98766905
ENST00000350532ENST00000394127IKZF3chr1737985640-MED24chr1738176186-0.0113707660.9886292
ENST00000350532ENST00000501516IKZF3chr1737985640-MED24chr1738176186-0.0077605220.9922395
ENST00000351680ENST00000394126IKZF3chr1737985640-MED24chr1738176186-0.0124575180.9875425
ENST00000351680ENST00000356271IKZF3chr1737985640-MED24chr1738176186-0.0124750470.987525
ENST00000351680ENST00000394128IKZF3chr1737985640-MED24chr1738176186-0.0123309320.98766905
ENST00000351680ENST00000394127IKZF3chr1737985640-MED24chr1738176186-0.0113707660.9886292
ENST00000351680ENST00000501516IKZF3chr1737985640-MED24chr1738176186-0.0077605220.9922395
ENST00000467757ENST00000394126IKZF3chr1737985640-MED24chr1738176186-0.0124575180.9875425
ENST00000467757ENST00000356271IKZF3chr1737985640-MED24chr1738176186-0.0124750470.987525
ENST00000467757ENST00000394128IKZF3chr1737985640-MED24chr1738176186-0.0123309320.98766905
ENST00000467757ENST00000394127IKZF3chr1737985640-MED24chr1738176186-0.0113707660.9886292
ENST00000467757ENST00000501516IKZF3chr1737985640-MED24chr1738176186-0.0077605220.9922395
ENST00000439016ENST00000394126IKZF3chr1737985640-MED24chr1738176186-0.0124490270.98755103
ENST00000439016ENST00000356271IKZF3chr1737985640-MED24chr1738176186-0.0124725690.98752743
ENST00000439016ENST00000394128IKZF3chr1737985640-MED24chr1738176186-0.0123530650.98764694
ENST00000439016ENST00000394127IKZF3chr1737985640-MED24chr1738176186-0.0113313480.9886686
ENST00000439016ENST00000501516IKZF3chr1737985640-MED24chr1738176186-0.0078335020.9921665
ENST00000346872ENST00000394126IKZF3chr1737985639-MED24chr1738176186-0.0099014910.99009854
ENST00000346872ENST00000356271IKZF3chr1737985639-MED24chr1738176186-0.0100612940.98993874
ENST00000346872ENST00000394128IKZF3chr1737985639-MED24chr1738176186-0.0095692160.9904308
ENST00000346872ENST00000394127IKZF3chr1737985639-MED24chr1738176186-0.0087288030.99127126
ENST00000346872ENST00000501516IKZF3chr1737985639-MED24chr1738176186-0.004244140.99575585
ENST00000394189ENST00000394126IKZF3chr1737985639-MED24chr1738176186-0.0099014910.99009854
ENST00000394189ENST00000356271IKZF3chr1737985639-MED24chr1738176186-0.0100612940.98993874
ENST00000394189ENST00000394128IKZF3chr1737985639-MED24chr1738176186-0.0095692160.9904308
ENST00000394189ENST00000394127IKZF3chr1737985639-MED24chr1738176186-0.0087288030.99127126
ENST00000394189ENST00000501516IKZF3chr1737985639-MED24chr1738176186-0.004244140.99575585
ENST00000377944ENST00000394126IKZF3chr1737985639-MED24chr1738176186-0.0099014910.99009854
ENST00000377944ENST00000356271IKZF3chr1737985639-MED24chr1738176186-0.0100612940.98993874
ENST00000377944ENST00000394128IKZF3chr1737985639-MED24chr1738176186-0.0095692160.9904308
ENST00000377944ENST00000394127IKZF3chr1737985639-MED24chr1738176186-0.0087288030.99127126
ENST00000377944ENST00000501516IKZF3chr1737985639-MED24chr1738176186-0.004244140.99575585
ENST00000377945ENST00000394126IKZF3chr1737985639-MED24chr1738176186-0.0099014910.99009854
ENST00000377945ENST00000356271IKZF3chr1737985639-MED24chr1738176186-0.0100612940.98993874
ENST00000377945ENST00000394128IKZF3chr1737985639-MED24chr1738176186-0.0095692160.9904308
ENST00000377945ENST00000394127IKZF3chr1737985639-MED24chr1738176186-0.0087288030.99127126
ENST00000377945ENST00000501516IKZF3chr1737985639-MED24chr1738176186-0.004244140.99575585
ENST00000377952ENST00000394126IKZF3chr1737985639-MED24chr1738176186-0.0099014910.99009854
ENST00000377952ENST00000356271IKZF3chr1737985639-MED24chr1738176186-0.0100612940.98993874
ENST00000377952ENST00000394128IKZF3chr1737985639-MED24chr1738176186-0.0095692160.9904308
ENST00000377952ENST00000394127IKZF3chr1737985639-MED24chr1738176186-0.0087288030.99127126
ENST00000377952ENST00000501516IKZF3chr1737985639-MED24chr1738176186-0.004244140.99575585
ENST00000377958ENST00000394126IKZF3chr1737985639-MED24chr1738176186-0.0099014910.99009854
ENST00000377958ENST00000356271IKZF3chr1737985639-MED24chr1738176186-0.0100612940.98993874
ENST00000377958ENST00000394128IKZF3chr1737985639-MED24chr1738176186-0.0095692160.9904308
ENST00000377958ENST00000394127IKZF3chr1737985639-MED24chr1738176186-0.0087288030.99127126
ENST00000377958ENST00000501516IKZF3chr1737985639-MED24chr1738176186-0.004244140.99575585
ENST00000346243ENST00000394126IKZF3chr1737985639-MED24chr1738176186-0.0124575180.9875425
ENST00000346243ENST00000356271IKZF3chr1737985639-MED24chr1738176186-0.0124750470.987525
ENST00000346243ENST00000394128IKZF3chr1737985639-MED24chr1738176186-0.0123309320.98766905
ENST00000346243ENST00000394127IKZF3chr1737985639-MED24chr1738176186-0.0113707660.9886292
ENST00000346243ENST00000501516IKZF3chr1737985639-MED24chr1738176186-0.0077605220.9922395
ENST00000350532ENST00000394126IKZF3chr1737985639-MED24chr1738176186-0.0124575180.9875425
ENST00000350532ENST00000356271IKZF3chr1737985639-MED24chr1738176186-0.0124750470.987525
ENST00000350532ENST00000394128IKZF3chr1737985639-MED24chr1738176186-0.0123309320.98766905
ENST00000350532ENST00000394127IKZF3chr1737985639-MED24chr1738176186-0.0113707660.9886292
ENST00000350532ENST00000501516IKZF3chr1737985639-MED24chr1738176186-0.0077605220.9922395
ENST00000351680ENST00000394126IKZF3chr1737985639-MED24chr1738176186-0.0124575180.9875425
ENST00000351680ENST00000356271IKZF3chr1737985639-MED24chr1738176186-0.0124750470.987525
ENST00000351680ENST00000394128IKZF3chr1737985639-MED24chr1738176186-0.0123309320.98766905
ENST00000351680ENST00000394127IKZF3chr1737985639-MED24chr1738176186-0.0113707660.9886292
ENST00000351680ENST00000501516IKZF3chr1737985639-MED24chr1738176186-0.0077605220.9922395
ENST00000467757ENST00000394126IKZF3chr1737985639-MED24chr1738176186-0.0124575180.9875425
ENST00000467757ENST00000356271IKZF3chr1737985639-MED24chr1738176186-0.0124750470.987525
ENST00000467757ENST00000394128IKZF3chr1737985639-MED24chr1738176186-0.0123309320.98766905
ENST00000467757ENST00000394127IKZF3chr1737985639-MED24chr1738176186-0.0113707660.9886292
ENST00000467757ENST00000501516IKZF3chr1737985639-MED24chr1738176186-0.0077605220.9922395
ENST00000439016ENST00000394126IKZF3chr1737985639-MED24chr1738176186-0.0124490270.98755103
ENST00000439016ENST00000356271IKZF3chr1737985639-MED24chr1738176186-0.0124725690.98752743
ENST00000439016ENST00000394128IKZF3chr1737985639-MED24chr1738176186-0.0123530650.98764694
ENST00000439016ENST00000394127IKZF3chr1737985639-MED24chr1738176186-0.0113313480.9886686
ENST00000439016ENST00000501516IKZF3chr1737985639-MED24chr1738176186-0.0078335020.9921665

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-MED24

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
IKZF3chr1737985639MED24chr173817618616354SGEGPANEDEDIGANLFLLISSILGS
IKZF3chr1737985639MED24chr173817618616454SGEGPANEDEDIGANLFLLISSILGS
IKZF3chr1737985639MED24chr173817618622554SGEGPANEDEDIGANLFLLISSILGS
IKZF3chr1737985640MED24chr173817618616354SGEGPANEDEDIGANLFLLISSILGS
IKZF3chr1737985640MED24chr173817618616454SGEGPANEDEDIGANLFLLISSILGS
IKZF3chr1737985640MED24chr173817618622554SGEGPANEDEDIGANLFLLISSILGS

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Potential FusionNeoAntigen Information of IKZF3-MED24 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-MED24_37985639_38176186.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-MED24chr1737985639chr1738176186163HLA-B18:01DEDIGANL0.9940.9313816
IKZF3-MED24chr1737985639chr1738176186163HLA-B18:01DEDIGANLF0.97920.9208817
IKZF3-MED24chr1737985639chr1738176186163HLA-B44:03DEDIGANLF0.96060.9091817
IKZF3-MED24chr1737985639chr1738176186163HLA-B39:08NEDEDIGANL0.91510.7024616
IKZF3-MED24chr1737985639chr1738176186163HLA-B18:05DEDIGANL0.9940.9313816
IKZF3-MED24chr1737985639chr1738176186163HLA-B18:03DEDIGANL0.9920.9276816
IKZF3-MED24chr1737985639chr1738176186163HLA-B18:06DEDIGANL0.99150.9307816
IKZF3-MED24chr1737985639chr1738176186163HLA-B18:07DEDIGANLF0.98660.8896817
IKZF3-MED24chr1737985639chr1738176186163HLA-B18:06DEDIGANLF0.9820.9207817
IKZF3-MED24chr1737985639chr1738176186163HLA-B18:04DEDIGANLF0.98020.9314817
IKZF3-MED24chr1737985639chr1738176186163HLA-B18:05DEDIGANLF0.97920.9208817
IKZF3-MED24chr1737985639chr1738176186163HLA-B18:08DEDIGANLF0.97740.7899817
IKZF3-MED24chr1737985639chr1738176186163HLA-B18:03DEDIGANLF0.96480.9145817
IKZF3-MED24chr1737985639chr1738176186163HLA-B44:26DEDIGANLF0.96060.9091817
IKZF3-MED24chr1737985639chr1738176186163HLA-B44:13DEDIGANLF0.96060.9091817
IKZF3-MED24chr1737985639chr1738176186163HLA-B44:07DEDIGANLF0.96060.9091817
IKZF3-MED24chr1737985639chr1738176186163HLA-B18:11DEDIGANLF0.64680.8511817
IKZF3-MED24chr1737985639chr1738176186163HLA-B39:11NEDEDIGANL0.93850.6523616

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Potential FusionNeoAntigen Information of IKZF3-MED24 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-MED24

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
6127NEDEDIGANLFLLIIKZF3MED24chr1737985639chr1738176186163

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of IKZF3-MED24

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-B14:023BVN6127NEDEDIGANLFLLI-7.15543-7.26883
HLA-B14:023BVN6127NEDEDIGANLFLLI-4.77435-5.80965
HLA-B52:013W396127NEDEDIGANLFLLI-6.80875-6.92215
HLA-B52:013W396127NEDEDIGANLFLLI-4.20386-5.23916
HLA-A11:014UQ26127NEDEDIGANLFLLI-7.5194-8.5547
HLA-A11:014UQ26127NEDEDIGANLFLLI-6.9601-7.0735
HLA-A24:025HGA6127NEDEDIGANLFLLI-7.52403-7.63743
HLA-A24:025HGA6127NEDEDIGANLFLLI-5.82433-6.85963
HLA-B27:056PYJ6127NEDEDIGANLFLLI-3.28285-4.31815
HLA-B44:053DX86127NEDEDIGANLFLLI-5.91172-6.94702
HLA-B44:053DX86127NEDEDIGANLFLLI-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of IKZF3-MED24

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-MED24chr1737985639chr1738176186616NEDEDIGANLATGAAGATGAAGACATAGGAGCCAACCTGT
IKZF3-MED24chr1737985639chr1738176186816DEDIGANLATGAAGACATAGGAGCCAACCTGT
IKZF3-MED24chr1737985639chr1738176186817DEDIGANLFATGAAGACATAGGAGCCAACCTGTTCC

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-MED24

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
BLCAIKZF3-MED24chr1737985639ENST00000346243chr1738176186ENST00000394127TCGA-FD-A3SL

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Potential target of CAR-T therapy development for IKZF3-MED24

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-MED24

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-MED24

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