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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:EWSR1-KREMEN1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: EWSR1-KREMEN1
FusionPDB ID: 27837
FusionGDB2.0 ID: 27837
HgeneTgene
Gene symbol

EWSR1

KREMEN1

Gene ID

2130

83999

Gene nameEWS RNA binding protein 1kringle containing transmembrane protein 1
SynonymsEWS|EWS-FLI1|bK984G1.4ECTD13|KREMEN|KRM1
Cytomap

22q12.2

22q12.1

Type of geneprotein-codingprotein-coding
DescriptionRNA-binding protein EWSEWS RNA-binding protein variant 6Ewing sarcoma breakpoint region 1Ewings sarcoma EWS-Fli1 (type 1) oncogenekremen protein 1dickkopf receptorkringle domain-containing transmembrane protein 1kringle-coding gene marking the eye and the nosekringle-containing protein marking the eye and the nose
Modification date2020032920200313
UniProtAcc

Q01844

Main function of 5'-partner protein: FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

Q96MU8

Main function of 5'-partner protein: FUNCTION: Receptor for Dickkopf proteins. Cooperates with DKK1/2 to inhibit Wnt/beta-catenin signaling by promoting the endocytosis of Wnt receptors LRP5 and LRP6. In the absence of DKK1, potentiates Wnt-beta-catenin signaling by maintaining LRP5 or LRP6 at the cell membrane. Can trigger apoptosis in a Wnt-independent manner and this apoptotic activity is inhibited upon binding of the ligand DKK1. Plays a role in limb development; attenuates Wnt signaling in the developing limb to allow normal limb patterning and can also negatively regulate bone formation. Modulates cell fate decisions in the developing cochlea with an inhibitory role in hair cell fate specification. {ECO:0000250|UniProtKB:Q90Y90, ECO:0000250|UniProtKB:Q99N43}.
Ensembl transtripts involved in fusion geneENST idsENST00000331029, ENST00000332035, 
ENST00000332050, ENST00000333395, 
ENST00000397938, ENST00000406548, 
ENST00000414183, 		ENST00000479755, 
ENST00000327813, ENST00000400335, 
ENST00000400338, ENST00000407188, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score44 X 91 X 16=640645 X 9 X 5=225
# samples 989
** MAII scorelog2(98/64064*10)=-6.03058831983342
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/225*10)=-1.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: EWSR1 [Title/Abstract] AND KREMEN1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: EWSR1 [Title/Abstract] AND KREMEN1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)EWSR1(29668420)-KREMEN1(29517344), # samples:2
Anticipated loss of major functional domain due to fusion event.EWSR1-KREMEN1 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.
EWSR1-KREMEN1 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.
EWSR1-KREMEN1 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.
EWSR1-KREMEN1 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.
EWSR1-KREMEN1 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
EWSR1-KREMEN1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
EWSR1-KREMEN1 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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


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/chr22:29668420/chr22:29517344)
- 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 EWSR1 (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 KREMEN1 (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)
ENST00000332050EWSR1chr2229688595+ENST00000400338KREMEN1chr2229521250+692512733282223631
ENST00000332050EWSR1chr2229688595+ENST00000400335KREMEN1chr2229521250+688112733282172614
ENST00000332050EWSR1chr2229688595+ENST00000327813KREMEN1chr2229521250+350212733282274648
ENST00000332050EWSR1chr2229688595+ENST00000407188KREMEN1chr2229521250+222412733282223632
ENST00000397938EWSR1chr2229688595+ENST00000400338KREMEN1chr2229521250+713514833192433704
ENST00000397938EWSR1chr2229688595+ENST00000400335KREMEN1chr2229521250+709114833192382687
ENST00000397938EWSR1chr2229688595+ENST00000327813KREMEN1chr2229521250+371214833192484721
ENST00000397938EWSR1chr2229688595+ENST00000407188KREMEN1chr2229521250+243414833192433705
ENST00000406548EWSR1chr2229688595+ENST00000400338KREMEN1chr2229521250+68771225642175703
ENST00000406548EWSR1chr2229688595+ENST00000400335KREMEN1chr2229521250+68331225642124686
ENST00000406548EWSR1chr2229688595+ENST00000327813KREMEN1chr2229521250+34541225642226720
ENST00000406548EWSR1chr2229688595+ENST00000407188KREMEN1chr2229521250+21761225642175704
ENST00000331029EWSR1chr2229688595+ENST00000400338KREMEN1chr2229521250+67481096462046666
ENST00000331029EWSR1chr2229688595+ENST00000400335KREMEN1chr2229521250+67041096461995649
ENST00000331029EWSR1chr2229688595+ENST00000327813KREMEN1chr2229521250+33251096462097683
ENST00000331029EWSR1chr2229688595+ENST00000407188KREMEN1chr2229521250+20471096462046667
ENST00000414183EWSR1chr2229688595+ENST00000400338KREMEN1chr2229521250+68521200212150709
ENST00000414183EWSR1chr2229688595+ENST00000400335KREMEN1chr2229521250+68081200212099692
ENST00000414183EWSR1chr2229688595+ENST00000327813KREMEN1chr2229521250+34291200212201726
ENST00000414183EWSR1chr2229688595+ENST00000407188KREMEN1chr2229521250+21511200212150709
ENST00000332035EWSR1chr2229688595+ENST00000400338KREMEN1chr2229521250+66591007111957648
ENST00000332035EWSR1chr2229688595+ENST00000400335KREMEN1chr2229521250+66151007111906631
ENST00000332035EWSR1chr2229688595+ENST00000327813KREMEN1chr2229521250+32361007112008665
ENST00000332035EWSR1chr2229688595+ENST00000407188KREMEN1chr2229521250+19581007111957649
ENST00000332050EWSR1chr2229688595+ENST00000400338KREMEN1chr2229521251+692512733282223631
ENST00000332050EWSR1chr2229688595+ENST00000400335KREMEN1chr2229521251+688112733282172614
ENST00000332050EWSR1chr2229688595+ENST00000327813KREMEN1chr2229521251+350212733282274648
ENST00000332050EWSR1chr2229688595+ENST00000407188KREMEN1chr2229521251+222412733282223632
ENST00000397938EWSR1chr2229688595+ENST00000400338KREMEN1chr2229521251+713514833192433704
ENST00000397938EWSR1chr2229688595+ENST00000400335KREMEN1chr2229521251+709114833192382687
ENST00000397938EWSR1chr2229688595+ENST00000327813KREMEN1chr2229521251+371214833192484721
ENST00000397938EWSR1chr2229688595+ENST00000407188KREMEN1chr2229521251+243414833192433705
ENST00000406548EWSR1chr2229688595+ENST00000400338KREMEN1chr2229521251+68771225642175703
ENST00000406548EWSR1chr2229688595+ENST00000400335KREMEN1chr2229521251+68331225642124686
ENST00000406548EWSR1chr2229688595+ENST00000327813KREMEN1chr2229521251+34541225642226720
ENST00000406548EWSR1chr2229688595+ENST00000407188KREMEN1chr2229521251+21761225642175704
ENST00000331029EWSR1chr2229688595+ENST00000400338KREMEN1chr2229521251+67481096462046666
ENST00000331029EWSR1chr2229688595+ENST00000400335KREMEN1chr2229521251+67041096461995649
ENST00000331029EWSR1chr2229688595+ENST00000327813KREMEN1chr2229521251+33251096462097683
ENST00000331029EWSR1chr2229688595+ENST00000407188KREMEN1chr2229521251+20471096462046667
ENST00000414183EWSR1chr2229688595+ENST00000400338KREMEN1chr2229521251+68521200212150709
ENST00000414183EWSR1chr2229688595+ENST00000400335KREMEN1chr2229521251+68081200212099692
ENST00000414183EWSR1chr2229688595+ENST00000327813KREMEN1chr2229521251+34291200212201726
ENST00000414183EWSR1chr2229688595+ENST00000407188KREMEN1chr2229521251+21511200212150709
ENST00000332035EWSR1chr2229688595+ENST00000400338KREMEN1chr2229521251+66591007111957648
ENST00000332035EWSR1chr2229688595+ENST00000400335KREMEN1chr2229521251+66151007111906631
ENST00000332035EWSR1chr2229688595+ENST00000327813KREMEN1chr2229521251+32361007112008665
ENST00000332035EWSR1chr2229688595+ENST00000407188KREMEN1chr2229521251+19581007111957649

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
ENST00000332050ENST00000400338EWSR1chr2229688595+KREMEN1chr2229521250+0.0021863970.9978136
ENST00000332050ENST00000400335EWSR1chr2229688595+KREMEN1chr2229521250+0.0021116820.99788827
ENST00000332050ENST00000327813EWSR1chr2229688595+KREMEN1chr2229521250+0.0045907380.9954092
ENST00000332050ENST00000407188EWSR1chr2229688595+KREMEN1chr2229521250+0.0039292380.99607074
ENST00000397938ENST00000400338EWSR1chr2229688595+KREMEN1chr2229521250+0.0021063980.99789363
ENST00000397938ENST00000400335EWSR1chr2229688595+KREMEN1chr2229521250+0.0021645060.99783546
ENST00000397938ENST00000327813EWSR1chr2229688595+KREMEN1chr2229521250+0.0048867410.9951133
ENST00000397938ENST00000407188EWSR1chr2229688595+KREMEN1chr2229521250+0.0051240840.99487597
ENST00000406548ENST00000400338EWSR1chr2229688595+KREMEN1chr2229521250+0.0017725230.99822754
ENST00000406548ENST00000400335EWSR1chr2229688595+KREMEN1chr2229521250+0.0018889180.9981111
ENST00000406548ENST00000327813EWSR1chr2229688595+KREMEN1chr2229521250+0.0044104150.9955896
ENST00000406548ENST00000407188EWSR1chr2229688595+KREMEN1chr2229521250+0.0046517040.9953483
ENST00000331029ENST00000400338EWSR1chr2229688595+KREMEN1chr2229521250+0.0021821160.9978179
ENST00000331029ENST00000400335EWSR1chr2229688595+KREMEN1chr2229521250+0.0022315750.9977684
ENST00000331029ENST00000327813EWSR1chr2229688595+KREMEN1chr2229521250+0.005832560.99416745
ENST00000331029ENST00000407188EWSR1chr2229688595+KREMEN1chr2229521250+0.0055615820.9944384
ENST00000414183ENST00000400338EWSR1chr2229688595+KREMEN1chr2229521250+0.001600770.9983992
ENST00000414183ENST00000400335EWSR1chr2229688595+KREMEN1chr2229521250+0.0018563350.9981437
ENST00000414183ENST00000327813EWSR1chr2229688595+KREMEN1chr2229521250+0.0044525650.9955474
ENST00000414183ENST00000407188EWSR1chr2229688595+KREMEN1chr2229521250+0.0044534090.9955466
ENST00000332035ENST00000400338EWSR1chr2229688595+KREMEN1chr2229521250+0.002518840.99748117
ENST00000332035ENST00000400335EWSR1chr2229688595+KREMEN1chr2229521250+0.0023939960.99760604
ENST00000332035ENST00000327813EWSR1chr2229688595+KREMEN1chr2229521250+0.0068262110.9931738
ENST00000332035ENST00000407188EWSR1chr2229688595+KREMEN1chr2229521250+0.0063125020.99368757
ENST00000332050ENST00000400338EWSR1chr2229688595+KREMEN1chr2229521251+0.0021863970.9978136
ENST00000332050ENST00000400335EWSR1chr2229688595+KREMEN1chr2229521251+0.0021116820.99788827
ENST00000332050ENST00000327813EWSR1chr2229688595+KREMEN1chr2229521251+0.0045907380.9954092
ENST00000332050ENST00000407188EWSR1chr2229688595+KREMEN1chr2229521251+0.0039292380.99607074
ENST00000397938ENST00000400338EWSR1chr2229688595+KREMEN1chr2229521251+0.0021063980.99789363
ENST00000397938ENST00000400335EWSR1chr2229688595+KREMEN1chr2229521251+0.0021645060.99783546
ENST00000397938ENST00000327813EWSR1chr2229688595+KREMEN1chr2229521251+0.0048867410.9951133
ENST00000397938ENST00000407188EWSR1chr2229688595+KREMEN1chr2229521251+0.0051240840.99487597
ENST00000406548ENST00000400338EWSR1chr2229688595+KREMEN1chr2229521251+0.0017725230.99822754
ENST00000406548ENST00000400335EWSR1chr2229688595+KREMEN1chr2229521251+0.0018889180.9981111
ENST00000406548ENST00000327813EWSR1chr2229688595+KREMEN1chr2229521251+0.0044104150.9955896
ENST00000406548ENST00000407188EWSR1chr2229688595+KREMEN1chr2229521251+0.0046517040.9953483
ENST00000331029ENST00000400338EWSR1chr2229688595+KREMEN1chr2229521251+0.0021821160.9978179
ENST00000331029ENST00000400335EWSR1chr2229688595+KREMEN1chr2229521251+0.0022315750.9977684
ENST00000331029ENST00000327813EWSR1chr2229688595+KREMEN1chr2229521251+0.005832560.99416745
ENST00000331029ENST00000407188EWSR1chr2229688595+KREMEN1chr2229521251+0.0055615820.9944384
ENST00000414183ENST00000400338EWSR1chr2229688595+KREMEN1chr2229521251+0.001600770.9983992
ENST00000414183ENST00000400335EWSR1chr2229688595+KREMEN1chr2229521251+0.0018563350.9981437
ENST00000414183ENST00000327813EWSR1chr2229688595+KREMEN1chr2229521251+0.0044525650.9955474
ENST00000414183ENST00000407188EWSR1chr2229688595+KREMEN1chr2229521251+0.0044534090.9955466
ENST00000332035ENST00000400338EWSR1chr2229688595+KREMEN1chr2229521251+0.002518840.99748117
ENST00000332035ENST00000400335EWSR1chr2229688595+KREMEN1chr2229521251+0.0023939960.99760604
ENST00000332035ENST00000327813EWSR1chr2229688595+KREMEN1chr2229521251+0.0068262110.9931738
ENST00000332035ENST00000407188EWSR1chr2229688595+KREMEN1chr2229521251+0.0063125020.99368757

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 EWSR1-KREMEN1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
EWSR1chr2229688595KREMEN1chr22295212501007332DLADFFKQCGVVKFAGMESGYACFCG
EWSR1chr2229688595KREMEN1chr22295212501096350DLADFFKQCGVVKFAGMESGYACFCG
EWSR1chr2229688595KREMEN1chr22295212501200393DLADFFKQCGVVKFAGMESGYACFCG
EWSR1chr2229688595KREMEN1chr22295212501225387DLADFFKQCGVVKFAGMESGYACFCG
EWSR1chr2229688595KREMEN1chr22295212501273315DLADFFKQCGVVKFAGMESGYACFCG
EWSR1chr2229688595KREMEN1chr22295212501483388DLADFFKQCGVVKFAGMESGYACFCG
EWSR1chr2229688595KREMEN1chr22295212511007332DLADFFKQCGVVKFAGMESGYACFCG
EWSR1chr2229688595KREMEN1chr22295212511096350DLADFFKQCGVVKFAGMESGYACFCG
EWSR1chr2229688595KREMEN1chr22295212511200393DLADFFKQCGVVKFAGMESGYACFCG
EWSR1chr2229688595KREMEN1chr22295212511225387DLADFFKQCGVVKFAGMESGYACFCG
EWSR1chr2229688595KREMEN1chr22295212511273315DLADFFKQCGVVKFAGMESGYACFCG
EWSR1chr2229688595KREMEN1chr22295212511483388DLADFFKQCGVVKFAGMESGYACFCG

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Potential FusionNeoAntigen Information of EWSR1-KREMEN1 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.
EWSR1-KREMEN1_29688595_29521250.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)
EWSR1-KREMEN1chr2229688595chr22295212501096HLA-B15:03KQCGVVKF0.98020.7846614
EWSR1-KREMEN1chr2229688595chr22295212501096HLA-B15:03FKQCGVVKF0.50260.752514
EWSR1-KREMEN1chr2229688595chr22295212501096HLA-B15:03VKFAGMESGY0.86360.90411121
EWSR1-KREMEN1chr2229688595chr22295212501096HLA-B15:54KQCGVVKF0.99680.8412614
EWSR1-KREMEN1chr2229688595chr22295212501096HLA-B15:68KQCGVVKF0.99330.5534614
EWSR1-KREMEN1chr2229688595chr22295212501096HLA-B48:02FKQCGVVKF0.51830.9463514
EWSR1-KREMEN1chr2229688595chr22295212501096HLA-B15:54FKQCGVVKF0.12880.8467514
EWSR1-KREMEN1chr2229688595chr22295212501096HLA-B15:53VKFAGMESGY0.94070.95531121
EWSR1-KREMEN1chr2229688595chr22295212501096HLA-B15:54VKFAGMESGY0.87310.9471121
EWSR1-KREMEN1chr2229688595chr22295212501096HLA-B48:02VKFAGMESGY0.81780.95651121
EWSR1-KREMEN1chr2229688595chr22295212501096HLA-B15:68VKFAGMESGY0.75940.82741121

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Potential FusionNeoAntigen Information of EWSR1-KREMEN1 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 EWSR1-KREMEN1

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
4512KQCGVVKFAGMESGEWSR1KREMEN1chr2229688595chr22295212501096

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of EWSR1-KREMEN1

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-B14:023BVN4512KQCGVVKFAGMESG-7.9962-8.1096
HLA-B14:023BVN4512KQCGVVKFAGMESG-5.70842-6.74372
HLA-B52:013W394512KQCGVVKFAGMESG-6.83737-6.95077
HLA-B52:013W394512KQCGVVKFAGMESG-4.4836-5.5189
HLA-A11:014UQ24512KQCGVVKFAGMESG-10.0067-10.1201
HLA-A11:014UQ24512KQCGVVKFAGMESG-9.03915-10.0745
HLA-A24:025HGA4512KQCGVVKFAGMESG-6.56204-6.67544
HLA-A24:025HGA4512KQCGVVKFAGMESG-5.42271-6.45801
HLA-B44:053DX84512KQCGVVKFAGMESG-7.85648-8.89178
HLA-B44:053DX84512KQCGVVKFAGMESG-5.3978-5.5112
HLA-A02:016TDR4512KQCGVVKFAGMESG-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of EWSR1-KREMEN1

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
EWSR1-KREMEN1chr2229688595chr22295212501121VKFAGMESGYGTTAAGTTTGCTGGGATGGAGTCAGGCTAT
EWSR1-KREMEN1chr2229688595chr2229521250514FKQCGVVKFTTTAAGCAGTGTGGGGTTGTTAAGTTT
EWSR1-KREMEN1chr2229688595chr2229521250614KQCGVVKFAAGCAGTGTGGGGTTGTTAAGTTT

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 EWSR1-KREMEN1

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
UCECEWSR1-KREMEN1chr2229688595ENST00000331029chr2229521250ENST00000327813TCGA-D1-A16R

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Potential target of CAR-T therapy development for EWSR1-KREMEN1

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
TgeneKREMEN1chr22:29688595chr22:29521250ENST00000327813310393_4130493.0TransmembraneHelical
TgeneKREMEN1chr22:29688595chr22:29521250ENST0000040033539393_4130459.0TransmembraneHelical
TgeneKREMEN1chr22:29688595chr22:29521250ENST0000040718839393_4130474.0TransmembraneHelical
TgeneKREMEN1chr22:29688595chr22:29521251ENST00000327813310393_4130493.0TransmembraneHelical
TgeneKREMEN1chr22:29688595chr22:29521251ENST0000040033539393_4130459.0TransmembraneHelical
TgeneKREMEN1chr22:29688595chr22:29521251ENST0000040718839393_4130474.0TransmembraneHelical

check button Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result

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Related Drugs to EWSR1-KREMEN1

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 EWSR1-KREMEN1

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
HgeneEWSR1C0553580Ewings sarcoma3CTD_human;ORPHANET
HgeneEWSR1C0002736Amyotrophic Lateral Sclerosis1GENOMICS_ENGLAND
HgeneEWSR1C0033578Prostatic Neoplasms1CTD_human
HgeneEWSR1C0206651Clear Cell Sarcoma of Soft Tissue1ORPHANET
HgeneEWSR1C0206663Neuroectodermal Tumor, Primitive1CTD_human
HgeneEWSR1C0279980Extra-osseous Ewing's sarcoma1ORPHANET
HgeneEWSR1C0334584Spongioblastoma1CTD_human
HgeneEWSR1C0334596Medulloepithelioma1CTD_human
HgeneEWSR1C0376358Malignant neoplasm of prostate1CTD_human
HgeneEWSR1C0700367Ependymoblastoma1CTD_human
HgeneEWSR1C0751675Cerebral Primitive Neuroectodermal Tumor1CTD_human
HgeneEWSR1C1275278Extraskeletal Myxoid Chondrosarcoma1ORPHANET