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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:ECE1-SRSF10

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ECE1-SRSF10
FusionPDB ID: 24862
FusionGDB2.0 ID: 24862
HgeneTgene
Gene symbol

ECE1

SRSF10

Gene ID

1889

10772

Gene nameendothelin converting enzyme 1serine and arginine rich splicing factor 10
SynonymsECEFUSIP1|FUSIP2|NSSR|PPP1R149|SFRS13|SFRS13A|SRp38|SRrp40|TASR|TASR1|TASR2
Cytomap

1p36.12

1p36.11

Type of geneprotein-codingprotein-coding
Descriptionendothelin-converting enzyme 1ECE-1serine/arginine-rich splicing factor 1040 kDa SR-repressor proteinFUS interacting protein (serine-arginine rich) 1FUS-interacting protein (serine-arginine rich) 2SR splicing factor 10TLS-associated SR proteinTLS-associated protein TASRTLS-associate
Modification date2020031320200313
UniProtAcc

P42892

Main function of 5'-partner protein: FUNCTION: Converts big endothelin-1 to endothelin-1. {ECO:0000269|PubMed:9396733}.
.
Ensembl transtripts involved in fusion geneENST idsENST00000264205, ENST00000357071, 
ENST00000374893, ENST00000415912, 
ENST00000436918, ENST00000528294, 
ENST00000341154, ENST00000343255, 
ENST00000374452, ENST00000374453, 
ENST00000484146, ENST00000492112, 
ENST00000374449, ENST00000374457, 
ENST00000433682, ENST00000344989, 
ENST00000453840, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score16 X 15 X 9=21604 X 4 X 2=32
# samples 184
** MAII scorelog2(18/2160*10)=-3.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/32*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Fusion gene context

PubMed: ECE1 [Title/Abstract] AND SRSF10 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ECE1 [Title/Abstract] AND SRSF10 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ECE1(21573714)-SRSF10(24305307), # samples:2
Anticipated loss of major functional domain due to fusion event.ECE1-SRSF10 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.
ECE1-SRSF10 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.
ECE1-SRSF10 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.
ECE1-SRSF10 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
HgeneECE1

GO:0010814

substance P catabolic process

18039931

HgeneECE1

GO:0010815

bradykinin catabolic process

18039931

HgeneECE1

GO:0010816

calcitonin catabolic process

18039931

HgeneECE1

GO:0016485

protein processing

7805846

HgeneECE1

GO:0016486

peptide hormone processing

7864876

HgeneECE1

GO:0034959

endothelin maturation

7805846

HgeneECE1

GO:0042447

hormone catabolic process

7864876

TgeneSRSF10

GO:0000375

RNA splicing, via transesterification reactions

9774382

TgeneSRSF10

GO:0000398

mRNA splicing, via spliceosome

9774382

TgeneSRSF10

GO:0006376

mRNA splice site selection

9774382

TgeneSRSF10

GO:0048024

regulation of mRNA splicing, via spliceosome

26876937

TgeneSRSF10

GO:0048025

negative regulation of mRNA splicing, via spliceosome

11684676



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/chr1:21573714/chr1:24305307)
- 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 ECE1 (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 SRSF10 (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)
ENST00000415912ECE1chr121573714-ENST00000344989SRSF10chr124305307-458712411261727533
ENST00000415912ECE1chr121573714-ENST00000453840SRSF10chr124305307-294312411261724532
ENST00000357071ECE1chr121573714-ENST00000344989SRSF10chr124305307-45881242461728560
ENST00000357071ECE1chr121573714-ENST00000453840SRSF10chr124305307-29441242461725559
ENST00000374893ECE1chr121573714-ENST00000344989SRSF10chr124305307-45841238631724553
ENST00000374893ECE1chr121573714-ENST00000453840SRSF10chr124305307-29401238631721552
ENST00000436918ECE1chr121573714-ENST00000344989SRSF10chr124305307-45591213381699553
ENST00000436918ECE1chr121573714-ENST00000453840SRSF10chr124305307-29151213381696552
ENST00000264205ECE1chr121573714-ENST00000344989SRSF10chr124305307-45591213591699546
ENST00000264205ECE1chr121573714-ENST00000453840SRSF10chr124305307-29151213591696545

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
ENST00000415912ENST00000344989ECE1chr121573714-SRSF10chr124305307-0.0004520030.999548
ENST00000415912ENST00000453840ECE1chr121573714-SRSF10chr124305307-0.0010602980.9989397
ENST00000357071ENST00000344989ECE1chr121573714-SRSF10chr124305307-0.0002146720.99978536
ENST00000357071ENST00000453840ECE1chr121573714-SRSF10chr124305307-0.0005122780.99948764
ENST00000374893ENST00000344989ECE1chr121573714-SRSF10chr124305307-0.0001473220.99985266
ENST00000374893ENST00000453840ECE1chr121573714-SRSF10chr124305307-0.0003475840.9996524
ENST00000436918ENST00000344989ECE1chr121573714-SRSF10chr124305307-0.0001474340.99985254
ENST00000436918ENST00000453840ECE1chr121573714-SRSF10chr124305307-0.0003446880.99965537
ENST00000264205ENST00000344989ECE1chr121573714-SRSF10chr124305307-0.0001792350.99982077
ENST00000264205ENST00000453840ECE1chr121573714-SRSF10chr124305307-0.0003976880.9996024

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 ECE1-SRSF10

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ECE1chr121573714SRSF10chr1243053071213385EQISTLINTTDRWSEDLRREFGRYGP
ECE1chr121573714SRSF10chr1243053071213392EQISTLINTTDRWSEDLRREFGRYGP
ECE1chr121573714SRSF10chr1243053071238392EQISTLINTTDRWSEDLRREFGRYGP
ECE1chr121573714SRSF10chr1243053071241372EQISTLINTTDRWSEDLRREFGRYGP
ECE1chr121573714SRSF10chr1243053071242399EQISTLINTTDRWSEDLRREFGRYGP

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Potential FusionNeoAntigen Information of ECE1-SRSF10 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.
ECE1-SRSF10_21573714_24305307.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)
ECE1-SRSF10chr121573714chr1243053071213HLA-A24:25RWSEDLRREF0.99840.571121
ECE1-SRSF10chr121573714chr1243053071213HLA-A24:20RWSEDLRREF0.99830.56931121
ECE1-SRSF10chr121573714chr1243053071213HLA-A24:15RWSEDLRREF0.99810.56291121
ECE1-SRSF10chr121573714chr1243053071213HLA-A24:17RWSEDLRREF0.99330.68231121
ECE1-SRSF10chr121573714chr1243053071213HLA-A31:08RWSEDLRREF0.95190.54831121
ECE1-SRSF10chr121573714chr1243053071213HLA-C05:09TTDRWSEDL0.99960.9442817
ECE1-SRSF10chr121573714chr1243053071213HLA-C08:15TTDRWSEDL0.9990.9651817
ECE1-SRSF10chr121573714chr1243053071213HLA-C03:07WSEDLRREF0.91540.95741221
ECE1-SRSF10chr121573714chr1243053071213HLA-C03:14WSEDLRREF0.89180.9731221
ECE1-SRSF10chr121573714chr1243053071213HLA-C12:12WSEDLRREF0.19630.94741221
ECE1-SRSF10chr121573714chr1243053071213HLA-A24:02RWSEDLRREF0.99830.56931121
ECE1-SRSF10chr121573714chr1243053071213HLA-C05:01TTDRWSEDL0.99960.9442817
ECE1-SRSF10chr121573714chr1243053071213HLA-C04:03TTDRWSEDL0.99950.9226817
ECE1-SRSF10chr121573714chr1243053071213HLA-C08:02TTDRWSEDL0.9990.9651817
ECE1-SRSF10chr121573714chr1243053071213HLA-C03:02WSEDLRREF0.98840.96071221
ECE1-SRSF10chr121573714chr1243053071213HLA-C16:04WSEDLRREF0.7340.98241221
ECE1-SRSF10chr121573714chr1243053071213HLA-C16:01WSEDLRREF0.62850.98141221
ECE1-SRSF10chr121573714chr1243053071213HLA-C16:02WSEDLRREF0.51710.99361221
ECE1-SRSF10chr121573714chr1243053071213HLA-C12:02WSEDLRREF0.35530.96991221
ECE1-SRSF10chr121573714chr1243053071213HLA-C02:10WSEDLRREF0.18240.96461221
ECE1-SRSF10chr121573714chr1243053071213HLA-C02:02WSEDLRREF0.18240.96461221

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Potential FusionNeoAntigen Information of ECE1-SRSF10 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.
ECE1-SRSF10_21573714_24305307.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)
ECE1-SRSF10chr121573714chr1243053071213DRB1-1389STLINTTDRWSEDLR318

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Fusion breakpoint peptide structures of ECE1-SRSF10

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
3866INTTDRWSEDLRREECE1SRSF10chr121573714chr1243053071213

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ECE1-SRSF10

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-B14:023BVN3866INTTDRWSEDLRRE-5.50071-6.53601
HLA-B14:023BVN3866INTTDRWSEDLRRE-5.44997-5.56337
HLA-B52:013W393866INTTDRWSEDLRRE-6.87928-6.99268
HLA-B52:013W393866INTTDRWSEDLRRE-3.95744-4.99274
HLA-A24:025HGA3866INTTDRWSEDLRRE-7.30598-7.41938
HLA-A24:025HGA3866INTTDRWSEDLRRE-5.09366-6.12896
HLA-B44:053DX83866INTTDRWSEDLRRE-5.64505-5.75845
HLA-B44:053DX83866INTTDRWSEDLRRE-4.1878-5.2231
HLA-A02:016TDR3866INTTDRWSEDLRRE-0.0912853-1.12659

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Vaccine Design for the FusionNeoAntigens of ECE1-SRSF10

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
ECE1-SRSF10chr121573714chr1243053071121RWSEDLRREFCAGATGGTCTGAAGACTTGCGGCGTGAATT
ECE1-SRSF10chr121573714chr1243053071221WSEDLRREFATGGTCTGAAGACTTGCGGCGTGAATT
ECE1-SRSF10chr121573714chr124305307817TTDRWSEDLCACCACCGACAGATGGTCTGAAGACTT

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
ECE1-SRSF10chr121573714chr124305307318STLINTTDRWSEDLRCTCCACTCTCATCAACACCACCGACAGATGGTCTGAAGACTTGCG

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Information of the samples that have these potential fusion neoantigens of ECE1-SRSF10

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
OVECE1-SRSF10chr121573714ENST00000264205chr124305307ENST00000344989TCGA-09-1673-01A

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Potential target of CAR-T therapy development for ECE1-SRSF10

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
HgeneECE1chr1:21573714chr1:24305307ENST00000264205-81869_89384768.0TransmembraneHelical%3B Signal-anchor for type II membrane protein
HgeneECE1chr1:21573714chr1:24305307ENST00000357071-71769_89375759.0TransmembraneHelical%3B Signal-anchor for type II membrane protein
HgeneECE1chr1:21573714chr1:24305307ENST00000374893-91969_89387771.0TransmembraneHelical%3B Signal-anchor for type II membrane protein
HgeneECE1chr1:21573714chr1:24305307ENST00000415912-91969_89371755.0TransmembraneHelical%3B Signal-anchor for type II membrane protein

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 ECE1-SRSF10

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 ECE1-SRSF10

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