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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:SSFA2-SMARCE1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SSFA2-SMARCE1
FusionPDB ID: 86749
FusionGDB2.0 ID: 86749
HgeneTgene
Gene symbol

SSFA2

SMARCE1

Gene ID

6744

6605

Gene nameITPR interacting domain containing 2SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1
SynonymsCS-1|CS1|KRAP|SPAG13|SSFA2BAF57|CSS5
Cytomap

2q31.3

17q21.2

Type of geneprotein-codingprotein-coding
Descriptionprotein ITPRID2ITPR-interacting domain-containing protein 2KRAS-induced actin-interacting proteincleavage signal-1 proteinki-ras-induced actin-interacting proteinsperm associated antigen 13sperm specific antigen 2SWI/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 date2020032020200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000320370, ENST00000409001, 
ENST00000428267, ENST00000431877, 
ENST00000409136, ENST00000467172, 
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 6=54010 X 11 X 5=550
# samples 1112
** MAII scorelog2(11/540*10)=-2.29545588352617
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: SSFA2 [Title/Abstract] AND SMARCE1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: SSFA2 [Title/Abstract] AND SMARCE1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SSFA2(182774697)-SMARCE1(38788462), # samples:1
Anticipated loss of major functional domain due to fusion event.SSFA2-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.
SSFA2-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/chr2:182774697/chr17:38788462)
- 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 SSFA2 (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


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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)
ENST00000431877SSFA2chr2182774697+ENST00000348513SMARCE1chr1738788462+60261665261873615
ENST00000431877SSFA2chr2182774697+ENST00000544009SMARCE1chr1738788462+27141665261873615
ENST00000431877SSFA2chr2182774697+ENST00000431889SMARCE1chr1738788462+25201665261873615
ENST00000431877SSFA2chr2182774697+ENST00000580419SMARCE1chr1738788462+22091665261873615
ENST00000431877SSFA2chr2182774697+ENST00000377808SMARCE1chr1738788462+22881665261873615
ENST00000431877SSFA2chr2182774697+ENST00000400122SMARCE1chr1738788462+22881665261873615
ENST00000431877SSFA2chr2182774697+ENST00000578044SMARCE1chr1738788462+22091665261873615
ENST00000320370SSFA2chr2182774697+ENST00000348513SMARCE1chr1738788462+59591598161806596
ENST00000320370SSFA2chr2182774697+ENST00000544009SMARCE1chr1738788462+26471598161806596
ENST00000320370SSFA2chr2182774697+ENST00000431889SMARCE1chr1738788462+24531598161806596
ENST00000320370SSFA2chr2182774697+ENST00000580419SMARCE1chr1738788462+21421598161806596
ENST00000320370SSFA2chr2182774697+ENST00000377808SMARCE1chr1738788462+22211598161806596
ENST00000320370SSFA2chr2182774697+ENST00000400122SMARCE1chr1738788462+22211598161806596
ENST00000320370SSFA2chr2182774697+ENST00000578044SMARCE1chr1738788462+21421598161806596
ENST00000409001SSFA2chr2182774697+ENST00000348513SMARCE1chr1738788462+5929156811776591
ENST00000409001SSFA2chr2182774697+ENST00000544009SMARCE1chr1738788462+2617156811776591
ENST00000409001SSFA2chr2182774697+ENST00000431889SMARCE1chr1738788462+2423156811776591
ENST00000409001SSFA2chr2182774697+ENST00000580419SMARCE1chr1738788462+2112156811776591
ENST00000409001SSFA2chr2182774697+ENST00000377808SMARCE1chr1738788462+2191156811776591
ENST00000409001SSFA2chr2182774697+ENST00000400122SMARCE1chr1738788462+2191156811776591
ENST00000409001SSFA2chr2182774697+ENST00000578044SMARCE1chr1738788462+2112156811776591
ENST00000428267SSFA2chr2182774697+ENST00000348513SMARCE1chr1738788462+566813071661515449
ENST00000428267SSFA2chr2182774697+ENST00000544009SMARCE1chr1738788462+235613071661515449
ENST00000428267SSFA2chr2182774697+ENST00000431889SMARCE1chr1738788462+216213071661515449
ENST00000428267SSFA2chr2182774697+ENST00000580419SMARCE1chr1738788462+185113071661515449
ENST00000428267SSFA2chr2182774697+ENST00000377808SMARCE1chr1738788462+193013071661515449
ENST00000428267SSFA2chr2182774697+ENST00000400122SMARCE1chr1738788462+193013071661515449
ENST00000428267SSFA2chr2182774697+ENST00000578044SMARCE1chr1738788462+185113071661515449

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
ENST00000431877ENST00000348513SSFA2chr2182774697+SMARCE1chr1738788462+0.000311050.999689
ENST00000431877ENST00000544009SSFA2chr2182774697+SMARCE1chr1738788462+0.0012190660.9987809
ENST00000431877ENST00000431889SSFA2chr2182774697+SMARCE1chr1738788462+0.0019180080.99808204
ENST00000431877ENST00000580419SSFA2chr2182774697+SMARCE1chr1738788462+0.0041007510.99589926
ENST00000431877ENST00000377808SSFA2chr2182774697+SMARCE1chr1738788462+0.0039294340.9960705
ENST00000431877ENST00000400122SSFA2chr2182774697+SMARCE1chr1738788462+0.0039294340.9960705
ENST00000431877ENST00000578044SSFA2chr2182774697+SMARCE1chr1738788462+0.0041007510.99589926
ENST00000320370ENST00000348513SSFA2chr2182774697+SMARCE1chr1738788462+0.0002942570.99970573
ENST00000320370ENST00000544009SSFA2chr2182774697+SMARCE1chr1738788462+0.0010252150.9989748
ENST00000320370ENST00000431889SSFA2chr2182774697+SMARCE1chr1738788462+0.0015283090.9984717
ENST00000320370ENST00000580419SSFA2chr2182774697+SMARCE1chr1738788462+0.0036317150.9963683
ENST00000320370ENST00000377808SSFA2chr2182774697+SMARCE1chr1738788462+0.0035909810.996409
ENST00000320370ENST00000400122SSFA2chr2182774697+SMARCE1chr1738788462+0.0035909810.996409
ENST00000320370ENST00000578044SSFA2chr2182774697+SMARCE1chr1738788462+0.0036317150.9963683
ENST00000409001ENST00000348513SSFA2chr2182774697+SMARCE1chr1738788462+0.0002895670.9997104
ENST00000409001ENST00000544009SSFA2chr2182774697+SMARCE1chr1738788462+0.0009630710.9990369
ENST00000409001ENST00000431889SSFA2chr2182774697+SMARCE1chr1738788462+0.0014532920.99854666
ENST00000409001ENST00000580419SSFA2chr2182774697+SMARCE1chr1738788462+0.003903290.9960968
ENST00000409001ENST00000377808SSFA2chr2182774697+SMARCE1chr1738788462+0.003897260.9961028
ENST00000409001ENST00000400122SSFA2chr2182774697+SMARCE1chr1738788462+0.003897260.9961028
ENST00000409001ENST00000578044SSFA2chr2182774697+SMARCE1chr1738788462+0.003903290.9960968
ENST00000428267ENST00000348513SSFA2chr2182774697+SMARCE1chr1738788462+0.0005219050.99947816
ENST00000428267ENST00000544009SSFA2chr2182774697+SMARCE1chr1738788462+0.0014984190.99850154
ENST00000428267ENST00000431889SSFA2chr2182774697+SMARCE1chr1738788462+0.0023844540.9976156
ENST00000428267ENST00000580419SSFA2chr2182774697+SMARCE1chr1738788462+0.00692320.9930768
ENST00000428267ENST00000377808SSFA2chr2182774697+SMARCE1chr1738788462+0.006710770.9932893
ENST00000428267ENST00000400122SSFA2chr2182774697+SMARCE1chr1738788462+0.006710770.9932893
ENST00000428267ENST00000578044SSFA2chr2182774697+SMARCE1chr1738788462+0.00692320.9930768

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 SSFA2-SMARCE1

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

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Potential FusionNeoAntigen Information of SSFA2-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.

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)

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Potential FusionNeoAntigen Information of SSFA2-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 SSFA2-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.

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SSFA2-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

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Vaccine Design for the FusionNeoAntigens of SSFA2-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

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 SSFA2-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

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Potential target of CAR-T therapy development for SSFA2-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 SSFA2-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 SSFA2-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