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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:EPB41L1-HTR3C

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: EPB41L1-HTR3C
FusionPDB ID: 26814
FusionGDB2.0 ID: 26814
HgeneTgene
Gene symbol

EPB41L1

HTR3C

Gene ID

2036

170572

Gene nameerythrocyte membrane protein band 4.1 like 15-hydroxytryptamine receptor 3C
Synonyms4.1N|MRD11-
Cytomap

20q11.23

3q27.1

Type of geneprotein-codingprotein-coding
Descriptionband 4.1-like protein 1neuron-type nonerythroid protein 4.1neuronal protein 4.15-hydroxytryptamine receptor 3C5-HT3-C5-HT3C5-hydroxytryptamine (serotonin) receptor 3, family member C5-hydroxytryptamine (serotonin) receptor 3C, ionotropic5-hydroxytryptamine receptor 3 subunit Cserotonin receptor 3C
Modification date2020031320200313
UniProtAcc

Q9H4G0

Main function of 5'-partner protein: FUNCTION: May function to confer stability and plasticity to neuronal membrane via multiple interactions, including the spectrin-actin-based cytoskeleton, integral membrane channels and membrane-associated guanylate kinases.		.
Ensembl transtripts involved in fusion geneENST idsENST00000202028, ENST00000338074, 
ENST00000373950, ENST00000441639, 
ENST00000373946, ENST00000373941, 
ENST00000479336, 		ENST00000318351, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score24 X 23 X 12=66244 X 7 X 4=112
# samples 345
** MAII scorelog2(34/6624*10)=-4.28409602136162
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/112*10)=-1.16349873228288
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: EPB41L1 [Title/Abstract] AND HTR3C [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: EPB41L1 [Title/Abstract] AND HTR3C [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)EPB41L1(34700402)-HTR3C(183773100), # samples:2
Anticipated loss of major functional domain due to fusion event.EPB41L1-HTR3C 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.
EPB41L1-HTR3C 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.
EPB41L1-HTR3C seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
EPB41L1-HTR3C seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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/chr20:34700402/chr3:183773100)
- 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 EPB41L1 (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 HTR3C (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)
ENST00000373946EPB41L1chr2034713449+ENST00000318351HTR3Cchr3183773100+15138401193397

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
ENST00000373946ENST00000318351EPB41L1chr2034713449+HTR3Cchr3183773100+0.022334320.97766566

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 EPB41L1-HTR3C

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
EPB41L1chr2034713449HTR3Cchr31837731008428LAESLAPTERSVKDAQLQLLTSFLWM
EPB41L1chr2034713449HTR3Cchr31837731008431SLAPTERSVKDAQLQLLTSFLWMDLV

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Potential FusionNeoAntigen Information of EPB41L1-HTR3C 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.
EPB41L1-HTR3C_34713449_183773100.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)
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B39:01ERSVKDAQL0.99680.7348514
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B14:01ERSVKDAQL0.99670.7557514
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B14:02ERSVKDAQL0.99670.7557514
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B38:02ERSVKDAQL0.99310.8517514
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B38:01ERSVKDAQL0.99250.8533514
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-A66:01SVKDAQLQL0.97830.6373716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-A30:08SVKDAQLQL0.96730.814716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B39:13VKDAQLQLL0.95930.9418817
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B15:17SVKDAQLQL0.95420.8623716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B38:01VKDAQLQLL0.93770.9741817
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B38:02VKDAQLQLL0.93070.9733817
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-A26:02SVKDAQLQL0.92670.6224716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B15:16SVKDAQLQL0.90230.9134716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B46:01SVKDAQLQL0.88720.6689716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-A26:03SVKDAQLQL0.88130.6388716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-A26:08SVKDAQLQL0.84810.5606716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B07:10SVKDAQLQL0.79130.7716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-A26:15SVKDAQLQL0.7340.6679716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-A26:14SVKDAQLQL0.7340.6679716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-A32:13SVKDAQLQL0.46050.9723716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B81:01SVKDAQLQL0.4460.672716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B48:01SVKDAQLQL0.43470.8086716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B13:02SVKDAQLQL0.27280.7858716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B82:01SVKDAQLQL0.2250.7102716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B13:01SVKDAQLQL0.16780.971716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B15:16RSVKDAQLQL0.99480.9354616
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B15:17RSVKDAQLQL0.9930.8955616
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B57:03RSVKDAQLQL0.98680.9882616
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-A30:08RSVKDAQLQL0.90760.8385616
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B39:01ERSVKDAQLQL0.99930.9186516
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B57:03RSVKDAQLQLL0.99840.9881617
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B38:02ERSVKDAQLQL0.99830.9723516
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C15:04SVKDAQLQL0.99920.8572716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C15:06SVKDAQLQL0.99910.8684716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C03:07SVKDAQLQL0.99810.94716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C03:19SVKDAQLQL0.9980.9559716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C03:08SVKDAQLQL0.99740.8826716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B39:09ERSVKDAQL0.99680.5897514
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C06:03SVKDAQLQL0.99670.9913716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C12:04SVKDAQLQL0.99670.9923716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C12:12SVKDAQLQL0.99580.9439716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B39:12ERSVKDAQL0.99520.7445514
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B39:05ERSVKDAQL0.99210.7048514
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C04:06SVKDAQLQL0.98940.9819716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C12:16SVKDAQLQL0.98830.9679716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B39:09VKDAQLQLL0.98670.8742817
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B15:04SVKDAQLQL0.98410.9256716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C02:06SVKDAQLQL0.96460.9335716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-A02:05SVKDAQLQL0.9540.5011716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C08:04SVKDAQLQL0.9430.9755716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C08:13SVKDAQLQL0.9430.9755716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C07:13VKDAQLQLL0.94290.8716817
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C07:29VKDAQLQLL0.93990.8544817
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B42:02SVKDAQLQL0.92020.7263716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C07:05SVKDAQLQL0.90620.9385716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B07:04SVKDAQLQL0.88660.6435716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B39:05VKDAQLQLL0.8840.8715817
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C01:17SVKDAQLQL0.84870.9765716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C03:14SVKDAQLQL0.84760.9367716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C07:13SVKDAQLQL0.82040.9258716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B07:12SVKDAQLQL0.80310.74716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C07:27SVKDAQLQL0.8010.923716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C07:29SVKDAQLQL0.7770.9069716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C07:19SVKDAQLQL0.77510.8013716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C01:30SVKDAQLQL0.7540.9804716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-A26:01SVKDAQLQL0.7340.6679716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C08:03SVKDAQLQL0.72940.9861716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C07:95SVKDAQLQL0.67840.7086716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B39:08VKDAQLQLL0.60690.9647817
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B14:03ERSVKDAQL0.44330.8281514
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B48:03VKDAQLQLL0.17960.6658817
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C15:06RSVKDAQLQL0.99890.8641616
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B39:12ERSVKDAQLQL0.99920.9201516
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C18:01VKDAQLQLL0.99970.9704817
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C15:09SVKDAQLQL0.99920.8572716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C15:05SVKDAQLQL0.99880.9229716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C15:02SVKDAQLQL0.99840.8007716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C16:04SVKDAQLQL0.99720.977716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C03:03SVKDAQLQL0.99710.9714716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C03:04SVKDAQLQL0.99710.9714716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C12:03SVKDAQLQL0.9970.9819716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B39:31ERSVKDAQL0.99680.7334514
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C06:02SVKDAQLQL0.99660.9919716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C06:17SVKDAQLQL0.99660.9919716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C06:06SVKDAQLQL0.99520.9902716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C03:67SVKDAQLQL0.9930.9626716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B39:02VKDAQLQLL0.99280.9355817
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B38:05ERSVKDAQL0.99250.8533514
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C03:17SVKDAQLQL0.99250.9612716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C12:02SVKDAQLQL0.99160.9715716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C03:02SVKDAQLQL0.99120.9631716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C03:05SVKDAQLQL0.98220.9214716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C16:02SVKDAQLQL0.98180.9892716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C04:04SVKDAQLQL0.97620.9769716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C03:06SVKDAQLQL0.97450.9732716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C16:01SVKDAQLQL0.9690.9761716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-A30:01SVKDAQLQL0.96420.8919716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C07:04SVKDAQLQL0.95170.9679716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C02:10SVKDAQLQL0.94480.965716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C02:02SVKDAQLQL0.94480.965716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B38:05VKDAQLQLL0.93770.9741817
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-A32:01SVKDAQLQL0.93270.9438716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B15:73SVKDAQLQL0.92520.9382716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C06:08SVKDAQLQL0.90880.9865716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C01:03SVKDAQLQL0.89780.9748716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-A25:01SVKDAQLQL0.89030.9111716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C06:06VKDAQLQLL0.88370.9895817
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B15:30SVKDAQLQL0.87890.9324716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-A30:04SVKDAQLQL0.87270.6052716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C01:02SVKDAQLQL0.8680.9766716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C07:22SVKDAQLQL0.85880.7376716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B07:13SVKDAQLQL0.82630.9085716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B48:05SVKDAQLQL0.82280.5242716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B08:12SVKDAQLQL0.79080.8035716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B07:26SVKDAQLQL0.75130.5677716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-A02:14SVKDAQLQL0.73360.5795716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C08:01SVKDAQLQL0.72940.9861716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B15:09VKDAQLQLL0.71340.7615817
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C07:01SVKDAQLQL0.69890.6757716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C07:04VKDAQLQLL0.69880.9532817
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B39:11VKDAQLQLL0.62450.9161817
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C17:01SVKDAQLQL0.47330.9553716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B82:02SVKDAQLQL0.2250.7102716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B40:12VKDAQLQLL0.17960.6658817
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B40:21SVKDAQLQL0.12360.6757716
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B48:05VKDAQLQLL0.03420.6051817
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C15:05RSVKDAQLQL0.99890.9285616
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-C15:02RSVKDAQLQL0.99870.8841616
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B58:06RSVKDAQLQL0.99690.922616
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B15:30SVKDAQLQLL0.97090.935717
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-A30:01RSVKDAQLQL0.91270.9283616
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B15:73RSVKDAQLQL0.89850.9814616
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B15:30RSVKDAQLQL0.85430.9812616
EPB41L1-HTR3Cchr2034713449chr318377310084HLA-B39:31ERSVKDAQLQL0.99950.9187516

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Potential FusionNeoAntigen Information of EPB41L1-HTR3C 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 EPB41L1-HTR3C

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
8257RSVKDAQLQLLTSFEPB41L1HTR3Cchr2034713449chr318377310084

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of EPB41L1-HTR3C

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-B14:023BVN8257RSVKDAQLQLLTSF-7.9962-8.1096
HLA-B14:023BVN8257RSVKDAQLQLLTSF-5.70842-6.74372
HLA-B52:013W398257RSVKDAQLQLLTSF-6.83737-6.95077
HLA-B52:013W398257RSVKDAQLQLLTSF-4.4836-5.5189
HLA-A11:014UQ28257RSVKDAQLQLLTSF-10.0067-10.1201
HLA-A11:014UQ28257RSVKDAQLQLLTSF-9.03915-10.0745
HLA-A24:025HGA8257RSVKDAQLQLLTSF-6.56204-6.67544
HLA-A24:025HGA8257RSVKDAQLQLLTSF-5.42271-6.45801
HLA-B44:053DX88257RSVKDAQLQLLTSF-7.85648-8.89178
HLA-B44:053DX88257RSVKDAQLQLLTSF-5.3978-5.5112
HLA-A02:016TDR8257RSVKDAQLQLLTSF-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of EPB41L1-HTR3C

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
EPB41L1-HTR3Cchr2034713449chr3183773100514ERSVKDAQLGCACCTACTGAGCGCTCAGTAAAGGAT
EPB41L1-HTR3Cchr2034713449chr3183773100516ERSVKDAQLQLGCACCTACTGAGCGCTCAGTAAAGGATGCACAG
EPB41L1-HTR3Cchr2034713449chr3183773100616RSVKDAQLQLCCTACTGAGCGCTCAGTAAAGGATGCACAG
EPB41L1-HTR3Cchr2034713449chr3183773100617RSVKDAQLQLLCCTACTGAGCGCTCAGTAAAGGATGCACAGCTC
EPB41L1-HTR3Cchr2034713449chr3183773100716SVKDAQLQLACTGAGCGCTCAGTAAAGGATGCACAG
EPB41L1-HTR3Cchr2034713449chr3183773100717SVKDAQLQLLACTGAGCGCTCAGTAAAGGATGCACAGCTC
EPB41L1-HTR3Cchr2034713449chr3183773100817VKDAQLQLLGAGCGCTCAGTAAAGGATGCACAGCTC

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 EPB41L1-HTR3C

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
OVEPB41L1-HTR3Cchr2034713449ENST00000373946chr3183773100ENST00000318351TCGA-13-1405-01A

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Potential target of CAR-T therapy development for EPB41L1-HTR3C

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
TgeneHTR3Cchr20:34713449chr3:183773100ENST0000031835119249_2690448.0TransmembraneHelical%3B Name%3D1
TgeneHTR3Cchr20:34713449chr3:183773100ENST0000031835119283_3030448.0TransmembraneHelical%3B Name%3D2
TgeneHTR3Cchr20:34713449chr3:183773100ENST0000031835119307_3290448.0TransmembraneHelical%3B Name%3D3
TgeneHTR3Cchr20:34713449chr3:183773100ENST0000031835119425_4450448.0TransmembraneHelical%3B Name%3D4

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 EPB41L1-HTR3C

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 EPB41L1-HTR3C

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