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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:EXOSC4-NEIL2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: EXOSC4-NEIL2
FusionPDB ID: 27981
FusionGDB2.0 ID: 27981
HgeneTgene
Gene symbol

EXOSC4

NEIL2

Gene ID

54512

252969

Gene nameexosome component 4nei like DNA glycosylase 2
SynonymsRRP41|RRP41A|Rrp41p|SKI6|Ski6p|hRrp41p|p12ANEH2|NEI2
Cytomap

8q24.3

8p23.1

Type of geneprotein-codingprotein-coding
Descriptionexosome complex component RRP41exosome complex exonuclease RRP41exosome component Rrp41ribosomal RNA-processing protein 41endonuclease 8-like 2DNA glycosylase/AP lyase Neil2DNA-(apurinic or apyrimidinic site) lyase Neil2nei endonuclease VIII-like 2nei homolog 2nei-like protein 2
Modification date2020031320200313
UniProtAcc

Q9NPD3

Main function of 5'-partner protein: FUNCTION: Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. EXOSC4 binds to ARE-containing RNAs. {ECO:0000269|PubMed:16912217, ECO:0000269|PubMed:17545563, ECO:0000269|PubMed:18172165, ECO:0000269|PubMed:20368444, ECO:0000269|PubMed:21255825}.

Q969S2

Main function of 5'-partner protein: FUNCTION: Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Has DNA glycosylase activity towards 5-hydroxyuracil and other oxidized derivatives of cytosine with a preference for mismatched double-stranded DNA (DNA bubbles). Has low or no DNA glycosylase activity towards thymine glycol, 2-hydroxyadenine, hypoxanthine and 8-oxoguanine. Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. {ECO:0000269|PubMed:12097317, ECO:0000269|PubMed:14522990, ECO:0000269|PubMed:15175427, ECO:0000269|PubMed:15339932}.
Ensembl transtripts involved in fusion geneENST idsENST00000316052, ENST00000525936, 
ENST00000403422, ENST00000284503, 
ENST00000528323, ENST00000436750, 
ENST00000455213, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score2 X 4 X 2=162 X 6 X 3=36
# samples 34
** MAII scorelog2(3/16*10)=0.906890595608518
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Fusion gene context

PubMed: EXOSC4 [Title/Abstract] AND NEIL2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: EXOSC4 [Title/Abstract] AND NEIL2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)EXOSC4(145133803)-NEIL2(11637108), # samples:1
EXOSC4(145133802)-NEIL2(11637106), # samples:1
EXOSC4(145133800)-NEIL2(11637105), # samples:1
EXOSC4(145133802)-NEIL2(11637107), # samples:1
Anticipated loss of major functional domain due to fusion event.EXOSC4-NEIL2 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.
EXOSC4-NEIL2 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
HgeneEXOSC4

GO:0045006

DNA deamination

21255825



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/chr8:145133803/chr8:11637108)
- 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 EXOSC4 (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 NEIL2 (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)
ENST00000316052EXOSC4chr8145133803+ENST00000436750NEIL2chr811637108+22072741031134343
ENST00000316052EXOSC4chr8145133803+ENST00000455213NEIL2chr811637108+22022741031134343
ENST00000525936EXOSC4chr8145133803+ENST00000436750NEIL2chr811637108+2185252811112343
ENST00000525936EXOSC4chr8145133803+ENST00000455213NEIL2chr811637108+2180252811112343
ENST00000316052EXOSC4chr8145133802+ENST00000436750NEIL2chr811637106+22072741031134343
ENST00000316052EXOSC4chr8145133802+ENST00000455213NEIL2chr811637106+22022741031134343
ENST00000525936EXOSC4chr8145133802+ENST00000436750NEIL2chr811637106+2185252811112343
ENST00000525936EXOSC4chr8145133802+ENST00000455213NEIL2chr811637106+2180252811112343
ENST00000316052EXOSC4chr8145133800+ENST00000436750NEIL2chr811637105+22072741031134343
ENST00000316052EXOSC4chr8145133800+ENST00000455213NEIL2chr811637105+22022741031134343
ENST00000525936EXOSC4chr8145133800+ENST00000436750NEIL2chr811637105+2185252811112343
ENST00000525936EXOSC4chr8145133800+ENST00000455213NEIL2chr811637105+2180252811112343
ENST00000316052EXOSC4chr8145133802-ENST00000436750NEIL2chr811637107+22072741031134343
ENST00000316052EXOSC4chr8145133802-ENST00000455213NEIL2chr811637107+22022741031134343
ENST00000525936EXOSC4chr8145133802-ENST00000436750NEIL2chr811637107+2185252811112343
ENST00000525936EXOSC4chr8145133802-ENST00000455213NEIL2chr811637107+2180252811112343

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
ENST00000316052ENST00000436750EXOSC4chr8145133803+NEIL2chr811637108+0.0065142390.99348575
ENST00000316052ENST00000455213EXOSC4chr8145133803+NEIL2chr811637108+0.0065257750.9934742
ENST00000525936ENST00000436750EXOSC4chr8145133803+NEIL2chr811637108+0.0065187710.9934813
ENST00000525936ENST00000455213EXOSC4chr8145133803+NEIL2chr811637108+0.0064917440.9935082
ENST00000316052ENST00000436750EXOSC4chr8145133802+NEIL2chr811637106+0.0065142390.99348575
ENST00000316052ENST00000455213EXOSC4chr8145133802+NEIL2chr811637106+0.0065257750.9934742
ENST00000525936ENST00000436750EXOSC4chr8145133802+NEIL2chr811637106+0.0065187710.9934813
ENST00000525936ENST00000455213EXOSC4chr8145133802+NEIL2chr811637106+0.0064917440.9935082
ENST00000316052ENST00000436750EXOSC4chr8145133800+NEIL2chr811637105+0.0065142390.99348575
ENST00000316052ENST00000455213EXOSC4chr8145133800+NEIL2chr811637105+0.0065257750.9934742
ENST00000525936ENST00000436750EXOSC4chr8145133800+NEIL2chr811637105+0.0065187710.9934813
ENST00000525936ENST00000455213EXOSC4chr8145133800+NEIL2chr811637105+0.0064917440.9935082
ENST00000316052ENST00000436750EXOSC4chr8145133802-NEIL2chr811637107+0.0065142390.99348575
ENST00000316052ENST00000455213EXOSC4chr8145133802-NEIL2chr811637107+0.0065257750.9934742
ENST00000525936ENST00000436750EXOSC4chr8145133802-NEIL2chr811637107+0.0065187710.9934813
ENST00000525936ENST00000455213EXOSC4chr8145133802-NEIL2chr811637107+0.0064917440.9935082

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 EXOSC4-NEIL2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
EXOSC4chr8145133800NEIL2chr81163710525257NTKALAVVYGPHEVHGKKLFLRFDLD
EXOSC4chr8145133800NEIL2chr81163710527457NTKALAVVYGPHEVHGKKLFLRFDLD
EXOSC4chr8145133802NEIL2chr81163710625257NTKALAVVYGPHEVHGKKLFLRFDLD
EXOSC4chr8145133802NEIL2chr81163710627457NTKALAVVYGPHEVHGKKLFLRFDLD
EXOSC4chr8145133802NEIL2chr81163710725257NTKALAVVYGPHEVHGKKLFLRFDLD
EXOSC4chr8145133802NEIL2chr81163710727457NTKALAVVYGPHEVHGKKLFLRFDLD
EXOSC4chr8145133803NEIL2chr81163710825257NTKALAVVYGPHEVHGKKLFLRFDLD
EXOSC4chr8145133803NEIL2chr81163710827457NTKALAVVYGPHEVHGKKLFLRFDLD

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Potential FusionNeoAntigen Information of EXOSC4-NEIL2 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.
EXOSC4-NEIL2_145133800_11637105.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)
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B52:01VVYGPHEV0.99680.9963614
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A66:01EVHGKKLFL0.99190.66091221
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A26:03EVHGKKLFL0.9850.6191221
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B18:01HEVHGKKLF0.97390.83451120
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B44:03HEVHGKKLF0.96920.95891120
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:38AVVYGPHEV0.96010.79514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A26:15EVHGKKLFL0.9590.57541221
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A26:14EVHGKKLFL0.9590.57541221
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:21AVVYGPHEV0.93440.7439514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:29AVVYGPHEV0.92540.6372514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:35AVVYGPHEV0.91630.663514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:20AVVYGPHEV0.91570.6441514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:60AVVYGPHEV0.90370.6329514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:24AVVYGPHEV0.90170.6367514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:30AVVYGPHEV0.90170.6367514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:67AVVYGPHEV0.90170.6367514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B08:01EVHGKKLFL0.89740.69931221
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:11AVVYGPHEV0.89540.6555514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:22AVVYGPHEV0.87530.57514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:16AVVYGPHEV0.84120.5777514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:13AVVYGPHEV0.83960.828514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B08:09EVHGKKLFL0.82510.68051221
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:27AVVYGPHEV0.81470.6618514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B13:02AVVYGPHEV0.54970.9881514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B07:05GPHEVHGKKL0.99290.5398919
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B81:01GPHEVHGKKL0.34830.5845919
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B82:01GPHEVHGKKL0.17280.5126919
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A30:08VVYGPHEVHGK0.99720.6364617
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:22ALAVVYGPHEV0.99630.672314
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:27ALAVVYGPHEV0.99590.7733314
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:13ALAVVYGPHEV0.99570.8541314
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:19ALAVVYGPHEV0.96120.6151314
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B44:03GPHEVHGKKLF0.74250.9724920
EXOSC4-NEIL2chr8145133800chr811637105274HLA-C15:06VVYGPHEV0.99960.956614
EXOSC4-NEIL2chr8145133800chr811637105274HLA-C04:06VVYGPHEV0.99960.9923614
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B51:07VVYGPHEV0.99730.9914614
EXOSC4-NEIL2chr8145133800chr811637105274HLA-C06:03VVYGPHEV0.99690.9953614
EXOSC4-NEIL2chr8145133800chr811637105274HLA-C12:04VVYGPHEV0.99620.9955614
EXOSC4-NEIL2chr8145133800chr811637105274HLA-C15:06AVVYGPHEV0.99540.9543514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A26:01EVHGKKLFL0.9590.57541221
EXOSC4-NEIL2chr8145133800chr811637105274HLA-C12:04AVVYGPHEV0.95120.9952514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-C06:03AVVYGPHEV0.94630.9956514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:01AVVYGPHEV0.90170.6367514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-C02:06AVVYGPHEV0.86770.9896514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B15:04VVYGPHEVH0.80190.9706615
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B07:12GPHEVHGKKL0.95160.6771919
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B42:02GPHEVHGKKL0.43630.8749919
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B42:01GPHEVHGKKL0.39430.8673919
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:02ALAVVYGPHEV0.99650.5382314
EXOSC4-NEIL2chr8145133800chr811637105274HLA-C15:02VVYGPHEV0.99960.9756614
EXOSC4-NEIL2chr8145133800chr811637105274HLA-C15:05VVYGPHEV0.99950.9848614
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B41:03HEVHGKKL0.9120.6321119
EXOSC4-NEIL2chr8145133800chr811637105274HLA-C15:02AVVYGPHEV0.99820.9738514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-C15:05AVVYGPHEV0.99710.9816514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A25:01EVHGKKLFL0.98360.97921221
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B18:07HEVHGKKLF0.97960.81141120
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B18:04HEVHGKKLF0.97690.84481120
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B18:08HEVHGKKLF0.97580.60781120
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B18:05HEVHGKKLF0.97390.83451120
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A68:02AVVYGPHEV0.97320.6413514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B44:07HEVHGKKLF0.96920.95891120
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B44:13HEVHGKKLF0.96920.95891120
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B44:26HEVHGKKLF0.96920.95891120
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B18:06HEVHGKKLF0.96730.83951120
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B18:03HEVHGKKLF0.96290.8291120
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A69:01AVVYGPHEV0.94050.8177514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B40:04HEVHGKKLF0.93610.59611120
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:14AVVYGPHEV0.93510.6827514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:06AVVYGPHEV0.93440.7439514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A68:02EVHGKKLFL0.91480.59191221
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:03AVVYGPHEV0.91060.7633514
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B08:18EVHGKKLFL0.89740.69931221
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B18:11HEVHGKKLF0.89730.8531120
EXOSC4-NEIL2chr8145133800chr811637105274HLA-C12:02VVYGPHEVH0.72640.9545615
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A69:01EVHGKKLFL0.69420.681221
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B08:12EVHGKKLFL0.45850.80711221
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B41:03HEVHGKKLF0.27010.61011120
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B48:02HEVHGKKLF0.09420.81521120
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B15:53HEVHGKKLF0.03870.771120
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B15:54HEVHGKKLF0.01630.74231120
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B07:09GPHEVHGKKL0.99440.5049919
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B55:04GPHEVHGKKL0.39190.5814919
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B82:02GPHEVHGKKL0.17280.5126919
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A02:03ALAVVYGPHEV0.99840.8176314
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A25:01EVHGKKLFLRF0.99750.95441223
EXOSC4-NEIL2chr8145133800chr811637105274HLA-A30:01VVYGPHEVHGK0.99670.6806617
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B44:07GPHEVHGKKLF0.74250.9724920
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B44:13GPHEVHGKKLF0.74250.9724920
EXOSC4-NEIL2chr8145133800chr811637105274HLA-B44:26GPHEVHGKKLF0.74250.9724920

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Potential FusionNeoAntigen Information of EXOSC4-NEIL2 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 EXOSC4-NEIL2

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
10385VVYGPHEVHGKKLFEXOSC4NEIL2chr8145133800chr811637105274

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of EXOSC4-NEIL2

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-B14:023BVN10385VVYGPHEVHGKKLF-6.80686-6.92026
HLA-B14:023BVN10385VVYGPHEVHGKKLF-5.01234-6.04764
HLA-B52:013W3910385VVYGPHEVHGKKLF-6.71251-6.82591
HLA-B52:013W3910385VVYGPHEVHGKKLF-4.13165-5.16695
HLA-A11:014UQ210385VVYGPHEVHGKKLF-4.31699-4.43039
HLA-A11:014UQ210385VVYGPHEVHGKKLF-4.19959-5.23489
HLA-A24:025HGA10385VVYGPHEVHGKKLF-7.74913-7.86253
HLA-A24:025HGA10385VVYGPHEVHGKKLF-5.75888-6.79418
HLA-B27:036PZ510385VVYGPHEVHGKKLF1000110000
HLA-B44:053DX810385VVYGPHEVHGKKLF-4.89721-5.01061
HLA-B44:053DX810385VVYGPHEVHGKKLF-3.74482-4.78012
HLA-B35:011A1N10385VVYGPHEVHGKKLF-8.42572-8.53912
HLA-B35:011A1N10385VVYGPHEVHGKKLF-6.4428-7.4781
HLA-A02:016TDR10385VVYGPHEVHGKKLF-5.01451-6.04981

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Vaccine Design for the FusionNeoAntigens of EXOSC4-NEIL2

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
EXOSC4-NEIL2chr8145133800chr8116371051119HEVHGKKLCACGAGGTCCATGGAAAGAAATTA
EXOSC4-NEIL2chr8145133800chr8116371051120HEVHGKKLFCACGAGGTCCATGGAAAGAAATTATTC
EXOSC4-NEIL2chr8145133800chr8116371051221EVHGKKLFLGAGGTCCATGGAAAGAAATTATTCCTT
EXOSC4-NEIL2chr8145133800chr8116371051223EVHGKKLFLRFGAGGTCCATGGAAAGAAATTATTCCTTAGATTT
EXOSC4-NEIL2chr8145133800chr811637105314ALAVVYGPHEVGCACTGGCTGTGGTCTACGGCCCGCACGAGGTC
EXOSC4-NEIL2chr8145133800chr811637105514AVVYGPHEVGCTGTGGTCTACGGCCCGCACGAGGTC
EXOSC4-NEIL2chr8145133800chr811637105614VVYGPHEVGTGGTCTACGGCCCGCACGAGGTC
EXOSC4-NEIL2chr8145133800chr811637105615VVYGPHEVHGTGGTCTACGGCCCGCACGAGGTCCAT
EXOSC4-NEIL2chr8145133800chr811637105617VVYGPHEVHGKGTGGTCTACGGCCCGCACGAGGTCCATGGAAAG
EXOSC4-NEIL2chr8145133800chr811637105919GPHEVHGKKLGGCCCGCACGAGGTCCATGGAAAGAAATTA
EXOSC4-NEIL2chr8145133800chr811637105920GPHEVHGKKLFGGCCCGCACGAGGTCCATGGAAAGAAATTATTC

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 EXOSC4-NEIL2

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
MESOEXOSC4-NEIL2chr8145133800ENST00000316052chr811637105ENST00000436750TCGA-UD-AAC4

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Potential target of CAR-T therapy development for EXOSC4-NEIL2

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 EXOSC4-NEIL2

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 EXOSC4-NEIL2

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