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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:SCYL1-MICAL2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SCYL1-MICAL2
FusionPDB ID: 79772
FusionGDB2.0 ID: 79772
HgeneTgene
Gene symbol

SCYL1

MICAL2

Gene ID

57410

9645

Gene nameSCY1 like pseudokinase 1microtubule associated monooxygenase, calponin and LIM domain containing 2
SynonymsGKLP|HT019|NKTL|NTKL|P105|SCAR21|TAPK|TEIF|TRAPMICAL-2|MICAL2PV1|MICAL2PV2
Cytomap

11q13.1

11p15.3

Type of geneprotein-codingprotein-coding
DescriptionN-terminal kinase-like proteinSCY1-like protein 1SCY1-like, kinase-like 1coated vesicle-associated kinase of 90 kDalikely ortholog of mouse N-terminal kinase-like proteintelomerase regulation-associated proteintelomerase transcriptional elements-int[F-actin]-monooxygenase MICAL2[F-actin]-methionine sulfoxide oxidase MICAL2flavoprotein oxidoreductase MICAL2microtubule associated monoxygenase, calponin and LIM domain containing 2molecule interacting with CasL protein 2protein-methionine sulfoxide
Modification date2020031320200320
UniProtAcc.

O94851

Main function of 5'-partner protein: FUNCTION: Nuclear monooxygenase that promotes depolymerization of F-actin by mediating oxidation of specific methionine residues on actin to form methionine-sulfoxide, resulting in actin filament disassembly and preventing repolymerization (PubMed:24440334). In the absence of actin, it also functions as a NADPH oxidase producing H(2)O(2) (By similarity). Acts as a key regulator of the SRF signaling pathway elicited by nerve growth factor and serum: mediates oxidation and subsequent depolymerization of nuclear actin, leading to increase MKL1/MRTF-A presence in the nucleus and promote SRF:MKL1/MRTF-A-dependent gene transcription. Does not activate SRF:MKL1/MRTF-A through RhoA (PubMed:24440334). {ECO:0000250|UniProtKB:Q8TDZ2, ECO:0000269|PubMed:24440334}.
Ensembl transtripts involved in fusion geneENST idsENST00000270176, ENST00000279270, 
ENST00000420247, ENST00000524944, 
ENST00000525364, ENST00000527009, 
ENST00000533862, ENST00000534462, 
ENST00000527195, ENST00000256194, 
ENST00000342902, ENST00000379612, 
ENST00000527546, ENST00000537344, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score8 X 8 X 7=4489 X 10 X 6=540
# samples 1410
** MAII scorelog2(14/448*10)=-1.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/540*10)=-2.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: SCYL1 [Title/Abstract] AND MICAL2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: SCYL1 [Title/Abstract] AND MICAL2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SCYL1(65294588)-MICAL2(12278331), # samples:1
Anticipated loss of major functional domain due to fusion event.SCYL1-MICAL2 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.
SCYL1-MICAL2 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.
SCYL1-MICAL2 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.
SCYL1-MICAL2 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
HgeneSCYL1

GO:0006890

retrograde vesicle-mediated transport, Golgi to ER

18556652

TgeneMICAL2

GO:0007010

cytoskeleton organization

24440334

TgeneMICAL2

GO:0030042

actin filament depolymerization

24440334

TgeneMICAL2

GO:0055114

oxidation-reduction process

24440334



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/chr11:65294588/chr11:12278331)
- 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 SCYL1 (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 MICAL2 (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)
ENST00000525364SCYL1chr1165294588+ENST00000537344MICAL2chr1112278331+1745926771345422
ENST00000525364SCYL1chr1165294588+ENST00000256194MICAL2chr1112278331+1589926771345422
ENST00000525364SCYL1chr1165294588+ENST00000527546MICAL2chr1112278331+1745926771345422
ENST00000525364SCYL1chr1165294588+ENST00000342902MICAL2chr1112278331+1392926771345422
ENST00000525364SCYL1chr1165294588+ENST00000379612MICAL2chr1112278331+1580926771579501
ENST00000270176SCYL1chr1165294588+ENST00000537344MICAL2chr1112278331+1745926771345422
ENST00000270176SCYL1chr1165294588+ENST00000256194MICAL2chr1112278331+1589926771345422
ENST00000270176SCYL1chr1165294588+ENST00000527546MICAL2chr1112278331+1745926771345422
ENST00000270176SCYL1chr1165294588+ENST00000342902MICAL2chr1112278331+1392926771345422
ENST00000270176SCYL1chr1165294588+ENST00000379612MICAL2chr1112278331+1580926771579501
ENST00000420247SCYL1chr1165294588+ENST00000537344MICAL2chr1112278331+1737918691337422
ENST00000420247SCYL1chr1165294588+ENST00000256194MICAL2chr1112278331+1581918691337422
ENST00000420247SCYL1chr1165294588+ENST00000527546MICAL2chr1112278331+1737918691337422
ENST00000420247SCYL1chr1165294588+ENST00000342902MICAL2chr1112278331+1384918691337422
ENST00000420247SCYL1chr1165294588+ENST00000379612MICAL2chr1112278331+1572918691571500
ENST00000533862SCYL1chr1165294588+ENST00000537344MICAL2chr1112278331+1710891421310422
ENST00000533862SCYL1chr1165294588+ENST00000256194MICAL2chr1112278331+1554891421310422
ENST00000533862SCYL1chr1165294588+ENST00000527546MICAL2chr1112278331+1710891421310422
ENST00000533862SCYL1chr1165294588+ENST00000342902MICAL2chr1112278331+1357891421310422
ENST00000533862SCYL1chr1165294588+ENST00000379612MICAL2chr1112278331+1545891421544500
ENST00000279270SCYL1chr1165294588+ENST00000537344MICAL2chr1112278331+1709890411309422
ENST00000279270SCYL1chr1165294588+ENST00000256194MICAL2chr1112278331+1553890411309422
ENST00000279270SCYL1chr1165294588+ENST00000527546MICAL2chr1112278331+1709890411309422
ENST00000279270SCYL1chr1165294588+ENST00000342902MICAL2chr1112278331+1356890411309422
ENST00000279270SCYL1chr1165294588+ENST00000379612MICAL2chr1112278331+1544890411543501
ENST00000524944SCYL1chr1165294588+ENST00000537344MICAL2chr1112278331+1701882331301422
ENST00000524944SCYL1chr1165294588+ENST00000256194MICAL2chr1112278331+1545882331301422
ENST00000524944SCYL1chr1165294588+ENST00000527546MICAL2chr1112278331+1701882331301422
ENST00000524944SCYL1chr1165294588+ENST00000342902MICAL2chr1112278331+1348882331301422
ENST00000524944SCYL1chr1165294588+ENST00000379612MICAL2chr1112278331+1536882331535500
ENST00000527009SCYL1chr1165294588+ENST00000537344MICAL2chr1112278331+17188992781318346
ENST00000527009SCYL1chr1165294588+ENST00000256194MICAL2chr1112278331+15628992781318346
ENST00000527009SCYL1chr1165294588+ENST00000527546MICAL2chr1112278331+17188992781318346
ENST00000527009SCYL1chr1165294588+ENST00000342902MICAL2chr1112278331+13658992781318346
ENST00000527009SCYL1chr1165294588+ENST00000379612MICAL2chr1112278331+15538992781552425

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
ENST00000525364ENST00000537344SCYL1chr1165294588+MICAL2chr1112278331+0.0091651440.99083483
ENST00000525364ENST00000256194SCYL1chr1165294588+MICAL2chr1112278331+0.0084044920.99159545
ENST00000525364ENST00000527546SCYL1chr1165294588+MICAL2chr1112278331+0.0091651440.99083483
ENST00000525364ENST00000342902SCYL1chr1165294588+MICAL2chr1112278331+0.0128114530.9871885
ENST00000525364ENST00000379612SCYL1chr1165294588+MICAL2chr1112278331+0.0171881360.98281187
ENST00000270176ENST00000537344SCYL1chr1165294588+MICAL2chr1112278331+0.0091651440.99083483
ENST00000270176ENST00000256194SCYL1chr1165294588+MICAL2chr1112278331+0.0084044920.99159545
ENST00000270176ENST00000527546SCYL1chr1165294588+MICAL2chr1112278331+0.0091651440.99083483
ENST00000270176ENST00000342902SCYL1chr1165294588+MICAL2chr1112278331+0.0128114530.9871885
ENST00000270176ENST00000379612SCYL1chr1165294588+MICAL2chr1112278331+0.0171881360.98281187
ENST00000420247ENST00000537344SCYL1chr1165294588+MICAL2chr1112278331+0.0089542860.99104565
ENST00000420247ENST00000256194SCYL1chr1165294588+MICAL2chr1112278331+0.008395410.9916046
ENST00000420247ENST00000527546SCYL1chr1165294588+MICAL2chr1112278331+0.0089542860.99104565
ENST00000420247ENST00000342902SCYL1chr1165294588+MICAL2chr1112278331+0.0125464860.9874535
ENST00000420247ENST00000379612SCYL1chr1165294588+MICAL2chr1112278331+0.01665680.98334324
ENST00000533862ENST00000537344SCYL1chr1165294588+MICAL2chr1112278331+0.0084871210.99151284
ENST00000533862ENST00000256194SCYL1chr1165294588+MICAL2chr1112278331+0.0081502720.9918498
ENST00000533862ENST00000527546SCYL1chr1165294588+MICAL2chr1112278331+0.0084871210.99151284
ENST00000533862ENST00000342902SCYL1chr1165294588+MICAL2chr1112278331+0.0120880010.987912
ENST00000533862ENST00000379612SCYL1chr1165294588+MICAL2chr1112278331+0.0161132070.9838868
ENST00000279270ENST00000537344SCYL1chr1165294588+MICAL2chr1112278331+0.0086063070.9913936
ENST00000279270ENST00000256194SCYL1chr1165294588+MICAL2chr1112278331+0.008208930.9917911
ENST00000279270ENST00000527546SCYL1chr1165294588+MICAL2chr1112278331+0.0086063070.9913936
ENST00000279270ENST00000342902SCYL1chr1165294588+MICAL2chr1112278331+0.0120958960.98790413
ENST00000279270ENST00000379612SCYL1chr1165294588+MICAL2chr1112278331+0.0163549180.9836451
ENST00000524944ENST00000537344SCYL1chr1165294588+MICAL2chr1112278331+0.0084502450.99154973
ENST00000524944ENST00000256194SCYL1chr1165294588+MICAL2chr1112278331+0.0078758040.99212414
ENST00000524944ENST00000527546SCYL1chr1165294588+MICAL2chr1112278331+0.0084502450.99154973
ENST00000524944ENST00000342902SCYL1chr1165294588+MICAL2chr1112278331+0.0116369860.9883631
ENST00000524944ENST00000379612SCYL1chr1165294588+MICAL2chr1112278331+0.0160647740.98393524
ENST00000527009ENST00000537344SCYL1chr1165294588+MICAL2chr1112278331+0.129435660.87056434
ENST00000527009ENST00000256194SCYL1chr1165294588+MICAL2chr1112278331+0.170816020.829184
ENST00000527009ENST00000527546SCYL1chr1165294588+MICAL2chr1112278331+0.129435660.87056434
ENST00000527009ENST00000342902SCYL1chr1165294588+MICAL2chr1112278331+0.212243930.7877561
ENST00000527009ENST00000379612SCYL1chr1165294588+MICAL2chr1112278331+0.0780603440.9219396

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 SCYL1-MICAL2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
SCYL1chr1165294588MICAL2chr1112278331882282NRFVETNLFLEEIQESMRKSFPLNLG
SCYL1chr1165294588MICAL2chr1112278331890282NRFVETNLFLEEIQESMRKSFPLNLG
SCYL1chr1165294588MICAL2chr1112278331891282NRFVETNLFLEEIQESMRKSFPLNLG
SCYL1chr1165294588MICAL2chr1112278331899206NRFVETNLFLEEIQESMRKSFPLNLG
SCYL1chr1165294588MICAL2chr1112278331918282NRFVETNLFLEEIQESMRKSFPLNLG
SCYL1chr1165294588MICAL2chr1112278331926282NRFVETNLFLEEIQESMRKSFPLNLG

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Potential FusionNeoAntigen Information of SCYL1-MICAL2 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.
SCYL1-MICAL2_65294588_12278331.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)
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B18:01LEEIQESM0.99320.9251917
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:22FLEEIQESM0.99540.7188817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:24FLEEIQESM0.99430.6122817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:67FLEEIQESM0.99430.6122817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:30FLEEIQESM0.99430.6122817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:60FLEEIQESM0.99380.6204817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:11FLEEIQESM0.99350.6599817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:21FLEEIQESM0.9910.7434817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:04FLEEIQESM0.98950.638817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:16FLEEIQESM0.98710.5551817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:01IQESMRKSF0.98650.8451221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:27FLEEIQESM0.98450.691817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:17FLEEIQESM0.98390.5451817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:13FLEEIQESM0.97170.7597817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:35FLEEIQESM0.96070.657817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:38FLEEIQESM0.94530.6187817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B35:08FLEEIQESM0.94440.9005817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:29FLEEIQESM0.93540.623817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:20FLEEIQESM0.89360.6196817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:02FLEEIQESM0.88980.9675817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:25IQESMRKSF0.84460.85921221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B35:03FLEEIQESM0.78920.9423817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:03IQESMRKSF0.68230.66921221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B35:02FLEEIQESM0.51460.9712817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B35:04FLEEIQESM0.51460.9712817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B44:03EEIQESMRKSF0.99990.96951021
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B18:01EEIQESMRKSF0.98970.91261021
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C05:09FLEEIQESM0.99990.9519817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C04:07FLEEIQESM0.99980.8486817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C04:10FLEEIQESM0.99980.8709817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C08:15FLEEIQESM0.99970.9828817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C01:17FLEEIQESM0.99830.9606817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:02FLEEIQESM0.99550.5353817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:07FLEEIQESM0.99450.642817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:01FLEEIQESM0.99430.6122817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C03:19FLEEIQESM0.9930.9936817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:05FLEEIQESM0.99170.6716817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C04:06FLEEIQESM0.99150.9439817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C08:04FLEEIQESM0.96620.9762817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C08:13FLEEIQESM0.96620.9762817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C04:14FLEEIQESM0.96470.9021817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:07IQESMRKSF0.95040.64331221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C08:03FLEEIQESM0.91280.9912817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:21FLEEIQESM0.89680.9493817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:31FLEEIQESM0.860.9468817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C07:13FLEEIQESM0.82330.9693817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C07:29FLEEIQESM0.79580.9723817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B39:08FLEEIQESM0.70080.9285817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:05IQESMRKSF0.62320.84781221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B39:09FLEEIQESM0.54430.7305817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B35:12FLEEIQESM0.51460.9712817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B40:04LEEIQESM0.99810.7692917
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B18:05LEEIQESM0.99320.9251917
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B18:11LEEIQESM0.98460.9355917
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C04:03FLEEIQESM0.99990.8585817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C05:01FLEEIQESM0.99990.9519817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C04:01FLEEIQESM0.99980.8486817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C18:01FLEEIQESM0.99980.8686817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C08:02FLEEIQESM0.99970.9828817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C01:03FLEEIQESM0.99970.9697817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C03:03FLEEIQESM0.99610.9931817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C03:04FLEEIQESM0.99610.9931817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:14FLEEIQESM0.9910.7053817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:06FLEEIQESM0.9910.7434817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C03:67FLEEIQESM0.99010.9881817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A02:03FLEEIQESM0.98950.799817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:33IQESMRKSF0.98650.8451221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:125IQESMRKSF0.98650.8451221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:34IQESMRKSF0.98650.8451221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:27IQESMRKSF0.98620.82791221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:135IQESMRKSF0.98530.82491221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C03:06FLEEIQESM0.9810.994817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:50IQESMRKSF0.98070.83811221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C04:04FLEEIQESM0.97990.9505817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:24IQESMRKSF0.9710.80361221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:35IQESMRKSF0.91890.81221221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C08:01FLEEIQESM0.91280.9912817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:73FLEEIQESM0.85650.9246817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:39IQESMRKSF0.85460.74571221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C07:04FLEEIQESM0.85280.947817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-C17:01FLEEIQESM0.84860.9589817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B35:20FLEEIQESM0.84470.9704817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:12IQESMRKSF0.84020.79991221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:53IQESMRKSF0.8280.79631221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B35:13FLEEIQESM0.80740.9475817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:54IQESMRKSF0.77460.78321221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:30FLEEIQESM0.77320.9091817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B39:11FLEEIQESM0.68090.9198817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:20IQESMRKSF0.60740.87671221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B15:68IQESMRKSF0.59630.54581221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B48:02IQESMRKSF0.57660.87281221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B35:28IQESMRKSF0.56040.87541221
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B08:12FLEEIQESM0.55690.916817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B35:09FLEEIQESM0.51460.9712817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B07:13FLEEIQESM0.27080.8794817
SCYL1-MICAL2chr1165294588chr1112278331926HLA-A25:01EIQESMRKSF0.95610.8241121
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B44:13EEIQESMRKSF0.99990.96951021
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B44:07EEIQESMRKSF0.99990.96951021
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B44:26EEIQESMRKSF0.99990.96951021
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B18:11EEIQESMRKSF0.99640.83171021
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B18:08EEIQESMRKSF0.99160.8291021
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B18:04EEIQESMRKSF0.99160.92361021
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B18:06EEIQESMRKSF0.99150.92121021
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B18:05EEIQESMRKSF0.98970.91261021
SCYL1-MICAL2chr1165294588chr1112278331926HLA-B18:03EEIQESMRKSF0.98620.90491021

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Potential FusionNeoAntigen Information of SCYL1-MICAL2 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 SCYL1-MICAL2

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
6246NLFLEEIQESMRKSSCYL1MICAL2chr1165294588chr1112278331926

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SCYL1-MICAL2

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-B14:023BVN6246NLFLEEIQESMRKS-7.9962-8.1096
HLA-B14:023BVN6246NLFLEEIQESMRKS-5.70842-6.74372
HLA-B52:013W396246NLFLEEIQESMRKS-6.83737-6.95077
HLA-B52:013W396246NLFLEEIQESMRKS-4.4836-5.5189
HLA-A11:014UQ26246NLFLEEIQESMRKS-10.0067-10.1201
HLA-A11:014UQ26246NLFLEEIQESMRKS-9.03915-10.0745
HLA-A24:025HGA6246NLFLEEIQESMRKS-6.56204-6.67544
HLA-A24:025HGA6246NLFLEEIQESMRKS-5.42271-6.45801
HLA-B44:053DX86246NLFLEEIQESMRKS-7.85648-8.89178
HLA-B44:053DX86246NLFLEEIQESMRKS-5.3978-5.5112
HLA-A02:016TDR6246NLFLEEIQESMRKS-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of SCYL1-MICAL2

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
SCYL1-MICAL2chr1165294588chr11122783311021EEIQESMRKSFGAGATTCAGGAATCTATGCGAAAGTCATTTCCC
SCYL1-MICAL2chr1165294588chr11122783311121EIQESMRKSFATTCAGGAATCTATGCGAAAGTCATTTCCC
SCYL1-MICAL2chr1165294588chr11122783311221IQESMRKSFCAGGAATCTATGCGAAAGTCATTTCCC
SCYL1-MICAL2chr1165294588chr1112278331817FLEEIQESMCTGGAGGAGATTCAGGAATCTATGCGA
SCYL1-MICAL2chr1165294588chr1112278331917LEEIQESMGAGGAGATTCAGGAATCTATGCGA

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 SCYL1-MICAL2

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
OVSCYL1-MICAL2chr1165294588ENST00000270176chr1112278331ENST00000256194TCGA-24-2280

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Potential target of CAR-T therapy development for SCYL1-MICAL2

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 SCYL1-MICAL2

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 SCYL1-MICAL2

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