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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:SLMAP-ELN

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SLMAP-ELN
FusionPDB ID: 83690
FusionGDB2.0 ID: 83690
HgeneTgene
Gene symbol

SLMAP

ELN

Gene ID

7871

100130933

Gene namesarcolemma associated proteinsmall integral membrane protein 6
SynonymsSLAPC17orf110|ELN
Cytomap

3p14.3

17q25.1

Type of geneprotein-codingprotein-coding
Descriptionsarcolemmal membrane-associated proteinsmall integral membrane protein 6endoregulin
Modification date2020031320200313
UniProtAcc.

P15502

Main function of 5'-partner protein: FUNCTION: Major structural protein of tissues such as aorta and nuchal ligament, which must expand rapidly and recover completely. Molecular determinant of the late arterial morphogenesis, stabilizing arterial structure by regulating proliferation and organization of vascular smooth muscle (By similarity). {ECO:0000250|UniProtKB:P54320}.
Ensembl transtripts involved in fusion geneENST idsENST00000472546, ENST00000295951, 
ENST00000295952, ENST00000383718, 
ENST00000428312, ENST00000449503, 
ENST00000416870, ENST00000442599, 
ENST00000494088, ENST00000495364, 
ENST00000252034, ENST00000320399, 
ENST00000320492, ENST00000357036, 
ENST00000358929, ENST00000380553, 
ENST00000380562, ENST00000380575, 
ENST00000380576, ENST00000380584, 
ENST00000414324, ENST00000429192, 
ENST00000445912, ENST00000458204, 
ENST00000466878, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score8 X 5 X 8=3203 X 4 X 3=36
# samples 94
** MAII scorelog2(9/320*10)=-1.83007499855769
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
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: SLMAP [Title/Abstract] AND ELN [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: SLMAP [Title/Abstract] AND ELN [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SLMAP(57875827)-ELN(73480024), # samples:1
Anticipated loss of major functional domain due to fusion event.SLMAP-ELN 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.
SLMAP-ELN 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.
SLMAP-ELN 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.
SLMAP-ELN 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


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/chr3:57875827/chr7:73480024)
- 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 SLMAP (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 ELN (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)
ENST00000295951SLMAPchr357875827+ENST00000445912ELNchr773480024+2666247512172602461
ENST00000295951SLMAPchr357875827+ENST00000252034ELNchr773480024+3864247512172656479
ENST00000295951SLMAPchr357875827+ENST00000358929ELNchr773480024+3861247512172656479
ENST00000295951SLMAPchr357875827+ENST00000320492ELNchr773480024+3634247512172656479
ENST00000295951SLMAPchr357875827+ENST00000414324ELNchr773480024+3634247512172656479
ENST00000295951SLMAPchr357875827+ENST00000380562ELNchr773480024+2657247512172656480
ENST00000295951SLMAPchr357875827+ENST00000380575ELNchr773480024+3581247512172602461
ENST00000295951SLMAPchr357875827+ENST00000380584ELNchr773480024+3810247512172602461
ENST00000295951SLMAPchr357875827+ENST00000458204ELNchr773480024+3634247512172656479
ENST00000295951SLMAPchr357875827+ENST00000357036ELNchr773480024+3810247512172602461
ENST00000295951SLMAPchr357875827+ENST00000429192ELNchr773480024+3807247512172602461
ENST00000295951SLMAPchr357875827+ENST00000380553ELNchr773480024+3580247512172602461
ENST00000295951SLMAPchr357875827+ENST00000380576ELNchr773480024+3635247512172656479
ENST00000295951SLMAPchr357875827+ENST00000320399ELNchr773480024+2657247512172656480
ENST00000295952SLMAPchr357875827+ENST00000445912ELNchr773480024+165414632051590461
ENST00000295952SLMAPchr357875827+ENST00000252034ELNchr773480024+285214632051644479
ENST00000295952SLMAPchr357875827+ENST00000358929ELNchr773480024+284914632051644479
ENST00000295952SLMAPchr357875827+ENST00000320492ELNchr773480024+262214632051644479
ENST00000295952SLMAPchr357875827+ENST00000414324ELNchr773480024+262214632051644479
ENST00000295952SLMAPchr357875827+ENST00000380562ELNchr773480024+164514632051644480
ENST00000295952SLMAPchr357875827+ENST00000380575ELNchr773480024+256914632051590461
ENST00000295952SLMAPchr357875827+ENST00000380584ELNchr773480024+279814632051590461
ENST00000295952SLMAPchr357875827+ENST00000458204ELNchr773480024+262214632051644479
ENST00000295952SLMAPchr357875827+ENST00000357036ELNchr773480024+279814632051590461
ENST00000295952SLMAPchr357875827+ENST00000429192ELNchr773480024+279514632051590461
ENST00000295952SLMAPchr357875827+ENST00000380553ELNchr773480024+256814632051590461
ENST00000295952SLMAPchr357875827+ENST00000380576ELNchr773480024+262314632051644479
ENST00000295952SLMAPchr357875827+ENST00000320399ELNchr773480024+164514632051644480
ENST00000383718SLMAPchr357875827+ENST00000445912ELNchr773480024+15861395981522474
ENST00000383718SLMAPchr357875827+ENST00000252034ELNchr773480024+27841395981576492
ENST00000383718SLMAPchr357875827+ENST00000358929ELNchr773480024+27811395981576492
ENST00000383718SLMAPchr357875827+ENST00000320492ELNchr773480024+25541395981576492
ENST00000383718SLMAPchr357875827+ENST00000414324ELNchr773480024+25541395981576492
ENST00000383718SLMAPchr357875827+ENST00000380562ELNchr773480024+15771395981576493
ENST00000383718SLMAPchr357875827+ENST00000380575ELNchr773480024+25011395981522474
ENST00000383718SLMAPchr357875827+ENST00000380584ELNchr773480024+27301395981522474
ENST00000383718SLMAPchr357875827+ENST00000458204ELNchr773480024+25541395981576492
ENST00000383718SLMAPchr357875827+ENST00000357036ELNchr773480024+27301395981522474
ENST00000383718SLMAPchr357875827+ENST00000429192ELNchr773480024+27271395981522474
ENST00000383718SLMAPchr357875827+ENST00000380553ELNchr773480024+25001395981522474
ENST00000383718SLMAPchr357875827+ENST00000380576ELNchr773480024+25551395981576492
ENST00000383718SLMAPchr357875827+ENST00000320399ELNchr773480024+15771395981576493
ENST00000428312SLMAPchr357875827+ENST00000445912ELNchr773480024+15941403941530478
ENST00000428312SLMAPchr357875827+ENST00000252034ELNchr773480024+27921403941584496
ENST00000428312SLMAPchr357875827+ENST00000358929ELNchr773480024+27891403941584496
ENST00000428312SLMAPchr357875827+ENST00000320492ELNchr773480024+25621403941584496
ENST00000428312SLMAPchr357875827+ENST00000414324ELNchr773480024+25621403941584496
ENST00000428312SLMAPchr357875827+ENST00000380562ELNchr773480024+15851403941584497
ENST00000428312SLMAPchr357875827+ENST00000380575ELNchr773480024+25091403941530478
ENST00000428312SLMAPchr357875827+ENST00000380584ELNchr773480024+27381403941530478
ENST00000428312SLMAPchr357875827+ENST00000458204ELNchr773480024+25621403941584496
ENST00000428312SLMAPchr357875827+ENST00000357036ELNchr773480024+27381403941530478
ENST00000428312SLMAPchr357875827+ENST00000429192ELNchr773480024+27351403941530478
ENST00000428312SLMAPchr357875827+ENST00000380553ELNchr773480024+25081403941530478
ENST00000428312SLMAPchr357875827+ENST00000380576ELNchr773480024+25631403941584496
ENST00000428312SLMAPchr357875827+ENST00000320399ELNchr773480024+15851403941584497
ENST00000449503SLMAPchr357875827+ENST00000445912ELNchr773480024+14801289941416440
ENST00000449503SLMAPchr357875827+ENST00000252034ELNchr773480024+26781289941470458
ENST00000449503SLMAPchr357875827+ENST00000358929ELNchr773480024+26751289941470458
ENST00000449503SLMAPchr357875827+ENST00000320492ELNchr773480024+24481289941470458
ENST00000449503SLMAPchr357875827+ENST00000414324ELNchr773480024+24481289941470458
ENST00000449503SLMAPchr357875827+ENST00000380562ELNchr773480024+14711289941470459
ENST00000449503SLMAPchr357875827+ENST00000380575ELNchr773480024+23951289941416440
ENST00000449503SLMAPchr357875827+ENST00000380584ELNchr773480024+26241289941416440
ENST00000449503SLMAPchr357875827+ENST00000458204ELNchr773480024+24481289941470458
ENST00000449503SLMAPchr357875827+ENST00000357036ELNchr773480024+26241289941416440
ENST00000449503SLMAPchr357875827+ENST00000429192ELNchr773480024+26211289941416440
ENST00000449503SLMAPchr357875827+ENST00000380553ELNchr773480024+23941289941416440
ENST00000449503SLMAPchr357875827+ENST00000380576ELNchr773480024+24491289941470458
ENST00000449503SLMAPchr357875827+ENST00000320399ELNchr773480024+14711289941470459

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
ENST00000295951ENST00000445912SLMAPchr357875827+ELNchr773480024+0.0036228260.99637717
ENST00000295951ENST00000252034SLMAPchr357875827+ELNchr773480024+0.0024152020.9975848
ENST00000295951ENST00000358929SLMAPchr357875827+ELNchr773480024+0.0024400880.9975599
ENST00000295951ENST00000320492SLMAPchr357875827+ELNchr773480024+0.0033198820.99668014
ENST00000295951ENST00000414324SLMAPchr357875827+ELNchr773480024+0.0033198820.99668014
ENST00000295951ENST00000380562SLMAPchr357875827+ELNchr773480024+0.0035176710.99648225
ENST00000295951ENST00000380575SLMAPchr357875827+ELNchr773480024+0.0033334590.9966665
ENST00000295951ENST00000380584SLMAPchr357875827+ELNchr773480024+0.002463220.9975368
ENST00000295951ENST00000458204SLMAPchr357875827+ELNchr773480024+0.0033198820.99668014
ENST00000295951ENST00000357036SLMAPchr357875827+ELNchr773480024+0.002463220.9975368
ENST00000295951ENST00000429192SLMAPchr357875827+ELNchr773480024+0.0024889770.997511
ENST00000295951ENST00000380553SLMAPchr357875827+ELNchr773480024+0.0033222380.99667776
ENST00000295951ENST00000380576SLMAPchr357875827+ELNchr773480024+0.0033364420.9966635
ENST00000295951ENST00000320399SLMAPchr357875827+ELNchr773480024+0.0035176710.99648225
ENST00000295952ENST00000445912SLMAPchr357875827+ELNchr773480024+0.0019743750.99802566
ENST00000295952ENST00000252034SLMAPchr357875827+ELNchr773480024+0.0013956810.99860436
ENST00000295952ENST00000358929SLMAPchr357875827+ELNchr773480024+0.001410760.9985892
ENST00000295952ENST00000320492SLMAPchr357875827+ELNchr773480024+0.0020890180.9979109
ENST00000295952ENST00000414324SLMAPchr357875827+ELNchr773480024+0.0020890180.9979109
ENST00000295952ENST00000380562SLMAPchr357875827+ELNchr773480024+0.001760630.9982394
ENST00000295952ENST00000380575SLMAPchr357875827+ELNchr773480024+0.002210060.99779
ENST00000295952ENST00000380584SLMAPchr357875827+ELNchr773480024+0.0013993940.99860066
ENST00000295952ENST00000458204SLMAPchr357875827+ELNchr773480024+0.0020890180.9979109
ENST00000295952ENST00000357036SLMAPchr357875827+ELNchr773480024+0.0013993940.99860066
ENST00000295952ENST00000429192SLMAPchr357875827+ELNchr773480024+0.0014159180.99858415
ENST00000295952ENST00000380553SLMAPchr357875827+ELNchr773480024+0.0021982120.9978017
ENST00000295952ENST00000380576SLMAPchr357875827+ELNchr773480024+0.0021008230.9978992
ENST00000295952ENST00000320399SLMAPchr357875827+ELNchr773480024+0.001760630.9982394
ENST00000383718ENST00000445912SLMAPchr357875827+ELNchr773480024+0.003044830.99695516
ENST00000383718ENST00000252034SLMAPchr357875827+ELNchr773480024+0.00126080.9987392
ENST00000383718ENST00000358929SLMAPchr357875827+ELNchr773480024+0.0012753520.99872464
ENST00000383718ENST00000320492SLMAPchr357875827+ELNchr773480024+0.0018716650.99812835
ENST00000383718ENST00000414324SLMAPchr357875827+ELNchr773480024+0.0018716650.99812835
ENST00000383718ENST00000380562SLMAPchr357875827+ELNchr773480024+0.0019979340.9980021
ENST00000383718ENST00000380575SLMAPchr357875827+ELNchr773480024+0.0023345010.9976655
ENST00000383718ENST00000380584SLMAPchr357875827+ELNchr773480024+0.0015434960.9984565
ENST00000383718ENST00000458204SLMAPchr357875827+ELNchr773480024+0.0018716650.99812835
ENST00000383718ENST00000357036SLMAPchr357875827+ELNchr773480024+0.0015434960.9984565
ENST00000383718ENST00000429192SLMAPchr357875827+ELNchr773480024+0.0015596370.9984403
ENST00000383718ENST00000380553SLMAPchr357875827+ELNchr773480024+0.0023248840.9976751
ENST00000383718ENST00000380576SLMAPchr357875827+ELNchr773480024+0.0018813050.9981187
ENST00000383718ENST00000320399SLMAPchr357875827+ELNchr773480024+0.0019979340.9980021
ENST00000428312ENST00000445912SLMAPchr357875827+ELNchr773480024+0.0035333210.99646664
ENST00000428312ENST00000252034SLMAPchr357875827+ELNchr773480024+0.0016393970.9983606
ENST00000428312ENST00000358929SLMAPchr357875827+ELNchr773480024+0.0016573050.99834263
ENST00000428312ENST00000320492SLMAPchr357875827+ELNchr773480024+0.0024522060.9975478
ENST00000428312ENST00000414324SLMAPchr357875827+ELNchr773480024+0.0024522060.9975478
ENST00000428312ENST00000380562SLMAPchr357875827+ELNchr773480024+0.0028511380.99714893
ENST00000428312ENST00000380575SLMAPchr357875827+ELNchr773480024+0.0030575220.99694246
ENST00000428312ENST00000380584SLMAPchr357875827+ELNchr773480024+0.0020014880.99799854
ENST00000428312ENST00000458204SLMAPchr357875827+ELNchr773480024+0.0024522060.9975478
ENST00000428312ENST00000357036SLMAPchr357875827+ELNchr773480024+0.0020014880.99799854
ENST00000428312ENST00000429192SLMAPchr357875827+ELNchr773480024+0.0020239170.9979761
ENST00000428312ENST00000380553SLMAPchr357875827+ELNchr773480024+0.0030409770.9969591
ENST00000428312ENST00000380576SLMAPchr357875827+ELNchr773480024+0.0024684780.99753153
ENST00000428312ENST00000320399SLMAPchr357875827+ELNchr773480024+0.0028511380.99714893
ENST00000449503ENST00000445912SLMAPchr357875827+ELNchr773480024+0.0029048490.9970951
ENST00000449503ENST00000252034SLMAPchr357875827+ELNchr773480024+0.0015200810.9984799
ENST00000449503ENST00000358929SLMAPchr357875827+ELNchr773480024+0.0015344050.99846566
ENST00000449503ENST00000320492SLMAPchr357875827+ELNchr773480024+0.0022226060.9977774
ENST00000449503ENST00000414324SLMAPchr357875827+ELNchr773480024+0.0022226060.9977774
ENST00000449503ENST00000380562SLMAPchr357875827+ELNchr773480024+0.0023215230.99767846
ENST00000449503ENST00000380575SLMAPchr357875827+ELNchr773480024+0.0024719070.99752814
ENST00000449503ENST00000380584SLMAPchr357875827+ELNchr773480024+0.0016291660.9983708
ENST00000449503ENST00000458204SLMAPchr357875827+ELNchr773480024+0.0022226060.9977774
ENST00000449503ENST00000357036SLMAPchr357875827+ELNchr773480024+0.0016291660.9983708
ENST00000449503ENST00000429192SLMAPchr357875827+ELNchr773480024+0.0016464390.9983536
ENST00000449503ENST00000380553SLMAPchr357875827+ELNchr773480024+0.0024596940.99754035
ENST00000449503ENST00000380576SLMAPchr357875827+ELNchr773480024+0.0022364660.9977635
ENST00000449503ENST00000320399SLMAPchr357875827+ELNchr773480024+0.0023215230.99767846

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 SLMAP-ELN

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
SLMAPchr357875827ELNchr7734800241289396EGHLTKAVEETKLSKGIPPAAAAKAA
SLMAPchr357875827ELNchr7734800241395430EGHLTKAVEETKLSKGIPPAAAAKAA
SLMAPchr357875827ELNchr7734800241403434EGHLTKAVEETKLSKGIPPAAAAKAA
SLMAPchr357875827ELNchr7734800241463417EGHLTKAVEETKLSKGIPPAAAAKAA
SLMAPchr357875827ELNchr7734800242475417EGHLTKAVEETKLSKGIPPAAAAKAA

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Potential FusionNeoAntigen Information of SLMAP-ELN 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.
SLMAP-ELN_57875827_73480024.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)
SLMAP-ELNchr357875827chr7734800242475HLA-B44:03EETKLSKGI0.98050.8901817
SLMAP-ELNchr357875827chr7734800242475HLA-A30:08LSKGIPPAA0.88150.8181221
SLMAP-ELNchr357875827chr7734800242475HLA-A30:08KLSKGIPPAA0.84250.75961121
SLMAP-ELNchr357875827chr7734800242475HLA-B44:07EETKLSKGI0.98050.8901817
SLMAP-ELNchr357875827chr7734800242475HLA-B44:26EETKLSKGI0.98050.8901817
SLMAP-ELNchr357875827chr7734800242475HLA-B44:13EETKLSKGI0.98050.8901817
SLMAP-ELNchr357875827chr7734800242475HLA-A30:01LSKGIPPAA0.89020.90591221
SLMAP-ELNchr357875827chr7734800242475HLA-A30:01KAVEETKLSK0.97120.8556515
SLMAP-ELNchr357875827chr7734800242475HLA-A30:01KLSKGIPPAA0.85460.86141121

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Potential FusionNeoAntigen Information of SLMAP-ELN 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 SLMAP-ELN

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
682AVEETKLSKGIPPASLMAPELNchr357875827chr7734800242475

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

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-B53:011A1O682AVEETKLSKGIPPA-1.20162-2.23692
HLA-B51:011E28682AVEETKLSKGIPPA-4.67742-5.71272
HLA-B57:032BVO682AVEETKLSKGIPPA-3.57384-3.68724
HLA-A03:012XPG682AVEETKLSKGIPPA-2.81241-3.84771
HLA-A03:012XPG682AVEETKLSKGIPPA-2.75108-2.86448
HLA-B14:023BVN682AVEETKLSKGIPPA-6.6298-6.7432
HLA-B14:023BVN682AVEETKLSKGIPPA-5.03588-6.07118
HLA-B27:093CZF682AVEETKLSKGIPPA-2.72034-3.75564
HLA-B44:033DX7682AVEETKLSKGIPPA-0.953592-1.98889
HLA-B52:013W39682AVEETKLSKGIPPA-5.17052-5.28392
HLA-B52:013W39682AVEETKLSKGIPPA-2.67174-3.70704
HLA-B18:014JQV682AVEETKLSKGIPPA-3.88279-3.99619
HLA-B18:014JQV682AVEETKLSKGIPPA-2.06796-3.10326
HLA-A11:014UQ2682AVEETKLSKGIPPA-8.93359-9.04699
HLA-A11:014UQ2682AVEETKLSKGIPPA-8.08854-9.12384
HLA-A24:025HGA682AVEETKLSKGIPPA-6.7667-6.8801
HLA-A24:025HGA682AVEETKLSKGIPPA-4.92764-5.96294
HLA-B57:015VUD682AVEETKLSKGIPPA-2.30317-3.33847
HLA-B27:056PYJ682AVEETKLSKGIPPA-4.30074-4.41414
HLA-B27:056PYJ682AVEETKLSKGIPPA-2.70769-3.74299
HLA-B27:036PZ5682AVEETKLSKGIPPA-3.25646-4.29176
HLA-B27:036PZ5682AVEETKLSKGIPPA-1.00133-1.11473
HLA-B44:053DX8682AVEETKLSKGIPPA-5.00036-5.11376
HLA-B44:053DX8682AVEETKLSKGIPPA-4.13613-5.17143
HLA-B07:025EO0682AVEETKLSKGIPPA-1.03752-2.07282
HLA-A02:016TDR682AVEETKLSKGIPPA-5.74233-6.77763

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Vaccine Design for the FusionNeoAntigens of SLMAP-ELN

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
SLMAP-ELNchr357875827chr7734800241121KLSKGIPPAACAAAAGGTATACCTCCAGCTGCAGCCGCTA
SLMAP-ELNchr357875827chr7734800241221LSKGIPPAAAAGGTATACCTCCAGCTGCAGCCGCTA
SLMAP-ELNchr357875827chr773480024515KAVEETKLSKTAGAAGAAACAAAGCTTTCAAAAGGTATAC
SLMAP-ELNchr357875827chr773480024817EETKLSKGICAAAGCTTTCAAAAGGTATACCTCCAG

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 SLMAP-ELN

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
BRCASLMAP-ELNchr357875827ENST00000295951chr773480024ENST00000252034TCGA-LL-A441-01A

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Potential target of CAR-T therapy development for SLMAP-ELN

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 SLMAP-ELN

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 SLMAP-ELN

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