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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:SKIL-TNIK

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SKIL-TNIK
FusionPDB ID: 82097
FusionGDB2.0 ID: 82097
HgeneTgene
Gene symbol

SKIL

TNIK

Gene ID

6498

23043

Gene nameSKI like proto-oncogeneTRAF2 and NCK interacting kinase
SynonymsSNO|SnoA|SnoI|SnoNMRT54
Cytomap

3q26.2

3q26.2-q26.31

Type of geneprotein-codingprotein-coding
Descriptionski-like proteinSKI-like oncogeneski-related oncogene snoNTRAF2 and NCK-interacting protein kinase
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000259119, ENST00000413427, 
ENST00000426052, ENST00000458537, 
ENST00000490989, 		ENST00000464785, 
ENST00000465393, ENST00000284483, 
ENST00000341852, ENST00000357327, 
ENST00000369326, ENST00000436636, 
ENST00000460047, ENST00000470834, 
ENST00000475336, ENST00000488470, 
ENST00000538048, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score7 X 5 X 6=21013 X 13 X 4=676
# samples 816
** MAII scorelog2(8/210*10)=-1.39231742277876
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/676*10)=-2.07895134139482
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: SKIL [Title/Abstract] AND TNIK [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: SKIL [Title/Abstract] AND TNIK [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SKIL(170079215)-TNIK(171087476), # samples:1
SKIL(170079217)-TNIK(171087474), # samples:1
Anticipated loss of major functional domain due to fusion event.SKIL-TNIK 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.
SKIL-TNIK 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
TgeneTNIK

GO:0006468

protein phosphorylation

10521462|15342639|22797597

TgeneTNIK

GO:0007256

activation of JNKK activity

15342639

TgeneTNIK

GO:0031532

actin cytoskeleton reorganization

15342639

TgeneTNIK

GO:0035556

intracellular signal transduction

10521462

TgeneTNIK

GO:0046777

protein autophosphorylation

10521462|15342639

TgeneTNIK

GO:0048814

regulation of dendrite morphogenesis

20159449



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/chr3:170079215/chr3:171087476)
- 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 SKIL (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 TNIK (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


Top

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)
ENST00000259119SKILchr3170079215+ENST00000436636TNIKchr3171087476-8337176955757941745
ENST00000259119SKILchr3170079215+ENST00000538048TNIKchr3171087476-7029176955756501697
ENST00000259119SKILchr3170079215+ENST00000369326TNIKchr3171087476-7107176955757281723
ENST00000259119SKILchr3170079215+ENST00000341852TNIKchr3171087476-6094176955755421661
ENST00000259119SKILchr3170079215+ENST00000284483TNIKchr3171087476-5771176955757701738
ENST00000259119SKILchr3170079215+ENST00000470834TNIKchr3171087476-5684176955756831709
ENST00000259119SKILchr3170079215+ENST00000460047TNIKchr3171087476-5606176955756051683
ENST00000259119SKILchr3170079215+ENST00000475336TNIKchr3171087476-5519176955755181654
ENST00000259119SKILchr3170079215+ENST00000488470TNIKchr3171087476-5630176955756291691
ENST00000259119SKILchr3170079215+ENST00000357327TNIKchr3171087476-5708176955757071717
ENST00000426052SKILchr3170079215+ENST00000436636TNIKchr3171087476-7838127018152951704
ENST00000426052SKILchr3170079215+ENST00000538048TNIKchr3171087476-6530127018151511656
ENST00000426052SKILchr3170079215+ENST00000369326TNIKchr3171087476-6608127018152291682
ENST00000426052SKILchr3170079215+ENST00000341852TNIKchr3171087476-5595127018150431620
ENST00000426052SKILchr3170079215+ENST00000284483TNIKchr3171087476-5272127018152711697
ENST00000426052SKILchr3170079215+ENST00000470834TNIKchr3171087476-5185127018151841668
ENST00000426052SKILchr3170079215+ENST00000460047TNIKchr3171087476-5107127018151061642
ENST00000426052SKILchr3170079215+ENST00000475336TNIKchr3171087476-5020127018150191613
ENST00000426052SKILchr3170079215+ENST00000488470TNIKchr3171087476-5131127018151301650
ENST00000426052SKILchr3170079215+ENST00000357327TNIKchr3171087476-5209127018152081676
ENST00000413427SKILchr3170079215+ENST00000436636TNIKchr3171087476-8375180759558321745
ENST00000413427SKILchr3170079215+ENST00000538048TNIKchr3171087476-7067180759556881697
ENST00000413427SKILchr3170079215+ENST00000369326TNIKchr3171087476-7145180759557661723
ENST00000413427SKILchr3170079215+ENST00000341852TNIKchr3171087476-6132180759555801661
ENST00000413427SKILchr3170079215+ENST00000284483TNIKchr3171087476-5809180759558081738
ENST00000413427SKILchr3170079215+ENST00000470834TNIKchr3171087476-5722180759557211709
ENST00000413427SKILchr3170079215+ENST00000460047TNIKchr3171087476-5644180759556431683
ENST00000413427SKILchr3170079215+ENST00000475336TNIKchr3171087476-5557180759555561654
ENST00000413427SKILchr3170079215+ENST00000488470TNIKchr3171087476-5668180759556671691
ENST00000413427SKILchr3170079215+ENST00000357327TNIKchr3171087476-5746180759557451717
ENST00000458537SKILchr3170079215+ENST00000436636TNIKchr3171087476-8375180759558321745
ENST00000458537SKILchr3170079215+ENST00000538048TNIKchr3171087476-7067180759556881697
ENST00000458537SKILchr3170079215+ENST00000369326TNIKchr3171087476-7145180759557661723
ENST00000458537SKILchr3170079215+ENST00000341852TNIKchr3171087476-6132180759555801661
ENST00000458537SKILchr3170079215+ENST00000284483TNIKchr3171087476-5809180759558081738
ENST00000458537SKILchr3170079215+ENST00000470834TNIKchr3171087476-5722180759557211709
ENST00000458537SKILchr3170079215+ENST00000460047TNIKchr3171087476-5644180759556431683
ENST00000458537SKILchr3170079215+ENST00000475336TNIKchr3171087476-5557180759555561654
ENST00000458537SKILchr3170079215+ENST00000488470TNIKchr3171087476-5668180759556671691
ENST00000458537SKILchr3170079215+ENST00000357327TNIKchr3171087476-5746180759557451717
ENST00000259119SKILchr3170079217-ENST00000436636TNIKchr3171087474-8337176955757941745
ENST00000259119SKILchr3170079217-ENST00000538048TNIKchr3171087474-7029176955756501697
ENST00000259119SKILchr3170079217-ENST00000369326TNIKchr3171087474-7107176955757281723
ENST00000259119SKILchr3170079217-ENST00000341852TNIKchr3171087474-6094176955755421661
ENST00000259119SKILchr3170079217-ENST00000284483TNIKchr3171087474-5771176955757701738
ENST00000259119SKILchr3170079217-ENST00000470834TNIKchr3171087474-5684176955756831709
ENST00000259119SKILchr3170079217-ENST00000460047TNIKchr3171087474-5606176955756051683
ENST00000259119SKILchr3170079217-ENST00000475336TNIKchr3171087474-5519176955755181654
ENST00000259119SKILchr3170079217-ENST00000488470TNIKchr3171087474-5630176955756291691
ENST00000259119SKILchr3170079217-ENST00000357327TNIKchr3171087474-5708176955757071717
ENST00000426052SKILchr3170079217-ENST00000436636TNIKchr3171087474-7838127018152951704
ENST00000426052SKILchr3170079217-ENST00000538048TNIKchr3171087474-6530127018151511656
ENST00000426052SKILchr3170079217-ENST00000369326TNIKchr3171087474-6608127018152291682
ENST00000426052SKILchr3170079217-ENST00000341852TNIKchr3171087474-5595127018150431620
ENST00000426052SKILchr3170079217-ENST00000284483TNIKchr3171087474-5272127018152711697
ENST00000426052SKILchr3170079217-ENST00000470834TNIKchr3171087474-5185127018151841668
ENST00000426052SKILchr3170079217-ENST00000460047TNIKchr3171087474-5107127018151061642
ENST00000426052SKILchr3170079217-ENST00000475336TNIKchr3171087474-5020127018150191613
ENST00000426052SKILchr3170079217-ENST00000488470TNIKchr3171087474-5131127018151301650
ENST00000426052SKILchr3170079217-ENST00000357327TNIKchr3171087474-5209127018152081676
ENST00000413427SKILchr3170079217-ENST00000436636TNIKchr3171087474-8375180759558321745
ENST00000413427SKILchr3170079217-ENST00000538048TNIKchr3171087474-7067180759556881697
ENST00000413427SKILchr3170079217-ENST00000369326TNIKchr3171087474-7145180759557661723
ENST00000413427SKILchr3170079217-ENST00000341852TNIKchr3171087474-6132180759555801661
ENST00000413427SKILchr3170079217-ENST00000284483TNIKchr3171087474-5809180759558081738
ENST00000413427SKILchr3170079217-ENST00000470834TNIKchr3171087474-5722180759557211709
ENST00000413427SKILchr3170079217-ENST00000460047TNIKchr3171087474-5644180759556431683
ENST00000413427SKILchr3170079217-ENST00000475336TNIKchr3171087474-5557180759555561654
ENST00000413427SKILchr3170079217-ENST00000488470TNIKchr3171087474-5668180759556671691
ENST00000413427SKILchr3170079217-ENST00000357327TNIKchr3171087474-5746180759557451717
ENST00000458537SKILchr3170079217-ENST00000436636TNIKchr3171087474-8375180759558321745
ENST00000458537SKILchr3170079217-ENST00000538048TNIKchr3171087474-7067180759556881697
ENST00000458537SKILchr3170079217-ENST00000369326TNIKchr3171087474-7145180759557661723
ENST00000458537SKILchr3170079217-ENST00000341852TNIKchr3171087474-6132180759555801661
ENST00000458537SKILchr3170079217-ENST00000284483TNIKchr3171087474-5809180759558081738
ENST00000458537SKILchr3170079217-ENST00000470834TNIKchr3171087474-5722180759557211709
ENST00000458537SKILchr3170079217-ENST00000460047TNIKchr3171087474-5644180759556431683
ENST00000458537SKILchr3170079217-ENST00000475336TNIKchr3171087474-5557180759555561654
ENST00000458537SKILchr3170079217-ENST00000488470TNIKchr3171087474-5668180759556671691
ENST00000458537SKILchr3170079217-ENST00000357327TNIKchr3171087474-5746180759557451717

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
ENST00000259119ENST00000436636SKILchr3170079215+TNIKchr3171087476-0.0005861780.99941385
ENST00000259119ENST00000538048SKILchr3170079215+TNIKchr3171087476-0.001290330.9987097
ENST00000259119ENST00000369326SKILchr3170079215+TNIKchr3171087476-0.0009230510.99907696
ENST00000259119ENST00000341852SKILchr3170079215+TNIKchr3171087476-0.0018324150.9981675
ENST00000259119ENST00000284483SKILchr3170079215+TNIKchr3171087476-0.0024735880.99752647
ENST00000259119ENST00000470834SKILchr3170079215+TNIKchr3171087476-0.0020402010.99795985
ENST00000259119ENST00000460047SKILchr3170079215+TNIKchr3171087476-0.0012389980.99876106
ENST00000259119ENST00000475336SKILchr3170079215+TNIKchr3171087476-0.001228920.998771
ENST00000259119ENST00000488470SKILchr3170079215+TNIKchr3171087476-0.0025063970.9974936
ENST00000259119ENST00000357327SKILchr3170079215+TNIKchr3171087476-0.0022056360.9977944
ENST00000426052ENST00000436636SKILchr3170079215+TNIKchr3171087476-0.0004622370.9995378
ENST00000426052ENST00000538048SKILchr3170079215+TNIKchr3171087476-0.0011028860.9988971
ENST00000426052ENST00000369326SKILchr3170079215+TNIKchr3171087476-0.0007863550.9992136
ENST00000426052ENST00000341852SKILchr3170079215+TNIKchr3171087476-0.0016397690.9983602
ENST00000426052ENST00000284483SKILchr3170079215+TNIKchr3171087476-0.002525860.99747413
ENST00000426052ENST00000470834SKILchr3170079215+TNIKchr3171087476-0.0020230440.99797696
ENST00000426052ENST00000460047SKILchr3170079215+TNIKchr3171087476-0.0013419430.99865806
ENST00000426052ENST00000475336SKILchr3170079215+TNIKchr3171087476-0.001291640.99870837
ENST00000426052ENST00000488470SKILchr3170079215+TNIKchr3171087476-0.0024661230.9975339
ENST00000426052ENST00000357327SKILchr3170079215+TNIKchr3171087476-0.002180260.9978198
ENST00000413427ENST00000436636SKILchr3170079215+TNIKchr3171087476-0.0005807460.99941933
ENST00000413427ENST00000538048SKILchr3170079215+TNIKchr3171087476-0.0012646750.99873537
ENST00000413427ENST00000369326SKILchr3170079215+TNIKchr3171087476-0.0009031260.9990969
ENST00000413427ENST00000341852SKILchr3170079215+TNIKchr3171087476-0.0018061050.9981939
ENST00000413427ENST00000284483SKILchr3170079215+TNIKchr3171087476-0.0024124670.99758756
ENST00000413427ENST00000470834SKILchr3170079215+TNIKchr3171087476-0.0019721950.99802774
ENST00000413427ENST00000460047SKILchr3170079215+TNIKchr3171087476-0.0011843880.99881566
ENST00000413427ENST00000475336SKILchr3170079215+TNIKchr3171087476-0.0011721340.9988279
ENST00000413427ENST00000488470SKILchr3170079215+TNIKchr3171087476-0.0024357620.9975642
ENST00000413427ENST00000357327SKILchr3170079215+TNIKchr3171087476-0.002138360.9978617
ENST00000458537ENST00000436636SKILchr3170079215+TNIKchr3171087476-0.0005807460.99941933
ENST00000458537ENST00000538048SKILchr3170079215+TNIKchr3171087476-0.0012646750.99873537
ENST00000458537ENST00000369326SKILchr3170079215+TNIKchr3171087476-0.0009031260.9990969
ENST00000458537ENST00000341852SKILchr3170079215+TNIKchr3171087476-0.0018061050.9981939
ENST00000458537ENST00000284483SKILchr3170079215+TNIKchr3171087476-0.0024124670.99758756
ENST00000458537ENST00000470834SKILchr3170079215+TNIKchr3171087476-0.0019721950.99802774
ENST00000458537ENST00000460047SKILchr3170079215+TNIKchr3171087476-0.0011843880.99881566
ENST00000458537ENST00000475336SKILchr3170079215+TNIKchr3171087476-0.0011721340.9988279
ENST00000458537ENST00000488470SKILchr3170079215+TNIKchr3171087476-0.0024357620.9975642
ENST00000458537ENST00000357327SKILchr3170079215+TNIKchr3171087476-0.002138360.9978617
ENST00000259119ENST00000436636SKILchr3170079217-TNIKchr3171087474-0.0005861780.99941385
ENST00000259119ENST00000538048SKILchr3170079217-TNIKchr3171087474-0.001290330.9987097
ENST00000259119ENST00000369326SKILchr3170079217-TNIKchr3171087474-0.0009230510.99907696
ENST00000259119ENST00000341852SKILchr3170079217-TNIKchr3171087474-0.0018324150.9981675
ENST00000259119ENST00000284483SKILchr3170079217-TNIKchr3171087474-0.0024735880.99752647
ENST00000259119ENST00000470834SKILchr3170079217-TNIKchr3171087474-0.0020402010.99795985
ENST00000259119ENST00000460047SKILchr3170079217-TNIKchr3171087474-0.0012389980.99876106
ENST00000259119ENST00000475336SKILchr3170079217-TNIKchr3171087474-0.001228920.998771
ENST00000259119ENST00000488470SKILchr3170079217-TNIKchr3171087474-0.0025063970.9974936
ENST00000259119ENST00000357327SKILchr3170079217-TNIKchr3171087474-0.0022056360.9977944
ENST00000426052ENST00000436636SKILchr3170079217-TNIKchr3171087474-0.0004622370.9995378
ENST00000426052ENST00000538048SKILchr3170079217-TNIKchr3171087474-0.0011028860.9988971
ENST00000426052ENST00000369326SKILchr3170079217-TNIKchr3171087474-0.0007863550.9992136
ENST00000426052ENST00000341852SKILchr3170079217-TNIKchr3171087474-0.0016397690.9983602
ENST00000426052ENST00000284483SKILchr3170079217-TNIKchr3171087474-0.002525860.99747413
ENST00000426052ENST00000470834SKILchr3170079217-TNIKchr3171087474-0.0020230440.99797696
ENST00000426052ENST00000460047SKILchr3170079217-TNIKchr3171087474-0.0013419430.99865806
ENST00000426052ENST00000475336SKILchr3170079217-TNIKchr3171087474-0.001291640.99870837
ENST00000426052ENST00000488470SKILchr3170079217-TNIKchr3171087474-0.0024661230.9975339
ENST00000426052ENST00000357327SKILchr3170079217-TNIKchr3171087474-0.002180260.9978198
ENST00000413427ENST00000436636SKILchr3170079217-TNIKchr3171087474-0.0005807460.99941933
ENST00000413427ENST00000538048SKILchr3170079217-TNIKchr3171087474-0.0012646750.99873537
ENST00000413427ENST00000369326SKILchr3170079217-TNIKchr3171087474-0.0009031260.9990969
ENST00000413427ENST00000341852SKILchr3170079217-TNIKchr3171087474-0.0018061050.9981939
ENST00000413427ENST00000284483SKILchr3170079217-TNIKchr3171087474-0.0024124670.99758756
ENST00000413427ENST00000470834SKILchr3170079217-TNIKchr3171087474-0.0019721950.99802774
ENST00000413427ENST00000460047SKILchr3170079217-TNIKchr3171087474-0.0011843880.99881566
ENST00000413427ENST00000475336SKILchr3170079217-TNIKchr3171087474-0.0011721340.9988279
ENST00000413427ENST00000488470SKILchr3170079217-TNIKchr3171087474-0.0024357620.9975642
ENST00000413427ENST00000357327SKILchr3170079217-TNIKchr3171087474-0.002138360.9978617
ENST00000458537ENST00000436636SKILchr3170079217-TNIKchr3171087474-0.0005807460.99941933
ENST00000458537ENST00000538048SKILchr3170079217-TNIKchr3171087474-0.0012646750.99873537
ENST00000458537ENST00000369326SKILchr3170079217-TNIKchr3171087474-0.0009031260.9990969
ENST00000458537ENST00000341852SKILchr3170079217-TNIKchr3171087474-0.0018061050.9981939
ENST00000458537ENST00000284483SKILchr3170079217-TNIKchr3171087474-0.0024124670.99758756
ENST00000458537ENST00000470834SKILchr3170079217-TNIKchr3171087474-0.0019721950.99802774
ENST00000458537ENST00000460047SKILchr3170079217-TNIKchr3171087474-0.0011843880.99881566
ENST00000458537ENST00000475336SKILchr3170079217-TNIKchr3171087474-0.0011721340.9988279
ENST00000458537ENST00000488470SKILchr3170079217-TNIKchr3171087474-0.0024357620.9975642
ENST00000458537ENST00000357327SKILchr3170079217-TNIKchr3171087474-0.002138360.9978617

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 SKIL-TNIK

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
SKILchr3170079215TNIKchr31710874761270363KFSMRSGKRNQSKDPAGIFELVELVG
SKILchr3170079215TNIKchr31710874761769404KFSMRSGKRNQSKDPAGIFELVELVG
SKILchr3170079215TNIKchr31710874761807404KFSMRSGKRNQSKDPAGIFELVELVG
SKILchr3170079217TNIKchr31710874741270363KFSMRSGKRNQSKDPAGIFELVELVG
SKILchr3170079217TNIKchr31710874741769404KFSMRSGKRNQSKDPAGIFELVELVG
SKILchr3170079217TNIKchr31710874741807404KFSMRSGKRNQSKDPAGIFELVELVG

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Potential FusionNeoAntigen Information of SKIL-TNIK 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.
SKIL-TNIK_170079215_171087476.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)
SKIL-TNIKchr3170079215chr31710874761769HLA-B15:17QSKDPAGIF0.96580.85021019
SKIL-TNIKchr3170079215chr31710874761769HLA-B15:16QSKDPAGIF0.95680.81041019
SKIL-TNIKchr3170079215chr31710874761769HLA-B39:01SKDPAGIFEL0.99660.87981121
SKIL-TNIKchr3170079215chr31710874761769HLA-B39:13SKDPAGIFEL0.99290.89041121
SKIL-TNIKchr3170079215chr31710874761769HLA-B38:02SKDPAGIFEL0.9870.93551121
SKIL-TNIKchr3170079215chr31710874761769HLA-B38:01SKDPAGIFEL0.98690.94431121
SKIL-TNIKchr3170079215chr31710874761769HLA-B48:01SKDPAGIFEL0.92770.611121
SKIL-TNIKchr3170079215chr31710874761769HLA-B07:10SKDPAGIFEL0.65040.50321121
SKIL-TNIKchr3170079215chr31710874761769HLA-C15:04QSKDPAGIF0.87880.88111019
SKIL-TNIKchr3170079215chr31710874761769HLA-C12:12QSKDPAGIF0.73540.8271019
SKIL-TNIKchr3170079215chr31710874761769HLA-B39:09SKDPAGIFEL0.99660.67971121
SKIL-TNIKchr3170079215chr31710874761769HLA-B39:08SKDPAGIFEL0.98450.83351121
SKIL-TNIKchr3170079215chr31710874761769HLA-B39:05SKDPAGIFEL0.98390.84551121
SKIL-TNIKchr3170079215chr31710874761769HLA-B15:24QSKDPAGIF0.98520.84081019
SKIL-TNIKchr3170079215chr31710874761769HLA-B58:06QSKDPAGIF0.95070.84361019
SKIL-TNIKchr3170079215chr31710874761769HLA-B15:12QSKDPAGIF0.88140.92121019
SKIL-TNIKchr3170079215chr31710874761769HLA-C15:09QSKDPAGIF0.87880.88111019
SKIL-TNIKchr3170079215chr31710874761769HLA-C12:02QSKDPAGIF0.83010.91571019
SKIL-TNIKchr3170079215chr31710874761769HLA-C16:04QSKDPAGIF0.70920.96411019
SKIL-TNIKchr3170079215chr31710874761769HLA-C02:02QSKDPAGIF0.0820.95671019
SKIL-TNIKchr3170079215chr31710874761769HLA-C02:10QSKDPAGIF0.0820.95671019
SKIL-TNIKchr3170079215chr31710874761769HLA-B39:02SKDPAGIFEL0.99760.89431121
SKIL-TNIKchr3170079215chr31710874761769HLA-B15:53NQSKDPAGIF0.9930.6058919
SKIL-TNIKchr3170079215chr31710874761769HLA-B15:54NQSKDPAGIF0.98810.5621919
SKIL-TNIKchr3170079215chr31710874761769HLA-B39:11SKDPAGIFEL0.9880.76291121
SKIL-TNIKchr3170079215chr31710874761769HLA-B38:05SKDPAGIFEL0.98690.94431121
SKIL-TNIKchr3170079215chr31710874761769HLA-B15:12NQSKDPAGIF0.96820.6606919
SKIL-TNIKchr3170079215chr31710874761769HLA-B15:09SKDPAGIFEL0.88210.82061121
SKIL-TNIKchr3170079215chr31710874761769HLA-B59:01KDPAGIFELV0.62130.72621222

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Potential FusionNeoAntigen Information of SKIL-TNIK 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 SKIL-TNIK

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
2910GKRNQSKDPAGIFESKILTNIKchr3170079215chr31710874761769

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

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-B14:023BVN2910GKRNQSKDPAGIFE-7.9962-8.1096
HLA-B14:023BVN2910GKRNQSKDPAGIFE-5.70842-6.74372
HLA-B52:013W392910GKRNQSKDPAGIFE-6.83737-6.95077
HLA-B52:013W392910GKRNQSKDPAGIFE-4.4836-5.5189
HLA-A11:014UQ22910GKRNQSKDPAGIFE-10.0067-10.1201
HLA-A11:014UQ22910GKRNQSKDPAGIFE-9.03915-10.0745
HLA-A24:025HGA2910GKRNQSKDPAGIFE-6.56204-6.67544
HLA-A24:025HGA2910GKRNQSKDPAGIFE-5.42271-6.45801
HLA-B44:053DX82910GKRNQSKDPAGIFE-7.85648-8.89178
HLA-B44:053DX82910GKRNQSKDPAGIFE-5.3978-5.5112
HLA-A02:016TDR2910GKRNQSKDPAGIFE-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of SKIL-TNIK

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
SKIL-TNIKchr3170079215chr31710874761019QSKDPAGIFCAATCCAAGGACCCCGCAGGGATCTTT
SKIL-TNIKchr3170079215chr31710874761121SKDPAGIFELTCCAAGGACCCCGCAGGGATCTTTGAATTG
SKIL-TNIKchr3170079215chr31710874761222KDPAGIFELVAAGGACCCCGCAGGGATCTTTGAATTGGTG
SKIL-TNIKchr3170079215chr3171087476919NQSKDPAGIFAATCAATCCAAGGACCCCGCAGGGATCTTT

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 SKIL-TNIK

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
STADSKIL-TNIKchr3170079215ENST00000259119chr3171087476ENST00000284483TCGA-VQ-AA6B-01A

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Potential target of CAR-T therapy development for SKIL-TNIK

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 SKIL-TNIK

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 SKIL-TNIK

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