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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-FNDC3B

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SKIL-FNDC3B
FusionPDB ID: 82093
FusionGDB2.0 ID: 82093
HgeneTgene
Gene symbol

SKIL

FNDC3B

Gene ID

6498

64778

Gene nameSKI like proto-oncogenefibronectin type III domain containing 3B
SynonymsSNO|SnoA|SnoI|SnoNFAD104|PRO4979|YVTM2421
Cytomap

3q26.2

3q26.31

Type of geneprotein-codingprotein-coding
Descriptionski-like proteinSKI-like oncogeneski-related oncogene snoNfibronectin type III domain-containing protein 3BHCV NS5A-binding protein 37factor for adipocyte differentiation 104
Modification date2020031320200313
UniProtAcc.

Q53EP0

Main function of 5'-partner protein: FUNCTION: May be a positive regulator of adipogenesis. {ECO:0000269|PubMed:15564382}.
Ensembl transtripts involved in fusion geneENST idsENST00000259119, ENST00000413427, 
ENST00000426052, ENST00000458537, 
ENST00000490989, 		ENST00000392699, 
ENST00000421757, ENST00000423424, 
ENST00000476794, ENST00000336824, 
ENST00000415807, ENST00000416957, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score7 X 5 X 6=21021 X 23 X 11=5313
# samples 828
** MAII scorelog2(8/210*10)=-1.39231742277876
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(28/5313*10)=-4.2460279805281
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: SKIL [Title/Abstract] AND FNDC3B [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: SKIL [Title/Abstract] AND FNDC3B [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SKIL(170079217)-FNDC3B(172064117), # samples:2
Anticipated loss of major functional domain due to fusion event.SKIL-FNDC3B 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-FNDC3B 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-FNDC3B 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.
SKIL-FNDC3B 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/chr3:170079217/chr3:172064117)
- 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 FNDC3B (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)
ENST00000259119SKILchr3170079217+ENST00000415807FNDC3Bchr3172064117+443017695573133858
ENST00000259119SKILchr3170079217+ENST00000336824FNDC3Bchr3172064117+732417695573133858
ENST00000259119SKILchr3170079217+ENST00000416957FNDC3Bchr3172064117+314017695573133858
ENST00000426052SKILchr3170079217+ENST00000415807FNDC3Bchr3172064117+393112701812634817
ENST00000426052SKILchr3170079217+ENST00000336824FNDC3Bchr3172064117+682512701812634817
ENST00000426052SKILchr3170079217+ENST00000416957FNDC3Bchr3172064117+264112701812634817
ENST00000413427SKILchr3170079217+ENST00000415807FNDC3Bchr3172064117+446818075953171858
ENST00000413427SKILchr3170079217+ENST00000336824FNDC3Bchr3172064117+736218075953171858
ENST00000413427SKILchr3170079217+ENST00000416957FNDC3Bchr3172064117+317818075953171858
ENST00000458537SKILchr3170079217+ENST00000415807FNDC3Bchr3172064117+446818075953171858
ENST00000458537SKILchr3170079217+ENST00000336824FNDC3Bchr3172064117+736218075953171858
ENST00000458537SKILchr3170079217+ENST00000416957FNDC3Bchr3172064117+317818075953171858
ENST00000259119SKILchr3170079217+ENST00000415807FNDC3Bchr3172064116+443017695573133858
ENST00000259119SKILchr3170079217+ENST00000336824FNDC3Bchr3172064116+732417695573133858
ENST00000259119SKILchr3170079217+ENST00000416957FNDC3Bchr3172064116+314017695573133858
ENST00000426052SKILchr3170079217+ENST00000415807FNDC3Bchr3172064116+393112701812634817
ENST00000426052SKILchr3170079217+ENST00000336824FNDC3Bchr3172064116+682512701812634817
ENST00000426052SKILchr3170079217+ENST00000416957FNDC3Bchr3172064116+264112701812634817
ENST00000413427SKILchr3170079217+ENST00000415807FNDC3Bchr3172064116+446818075953171858
ENST00000413427SKILchr3170079217+ENST00000336824FNDC3Bchr3172064116+736218075953171858
ENST00000413427SKILchr3170079217+ENST00000416957FNDC3Bchr3172064116+317818075953171858
ENST00000458537SKILchr3170079217+ENST00000415807FNDC3Bchr3172064116+446818075953171858
ENST00000458537SKILchr3170079217+ENST00000336824FNDC3Bchr3172064116+736218075953171858
ENST00000458537SKILchr3170079217+ENST00000416957FNDC3Bchr3172064116+317818075953171858
ENST00000259119SKILchr3170079217+ENST00000415807FNDC3Bchr3172065001+431617695573019820
ENST00000259119SKILchr3170079217+ENST00000336824FNDC3Bchr3172065001+721017695573019820
ENST00000259119SKILchr3170079217+ENST00000416957FNDC3Bchr3172065001+302617695573019820
ENST00000426052SKILchr3170079217+ENST00000415807FNDC3Bchr3172065001+381712701812520779
ENST00000426052SKILchr3170079217+ENST00000336824FNDC3Bchr3172065001+671112701812520779
ENST00000426052SKILchr3170079217+ENST00000416957FNDC3Bchr3172065001+252712701812520779
ENST00000413427SKILchr3170079217+ENST00000415807FNDC3Bchr3172065001+435418075953057820
ENST00000413427SKILchr3170079217+ENST00000336824FNDC3Bchr3172065001+724818075953057820
ENST00000413427SKILchr3170079217+ENST00000416957FNDC3Bchr3172065001+306418075953057820
ENST00000458537SKILchr3170079217+ENST00000415807FNDC3Bchr3172065001+435418075953057820
ENST00000458537SKILchr3170079217+ENST00000336824FNDC3Bchr3172065001+724818075953057820
ENST00000458537SKILchr3170079217+ENST00000416957FNDC3Bchr3172065001+306418075953057820
ENST00000259119SKILchr3170079216+ENST00000415807FNDC3Bchr3172064116+443017695573133858
ENST00000259119SKILchr3170079216+ENST00000336824FNDC3Bchr3172064116+732417695573133858
ENST00000259119SKILchr3170079216+ENST00000416957FNDC3Bchr3172064116+314017695573133858
ENST00000426052SKILchr3170079216+ENST00000415807FNDC3Bchr3172064116+393112701812634817
ENST00000426052SKILchr3170079216+ENST00000336824FNDC3Bchr3172064116+682512701812634817
ENST00000426052SKILchr3170079216+ENST00000416957FNDC3Bchr3172064116+264112701812634817
ENST00000413427SKILchr3170079216+ENST00000415807FNDC3Bchr3172064116+446818075953171858
ENST00000413427SKILchr3170079216+ENST00000336824FNDC3Bchr3172064116+736218075953171858
ENST00000413427SKILchr3170079216+ENST00000416957FNDC3Bchr3172064116+317818075953171858
ENST00000458537SKILchr3170079216+ENST00000415807FNDC3Bchr3172064116+446818075953171858
ENST00000458537SKILchr3170079216+ENST00000336824FNDC3Bchr3172064116+736218075953171858
ENST00000458537SKILchr3170079216+ENST00000416957FNDC3Bchr3172064116+317818075953171858
ENST00000259119SKILchr3170079216+ENST00000415807FNDC3Bchr3172065001+431617695573019820
ENST00000259119SKILchr3170079216+ENST00000336824FNDC3Bchr3172065001+721017695573019820
ENST00000259119SKILchr3170079216+ENST00000416957FNDC3Bchr3172065001+302617695573019820
ENST00000426052SKILchr3170079216+ENST00000415807FNDC3Bchr3172065001+381712701812520779
ENST00000426052SKILchr3170079216+ENST00000336824FNDC3Bchr3172065001+671112701812520779
ENST00000426052SKILchr3170079216+ENST00000416957FNDC3Bchr3172065001+252712701812520779
ENST00000413427SKILchr3170079216+ENST00000415807FNDC3Bchr3172065001+435418075953057820
ENST00000413427SKILchr3170079216+ENST00000336824FNDC3Bchr3172065001+724818075953057820
ENST00000413427SKILchr3170079216+ENST00000416957FNDC3Bchr3172065001+306418075953057820
ENST00000458537SKILchr3170079216+ENST00000415807FNDC3Bchr3172065001+435418075953057820
ENST00000458537SKILchr3170079216+ENST00000336824FNDC3Bchr3172065001+724818075953057820
ENST00000458537SKILchr3170079216+ENST00000416957FNDC3Bchr3172065001+306418075953057820

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
ENST00000259119ENST00000415807SKILchr3170079217+FNDC3Bchr3172064117+0.0007431550.9992568
ENST00000259119ENST00000336824SKILchr3170079217+FNDC3Bchr3172064117+0.0005636430.9994363
ENST00000259119ENST00000416957SKILchr3170079217+FNDC3Bchr3172064117+0.0014908080.9985092
ENST00000426052ENST00000415807SKILchr3170079217+FNDC3Bchr3172064117+0.0004455850.99955434
ENST00000426052ENST00000336824SKILchr3170079217+FNDC3Bchr3172064117+0.0003205760.99967945
ENST00000426052ENST00000416957SKILchr3170079217+FNDC3Bchr3172064117+0.0018561740.9981438
ENST00000413427ENST00000415807SKILchr3170079217+FNDC3Bchr3172064117+0.0007826230.9992174
ENST00000413427ENST00000336824SKILchr3170079217+FNDC3Bchr3172064117+0.0005782290.99942183
ENST00000413427ENST00000416957SKILchr3170079217+FNDC3Bchr3172064117+0.0014701130.9985299
ENST00000458537ENST00000415807SKILchr3170079217+FNDC3Bchr3172064117+0.0007826230.9992174
ENST00000458537ENST00000336824SKILchr3170079217+FNDC3Bchr3172064117+0.0005782290.99942183
ENST00000458537ENST00000416957SKILchr3170079217+FNDC3Bchr3172064117+0.0014701130.9985299
ENST00000259119ENST00000415807SKILchr3170079217+FNDC3Bchr3172064116+0.0007431550.9992568
ENST00000259119ENST00000336824SKILchr3170079217+FNDC3Bchr3172064116+0.0005636430.9994363
ENST00000259119ENST00000416957SKILchr3170079217+FNDC3Bchr3172064116+0.0014908080.9985092
ENST00000426052ENST00000415807SKILchr3170079217+FNDC3Bchr3172064116+0.0004455850.99955434
ENST00000426052ENST00000336824SKILchr3170079217+FNDC3Bchr3172064116+0.0003205760.99967945
ENST00000426052ENST00000416957SKILchr3170079217+FNDC3Bchr3172064116+0.0018561740.9981438
ENST00000413427ENST00000415807SKILchr3170079217+FNDC3Bchr3172064116+0.0007826230.9992174
ENST00000413427ENST00000336824SKILchr3170079217+FNDC3Bchr3172064116+0.0005782290.99942183
ENST00000413427ENST00000416957SKILchr3170079217+FNDC3Bchr3172064116+0.0014701130.9985299
ENST00000458537ENST00000415807SKILchr3170079217+FNDC3Bchr3172064116+0.0007826230.9992174
ENST00000458537ENST00000336824SKILchr3170079217+FNDC3Bchr3172064116+0.0005782290.99942183
ENST00000458537ENST00000416957SKILchr3170079217+FNDC3Bchr3172064116+0.0014701130.9985299
ENST00000259119ENST00000415807SKILchr3170079217+FNDC3Bchr3172065001+0.0007025420.9992975
ENST00000259119ENST00000336824SKILchr3170079217+FNDC3Bchr3172065001+0.0005183850.9994816
ENST00000259119ENST00000416957SKILchr3170079217+FNDC3Bchr3172065001+0.0016964470.99830353
ENST00000426052ENST00000415807SKILchr3170079217+FNDC3Bchr3172065001+0.0005709770.99942905
ENST00000426052ENST00000336824SKILchr3170079217+FNDC3Bchr3172065001+0.0003995380.99960047
ENST00000426052ENST00000416957SKILchr3170079217+FNDC3Bchr3172065001+0.0025305570.9974694
ENST00000413427ENST00000415807SKILchr3170079217+FNDC3Bchr3172065001+0.000723680.99927634
ENST00000413427ENST00000336824SKILchr3170079217+FNDC3Bchr3172065001+0.0005263120.99947375
ENST00000413427ENST00000416957SKILchr3170079217+FNDC3Bchr3172065001+0.001623370.9983766
ENST00000458537ENST00000415807SKILchr3170079217+FNDC3Bchr3172065001+0.000723680.99927634
ENST00000458537ENST00000336824SKILchr3170079217+FNDC3Bchr3172065001+0.0005263120.99947375
ENST00000458537ENST00000416957SKILchr3170079217+FNDC3Bchr3172065001+0.001623370.9983766
ENST00000259119ENST00000415807SKILchr3170079216+FNDC3Bchr3172064116+0.0007431550.9992568
ENST00000259119ENST00000336824SKILchr3170079216+FNDC3Bchr3172064116+0.0005636430.9994363
ENST00000259119ENST00000416957SKILchr3170079216+FNDC3Bchr3172064116+0.0014908080.9985092
ENST00000426052ENST00000415807SKILchr3170079216+FNDC3Bchr3172064116+0.0004455850.99955434
ENST00000426052ENST00000336824SKILchr3170079216+FNDC3Bchr3172064116+0.0003205760.99967945
ENST00000426052ENST00000416957SKILchr3170079216+FNDC3Bchr3172064116+0.0018561740.9981438
ENST00000413427ENST00000415807SKILchr3170079216+FNDC3Bchr3172064116+0.0007826230.9992174
ENST00000413427ENST00000336824SKILchr3170079216+FNDC3Bchr3172064116+0.0005782290.99942183
ENST00000413427ENST00000416957SKILchr3170079216+FNDC3Bchr3172064116+0.0014701130.9985299
ENST00000458537ENST00000415807SKILchr3170079216+FNDC3Bchr3172064116+0.0007826230.9992174
ENST00000458537ENST00000336824SKILchr3170079216+FNDC3Bchr3172064116+0.0005782290.99942183
ENST00000458537ENST00000416957SKILchr3170079216+FNDC3Bchr3172064116+0.0014701130.9985299
ENST00000259119ENST00000415807SKILchr3170079216+FNDC3Bchr3172065001+0.0007025420.9992975
ENST00000259119ENST00000336824SKILchr3170079216+FNDC3Bchr3172065001+0.0005183850.9994816
ENST00000259119ENST00000416957SKILchr3170079216+FNDC3Bchr3172065001+0.0016964470.99830353
ENST00000426052ENST00000415807SKILchr3170079216+FNDC3Bchr3172065001+0.0005709770.99942905
ENST00000426052ENST00000336824SKILchr3170079216+FNDC3Bchr3172065001+0.0003995380.99960047
ENST00000426052ENST00000416957SKILchr3170079216+FNDC3Bchr3172065001+0.0025305570.9974694
ENST00000413427ENST00000415807SKILchr3170079216+FNDC3Bchr3172065001+0.000723680.99927634
ENST00000413427ENST00000336824SKILchr3170079216+FNDC3Bchr3172065001+0.0005263120.99947375
ENST00000413427ENST00000416957SKILchr3170079216+FNDC3Bchr3172065001+0.001623370.9983766
ENST00000458537ENST00000415807SKILchr3170079216+FNDC3Bchr3172065001+0.000723680.99927634
ENST00000458537ENST00000336824SKILchr3170079216+FNDC3Bchr3172065001+0.0005263120.99947375
ENST00000458537ENST00000416957SKILchr3170079216+FNDC3Bchr3172065001+0.001623370.9983766

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-FNDC3B

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
SKILchr3170079216FNDC3Bchr31720641161270363KFSMRSGKRNQSKYGPYSDVSEITTA
SKILchr3170079216FNDC3Bchr31720641161769404KFSMRSGKRNQSKYGPYSDVSEITTA
SKILchr3170079216FNDC3Bchr31720641161807404KFSMRSGKRNQSKYGPYSDVSEITTA
SKILchr3170079216FNDC3Bchr31720650011270363KFSMRSGKRNQSKSPDSSGADISEYR
SKILchr3170079216FNDC3Bchr31720650011769404KFSMRSGKRNQSKSPDSSGADISEYR
SKILchr3170079216FNDC3Bchr31720650011807404KFSMRSGKRNQSKSPDSSGADISEYR
SKILchr3170079217FNDC3Bchr31720641161270363KFSMRSGKRNQSKYGPYSDVSEITTA
SKILchr3170079217FNDC3Bchr31720641161769404KFSMRSGKRNQSKYGPYSDVSEITTA
SKILchr3170079217FNDC3Bchr31720641161807404KFSMRSGKRNQSKYGPYSDVSEITTA
SKILchr3170079217FNDC3Bchr31720641171270363KFSMRSGKRNQSKYGPYSDVSEITTA
SKILchr3170079217FNDC3Bchr31720641171769404KFSMRSGKRNQSKYGPYSDVSEITTA
SKILchr3170079217FNDC3Bchr31720641171807404KFSMRSGKRNQSKYGPYSDVSEITTA
SKILchr3170079217FNDC3Bchr31720650011270363KFSMRSGKRNQSKSPDSSGADISEYR
SKILchr3170079217FNDC3Bchr31720650011769404KFSMRSGKRNQSKSPDSSGADISEYR
SKILchr3170079217FNDC3Bchr31720650011807404KFSMRSGKRNQSKSPDSSGADISEYR

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Potential FusionNeoAntigen Information of SKIL-FNDC3B 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-FNDC3B_170079216_172064116.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-FNDC3Bchr3170079216chr31720641161769HLA-B27:05KRNQSKYGPY0.99980.6604717
SKIL-FNDC3Bchr3170079216chr31720641161769HLA-B27:04KRNQSKYGPY0.99970.636717
SKIL-FNDC3Bchr3170079216chr31720641161769HLA-B27:03KRNQSKYGPY0.9980.6626717
SKIL-FNDC3Bchr3170079216chr31720641161769HLA-B27:10KRNQSKYGPY0.99970.7597717
SKIL-FNDC3Bchr3170079216chr31720641161769HLA-B27:08KRNQSKYGPY0.99970.5306717

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Potential FusionNeoAntigen Information of SKIL-FNDC3B 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-FNDC3B

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
2912GKRNQSKYGPYSDVSKILFNDC3Bchr3170079216chr31720641161769

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SKIL-FNDC3B

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-B14:023BVN2912GKRNQSKYGPYSDV-7.9962-8.1096
HLA-B14:023BVN2912GKRNQSKYGPYSDV-5.70842-6.74372
HLA-B52:013W392912GKRNQSKYGPYSDV-6.83737-6.95077
HLA-B52:013W392912GKRNQSKYGPYSDV-4.4836-5.5189
HLA-A11:014UQ22912GKRNQSKYGPYSDV-10.0067-10.1201
HLA-A11:014UQ22912GKRNQSKYGPYSDV-9.03915-10.0745
HLA-A24:025HGA2912GKRNQSKYGPYSDV-6.56204-6.67544
HLA-A24:025HGA2912GKRNQSKYGPYSDV-5.42271-6.45801
HLA-B44:053DX82912GKRNQSKYGPYSDV-7.85648-8.89178
HLA-B44:053DX82912GKRNQSKYGPYSDV-5.3978-5.5112
HLA-A02:016TDR2912GKRNQSKYGPYSDV-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of SKIL-FNDC3B

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-FNDC3Bchr3170079216chr3172064116717KRNQSKYGPYAAGAGAAATCAATCCAAGTATGGTCCCTAT

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-FNDC3B

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
LUSCSKIL-FNDC3Bchr3170079216ENST00000259119chr3172064116ENST00000336824TCGA-56-7580-01A

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Potential target of CAR-T therapy development for SKIL-FNDC3B

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
TgeneFNDC3Bchr3:170079216chr3:172064116ENST0000033682418261182_120201205.0TransmembraneHelical
TgeneFNDC3Bchr3:170079216chr3:172064116ENST0000041580718261182_120201205.0TransmembraneHelical
TgeneFNDC3Bchr3:170079216chr3:172064116ENST0000041695718261182_120201205.0TransmembraneHelical
TgeneFNDC3Bchr3:170079216chr3:172064116ENST00000421757041182_1202072.0TransmembraneHelical
TgeneFNDC3Bchr3:170079216chr3:172064116ENST00000423424041182_1202072.0TransmembraneHelical
TgeneFNDC3Bchr3:170079216chr3:172065001ENST0000033682419261182_120201205.0TransmembraneHelical
TgeneFNDC3Bchr3:170079216chr3:172065001ENST0000041580719261182_120201205.0TransmembraneHelical
TgeneFNDC3Bchr3:170079216chr3:172065001ENST0000041695719261182_120201205.0TransmembraneHelical
TgeneFNDC3Bchr3:170079216chr3:172065001ENST00000421757041182_1202072.0TransmembraneHelical
TgeneFNDC3Bchr3:170079216chr3:172065001ENST00000423424041182_1202072.0TransmembraneHelical
TgeneFNDC3Bchr3:170079217chr3:172064116ENST0000033682418261182_120201205.0TransmembraneHelical
TgeneFNDC3Bchr3:170079217chr3:172064116ENST0000041580718261182_120201205.0TransmembraneHelical
TgeneFNDC3Bchr3:170079217chr3:172064116ENST0000041695718261182_120201205.0TransmembraneHelical
TgeneFNDC3Bchr3:170079217chr3:172064116ENST00000421757041182_1202072.0TransmembraneHelical
TgeneFNDC3Bchr3:170079217chr3:172064116ENST00000423424041182_1202072.0TransmembraneHelical
TgeneFNDC3Bchr3:170079217chr3:172064117ENST0000033682418261182_120201205.0TransmembraneHelical
TgeneFNDC3Bchr3:170079217chr3:172064117ENST0000041580718261182_120201205.0TransmembraneHelical
TgeneFNDC3Bchr3:170079217chr3:172064117ENST0000041695718261182_120201205.0TransmembraneHelical
TgeneFNDC3Bchr3:170079217chr3:172064117ENST00000421757041182_1202072.0TransmembraneHelical
TgeneFNDC3Bchr3:170079217chr3:172064117ENST00000423424041182_1202072.0TransmembraneHelical
TgeneFNDC3Bchr3:170079217chr3:172065001ENST0000033682419261182_120201205.0TransmembraneHelical
TgeneFNDC3Bchr3:170079217chr3:172065001ENST0000041580719261182_120201205.0TransmembraneHelical
TgeneFNDC3Bchr3:170079217chr3:172065001ENST0000041695719261182_120201205.0TransmembraneHelical
TgeneFNDC3Bchr3:170079217chr3:172065001ENST00000421757041182_1202072.0TransmembraneHelical
TgeneFNDC3Bchr3:170079217chr3:172065001ENST00000423424041182_1202072.0TransmembraneHelical

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-FNDC3B

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-FNDC3B

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