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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:CYP2S1-UPF1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CYP2S1-UPF1
FusionPDB ID: 21065
FusionGDB2.0 ID: 21065
HgeneTgene
Gene symbol

CYP2S1

UPF1

Gene ID

29785

5976

Gene namecytochrome P450 family 2 subfamily S member 1UPF1 RNA helicase and ATPase
SynonymsCYPIIS1HUPF1|NORF1|RENT1|pNORF1|smg-2
Cytomap

19q13.2

19p13.11

Type of geneprotein-codingprotein-coding
Descriptioncytochrome P450 2S1cytochrome P450, family 2, subfamily S, polypeptide 1cytochrome P540, subfamily IIS, polypeptide 1hydroperoxy icosatetraenoate dehydratasethromboxane-A synthaseregulator of nonsense transcripts 1ATP-dependent helicase RENT1UPF1 regulator of nonsense transcripts homologdelta helicasenonsense mRNA reducing factor 1smg-2 homolog, nonsense mediated mRNA decay factorup-frameshift mutation 1 homologup-frameshif
Modification date2020031320200313
UniProtAcc

Q96SQ9

Main function of 5'-partner protein: FUNCTION: A cytochrome P450 monooxygenase involved in the metabolism of retinoids and eicosanoids (PubMed:12711469, PubMed:21068195). In epidermis, may contribute to the oxidative metabolism of all-trans-retinoic acid. For this activity, uses molecular oxygen inserting one oxygen atom into a substrate, and reducing the second into a water molecule, with two electrons provided by NADPH via cytochrome P450 reductase (NADPH--hemoprotein reductase) (PubMed:12711469). Additionally, displays peroxidase and isomerase activities toward various oxygenated eicosanoids such as prostaglandin H2 (PGH2) and hydroperoxyeicosatetraenoates (HPETEs) (PubMed:21068195). Independently of cytochrome P450 reductase, NADPH, and O2, catalyzes the breakdown of PGH2 to hydroxyheptadecatrienoic acid (HHT) and malondialdehyde (MDA), which is known to act as a mediator of DNA damage (PubMed:21068195). {ECO:0000269|PubMed:12711469, ECO:0000269|PubMed:21068195}.
.
Ensembl transtripts involved in fusion geneENST idsENST00000310054, ENST00000542619, 
ENST00000600310, ENST00000262803, 
ENST00000599848, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score1 X 1 X 1=18 X 7 X 5=280
# samples 19
** MAII scorelog2(1/1*10)=3.32192809488736log2(9/280*10)=-1.63742992061529
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: CYP2S1 [Title/Abstract] AND UPF1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: CYP2S1 [Title/Abstract] AND UPF1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CYP2S1(41703833)-UPF1(18976098), # samples:1
Anticipated loss of major functional domain due to fusion event.CYP2S1-UPF1 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.
CYP2S1-UPF1 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.
CYP2S1-UPF1 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.
CYP2S1-UPF1 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
HgeneCYP2S1

GO:0006690

icosanoid metabolic process

21068195

HgeneCYP2S1

GO:0006693

prostaglandin metabolic process

21068195

HgeneCYP2S1

GO:0042573

retinoic acid metabolic process

12711469

TgeneUPF1

GO:0000184

nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

17468741

TgeneUPF1

GO:0006281

DNA repair

16488880

TgeneUPF1

GO:0032201

telomere maintenance via semi-conservative replication

21829167

TgeneUPF1

GO:0061014

positive regulation of mRNA catabolic process

24726324

TgeneUPF1

GO:0061158

3'-UTR-mediated mRNA destabilization

24726324

TgeneUPF1

GO:0071222

cellular response to lipopolysaccharide

26255671

TgeneUPF1

GO:0071347

cellular response to interleukin-1

26255671



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/chr19:41703833/chr19:18976098)
- 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 CYP2S1 (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 UPF1 (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)
ENST00000310054CYP2S1chr1941703833+ENST00000262803UPF1chr1918976098+29287091051208367
ENST00000310054CYP2S1chr1941703833+ENST00000599848UPF1chr1918976098+29217091051208367

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
ENST00000310054ENST00000262803CYP2S1chr1941703833+UPF1chr1918976098+0.0095184660.99048156
ENST00000310054ENST00000599848CYP2S1chr1941703833+UPF1chr1918976098+0.0094342850.9905657

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 CYP2S1-UPF1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
CYP2S1chr1941703833UPF1chr191897609870943RRSRPAEMEATGTWALLLALALLLLL

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Potential FusionNeoAntigen Information of CYP2S1-UPF1 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.
CYP2S1-UPF1_41703833_18976098.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)
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:03AEMEATGTW0.99960.9954514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:02AEMEATGTW0.99930.5784514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:05AEMEATGTW0.99870.7986514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:01MEATGTWAL0.99810.5911716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B13:01MEATGTWAL0.99540.9958716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B47:01AEMEATGTW0.98850.8847514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B50:02MEATGTWAL0.97780.8213716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:05MEATGTWAL0.95090.6653716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:03MEATGTWAL0.94660.9908716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B48:01MEATGTWAL0.94550.6863716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B18:01MEATGTWAL0.94430.9536716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B18:01AEMEATGTW0.94080.8978514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B45:01MEATGTWAL0.93270.9802716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B13:01AEMEATGTW0.93170.9964514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B47:01MEATGTWAL0.92870.9105716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B39:13MEATGTWAL0.78910.9979716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B39:01MEATGTWAL0.78420.9925716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:05MEATGTWAL0.75650.5572716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B38:01MEATGTWAL0.75440.9985716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B38:02MEATGTWAL0.75360.9986716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B39:24MEATGTWAL0.7250.8507716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B45:01AEMEATGTW0.7190.9894514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B15:10MEATGTWAL0.61310.8191716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B15:37MEATGTWAL0.5380.8766716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B41:02MEATGTWAL0.49060.7092716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B41:01MEATGTWAL0.48480.9966716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B50:01MEATGTWAL0.38850.9842716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:01MEATGTWALL0.99270.6062717
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B45:01AEMEATGTWA0.99230.9857515
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B50:02AEMEATGTWA0.98470.8216515
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:03AEMEATGTWA0.95510.9947515
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:02AEMEATGTWA0.94830.6896515
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:03PAEMEATGTW0.77410.9719414
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B50:01AEMEATGTWA0.73980.9875515
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B41:01AEMEATGTWA0.73670.991515
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:05EMEATGTWAL0.48370.5828616
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:01AEMEATGTWAL0.99970.701516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:03AEMEATGTWAL0.99950.9954516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:02AEMEATGTWAL0.99930.723516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B48:01AEMEATGTWAL0.99920.7847516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:05AEMEATGTWAL0.99910.8191516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:01MEATGTWALLL0.99880.6509718
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B47:01AEMEATGTWAL0.99870.9071516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B39:13AEMEATGTWAL0.99290.9981516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B53:01RPAEMEATGTW0.99230.5991314
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:05AEMEATGTWAL0.99170.5835516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:05RPAEMEATGTW0.97990.6047314
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:03RPAEMEATGTW0.97450.8462314
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B41:02AEMEATGTWAL0.93190.8304516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:08AEMEATGTW0.99930.7238514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:06MEATGTWAL0.99870.8973716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:09AEMEATGTW0.99830.727514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B48:03MEATGTWAL0.99570.6589716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:10MEATGTWAL0.98970.8284716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:03AEMEATGTW0.97730.7376514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:03MEATGTWAL0.92440.6917716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:08MEATGTWAL0.9130.6182716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:09MEATGTWAL0.90870.6778716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:10AEMEATGTW0.90210.9574514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B39:09MEATGTWAL0.80320.9289716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B39:08MEATGTWAL0.77560.9925716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B39:05MEATGTWAL0.7730.991716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B39:12MEATGTWAL0.75160.9929716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B14:03MEATGTWAL0.61140.982716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:10MEATGTWALL0.98420.824717
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:06AEMEATGTWA0.97860.954515
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:08PAEMEATGTW0.74480.62414
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:10EMEATGTWAL0.42550.8744616
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:06AEMEATGTWAL0.99990.7968516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:10AEMEATGTWAL0.99960.9454516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:09AEMEATGTWAL0.99950.8803516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B48:03AEMEATGTWAL0.99940.7375516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:08AEMEATGTWAL0.9990.8475516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:03AEMEATGTWAL0.9990.7109516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:08RPAEMEATGTW0.98660.5961314
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:09RPAEMEATGTW0.97990.5798314
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B39:08AEMEATGTWAL0.97930.9926516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:10RPAEMEATGTW0.59630.8501314
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:13AEMEATGTW0.99960.9954514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:07AEMEATGTW0.99960.9954514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:26AEMEATGTW0.99960.9954514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:22AEMEATGTW0.99930.5784514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:04MEATGTWAL0.99870.9774716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:36MEATGTWAL0.9980.5828716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:49MEATGTWAL0.99770.6051716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:21MEATGTWAL0.99590.6869716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:12MEATGTWAL0.99570.6589716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-A25:01EATGTWALL0.99290.9783817
CYP2S1-UPF1chr1941703833chr1918976098709HLA-A68:02EATGTWALL0.99270.9448817
CYP2S1-UPF1chr1941703833chr1918976098709HLA-A69:01EATGTWALL0.97960.8879817
CYP2S1-UPF1chr1941703833chr1918976098709HLA-C15:02ATGTWALLL0.96880.991918
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B18:04MEATGTWAL0.96780.9568716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-C15:05ATGTWALLL0.96730.9948918
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B18:07MEATGTWAL0.95550.9316716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B18:04AEMEATGTW0.9480.9028514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:26MEATGTWAL0.94660.9908716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:07MEATGTWAL0.94660.9908716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:13MEATGTWAL0.94660.9908716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B18:05MEATGTWAL0.94430.9536716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B18:05AEMEATGTW0.94080.8978514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B18:08MEATGTWAL0.93790.9748716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B18:08AEMEATGTW0.93650.9605514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B18:06MEATGTWAL0.9290.9677716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B18:03MEATGTWAL0.92760.9503716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B18:06AEMEATGTW0.89830.9314514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B18:03AEMEATGTW0.86250.8906514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B18:11MEATGTWAL0.81130.9708716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B39:11MEATGTWAL0.80680.9893716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B39:31MEATGTWAL0.79590.9924716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B18:11AEMEATGTW0.78650.924514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B39:02MEATGTWAL0.78330.9979716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:04AEMEATGTW0.76650.9758514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B38:05MEATGTWAL0.75440.9985716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B41:03MEATGTWAL0.65910.9303716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B48:02MEATGTWAL0.5920.978716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B15:09MEATGTWAL0.56130.9557716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B35:20MEATGTWAL0.4850.9837716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B15:13AEMEATGTW0.47360.9731514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B15:24AEMEATGTW0.41090.9924514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B50:04MEATGTWAL0.38850.9842716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B50:05MEATGTWAL0.38850.9842716
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B35:28AEMEATGTW0.28390.9523514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B41:03AEMEATGTW0.19610.8185514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B48:02AEMEATGTW0.1070.9477514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B15:53AEMEATGTW0.04420.9742514
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:04MEATGTWALL0.99550.9832717
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:36MEATGTWALL0.99370.597717
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:49MEATGTWALL0.99160.6302717
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:13AEMEATGTWA0.95510.9947515
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:26AEMEATGTWA0.95510.9947515
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:07AEMEATGTWA0.95510.9947515
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:22AEMEATGTWA0.94830.6896515
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:26PAEMEATGTW0.77410.9719414
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:13PAEMEATGTW0.77410.9719414
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:07PAEMEATGTW0.77410.9719414
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B50:04AEMEATGTWA0.73980.9875515
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B50:05AEMEATGTWA0.73980.9875515
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:36AEMEATGTWAL0.99970.7177516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:04AEMEATGTWAL0.99970.985516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:49AEMEATGTWAL0.99960.7093516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:07AEMEATGTWAL0.99950.9954516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:26AEMEATGTWAL0.99950.9954516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:13AEMEATGTWAL0.99950.9954516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:12AEMEATGTWAL0.99940.7375516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:22AEMEATGTWAL0.99930.723516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:36MEATGTWALLL0.99910.6461718
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B40:49MEATGTWALLL0.99870.6749718
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B39:02AEMEATGTWAL0.9910.9981516
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:26RPAEMEATGTW0.97450.8462314
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:07RPAEMEATGTW0.97450.8462314
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B44:13RPAEMEATGTW0.97450.8462314
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B53:02RPAEMEATGTW0.96880.7059314
CYP2S1-UPF1chr1941703833chr1918976098709HLA-B41:03AEMEATGTWAL0.93460.9895516

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Potential FusionNeoAntigen Information of CYP2S1-UPF1 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 CYP2S1-UPF1

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
1942EMEATGTWALLLALCYP2S1UPF1chr1941703833chr1918976098709

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CYP2S1-UPF1

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-B14:023BVN1942EMEATGTWALLLAL-6.12283-6.12283
HLA-A24:025HGA1942EMEATGTWALLLAL-7.36995-7.36995

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Vaccine Design for the FusionNeoAntigens of CYP2S1-UPF1

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
CYP2S1-UPF1chr1941703833chr1918976098314RPAEMEATGTWGTCTGGTGGAGACATTCCAGGGGACAGAAGGCC
CYP2S1-UPF1chr1941703833chr1918976098414PAEMEATGTWTGGTGGAGACATTCCAGGGGACAGAAGGCC
CYP2S1-UPF1chr1941703833chr1918976098514AEMEATGTWTGGAGACATTCCAGGGGACAGAAGGCC
CYP2S1-UPF1chr1941703833chr1918976098515AEMEATGTWATGGAGACATTCCAGGGGACAGAAGGCCGGC
CYP2S1-UPF1chr1941703833chr1918976098516AEMEATGTWALTGGAGACATTCCAGGGGACAGAAGGCCGGCCTT
CYP2S1-UPF1chr1941703833chr1918976098616EMEATGTWALAGACATTCCAGGGGACAGAAGGCCGGCCTT
CYP2S1-UPF1chr1941703833chr1918976098716MEATGTWALCATTCCAGGGGACAGAAGGCCGGCCTT
CYP2S1-UPF1chr1941703833chr1918976098717MEATGTWALLCATTCCAGGGGACAGAAGGCCGGCCTTCCA
CYP2S1-UPF1chr1941703833chr1918976098718MEATGTWALLLCATTCCAGGGGACAGAAGGCCGGCCTTCCAGCA
CYP2S1-UPF1chr1941703833chr1918976098817EATGTWALLTCCAGGGGACAGAAGGCCGGCCTTCCA
CYP2S1-UPF1chr1941703833chr1918976098918ATGTWALLLAGGGGACAGAAGGCCGGCCTTCCAGCA

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 CYP2S1-UPF1

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
LUSCCYP2S1-UPF1chr1941703833ENST00000310054chr1918976098ENST00000262803TCGA-34-5240-01A

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Potential target of CAR-T therapy development for CYP2S1-UPF1

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 CYP2S1-UPF1

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 CYP2S1-UPF1

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