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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:E2F6-STK36

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: E2F6-STK36
FusionPDB ID: 24791
FusionGDB2.0 ID: 24791
HgeneTgene
Gene symbol

E2F6

STK36

Gene ID

1876

27148

Gene nameE2F transcription factor 6serine/threonine kinase 36
SynonymsE2F-6FU
Cytomap

2p25.1

2q35

Type of geneprotein-codingprotein-coding
Descriptiontranscription factor E2F6serine/threonine-protein kinase 36fused homologtesticular tissue protein Li 188
Modification date2020031320200313
UniProtAcc

O75461

Main function of 5'-partner protein: FUNCTION: Inhibitor of E2F-dependent transcription (PubMed:9689056, PubMed:9704927, PubMed:9501179). Binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3' (PubMed:9501179). Has a preference for the 5'-TTTCCCGC-3' E2F recognition site (PubMed:9501179). E2F6 lacks the transcriptional activation and pocket protein binding domains (PubMed:9704927, PubMed:9501179). Appears to regulate a subset of E2F-dependent genes whose products are required for entry into the cell cycle but not for normal cell cycle progression (PubMed:9689056, PubMed:9501179). Represses expression of some meiosis-specific genes, including SLC25A31/ANT4 (By similarity). May silence expression via the recruitment of a chromatin remodeling complex containing histone H3-K9 methyltransferase activity. Overexpression delays the exit of cells from the S-phase (PubMed:9501179). {ECO:0000250|UniProtKB:O54917, ECO:0000269|PubMed:9501179, ECO:0000269|PubMed:9689056, ECO:0000269|PubMed:9704927}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000307236, ENST00000542100, 
ENST00000546212, ENST00000362009, 
ENST00000381525, 		ENST00000295709, 
ENST00000392105, ENST00000392106, 
ENST00000440309, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score2 X 2 X 2=86 X 7 X 4=168
# samples 26
** MAII scorelog2(2/8*10)=1.32192809488736log2(6/168*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: E2F6 [Title/Abstract] AND STK36 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: E2F6 [Title/Abstract] AND STK36 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)E2F6(11605898)-STK36(219545326), # samples:2
Anticipated loss of major functional domain due to fusion event.E2F6-STK36 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.
E2F6-STK36 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.
E2F6-STK36 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
E2F6-STK36 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
E2F6-STK36 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
E2F6-STK36 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
E2F6-STK36 seems lost the major protein functional domain in Tgene partner, which is a kinase due to the frame-shifted 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
HgeneE2F6

GO:0000122

negative regulation of transcription by RNA polymerase II

9501179

TgeneSTK36

GO:0051090

regulation of DNA-binding transcription factor activity

10806483



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/chr2:11605898/chr2:219545326)
- 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 E2F6 (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 STK36 (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)
ENST00000362009E2F6chr211597305-ENST00000295709STK36chr2219543891+440343343936961085
ENST00000362009E2F6chr211597305-ENST00000392106STK36chr2219543891+433643343936331064
ENST00000362009E2F6chr211597305-ENST00000392105STK36chr2219543891+433443343936331064
ENST00000362009E2F6chr211597305-ENST00000440309STK36chr2219543891+431143343936961085
ENST00000307236E2F6chr211597305-ENST00000295709STK36chr2219543891+420423424034971085
ENST00000307236E2F6chr211597305-ENST00000392106STK36chr2219543891+413723424034341064
ENST00000307236E2F6chr211597305-ENST00000392105STK36chr2219543891+413523424034341064
ENST00000307236E2F6chr211597305-ENST00000440309STK36chr2219543891+411223424034971085
ENST00000381525E2F6chr211597305-ENST00000295709STK36chr2219544283+430943327036021110
ENST00000381525E2F6chr211597305-ENST00000392106STK36chr2219544283+424243327035391089
ENST00000381525E2F6chr211597305-ENST00000392105STK36chr2219544283+424043327035391089
ENST00000381525E2F6chr211597305-ENST00000440309STK36chr2219544283+421743327036021110

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
ENST00000362009ENST00000295709E2F6chr211597305-STK36chr2219543891+0.0052394950.99476045
ENST00000362009ENST00000392106E2F6chr211597305-STK36chr2219543891+0.0051084970.9948915
ENST00000362009ENST00000392105E2F6chr211597305-STK36chr2219543891+0.0051098440.9948901
ENST00000362009ENST00000440309E2F6chr211597305-STK36chr2219543891+0.0055644050.99443555
ENST00000307236ENST00000295709E2F6chr211597305-STK36chr2219543891+0.0046935650.99530643
ENST00000307236ENST00000392106E2F6chr211597305-STK36chr2219543891+0.0045984820.9954015
ENST00000307236ENST00000392105E2F6chr211597305-STK36chr2219543891+0.0046160380.9953839
ENST00000307236ENST00000440309E2F6chr211597305-STK36chr2219543891+0.0050207740.9949792
ENST00000381525ENST00000295709E2F6chr211597305-STK36chr2219544283+0.003354470.9966455
ENST00000381525ENST00000392106E2F6chr211597305-STK36chr2219544283+0.0026973870.99730253
ENST00000381525ENST00000392105E2F6chr211597305-STK36chr2219544283+0.0026995060.99730057
ENST00000381525ENST00000440309E2F6chr211597305-STK36chr2219544283+0.0035868890.9964132

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 E2F6-STK36

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
E2F6chr211597305STK36chr221954428343355NLEDNVQYVSMRIITEPAGPDLGTPF

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Potential FusionNeoAntigen Information of E2F6-STK36 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.
E2F6-STK36_11597305_219544283.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)
E2F6-STK36chr211597305chr2219544283433HLA-B39:06MRIITEPA0.99940.90271018
E2F6-STK36chr211597305chr2219544283433HLA-B52:01VQYVSMRII0.33110.8733514
E2F6-STK36chr211597305chr2219544283433HLA-B73:01MRIITEPA0.99840.74261018
E2F6-STK36chr211597305chr2219544283433HLA-B15:04VQYVSMRII0.87110.845514
E2F6-STK36chr211597305chr2219544283433HLA-B51:07VQYVSMRII0.25020.7543514

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Potential FusionNeoAntigen Information of E2F6-STK36 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.
E2F6-STK36_11597305_219544283.msa

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)
E2F6-STK36chr211597305chr2219544283433DRB1-0405NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0405DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0409NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0409DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0417NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0417DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0424NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0424DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0429NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0429DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0430NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0430DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0445NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0445DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0447NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0447DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0448NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0448DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0454NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0457NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0457DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0467SMRIITEPAGPDLGT924
E2F6-STK36chr211597305chr2219544283433DRB1-0467VSMRIITEPAGPDLG823
E2F6-STK36chr211597305chr2219544283433DRB1-0477NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0477DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0480NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0480DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0482NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0482DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0483NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0483DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0484NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0484DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0486NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0486DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0486EDNVQYVSMRIITEP217
E2F6-STK36chr211597305chr2219544283433DRB1-0487NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0487DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0489NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0489DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0803NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0805NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0814NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0818NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0818DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0823NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0827NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0832NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0832DNVQYVSMRIITEPA318
E2F6-STK36chr211597305chr2219544283433DRB1-0832EDNVQYVSMRIITEP217
E2F6-STK36chr211597305chr2219544283433DRB1-0833NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0835NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0836NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0837NVQYVSMRIITEPAG419
E2F6-STK36chr211597305chr2219544283433DRB1-0838NVQYVSMRIITEPAG419

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Fusion breakpoint peptide structures of E2F6-STK36

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
7661QYVSMRIITEPAGPE2F6STK36chr211597305chr2219544283433

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of E2F6-STK36

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-B14:023BVN7661QYVSMRIITEPAGP-5.80164-5.91504
HLA-B52:013W397661QYVSMRIITEPAGP-5.81464-5.92804
HLA-A11:014UQ27661QYVSMRIITEPAGP-3.75955-4.79485
HLA-A24:025HGA7661QYVSMRIITEPAGP-7.62216-7.73556
HLA-A24:025HGA7661QYVSMRIITEPAGP-5.95577-6.99107
HLA-B44:053DX87661QYVSMRIITEPAGP-6.63562-7.67092
HLA-B44:053DX87661QYVSMRIITEPAGP-6.10696-6.22036

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Vaccine Design for the FusionNeoAntigens of E2F6-STK36

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
E2F6-STK36chr211597305chr22195442831018MRIITEPACCATGAGAATAATAACTGAGCCAG
E2F6-STK36chr211597305chr2219544283514VQYVSMRIIATGTACAATATGTGTCCATGAGAATAA

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
E2F6-STK36chr211597305chr2219544283217EDNVQYVSMRIITEPTAGAAGATAATGTACAATATGTGTCCATGAGAATAATAACTGAGC
E2F6-STK36chr211597305chr2219544283318DNVQYVSMRIITEPAAAGATAATGTACAATATGTGTCCATGAGAATAATAACTGAGCCAG
E2F6-STK36chr211597305chr2219544283419NVQYVSMRIITEPAGATAATGTACAATATGTGTCCATGAGAATAATAACTGAGCCAGCAG
E2F6-STK36chr211597305chr2219544283823VSMRIITEPAGPDLGATGTGTCCATGAGAATAATAACTGAGCCAGCAGGCCCAGATTTGG
E2F6-STK36chr211597305chr2219544283924SMRIITEPAGPDLGTTGTCCATGAGAATAATAACTGAGCCAGCAGGCCCAGATTTGGGGA

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Information of the samples that have these potential fusion neoantigens of E2F6-STK36

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
OVE2F6-STK36chr211597305ENST00000381525chr2219544283ENST00000295709TCGA-09-2044-01B

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Potential target of CAR-T therapy development for E2F6-STK36

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 E2F6-STK36

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 E2F6-STK36

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