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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:RTEL1-KCNH3

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: RTEL1-KCNH3
FusionPDB ID: 78506
FusionGDB2.0 ID: 78506
HgeneTgene
Gene symbol

RTEL1

KCNH3

Gene ID

51750

23416

Gene nameregulator of telomere elongation helicase 1potassium voltage-gated channel subfamily H member 3
SynonymsC20orf41|DKCA4|DKCB5|NHL|PFBMFT3|RTELBEC1|ELK2|Kv12.2
Cytomap

20q13.33

12q13.12

Type of geneprotein-codingprotein-coding
Descriptionregulator of telomere elongation helicase 1regulator of telomere lengthpotassium voltage-gated channel subfamily H member 3ELK channel 2brain-specific eag-like channel 1ether-a-go-go K(+) channel family memberether-a-go-go-like potassium channel 2potassium channel, voltage gated eag related subfamily H, member 3potassi
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000318100, ENST00000360203, 
ENST00000370018, ENST00000508582, 
ENST00000370003, ENST00000488316, 
ENST00000550434, ENST00000257981, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score2 X 3 X 2=122 X 3 X 2=12
# samples 33
** MAII scorelog2(3/12*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(3/12*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Fusion gene context

PubMed: RTEL1 [Title/Abstract] AND KCNH3 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: RTEL1 [Title/Abstract] AND KCNH3 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)RTEL1(62294242)-KCNH3(49934682), # samples:1
Anticipated loss of major functional domain due to fusion event.RTEL1-KCNH3 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.
RTEL1-KCNH3 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.
RTEL1-KCNH3 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.
RTEL1-KCNH3 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/chr20:62294242/chr12:49934682)
- 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 RTEL1 (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 KCNH3 (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)
ENST00000370018RTEL1chr2062294242+ENST00000257981KCNH3chr1249934682+4896136582745401237
ENST00000318100RTEL1chr2062294242+ENST00000257981KCNH3chr1249934682+4896136582745401237
ENST00000508582RTEL1chr2062294242+ENST00000257981KCNH3chr1249934682+448795634641311261
ENST00000360203RTEL1chr2062294242+ENST00000257981KCNH3chr1249934682+439486332540381237

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
ENST00000370018ENST00000257981RTEL1chr2062294242+KCNH3chr1249934682+0.0112255030.98877454
ENST00000318100ENST00000257981RTEL1chr2062294242+KCNH3chr1249934682+0.0112255030.98877454
ENST00000508582ENST00000257981RTEL1chr2062294242+KCNH3chr1249934682+0.0063365310.99366343
ENST00000360203ENST00000257981RTEL1chr2062294242+KCNH3chr1249934682+0.0062696980.9937303

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 RTEL1-KCNH3

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
RTEL1chr2062294242KCNH3chr12499346821365179VASRSCHFYNNVEDSNFVLGNAQVAG
RTEL1chr2062294242KCNH3chr1249934682863179VASRSCHFYNNVEDSNFVLGNAQVAG
RTEL1chr2062294242KCNH3chr1249934682956203VASRSCHFYNNVEDSNFVLGNAQVAG

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Potential FusionNeoAntigen Information of RTEL1-KCNH3 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.
RTEL1-KCNH3_62294242_49934682.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)
RTEL1-KCNH3chr2062294242chr12499346821365HLA-B39:13VEDSNFVL0.94890.93441119
RTEL1-KCNH3chr2062294242chr12499346821365HLA-B35:03NVEDSNFVL0.71250.94641019
RTEL1-KCNH3chr2062294242chr12499346821365HLA-B35:04NVEDSNFVL0.53320.86531019
RTEL1-KCNH3chr2062294242chr12499346821365HLA-B35:02NVEDSNFVL0.53320.86531019
RTEL1-KCNH3chr2062294242chr12499346821365HLA-B39:08VEDSNFVL0.97430.77811119
RTEL1-KCNH3chr2062294242chr12499346821365HLA-C05:09NVEDSNFVL0.99980.89381019
RTEL1-KCNH3chr2062294242chr12499346821365HLA-C08:15NVEDSNFVL0.99960.91331019
RTEL1-KCNH3chr2062294242chr12499346821365HLA-C08:13NVEDSNFVL0.92120.9641019
RTEL1-KCNH3chr2062294242chr12499346821365HLA-C08:04NVEDSNFVL0.92120.9641019
RTEL1-KCNH3chr2062294242chr12499346821365HLA-C04:06NVEDSNFVL0.9190.83161019
RTEL1-KCNH3chr2062294242chr12499346821365HLA-C08:03NVEDSNFVL0.84990.96421019
RTEL1-KCNH3chr2062294242chr12499346821365HLA-B35:12NVEDSNFVL0.53320.86531019
RTEL1-KCNH3chr2062294242chr12499346821365HLA-B40:04VEDSNFVL0.99970.69961119
RTEL1-KCNH3chr2062294242chr12499346821365HLA-B39:11VEDSNFVL0.96880.73031119
RTEL1-KCNH3chr2062294242chr12499346821365HLA-B39:02VEDSNFVL0.9620.94141119
RTEL1-KCNH3chr2062294242chr12499346821365HLA-C05:01NVEDSNFVL0.99980.89381019
RTEL1-KCNH3chr2062294242chr12499346821365HLA-C04:03NVEDSNFVL0.99980.6461019
RTEL1-KCNH3chr2062294242chr12499346821365HLA-C08:02NVEDSNFVL0.99960.91331019
RTEL1-KCNH3chr2062294242chr12499346821365HLA-C03:06NVEDSNFVL0.87470.99361019
RTEL1-KCNH3chr2062294242chr12499346821365HLA-C08:01NVEDSNFVL0.84990.96421019
RTEL1-KCNH3chr2062294242chr12499346821365HLA-B35:09NVEDSNFVL0.53320.86531019

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Potential FusionNeoAntigen Information of RTEL1-KCNH3 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.
RTEL1-KCNH3_62294242_49934682.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)
RTEL1-KCNH3chr2062294242chr12499346821365DRB1-0902VEDSNFVLGNAQVAG1126

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Fusion breakpoint peptide structures of RTEL1-KCNH3

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
3317HFYNNVEDSNFVLGRTEL1KCNH3chr2062294242chr12499346821365

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of RTEL1-KCNH3

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-B14:023BVN3317HFYNNVEDSNFVLG-7.9962-8.1096
HLA-B14:023BVN3317HFYNNVEDSNFVLG-5.70842-6.74372
HLA-B52:013W393317HFYNNVEDSNFVLG-6.83737-6.95077
HLA-B52:013W393317HFYNNVEDSNFVLG-4.4836-5.5189
HLA-A11:014UQ23317HFYNNVEDSNFVLG-10.0067-10.1201
HLA-A11:014UQ23317HFYNNVEDSNFVLG-9.03915-10.0745
HLA-A24:025HGA3317HFYNNVEDSNFVLG-6.56204-6.67544
HLA-A24:025HGA3317HFYNNVEDSNFVLG-5.42271-6.45801
HLA-B44:053DX83317HFYNNVEDSNFVLG-7.85648-8.89178
HLA-B44:053DX83317HFYNNVEDSNFVLG-5.3978-5.5112
HLA-A02:016TDR3317HFYNNVEDSNFVLG-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of RTEL1-KCNH3

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
RTEL1-KCNH3chr2062294242chr12499346821019NVEDSNFVLACGTAGAAGACAGTAACTTCGTGCTGG
RTEL1-KCNH3chr2062294242chr12499346821119VEDSNFVLTAGAAGACAGTAACTTCGTGCTGG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
RTEL1-KCNH3chr2062294242chr12499346821126VEDSNFVLGNAQVAGTAGAAGACAGTAACTTCGTGCTGGGCAACGCCCAGGTGGCGGGGC

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Information of the samples that have these potential fusion neoantigens of RTEL1-KCNH3

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
ACCRTEL1-KCNH3chr2062294242ENST00000318100chr1249934682ENST00000257981TCGA-OR-A5JP-01A

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Potential target of CAR-T therapy development for RTEL1-KCNH3

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
TgeneKCNH3chr20:62294242chr12:49934682ENST00000257981015454_47401084.0IntramembranePore-forming%3B Name%3DSegment H5
TgeneKCNH3chr20:62294242chr12:49934682ENST00000257981015229_24901084.0TransmembraneHelical%3B Name%3DSegment S1
TgeneKCNH3chr20:62294242chr12:49934682ENST00000257981015260_28001084.0TransmembraneHelical%3B Name%3DSegment S2
TgeneKCNH3chr20:62294242chr12:49934682ENST00000257981015303_32301084.0TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNH3chr20:62294242chr12:49934682ENST00000257981015332_35201084.0TransmembraneHelical%3B Voltage-sensor%3B Name%3DSegment S4
TgeneKCNH3chr20:62294242chr12:49934682ENST00000257981015362_38201084.0TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNH3chr20:62294242chr12:49934682ENST00000257981015480_50001084.0TransmembraneHelical%3B Name%3DSegment S6

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 RTEL1-KCNH3

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 RTEL1-KCNH3

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