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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:CEP128-TSHR

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CEP128-TSHR
FusionPDB ID: 15775
FusionGDB2.0 ID: 15775
HgeneTgene
Gene symbol

CEP128

TSHR

Gene ID

145508

7253

Gene namecentrosomal protein 128thyroid stimulating hormone receptor
SynonymsC14orf145|C14orf61|LEDP/132CHNG1|LGR3|hTSHR-I
Cytomap

14q31.1

14q31.1

Type of geneprotein-codingprotein-coding
Descriptioncentrosomal protein of 128 kDacentrosomal protein 128kDalens epithelium-derived proteinthyrotropin receptorTSH receptorseven transmembrane helix receptorthyrotropin receptor-I, hTSHR-I
Modification date2020031320200329
UniProtAcc

Q6ZU80

Main function of 5'-partner protein: 		.
Ensembl transtripts involved in fusion geneENST idsENST00000281129, ENST00000555265, 
ENST00000216517, ENST00000327841, 
ENST00000553717, 		ENST00000557096, 
ENST00000298171, ENST00000342443, 
ENST00000541158, ENST00000554263, 
ENST00000554435, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score6 X 7 X 2=848 X 7 X 7=392
# samples 79
** MAII scorelog2(7/84*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/392*10)=-2.12285674778553
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: CEP128 [Title/Abstract] AND TSHR [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: CEP128 [Title/Abstract] AND TSHR [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CEP128(81227781)-TSHR(81562983), # samples:3
TSHR(81424522)-CEP128(81425820), # samples:1
Anticipated loss of major functional domain due to fusion event.CEP128-TSHR 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.
CEP128-TSHR 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/chr14:81227781/chr14:81562983)
- 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 CEP128 (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 TSHR (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)
ENST00000281129CEP128chr1481227781-ENST00000541158TSHRchr1481562983+642327241412810889
ENST00000281129CEP128chr1481227781-ENST00000342443TSHRchr1481562983+321027241412810889
ENST00000281129CEP128chr1481227781-ENST00000298171TSHRchr1481562983+642327241412810889
ENST00000281129CEP128chr1481227781-ENST00000554263TSHRchr1481562983+333727241412810889
ENST00000281129CEP128chr1481227781-ENST00000554435TSHRchr1481562983+324227241412810889
ENST00000555265CEP128chr1481227781-ENST00000541158TSHRchr1481562983+662829293463015889
ENST00000555265CEP128chr1481227781-ENST00000342443TSHRchr1481562983+341529293463015889
ENST00000555265CEP128chr1481227781-ENST00000298171TSHRchr1481562983+662829293463015889
ENST00000555265CEP128chr1481227781-ENST00000554263TSHRchr1481562983+354229293463015889
ENST00000555265CEP128chr1481227781-ENST00000554435TSHRchr1481562983+344729293463015889
ENST00000281129CEP128chr1481227780-ENST00000541158TSHRchr1481562982+642327241412810889
ENST00000281129CEP128chr1481227780-ENST00000342443TSHRchr1481562982+321027241412810889
ENST00000281129CEP128chr1481227780-ENST00000298171TSHRchr1481562982+642327241412810889
ENST00000281129CEP128chr1481227780-ENST00000554263TSHRchr1481562982+333727241412810889
ENST00000281129CEP128chr1481227780-ENST00000554435TSHRchr1481562982+324227241412810889
ENST00000555265CEP128chr1481227780-ENST00000541158TSHRchr1481562982+662829293463015889
ENST00000555265CEP128chr1481227780-ENST00000342443TSHRchr1481562982+341529293463015889
ENST00000555265CEP128chr1481227780-ENST00000298171TSHRchr1481562982+662829293463015889
ENST00000555265CEP128chr1481227780-ENST00000554263TSHRchr1481562982+354229293463015889
ENST00000555265CEP128chr1481227780-ENST00000554435TSHRchr1481562982+344729293463015889

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
ENST00000281129ENST00000541158CEP128chr1481227781-TSHRchr1481562983+0.0012133070.99878675
ENST00000281129ENST00000342443CEP128chr1481227781-TSHRchr1481562983+0.0103729960.989627
ENST00000281129ENST00000298171CEP128chr1481227781-TSHRchr1481562983+0.0012133070.99878675
ENST00000281129ENST00000554263CEP128chr1481227781-TSHRchr1481562983+0.0072044550.9927955
ENST00000281129ENST00000554435CEP128chr1481227781-TSHRchr1481562983+0.00987550.9901245
ENST00000555265ENST00000541158CEP128chr1481227781-TSHRchr1481562983+0.0013232930.9986767
ENST00000555265ENST00000342443CEP128chr1481227781-TSHRchr1481562983+0.0099175550.99008244
ENST00000555265ENST00000298171CEP128chr1481227781-TSHRchr1481562983+0.0013232930.9986767
ENST00000555265ENST00000554263CEP128chr1481227781-TSHRchr1481562983+0.0071583740.9928416
ENST00000555265ENST00000554435CEP128chr1481227781-TSHRchr1481562983+0.0095077330.9904923
ENST00000281129ENST00000541158CEP128chr1481227780-TSHRchr1481562982+0.0012133070.99878675
ENST00000281129ENST00000342443CEP128chr1481227780-TSHRchr1481562982+0.0103729960.989627
ENST00000281129ENST00000298171CEP128chr1481227780-TSHRchr1481562982+0.0012133070.99878675
ENST00000281129ENST00000554263CEP128chr1481227780-TSHRchr1481562982+0.0072044550.9927955
ENST00000281129ENST00000554435CEP128chr1481227780-TSHRchr1481562982+0.00987550.9901245
ENST00000555265ENST00000541158CEP128chr1481227780-TSHRchr1481562982+0.0013232930.9986767
ENST00000555265ENST00000342443CEP128chr1481227780-TSHRchr1481562982+0.0099175550.99008244
ENST00000555265ENST00000298171CEP128chr1481227780-TSHRchr1481562982+0.0013232930.9986767
ENST00000555265ENST00000554263CEP128chr1481227780-TSHRchr1481562982+0.0071583740.9928416
ENST00000555265ENST00000554435CEP128chr1481227780-TSHRchr1481562982+0.0095077330.9904923

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 CEP128-TSHR

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
CEP128chr1481227780TSHRchr14815629822724859AACKTFSKDSVEKLKEAVQQWLYFSP
CEP128chr1481227780TSHRchr14815629822929859AACKTFSKDSVEKLKEAVQQWLYFSP
CEP128chr1481227781TSHRchr14815629832724859AACKTFSKDSVEKLKEAVQQWLYFSP
CEP128chr1481227781TSHRchr14815629832929859AACKTFSKDSVEKLKEAVQQWLYFSP

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Potential FusionNeoAntigen Information of CEP128-TSHR 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.
CEP128-TSHR_81227780_81562982.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)
CEP128-TSHRchr1481227780chr14815629822724HLA-B57:01KLKEAVQQW0.99840.99611221
CEP128-TSHRchr1481227780chr14815629822724HLA-A31:08KLKEAVQQW0.99710.94161221
CEP128-TSHRchr1481227780chr14815629822724HLA-B58:01KLKEAVQQW0.99560.99481221
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:16KLKEAVQQW0.99320.97421221
CEP128-TSHRchr1481227780chr14815629822724HLA-B58:02KLKEAVQQW0.99280.9961221
CEP128-TSHRchr1481227780chr14815629822724HLA-A32:13KLKEAVQQW0.99190.99251221
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:17KLKEAVQQW0.9880.95831221
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:16FSKDSVEKL0.98580.6928514
CEP128-TSHRchr1481227780chr14815629822724HLA-B57:03KLKEAVQQW0.96870.99831221
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:01KLKEAVQQW0.95030.95791221
CEP128-TSHRchr1481227780chr14815629822724HLA-A24:17KLKEAVQQW0.87850.74341221
CEP128-TSHRchr1481227780chr14815629822724HLA-A24:15KLKEAVQQW0.8740.78011221
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:25KLKEAVQQW0.75610.95981221
CEP128-TSHRchr1481227780chr14815629822724HLA-A24:14KLKEAVQQW0.5140.72361221
CEP128-TSHRchr1481227780chr14815629822724HLA-B13:01KLKEAVQQW0.00760.99691221
CEP128-TSHRchr1481227780chr14815629822724HLA-A02:22KLKEAVQQWL0.98330.60941222
CEP128-TSHRchr1481227780chr14815629822724HLA-A02:13KLKEAVQQWL0.97670.65621222
CEP128-TSHRchr1481227780chr14815629822724HLA-A02:27KLKEAVQQWL0.94430.62931222
CEP128-TSHRchr1481227780chr14815629822724HLA-A02:04KLKEAVQQWL0.90970.681222
CEP128-TSHRchr1481227780chr14815629822724HLA-A02:20KLKEAVQQWL0.76190.6691222
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:01KLKEAVQQWLY0.99990.74251223
CEP128-TSHRchr1481227780chr14815629822724HLA-B57:01VEKLKEAVQQW0.99980.97981021
CEP128-TSHRchr1481227780chr14815629822724HLA-B57:03KTFSKDSVEKL0.99970.9369314
CEP128-TSHRchr1481227780chr14815629822724HLA-B44:03VEKLKEAVQQW0.99890.88351021
CEP128-TSHRchr1481227780chr14815629822724HLA-B44:02VEKLKEAVQQW0.99860.76211021
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:25KLKEAVQQWLY0.9970.81971223
CEP128-TSHRchr1481227780chr14815629822724HLA-B44:05VEKLKEAVQQW0.9950.83761021
CEP128-TSHRchr1481227780chr14815629822724HLA-A32:13VEKLKEAVQQW0.99210.96161021
CEP128-TSHRchr1481227780chr14815629822724HLA-A32:13KLKEAVQQWLY0.95960.9291223
CEP128-TSHRchr1481227780chr14815629822724HLA-C03:08FSKDSVEKL0.99970.9377514
CEP128-TSHRchr1481227780chr14815629822724HLA-C03:19FSKDSVEKL0.99960.9911514
CEP128-TSHRchr1481227780chr14815629822724HLA-C03:07FSKDSVEKL0.99950.9827514
CEP128-TSHRchr1481227780chr14815629822724HLA-C15:04FSKDSVEKL0.99940.8896514
CEP128-TSHRchr1481227780chr14815629822724HLA-C15:06FSKDSVEKL0.99930.9222514
CEP128-TSHRchr1481227780chr14815629822724HLA-C06:03FSKDSVEKL0.99880.9943514
CEP128-TSHRchr1481227780chr14815629822724HLA-C12:04FSKDSVEKL0.99880.9946514
CEP128-TSHRchr1481227780chr14815629822724HLA-C04:06FSKDSVEKL0.99580.7479514
CEP128-TSHRchr1481227780chr14815629822724HLA-C12:16FSKDSVEKL0.99550.9564514
CEP128-TSHRchr1481227780chr14815629822724HLA-B78:01DSVEKLKEA0.99070.5234817
CEP128-TSHRchr1481227780chr14815629822724HLA-C12:12FSKDSVEKL0.98940.9148514
CEP128-TSHRchr1481227780chr14815629822724HLA-C08:04FSKDSVEKL0.98370.8994514
CEP128-TSHRchr1481227780chr14815629822724HLA-C08:13FSKDSVEKL0.98370.8994514
CEP128-TSHRchr1481227780chr14815629822724HLA-C01:17FSKDSVEKL0.98170.9003514
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:07KLKEAVQQW0.90790.94241221
CEP128-TSHRchr1481227780chr14815629822724HLA-A23:01KLKEAVQQW0.90620.57661221
CEP128-TSHRchr1481227780chr14815629822724HLA-C03:14FSKDSVEKL0.84860.9756514
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:04KLKEAVQQW0.84020.97851221
CEP128-TSHRchr1481227780chr14815629822724HLA-C08:03FSKDSVEKL0.81040.9552514
CEP128-TSHRchr1481227780chr14815629822724HLA-C07:05FSKDSVEKL0.79460.9629514
CEP128-TSHRchr1481227780chr14815629822724HLA-C07:19FSKDSVEKL0.77280.6637514
CEP128-TSHRchr1481227780chr14815629822724HLA-C07:27FSKDSVEKL0.74890.9488514
CEP128-TSHRchr1481227780chr14815629822724HLA-C07:29FSKDSVEKL0.70660.9338514
CEP128-TSHRchr1481227780chr14815629822724HLA-C07:13FSKDSVEKL0.64590.863514
CEP128-TSHRchr1481227780chr14815629822724HLA-C07:95FSKDSVEKL0.64470.7347514
CEP128-TSHRchr1481227780chr14815629822724HLA-C02:06FSKDSVEKL0.59050.956514
CEP128-TSHRchr1481227780chr14815629822724HLA-C01:30FSKDSVEKL0.53040.9518514
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:05KLKEAVQQW0.30870.9651221
CEP128-TSHRchr1481227780chr14815629822724HLA-B44:08KLKEAVQQW0.11770.82551221
CEP128-TSHRchr1481227780chr14815629822724HLA-B44:06KLKEAVQQW0.07960.52711221
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:04KLKEAVQQWL0.9840.81411222
CEP128-TSHRchr1481227780chr14815629822724HLA-A02:05KLKEAVQQWL0.98240.52191222
CEP128-TSHRchr1481227780chr14815629822724HLA-B44:06EKLKEAVQQW0.81170.5121121
CEP128-TSHRchr1481227780chr14815629822724HLA-B44:08EKLKEAVQQW0.73960.78241121
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:07KLKEAVQQWLY0.99980.66711223
CEP128-TSHRchr1481227780chr14815629822724HLA-B44:08VEKLKEAVQQW0.99850.80671021
CEP128-TSHRchr1481227780chr14815629822724HLA-B44:04VEKLKEAVQQW0.99790.63381021
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:04KLKEAVQQWLY0.99360.79281223
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:05KLKEAVQQWLY0.95240.78361223
CEP128-TSHRchr1481227780chr14815629822724HLA-B39:11SKDSVEKL0.96670.5836614
CEP128-TSHRchr1481227780chr14815629822724HLA-C03:04FSKDSVEKL0.99970.9914514
CEP128-TSHRchr1481227780chr14815629822724HLA-C03:03FSKDSVEKL0.99970.9914514
CEP128-TSHRchr1481227780chr14815629822724HLA-C15:09FSKDSVEKL0.99940.8896514
CEP128-TSHRchr1481227780chr14815629822724HLA-C03:17FSKDSVEKL0.99920.9727514
CEP128-TSHRchr1481227780chr14815629822724HLA-C15:05FSKDSVEKL0.99910.9025514
CEP128-TSHRchr1481227780chr14815629822724HLA-C03:05FSKDSVEKL0.99910.9147514
CEP128-TSHRchr1481227780chr14815629822724HLA-C15:02FSKDSVEKL0.9990.88514
CEP128-TSHRchr1481227780chr14815629822724HLA-C12:02FSKDSVEKL0.99890.9656514
CEP128-TSHRchr1481227780chr14815629822724HLA-C03:02FSKDSVEKL0.99880.971514
CEP128-TSHRchr1481227780chr14815629822724HLA-C03:67FSKDSVEKL0.99870.9857514
CEP128-TSHRchr1481227780chr14815629822724HLA-A32:01KLKEAVQQW0.99850.98961221
CEP128-TSHRchr1481227780chr14815629822724HLA-B57:10KLKEAVQQW0.99840.99611221
CEP128-TSHRchr1481227780chr14815629822724HLA-B57:04KLKEAVQQW0.99720.89941221
CEP128-TSHRchr1481227780chr14815629822724HLA-C06:06FSKDSVEKL0.99640.9794514
CEP128-TSHRchr1481227780chr14815629822724HLA-C06:02FSKDSVEKL0.99610.9936514
CEP128-TSHRchr1481227780chr14815629822724HLA-C06:17FSKDSVEKL0.99610.9936514
CEP128-TSHRchr1481227780chr14815629822724HLA-C12:03FSKDSVEKL0.99590.9787514
CEP128-TSHRchr1481227780chr14815629822724HLA-B58:06KLKEAVQQW0.99570.99281221
CEP128-TSHRchr1481227780chr14815629822724HLA-C03:06FSKDSVEKL0.99160.9913514
CEP128-TSHRchr1481227780chr14815629822724HLA-C01:03FSKDSVEKL0.99010.8882514
CEP128-TSHRchr1481227780chr14815629822724HLA-B78:02DSVEKLKEA0.98950.5645817
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:24KLKEAVQQW0.98770.99041221
CEP128-TSHRchr1481227780chr14815629822724HLA-C16:04FSKDSVEKL0.98080.9775514
CEP128-TSHRchr1481227780chr14815629822724HLA-C01:02FSKDSVEKL0.98040.8954514
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:27KLKEAVQQW0.95370.97621221
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:135KLKEAVQQW0.95330.95631221
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:34KLKEAVQQW0.95030.95791221
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:33KLKEAVQQW0.95030.95791221
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:125KLKEAVQQW0.95030.95791221
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:13KLKEAVQQW0.94210.96311221
CEP128-TSHRchr1481227780chr14815629822724HLA-C07:04FSKDSVEKL0.93670.8716514
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:50KLKEAVQQW0.93660.96781221
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:73FSKDSVEKL0.90430.7973514
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:35KLKEAVQQW0.89060.97741221
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:30FSKDSVEKL0.89010.7942514
CEP128-TSHRchr1481227780chr14815629822724HLA-C16:02FSKDSVEKL0.8760.9839514
CEP128-TSHRchr1481227780chr14815629822724HLA-C07:22FSKDSVEKL0.85650.7602514
CEP128-TSHRchr1481227780chr14815629822724HLA-B57:02KLKEAVQQW0.85560.99041221
CEP128-TSHRchr1481227780chr14815629822724HLA-C08:01FSKDSVEKL0.81040.9552514
CEP128-TSHRchr1481227780chr14815629822724HLA-A30:04KLKEAVQQW0.79170.82761221
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:39KLKEAVQQW0.77750.94511221
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:12KLKEAVQQW0.75060.97141221
CEP128-TSHRchr1481227780chr14815629822724HLA-B35:13FSKDSVEKL0.72540.9642514
CEP128-TSHRchr1481227780chr14815629822724HLA-C16:01FSKDSVEKL0.69170.9638514
CEP128-TSHRchr1481227780chr14815629822724HLA-C07:01FSKDSVEKL0.68190.673514
CEP128-TSHRchr1481227780chr14815629822724HLA-C02:02FSKDSVEKL0.47380.9728514
CEP128-TSHRchr1481227780chr14815629822724HLA-C02:10FSKDSVEKL0.47380.9728514
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:68KLKEAVQQW0.45440.91851221
CEP128-TSHRchr1481227780chr14815629822724HLA-C06:08FSKDSVEKL0.36880.9866514
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:20KLKEAVQQW0.28770.96811221
CEP128-TSHRchr1481227780chr14815629822724HLA-B35:28KLKEAVQQW0.26240.96871221
CEP128-TSHRchr1481227780chr14815629822724HLA-C17:01FSKDSVEKL0.25940.8127514
CEP128-TSHRchr1481227780chr14815629822724HLA-B07:13FSKDSVEKL0.10050.8218514
CEP128-TSHRchr1481227780chr14815629822724HLA-A25:01KLKEAVQQW0.05780.92471221
CEP128-TSHRchr1481227780chr14815629822724HLA-A02:03KLKEAVQQWL0.9830.65861222
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:73KLKEAVQQWL0.9520.90171222
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:30KLKEAVQQWL0.88120.90291222
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:13EKLKEAVQQW0.87870.91361121
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:24EKLKEAVQQW0.85350.91981121
CEP128-TSHRchr1481227780chr14815629822724HLA-A25:01EKLKEAVQQW0.30190.88741121
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:135KLKEAVQQWLY0.99990.74071223
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:50KLKEAVQQWLY0.99990.81291223
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:34KLKEAVQQWLY0.99990.74251223
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:33KLKEAVQQWLY0.99990.74251223
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:27KLKEAVQQWLY0.99990.7991223
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:125KLKEAVQQWLY0.99990.74251223
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:12KLKEAVQQWLY0.99990.75481223
CEP128-TSHRchr1481227780chr14815629822724HLA-B57:10VEKLKEAVQQW0.99980.97981021
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:35KLKEAVQQWLY0.99980.75651223
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:24KLKEAVQQWLY0.99960.86821223
CEP128-TSHRchr1481227780chr14815629822724HLA-B44:13VEKLKEAVQQW0.99890.88351021
CEP128-TSHRchr1481227780chr14815629822724HLA-B44:26VEKLKEAVQQW0.99890.88351021
CEP128-TSHRchr1481227780chr14815629822724HLA-B44:07VEKLKEAVQQW0.99890.88351021
CEP128-TSHRchr1481227780chr14815629822724HLA-B44:22VEKLKEAVQQW0.99860.76211021
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:39KLKEAVQQWLY0.99750.77551223
CEP128-TSHRchr1481227780chr14815629822724HLA-B44:21VEKLKEAVQQW0.9970.53311021
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:24VEKLKEAVQQW0.99660.91981021
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:13VEKLKEAVQQW0.99070.91421021
CEP128-TSHRchr1481227780chr14815629822724HLA-A32:01KLKEAVQQWLY0.98530.91281223
CEP128-TSHRchr1481227780chr14815629822724HLA-B15:20KLKEAVQQWLY0.95870.82111223

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Potential FusionNeoAntigen Information of CEP128-TSHR 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.
CEP128-TSHR_81227780_81562982.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)
CEP128-TSHRchr1481227780chr14815629822724DRB1-0338CKTFSKDSVEKLKEA217
CEP128-TSHRchr1481227780chr14815629822724DRB1-0338KTFSKDSVEKLKEAV318
CEP128-TSHRchr1481227780chr14815629822724DRB3-0101CKTFSKDSVEKLKEA217
CEP128-TSHRchr1481227780chr14815629822724DRB3-0101KTFSKDSVEKLKEAV318
CEP128-TSHRchr1481227780chr14815629822724DRB3-0101ACKTFSKDSVEKLKE116
CEP128-TSHRchr1481227780chr14815629822724DRB3-0101AACKTFSKDSVEKLK015
CEP128-TSHRchr1481227780chr14815629822724DRB3-0104CKTFSKDSVEKLKEA217
CEP128-TSHRchr1481227780chr14815629822724DRB3-0104KTFSKDSVEKLKEAV318
CEP128-TSHRchr1481227780chr14815629822724DRB3-0104ACKTFSKDSVEKLKE116
CEP128-TSHRchr1481227780chr14815629822724DRB3-0104AACKTFSKDSVEKLK015
CEP128-TSHRchr1481227780chr14815629822724DRB3-0105CKTFSKDSVEKLKEA217
CEP128-TSHRchr1481227780chr14815629822724DRB3-0105KTFSKDSVEKLKEAV318
CEP128-TSHRchr1481227780chr14815629822724DRB3-0105ACKTFSKDSVEKLKE116
CEP128-TSHRchr1481227780chr14815629822724DRB3-0105AACKTFSKDSVEKLK015
CEP128-TSHRchr1481227780chr14815629822724DRB3-0108CKTFSKDSVEKLKEA217
CEP128-TSHRchr1481227780chr14815629822724DRB3-0108KTFSKDSVEKLKEAV318
CEP128-TSHRchr1481227780chr14815629822724DRB3-0108ACKTFSKDSVEKLKE116
CEP128-TSHRchr1481227780chr14815629822724DRB3-0108AACKTFSKDSVEKLK015
CEP128-TSHRchr1481227780chr14815629822724DRB3-0109CKTFSKDSVEKLKEA217
CEP128-TSHRchr1481227780chr14815629822724DRB3-0109KTFSKDSVEKLKEAV318
CEP128-TSHRchr1481227780chr14815629822724DRB3-0109ACKTFSKDSVEKLKE116
CEP128-TSHRchr1481227780chr14815629822724DRB3-0111CKTFSKDSVEKLKEA217
CEP128-TSHRchr1481227780chr14815629822724DRB3-0111KTFSKDSVEKLKEAV318
CEP128-TSHRchr1481227780chr14815629822724DRB3-0111ACKTFSKDSVEKLKE116
CEP128-TSHRchr1481227780chr14815629822724DRB3-0111AACKTFSKDSVEKLK015
CEP128-TSHRchr1481227780chr14815629822724DRB3-0112CKTFSKDSVEKLKEA217
CEP128-TSHRchr1481227780chr14815629822724DRB3-0112KTFSKDSVEKLKEAV318
CEP128-TSHRchr1481227780chr14815629822724DRB3-0112ACKTFSKDSVEKLKE116
CEP128-TSHRchr1481227780chr14815629822724DRB3-0112AACKTFSKDSVEKLK015
CEP128-TSHRchr1481227780chr14815629822724DRB3-0113CKTFSKDSVEKLKEA217
CEP128-TSHRchr1481227780chr14815629822724DRB3-0113KTFSKDSVEKLKEAV318
CEP128-TSHRchr1481227780chr14815629822724DRB3-0113ACKTFSKDSVEKLKE116
CEP128-TSHRchr1481227780chr14815629822724DRB3-0113AACKTFSKDSVEKLK015
CEP128-TSHRchr1481227780chr14815629822724DRB3-0114CKTFSKDSVEKLKEA217
CEP128-TSHRchr1481227780chr14815629822724DRB3-0114KTFSKDSVEKLKEAV318
CEP128-TSHRchr1481227780chr14815629822724DRB3-0114ACKTFSKDSVEKLKE116
CEP128-TSHRchr1481227780chr14815629822724DRB3-0303CKTFSKDSVEKLKEA217
CEP128-TSHRchr1481227780chr14815629822724DRB3-0303KTFSKDSVEKLKEAV318

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Fusion breakpoint peptide structures of CEP128-TSHR

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
8681SKDSVEKLKEAVQQCEP128TSHRchr1481227780chr14815629822724

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CEP128-TSHR

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-B14:023BVN8681SKDSVEKLKEAVQQ-7.15543-7.26883
HLA-B14:023BVN8681SKDSVEKLKEAVQQ-4.77435-5.80965
HLA-B52:013W398681SKDSVEKLKEAVQQ-6.80875-6.92215
HLA-B52:013W398681SKDSVEKLKEAVQQ-4.20386-5.23916
HLA-A11:014UQ28681SKDSVEKLKEAVQQ-7.5194-8.5547
HLA-A11:014UQ28681SKDSVEKLKEAVQQ-6.9601-7.0735
HLA-A24:025HGA8681SKDSVEKLKEAVQQ-7.52403-7.63743
HLA-A24:025HGA8681SKDSVEKLKEAVQQ-5.82433-6.85963
HLA-B27:056PYJ8681SKDSVEKLKEAVQQ-3.28285-4.31815
HLA-B44:053DX88681SKDSVEKLKEAVQQ-5.91172-6.94702
HLA-B44:053DX88681SKDSVEKLKEAVQQ-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of CEP128-TSHR

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
CEP128-TSHRchr1481227780chr14815629821021VEKLKEAVQQWAAATTAAAAGAAGCTGTACAACAATGGCTTTAC
CEP128-TSHRchr1481227780chr14815629821121EKLKEAVQQWTTAAAAGAAGCTGTACAACAATGGCTTTAC
CEP128-TSHRchr1481227780chr14815629821221KLKEAVQQWAAAGAAGCTGTACAACAATGGCTTTAC
CEP128-TSHRchr1481227780chr14815629821222KLKEAVQQWLAAAGAAGCTGTACAACAATGGCTTTACTTC
CEP128-TSHRchr1481227780chr14815629821223KLKEAVQQWLYAAAGAAGCTGTACAACAATGGCTTTACTTCAGT
CEP128-TSHRchr1481227780chr1481562982314KTFSKDSVEKLTTCTCCAAGGACTCAGTGGAGAAATTAAAAGAA
CEP128-TSHRchr1481227780chr1481562982514FSKDSVEKLAAGGACTCAGTGGAGAAATTAAAAGAA
CEP128-TSHRchr1481227780chr1481562982614SKDSVEKLGACTCAGTGGAGAAATTAAAAGAA
CEP128-TSHRchr1481227780chr1481562982817DSVEKLKEAGTGGAGAAATTAAAAGAAGCTGTACAA

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
CEP128-TSHRchr1481227780chr1481562982015AACKTFSKDSVEKLKTGTAAAACATTCTCCAAGGACTCAGTGGAGAAATTAAAAGAAGCT
CEP128-TSHRchr1481227780chr1481562982116ACKTFSKDSVEKLKEAAAACATTCTCCAAGGACTCAGTGGAGAAATTAAAAGAAGCTGTA
CEP128-TSHRchr1481227780chr1481562982217CKTFSKDSVEKLKEAACATTCTCCAAGGACTCAGTGGAGAAATTAAAAGAAGCTGTACAA
CEP128-TSHRchr1481227780chr1481562982318KTFSKDSVEKLKEAVTTCTCCAAGGACTCAGTGGAGAAATTAAAAGAAGCTGTACAACAA

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Information of the samples that have these potential fusion neoantigens of CEP128-TSHR

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
BLCACEP128-TSHRchr1481227780ENST00000281129chr1481562982ENST00000298171TCGA-C4-A0F7

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Potential target of CAR-T therapy development for CEP128-TSHR

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
TgeneTSHRchr14:81227780chr14:81562982ENST0000034244359414_4410254.0TransmembraneHelical%3B Name%3D1
TgeneTSHRchr14:81227780chr14:81562982ENST0000034244359451_4730254.0TransmembraneHelical%3B Name%3D2
TgeneTSHRchr14:81227780chr14:81562982ENST0000034244359495_5170254.0TransmembraneHelical%3B Name%3D3
TgeneTSHRchr14:81227780chr14:81562982ENST0000034244359538_5600254.0TransmembraneHelical%3B Name%3D4
TgeneTSHRchr14:81227780chr14:81562982ENST0000034244359581_6020254.0TransmembraneHelical%3B Name%3D5
TgeneTSHRchr14:81227780chr14:81562982ENST0000034244359626_6490254.0TransmembraneHelical%3B Name%3D6
TgeneTSHRchr14:81227780chr14:81562982ENST0000034244359661_6820254.0TransmembraneHelical%3B Name%3D7
TgeneTSHRchr14:81227780chr14:81562982ENST0000055443559414_4410275.0TransmembraneHelical%3B Name%3D1
TgeneTSHRchr14:81227780chr14:81562982ENST0000055443559451_4730275.0TransmembraneHelical%3B Name%3D2
TgeneTSHRchr14:81227780chr14:81562982ENST0000055443559495_5170275.0TransmembraneHelical%3B Name%3D3
TgeneTSHRchr14:81227780chr14:81562982ENST0000055443559538_5600275.0TransmembraneHelical%3B Name%3D4
TgeneTSHRchr14:81227780chr14:81562982ENST0000055443559581_6020275.0TransmembraneHelical%3B Name%3D5
TgeneTSHRchr14:81227780chr14:81562982ENST0000055443559626_6490275.0TransmembraneHelical%3B Name%3D6
TgeneTSHRchr14:81227780chr14:81562982ENST0000055443559661_6820275.0TransmembraneHelical%3B Name%3D7
TgeneTSHRchr14:81227781chr14:81562983ENST0000034244359414_4410254.0TransmembraneHelical%3B Name%3D1
TgeneTSHRchr14:81227781chr14:81562983ENST0000034244359451_4730254.0TransmembraneHelical%3B Name%3D2
TgeneTSHRchr14:81227781chr14:81562983ENST0000034244359495_5170254.0TransmembraneHelical%3B Name%3D3
TgeneTSHRchr14:81227781chr14:81562983ENST0000034244359538_5600254.0TransmembraneHelical%3B Name%3D4
TgeneTSHRchr14:81227781chr14:81562983ENST0000034244359581_6020254.0TransmembraneHelical%3B Name%3D5
TgeneTSHRchr14:81227781chr14:81562983ENST0000034244359626_6490254.0TransmembraneHelical%3B Name%3D6
TgeneTSHRchr14:81227781chr14:81562983ENST0000034244359661_6820254.0TransmembraneHelical%3B Name%3D7
TgeneTSHRchr14:81227781chr14:81562983ENST0000055443559414_4410275.0TransmembraneHelical%3B Name%3D1
TgeneTSHRchr14:81227781chr14:81562983ENST0000055443559451_4730275.0TransmembraneHelical%3B Name%3D2
TgeneTSHRchr14:81227781chr14:81562983ENST0000055443559495_5170275.0TransmembraneHelical%3B Name%3D3
TgeneTSHRchr14:81227781chr14:81562983ENST0000055443559538_5600275.0TransmembraneHelical%3B Name%3D4
TgeneTSHRchr14:81227781chr14:81562983ENST0000055443559581_6020275.0TransmembraneHelical%3B Name%3D5
TgeneTSHRchr14:81227781chr14:81562983ENST0000055443559626_6490275.0TransmembraneHelical%3B Name%3D6
TgeneTSHRchr14:81227781chr14:81562983ENST0000055443559661_6820275.0TransmembraneHelical%3B Name%3D7

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 CEP128-TSHR

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 CEP128-TSHR

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