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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:NUMB-TSHR

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: NUMB-TSHR
FusionPDB ID: 60951
FusionGDB2.0 ID: 60951
HgeneTgene
Gene symbol

NUMB

TSHR

Gene ID

8650

7253

Gene nameNUMB endocytic adaptor proteinthyroid stimulating hormone receptor
SynonymsC14orf41|S171|c14_5527CHNG1|LGR3|hTSHR-I
Cytomap

14q24.2-q24.3

14q31.1

Type of geneprotein-codingprotein-coding
Descriptionprotein numb homologh-Numbnumb homologthyrotropin receptorTSH receptorseven transmembrane helix receptorthyrotropin receptor-I, hTSHR-I
Modification date2020031320200329
UniProtAcc

NUMBL

Main function of 5'-partner protein: 609		.
Ensembl transtripts involved in fusion geneENST idsENST00000355058, ENST00000356296, 
ENST00000359560, ENST00000454166, 
ENST00000535282, ENST00000544991, 
ENST00000554521, ENST00000554546, 
ENST00000555238, ENST00000555394, 
ENST00000555738, ENST00000557597, 
ENST00000559312, ENST00000560335, 
ENST00000556600, ENST00000556772, 
ENST00000557096, ENST00000298171, 
ENST00000342443, ENST00000541158, 
ENST00000554263, ENST00000554435, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score24 X 15 X 9=32408 X 7 X 7=392
# samples 269
** MAII scorelog2(26/3240*10)=-3.63941028474353
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: NUMB [Title/Abstract] AND TSHR [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

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

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)NUMB(73822334)-TSHR(81528492), # samples:2
Anticipated loss of major functional domain due to fusion event.NUMB-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.
NUMB-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.
NUMB-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.
NUMB-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.
NUMB-TSHR seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
NUMB-TSHR seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
NUMB-TSHR seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
NUMB-TSHR seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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


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/chr14:73822334/chr14:81528492)
- 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 NUMB (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)
ENST00000356296NUMBchr1473822334-ENST00000541158TSHRchr1481528492+44794053162529737
ENST00000356296NUMBchr1473822334-ENST00000342443TSHRchr1481528492+1266405316996226
ENST00000356296NUMBchr1473822334-ENST00000298171TSHRchr1481528492+44794053162529737
ENST00000356296NUMBchr1473822334-ENST00000554263TSHRchr1481528492+1393405316930204
ENST00000356296NUMBchr1473822334-ENST00000554435TSHRchr1481528492+12984053161059247
ENST00000355058NUMBchr1473822334-ENST00000541158TSHRchr1481528492+44794053162529737
ENST00000355058NUMBchr1473822334-ENST00000342443TSHRchr1481528492+1266405316996226
ENST00000355058NUMBchr1473822334-ENST00000298171TSHRchr1481528492+44794053162529737
ENST00000355058NUMBchr1473822334-ENST00000554263TSHRchr1481528492+1393405316930204
ENST00000355058NUMBchr1473822334-ENST00000554435TSHRchr1481528492+12984053161059247
ENST00000359560NUMBchr1473822334-ENST00000541158TSHRchr1481528492+44794053162529737
ENST00000359560NUMBchr1473822334-ENST00000342443TSHRchr1481528492+1266405316996226
ENST00000359560NUMBchr1473822334-ENST00000298171TSHRchr1481528492+44794053162529737
ENST00000359560NUMBchr1473822334-ENST00000554263TSHRchr1481528492+1393405316930204
ENST00000359560NUMBchr1473822334-ENST00000554435TSHRchr1481528492+12984053161059247
ENST00000535282NUMBchr1473822334-ENST00000541158TSHRchr1481528492+44013272382451737
ENST00000535282NUMBchr1473822334-ENST00000342443TSHRchr1481528492+1188327238918226
ENST00000535282NUMBchr1473822334-ENST00000298171TSHRchr1481528492+44013272382451737
ENST00000535282NUMBchr1473822334-ENST00000554263TSHRchr1481528492+1315327238852204
ENST00000535282NUMBchr1473822334-ENST00000554435TSHRchr1481528492+1220327238981247

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
ENST00000356296ENST00000541158NUMBchr1473822334-TSHRchr1481528492+0.001536440.99846363
ENST00000356296ENST00000342443NUMBchr1473822334-TSHRchr1481528492+0.0031371270.9968629
ENST00000356296ENST00000298171NUMBchr1473822334-TSHRchr1481528492+0.001536440.99846363
ENST00000356296ENST00000554263NUMBchr1473822334-TSHRchr1481528492+0.0039854960.9960145
ENST00000356296ENST00000554435NUMBchr1473822334-TSHRchr1481528492+0.0070025420.9929974
ENST00000355058ENST00000541158NUMBchr1473822334-TSHRchr1481528492+0.001536440.99846363
ENST00000355058ENST00000342443NUMBchr1473822334-TSHRchr1481528492+0.0031371270.9968629
ENST00000355058ENST00000298171NUMBchr1473822334-TSHRchr1481528492+0.001536440.99846363
ENST00000355058ENST00000554263NUMBchr1473822334-TSHRchr1481528492+0.0039854960.9960145
ENST00000355058ENST00000554435NUMBchr1473822334-TSHRchr1481528492+0.0070025420.9929974
ENST00000359560ENST00000541158NUMBchr1473822334-TSHRchr1481528492+0.001536440.99846363
ENST00000359560ENST00000342443NUMBchr1473822334-TSHRchr1481528492+0.0031371270.9968629
ENST00000359560ENST00000298171NUMBchr1473822334-TSHRchr1481528492+0.001536440.99846363
ENST00000359560ENST00000554263NUMBchr1473822334-TSHRchr1481528492+0.0039854960.9960145
ENST00000359560ENST00000554435NUMBchr1473822334-TSHRchr1481528492+0.0070025420.9929974
ENST00000535282ENST00000541158NUMBchr1473822334-TSHRchr1481528492+0.0014453280.99855465
ENST00000535282ENST00000342443NUMBchr1473822334-TSHRchr1481528492+0.001957270.9980427
ENST00000535282ENST00000298171NUMBchr1473822334-TSHRchr1481528492+0.0014453280.99855465
ENST00000535282ENST00000554263NUMBchr1473822334-TSHRchr1481528492+0.0029928190.9970072
ENST00000535282ENST00000554435NUMBchr1473822334-TSHRchr1481528492+0.0047381120.9952619

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 NUMB-TSHR

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
NUMBchr1473822334TSHRchr148152849232729KKAFAPENVASRLRKLIETHLRTIPS
NUMBchr1473822334TSHRchr148152849240529KKAFAPENVASRLRKLIETHLRTIPS

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Potential FusionNeoAntigen Information of NUMB-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.
NUMB-TSHR_73822334_81528492.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)
NUMB-TSHRchr1473822334chr1481528492405HLA-B27:07LRKLIETHL0.99880.70071221
NUMB-TSHRchr1473822334chr1481528492405HLA-B27:04LRKLIETHL0.99760.95161221
NUMB-TSHRchr1473822334chr1481528492405HLA-B27:02LRKLIETHL0.99730.9451221
NUMB-TSHRchr1473822334chr1481528492405HLA-B27:05LRKLIETHL0.99690.9811221
NUMB-TSHRchr1473822334chr1481528492405HLA-B14:01LRKLIETHL0.98910.94111221
NUMB-TSHRchr1473822334chr1481528492405HLA-B14:02LRKLIETHL0.98910.94111221
NUMB-TSHRchr1473822334chr1481528492405HLA-B08:01NVASRLRKL0.98220.5488716
NUMB-TSHRchr1473822334chr1481528492405HLA-B39:24LRKLIETHL0.97750.75281221
NUMB-TSHRchr1473822334chr1481528492405HLA-B08:09NVASRLRKL0.96130.6333716
NUMB-TSHRchr1473822334chr1481528492405HLA-B07:10LRKLIETHL0.00630.71031221
NUMB-TSHRchr1473822334chr1481528492405HLA-B27:07RLRKLIETHL0.880.72221121
NUMB-TSHRchr1473822334chr1481528492405HLA-B27:07SRLRKLIETHL10.75781021
NUMB-TSHRchr1473822334chr1481528492405HLA-A74:11RLRKLIETHLR0.98460.86851122
NUMB-TSHRchr1473822334chr1481528492405HLA-A74:09RLRKLIETHLR0.98460.86851122
NUMB-TSHRchr1473822334chr1481528492405HLA-A74:03RLRKLIETHLR0.98460.86851122
NUMB-TSHRchr1473822334chr1481528492405HLA-A31:02RLRKLIETHLR0.98190.88451122
NUMB-TSHRchr1473822334chr1481528492405HLA-A31:06RLRKLIETHLR0.90540.68971122
NUMB-TSHRchr1473822334chr1481528492405HLA-B27:14LRKLIETHL0.99720.95691221
NUMB-TSHRchr1473822334chr1481528492405HLA-C07:05LRKLIETHL0.98880.98661221
NUMB-TSHRchr1473822334chr1481528492405HLA-B73:01SRLRKLIET0.98790.72141019
NUMB-TSHRchr1473822334chr1481528492405HLA-C07:95LRKLIETHL0.9840.92861221
NUMB-TSHRchr1473822334chr1481528492405HLA-C07:27LRKLIETHL0.97270.98671221
NUMB-TSHRchr1473822334chr1481528492405HLA-C15:06NVASRLRKL0.96480.905716
NUMB-TSHRchr1473822334chr1481528492405HLA-C07:13LRKLIETHL0.94680.98391221
NUMB-TSHRchr1473822334chr1481528492405HLA-B39:12LRKLIETHL0.94360.98821221
NUMB-TSHRchr1473822334chr1481528492405HLA-C07:29LRKLIETHL0.93350.9821221
NUMB-TSHRchr1473822334chr1481528492405HLA-C07:46LRKLIETHL0.88340.96921221
NUMB-TSHRchr1473822334chr1481528492405HLA-B27:03LRKLIETHL0.8450.98341221
NUMB-TSHRchr1473822334chr1481528492405HLA-C07:19LRKLIETHL0.83680.93631221
NUMB-TSHRchr1473822334chr1481528492405HLA-B15:04RLRKLIETH0.83120.97691120
NUMB-TSHRchr1473822334chr1481528492405HLA-B15:07RLRKLIETH0.82640.92421120
NUMB-TSHRchr1473822334chr1481528492405HLA-C06:03NVASRLRKL0.68360.9972716
NUMB-TSHRchr1473822334chr1481528492405HLA-C12:04NVASRLRKL0.67620.9965716
NUMB-TSHRchr1473822334chr1481528492405HLA-C12:12NVASRLRKL0.6170.9533716
NUMB-TSHRchr1473822334chr1481528492405HLA-B14:03LRKLIETHL0.45640.94371221
NUMB-TSHRchr1473822334chr1481528492405HLA-C12:16LRKLIETHL0.0390.98921221
NUMB-TSHRchr1473822334chr1481528492405HLA-A31:01RLRKLIETHLR0.98930.86231122
NUMB-TSHRchr1473822334chr1481528492405HLA-C16:04VASRLRKL0.84460.9806816
NUMB-TSHRchr1473822334chr1481528492405HLA-C16:02VASRLRKL0.83770.9961816
NUMB-TSHRchr1473822334chr1481528492405HLA-C16:01VASRLRKL0.81320.9871816
NUMB-TSHRchr1473822334chr1481528492405HLA-B27:06LRKLIETHL0.99860.95471221
NUMB-TSHRchr1473822334chr1481528492405HLA-B27:08LRKLIETHL0.99760.96611221
NUMB-TSHRchr1473822334chr1481528492405HLA-B27:09LRKLIETHL0.99740.97831221
NUMB-TSHRchr1473822334chr1481528492405HLA-B27:10LRKLIETHL0.99710.97571221
NUMB-TSHRchr1473822334chr1481528492405HLA-C07:01LRKLIETHL0.98550.92331221
NUMB-TSHRchr1473822334chr1481528492405HLA-B08:18NVASRLRKL0.98220.5488716
NUMB-TSHRchr1473822334chr1481528492405HLA-A30:01RLRKLIETH0.96630.97621120
NUMB-TSHRchr1473822334chr1481528492405HLA-B15:50RLRKLIETH0.93660.96861120
NUMB-TSHRchr1473822334chr1481528492405HLA-A25:01NVASRLRKL0.92090.9367716
NUMB-TSHRchr1473822334chr1481528492405HLA-C03:67NVASRLRKL0.90480.9689716
NUMB-TSHRchr1473822334chr1481528492405HLA-C07:22LRKLIETHL0.88220.92531221
NUMB-TSHRchr1473822334chr1481528492405HLA-C06:08LRKLIETHL0.87530.99681221
NUMB-TSHRchr1473822334chr1481528492405HLA-B15:35RLRKLIETH0.85150.97261120
NUMB-TSHRchr1473822334chr1481528492405HLA-C06:06NVASRLRKL0.80530.9886716
NUMB-TSHRchr1473822334chr1481528492405HLA-C16:04NVASRLRKL0.77160.9819716
NUMB-TSHRchr1473822334chr1481528492405HLA-B08:12NVASRLRKL0.70880.7437716
NUMB-TSHRchr1473822334chr1481528492405HLA-C06:17NVASRLRKL0.66650.996716
NUMB-TSHRchr1473822334chr1481528492405HLA-C06:02NVASRLRKL0.66650.996716
NUMB-TSHRchr1473822334chr1481528492405HLA-C06:08NVASRLRKL0.65070.9929716
NUMB-TSHRchr1473822334chr1481528492405HLA-C12:03NVASRLRKL0.50320.9855716
NUMB-TSHRchr1473822334chr1481528492405HLA-C07:04NVASRLRKL0.47810.931716
NUMB-TSHRchr1473822334chr1481528492405HLA-C16:02NVASRLRKL0.47140.9944716
NUMB-TSHRchr1473822334chr1481528492405HLA-C06:02LRKLIETHL0.11780.99771221
NUMB-TSHRchr1473822334chr1481528492405HLA-C06:17LRKLIETHL0.11780.99771221
NUMB-TSHRchr1473822334chr1481528492405HLA-B27:08SRLRKLIETH0.99970.94241020
NUMB-TSHRchr1473822334chr1481528492405HLA-B27:10RLRKLIETHL0.96630.95481121
NUMB-TSHRchr1473822334chr1481528492405HLA-B27:06RLRKLIETHL0.93210.93121121
NUMB-TSHRchr1473822334chr1481528492405HLA-B27:09RLRKLIETHL0.83260.95521121
NUMB-TSHRchr1473822334chr1481528492405HLA-B27:06SRLRKLIETHL10.94491021
NUMB-TSHRchr1473822334chr1481528492405HLA-B27:09SRLRKLIETHL10.94571021
NUMB-TSHRchr1473822334chr1481528492405HLA-A74:01RLRKLIETHLR0.98460.86851122

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Potential FusionNeoAntigen Information of NUMB-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.
NUMB-TSHR_73822334_81528492.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)
NUMB-TSHRchr1473822334chr1481528492405DRB1-0340KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB1-0466KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB1-1179KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB1-1341KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB1-1385KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB1-1386KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB1-1396KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB1-1402KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB1-1419KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB1-1424KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB1-1441KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB1-1446KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB1-1447KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB1-1489KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB1-1494KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB1-1498KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB5-0101KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB5-0102KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB5-0103KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB5-0104KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB5-0105KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB5-0108NKKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB5-0111KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB5-0113KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB5-0114KKAFAPENVASRLRK015
NUMB-TSHRchr1473822334chr1481528492405DRB5-0203KKAFAPENVASRLRK015

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Fusion breakpoint peptide structures of NUMB-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
1996ENVASRLRKLIETHNUMBTSHRchr1473822334chr1481528492405

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of NUMB-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-B14:023BVN1996ENVASRLRKLIETH-7.9962-8.1096
HLA-B14:023BVN1996ENVASRLRKLIETH-5.70842-6.74372
HLA-B52:013W391996ENVASRLRKLIETH-6.83737-6.95077
HLA-B52:013W391996ENVASRLRKLIETH-4.4836-5.5189
HLA-A11:014UQ21996ENVASRLRKLIETH-10.0067-10.1201
HLA-A11:014UQ21996ENVASRLRKLIETH-9.03915-10.0745
HLA-A24:025HGA1996ENVASRLRKLIETH-6.56204-6.67544
HLA-A24:025HGA1996ENVASRLRKLIETH-5.42271-6.45801
HLA-B44:053DX81996ENVASRLRKLIETH-7.85648-8.89178
HLA-B44:053DX81996ENVASRLRKLIETH-5.3978-5.5112
HLA-A02:016TDR1996ENVASRLRKLIETH-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of NUMB-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
NUMB-TSHRchr1473822334chr14815284921019SRLRKLIETCCGGTTAAGGAAGCTTATTGAGACTCA
NUMB-TSHRchr1473822334chr14815284921020SRLRKLIETHCCGGTTAAGGAAGCTTATTGAGACTCACCT
NUMB-TSHRchr1473822334chr14815284921021SRLRKLIETHLCCGGTTAAGGAAGCTTATTGAGACTCACCTGAG
NUMB-TSHRchr1473822334chr14815284921120RLRKLIETHGTTAAGGAAGCTTATTGAGACTCACCT
NUMB-TSHRchr1473822334chr14815284921121RLRKLIETHLGTTAAGGAAGCTTATTGAGACTCACCTGAG
NUMB-TSHRchr1473822334chr14815284921122RLRKLIETHLRGTTAAGGAAGCTTATTGAGACTCACCTGAGAAC
NUMB-TSHRchr1473822334chr14815284921221LRKLIETHLAAGGAAGCTTATTGAGACTCACCTGAG
NUMB-TSHRchr1473822334chr1481528492716NVASRLRKLTGTAGCTTCCCGGTTAAGGAAGCTTAT
NUMB-TSHRchr1473822334chr1481528492816VASRLRKLAGCTTCCCGGTTAAGGAAGCTTAT

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
NUMB-TSHRchr1473822334chr1481528492015KKAFAPENVASRLRKGAAGGCGTTCGCACCGGAAAATGTAGCTTCCCGGTTAAGGAAGCT

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Information of the samples that have these potential fusion neoantigens of NUMB-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
SKCMNUMB-TSHRchr1473822334ENST00000355058chr1481528492ENST00000298171TCGA-WE-A8ZX-06A

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Potential target of CAR-T therapy development for NUMB-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
TgeneTSHRchr14:73822334chr14:81528492ENST0000034244309414_4410254.0TransmembraneHelical%3B Name%3D1
TgeneTSHRchr14:73822334chr14:81528492ENST0000034244309451_4730254.0TransmembraneHelical%3B Name%3D2
TgeneTSHRchr14:73822334chr14:81528492ENST0000034244309495_5170254.0TransmembraneHelical%3B Name%3D3
TgeneTSHRchr14:73822334chr14:81528492ENST0000034244309538_5600254.0TransmembraneHelical%3B Name%3D4
TgeneTSHRchr14:73822334chr14:81528492ENST0000034244309581_6020254.0TransmembraneHelical%3B Name%3D5
TgeneTSHRchr14:73822334chr14:81528492ENST0000034244309626_6490254.0TransmembraneHelical%3B Name%3D6
TgeneTSHRchr14:73822334chr14:81528492ENST0000034244309661_6820254.0TransmembraneHelical%3B Name%3D7
TgeneTSHRchr14:73822334chr14:81528492ENST0000055443509414_4410275.0TransmembraneHelical%3B Name%3D1
TgeneTSHRchr14:73822334chr14:81528492ENST0000055443509451_4730275.0TransmembraneHelical%3B Name%3D2
TgeneTSHRchr14:73822334chr14:81528492ENST0000055443509495_5170275.0TransmembraneHelical%3B Name%3D3
TgeneTSHRchr14:73822334chr14:81528492ENST0000055443509538_5600275.0TransmembraneHelical%3B Name%3D4
TgeneTSHRchr14:73822334chr14:81528492ENST0000055443509581_6020275.0TransmembraneHelical%3B Name%3D5
TgeneTSHRchr14:73822334chr14:81528492ENST0000055443509626_6490275.0TransmembraneHelical%3B Name%3D6
TgeneTSHRchr14:73822334chr14:81528492ENST0000055443509661_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 NUMB-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 NUMB-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