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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:NTM-CTNNA2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: NTM-CTNNA2
FusionPDB ID: 60652
FusionGDB2.0 ID: 60652
HgeneTgene
Gene symbol

NTM

CTNNA2

Gene ID

50863

1496

Gene nameneurotrimincatenin alpha 2
SynonymsCEPU-1|HNT|IGLON2|NTRICAP-R|CAPR|CDCBM9|CT114|CTNR
Cytomap

11q25

2p12

Type of geneprotein-codingprotein-coding
DescriptionneurotriminIgLON family member 2catenin alpha-2alpha-N-cateninalpha-catenin-related proteincadherin-associated protein, relatedcancer/testis antigen 114catenin (cadherin-associated protein), alpha 2
Modification date2020031320200313
UniProtAcc.

P26232

Main function of 5'-partner protein: FUNCTION: May function as a linker between cadherin adhesion receptors and the cytoskeleton to regulate cell-cell adhesion and differentiation in the nervous system (By similarity). Required for proper regulation of cortical neuronal migration and neurite growth (PubMed:30013181). It acts as negative regulator of Arp2/3 complex activity and Arp2/3-mediated actin polymerization (PubMed:30013181). It thereby suppresses excessive actin branching which would impair neurite growth and stability (PubMed:30013181). Regulates morphological plasticity of synapses and cerebellar and hippocampal lamination during development. Functions in the control of startle modulation (By similarity). {ECO:0000250|UniProtKB:Q61301, ECO:0000269|PubMed:30013181}.
Ensembl transtripts involved in fusion geneENST idsENST00000474900, ENST00000374784, 
ENST00000374786, ENST00000374791, 
ENST00000425719, ENST00000427481, 
ENST00000539799, 		ENST00000361291, 
ENST00000402739, ENST00000466387, 
ENST00000496558, ENST00000540488, 
ENST00000541047, ENST00000343114, 
ENST00000409266, ENST00000496251, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score15 X 15 X 7=157526 X 24 X 10=6240
# samples 1728
** MAII scorelog2(17/1575*10)=-3.21174517713694
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(28/6240*10)=-4.47804729680464
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: NTM [Title/Abstract] AND CTNNA2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: NTM [Title/Abstract] AND CTNNA2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)NTM(132082041)-CTNNA2(80085139), # samples:2
Anticipated loss of major functional domain due to fusion event.NTM-CTNNA2 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.
NTM-CTNNA2 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.
NTM-CTNNA2 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.
NTM-CTNNA2 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/chr11:132082041/chr2:80085139)
- 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 NTM (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 CTNNA2 (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)
ENST00000374791NTMchr11132082041+ENST00000466387CTNNA2chr280085139+41828553293274981
ENST00000374791NTMchr11132082041+ENST00000496558CTNNA2chr280085139+41838553293274981
ENST00000374791NTMchr11132082041+ENST00000361291CTNNA2chr280085139+32758553293274982
ENST00000374791NTMchr11132082041+ENST00000402739CTNNA2chr280085139+423685532934181029
ENST00000374791NTMchr11132082041+ENST00000540488CTNNA2chr280085139+31408553293139937
ENST00000374791NTMchr11132082041+ENST00000541047CTNNA2chr280085139+41828553293274981
ENST00000539799NTMchr11132082041+ENST00000466387CTNNA2chr280085139+385352602945981
ENST00000539799NTMchr11132082041+ENST00000496558CTNNA2chr280085139+385452602945981
ENST00000539799NTMchr11132082041+ENST00000361291CTNNA2chr280085139+294652602945981
ENST00000539799NTMchr11132082041+ENST00000402739CTNNA2chr280085139+3907526030891029
ENST00000539799NTMchr11132082041+ENST00000540488CTNNA2chr280085139+281152602810936
ENST00000539799NTMchr11132082041+ENST00000541047CTNNA2chr280085139+385352602945981
ENST00000427481NTMchr11132082041+ENST00000466387CTNNA2chr280085139+382649902918972
ENST00000427481NTMchr11132082041+ENST00000496558CTNNA2chr280085139+382749902918972
ENST00000427481NTMchr11132082041+ENST00000361291CTNNA2chr280085139+291949902918972
ENST00000427481NTMchr11132082041+ENST00000402739CTNNA2chr280085139+3880499030621020
ENST00000427481NTMchr11132082041+ENST00000540488CTNNA2chr280085139+278449902783927
ENST00000427481NTMchr11132082041+ENST00000541047CTNNA2chr280085139+382649902918972
ENST00000374786NTMchr11132082041+ENST00000466387CTNNA2chr280085139+4332100515534241089
ENST00000374786NTMchr11132082041+ENST00000496558CTNNA2chr280085139+4333100515534241089
ENST00000374786NTMchr11132082041+ENST00000361291CTNNA2chr280085139+3425100515534241090
ENST00000374786NTMchr11132082041+ENST00000402739CTNNA2chr280085139+4386100515535681137
ENST00000374786NTMchr11132082041+ENST00000540488CTNNA2chr280085139+3290100515532891045
ENST00000374786NTMchr11132082041+ENST00000541047CTNNA2chr280085139+4332100515534241089
ENST00000425719NTMchr11132082041+ENST00000466387CTNNA2chr280085139+387354652965986
ENST00000425719NTMchr11132082041+ENST00000496558CTNNA2chr280085139+387454652965986
ENST00000425719NTMchr11132082041+ENST00000361291CTNNA2chr280085139+296654652965987
ENST00000425719NTMchr11132082041+ENST00000402739CTNNA2chr280085139+3927546531091034
ENST00000425719NTMchr11132082041+ENST00000540488CTNNA2chr280085139+283154652830942
ENST00000425719NTMchr11132082041+ENST00000541047CTNNA2chr280085139+387354652965986
ENST00000374784NTMchr11132082041+ENST00000466387CTNNA2chr280085139+386754052959984
ENST00000374784NTMchr11132082041+ENST00000496558CTNNA2chr280085139+386854052959984
ENST00000374784NTMchr11132082041+ENST00000361291CTNNA2chr280085139+296054052959985
ENST00000374784NTMchr11132082041+ENST00000402739CTNNA2chr280085139+3921540531031032
ENST00000374784NTMchr11132082041+ENST00000540488CTNNA2chr280085139+282554052824940
ENST00000374784NTMchr11132082041+ENST00000541047CTNNA2chr280085139+386754052959984

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
ENST00000374791ENST00000466387NTMchr11132082041+CTNNA2chr280085139+0.0006787680.9993212
ENST00000374791ENST00000496558NTMchr11132082041+CTNNA2chr280085139+0.0006810750.99931896
ENST00000374791ENST00000361291NTMchr11132082041+CTNNA2chr280085139+0.0019864890.9980135
ENST00000374791ENST00000402739NTMchr11132082041+CTNNA2chr280085139+0.0015937640.99840623
ENST00000374791ENST00000540488NTMchr11132082041+CTNNA2chr280085139+0.0021286670.9978713
ENST00000374791ENST00000541047NTMchr11132082041+CTNNA2chr280085139+0.0006787680.9993212
ENST00000539799ENST00000466387NTMchr11132082041+CTNNA2chr280085139+0.0008894650.9991105
ENST00000539799ENST00000496558NTMchr11132082041+CTNNA2chr280085139+0.0008945480.9991054
ENST00000539799ENST00000361291NTMchr11132082041+CTNNA2chr280085139+0.0028767270.9971233
ENST00000539799ENST00000402739NTMchr11132082041+CTNNA2chr280085139+0.0017109650.99828905
ENST00000539799ENST00000540488NTMchr11132082041+CTNNA2chr280085139+0.0034992410.99650073
ENST00000539799ENST00000541047NTMchr11132082041+CTNNA2chr280085139+0.0008894650.9991105
ENST00000427481ENST00000466387NTMchr11132082041+CTNNA2chr280085139+0.0025650760.9974349
ENST00000427481ENST00000496558NTMchr11132082041+CTNNA2chr280085139+0.0025753740.9974246
ENST00000427481ENST00000361291NTMchr11132082041+CTNNA2chr280085139+0.0067685910.9932314
ENST00000427481ENST00000402739NTMchr11132082041+CTNNA2chr280085139+0.0017214540.9982785
ENST00000427481ENST00000540488NTMchr11132082041+CTNNA2chr280085139+0.0081756760.9918243
ENST00000427481ENST00000541047NTMchr11132082041+CTNNA2chr280085139+0.0025650760.9974349
ENST00000374786ENST00000466387NTMchr11132082041+CTNNA2chr280085139+0.0009599040.99904007
ENST00000374786ENST00000496558NTMchr11132082041+CTNNA2chr280085139+0.0009634290.99903655
ENST00000374786ENST00000361291NTMchr11132082041+CTNNA2chr280085139+0.0024654290.9975345
ENST00000374786ENST00000402739NTMchr11132082041+CTNNA2chr280085139+0.0020536810.9979463
ENST00000374786ENST00000540488NTMchr11132082041+CTNNA2chr280085139+0.0023914370.99760854
ENST00000374786ENST00000541047NTMchr11132082041+CTNNA2chr280085139+0.0009599040.99904007
ENST00000425719ENST00000466387NTMchr11132082041+CTNNA2chr280085139+0.0007837010.9992163
ENST00000425719ENST00000496558NTMchr11132082041+CTNNA2chr280085139+0.0007859910.99921393
ENST00000425719ENST00000361291NTMchr11132082041+CTNNA2chr280085139+0.0025480050.99745196
ENST00000425719ENST00000402739NTMchr11132082041+CTNNA2chr280085139+0.0014982510.9985018
ENST00000425719ENST00000540488NTMchr11132082041+CTNNA2chr280085139+0.0031988130.99680114
ENST00000425719ENST00000541047NTMchr11132082041+CTNNA2chr280085139+0.0007837010.9992163
ENST00000374784ENST00000466387NTMchr11132082041+CTNNA2chr280085139+0.0007750420.9992249
ENST00000374784ENST00000496558NTMchr11132082041+CTNNA2chr280085139+0.0007789330.9992211
ENST00000374784ENST00000361291NTMchr11132082041+CTNNA2chr280085139+0.0025279830.997472
ENST00000374784ENST00000402739NTMchr11132082041+CTNNA2chr280085139+0.0014747890.9985252
ENST00000374784ENST00000540488NTMchr11132082041+CTNNA2chr280085139+0.0031707440.9968292
ENST00000374784ENST00000541047NTMchr11132082041+CTNNA2chr280085139+0.0007750420.9992249

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 NTM-CTNNA2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
NTMchr11132082041CTNNA2chr2800851391005283PEPTVTWRHISPKGETMRIASSEFAD
NTMchr11132082041CTNNA2chr280085139499166PEPTVTWRHISPKGETMRIASSEFAD
NTMchr11132082041CTNNA2chr280085139526175PEPTVTWRHISPKGETMRIASSEFAD
NTMchr11132082041CTNNA2chr280085139540178PEPTVTWRHISPKGETMRIASSEFAD
NTMchr11132082041CTNNA2chr280085139546180PEPTVTWRHISPKGETMRIASSEFAD
NTMchr11132082041CTNNA2chr280085139855175PEPTVTWRHISPKGETMRIASSEFAD

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Potential FusionNeoAntigen Information of NTM-CTNNA2 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.
NTM-CTNNA2_132082041_80085139.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)
NTM-CTNNA2chr11132082041chr280085139540HLA-B15:02HISPKGETM0.95130.9492817
NTM-CTNNA2chr11132082041chr280085139540HLA-A26:03HISPKGETM0.71760.5538817
NTM-CTNNA2chr11132082041chr280085139540HLA-B35:03HISPKGETM0.58790.93817
NTM-CTNNA2chr11132082041chr280085139540HLA-B35:02HISPKGETM0.23460.9744817
NTM-CTNNA2chr11132082041chr280085139540HLA-B35:04HISPKGETM0.23460.9744817
NTM-CTNNA2chr11132082041chr280085139540HLA-B39:24RHISPKGETM0.99540.5973717
NTM-CTNNA2chr11132082041chr280085139540HLA-B39:01RHISPKGETM0.99020.8429717
NTM-CTNNA2chr11132082041chr280085139540HLA-B38:02RHISPKGETM0.96330.9027717
NTM-CTNNA2chr11132082041chr280085139540HLA-B38:01RHISPKGETM0.96270.9106717
NTM-CTNNA2chr11132082041chr280085139540HLA-B15:18RHISPKGETM0.96110.7899717
NTM-CTNNA2chr11132082041chr280085139540HLA-B15:10RHISPKGETM0.9560.664717
NTM-CTNNA2chr11132082041chr280085139540HLA-B39:13RHISPKGETM0.9550.8839717
NTM-CTNNA2chr11132082041chr280085139540HLA-B07:10RHISPKGETM0.94080.5014717
NTM-CTNNA2chr11132082041chr280085139540HLA-B48:01RHISPKGETM0.74170.5102717
NTM-CTNNA2chr11132082041chr280085139540HLA-B15:37RHISPKGETM0.64250.7135717
NTM-CTNNA2chr11132082041chr280085139540HLA-C01:17ISPKGETM0.99720.8751917
NTM-CTNNA2chr11132082041chr280085139540HLA-C01:30ISPKGETM0.97370.9261917
NTM-CTNNA2chr11132082041chr280085139540HLA-C03:07HISPKGETM0.99480.9693817
NTM-CTNNA2chr11132082041chr280085139540HLA-C03:08HISPKGETM0.99450.9076817
NTM-CTNNA2chr11132082041chr280085139540HLA-C03:19HISPKGETM0.9940.9883817
NTM-CTNNA2chr11132082041chr280085139540HLA-C12:12HISPKGETM0.97750.9817
NTM-CTNNA2chr11132082041chr280085139540HLA-C01:17HISPKGETM0.95320.8989817
NTM-CTNNA2chr11132082041chr280085139540HLA-B15:21HISPKGETM0.9530.8982817
NTM-CTNNA2chr11132082041chr280085139540HLA-C08:13HISPKGETM0.85760.9464817
NTM-CTNNA2chr11132082041chr280085139540HLA-C08:04HISPKGETM0.85760.9464817
NTM-CTNNA2chr11132082041chr280085139540HLA-B14:03HISPKGETM0.78050.8431817
NTM-CTNNA2chr11132082041chr280085139540HLA-B15:31HISPKGETM0.6510.9065817
NTM-CTNNA2chr11132082041chr280085139540HLA-C01:30HISPKGETM0.6270.9248817
NTM-CTNNA2chr11132082041chr280085139540HLA-C02:06HISPKGETM0.60180.9263817
NTM-CTNNA2chr11132082041chr280085139540HLA-C03:14HISPKGETM0.53340.985817
NTM-CTNNA2chr11132082041chr280085139540HLA-B51:07SPKGETMRI0.39270.74321019
NTM-CTNNA2chr11132082041chr280085139540HLA-C08:03HISPKGETM0.27930.974817
NTM-CTNNA2chr11132082041chr280085139540HLA-B35:12HISPKGETM0.23460.9744817
NTM-CTNNA2chr11132082041chr280085139540HLA-B39:10HISPKGETM0.13370.8737817
NTM-CTNNA2chr11132082041chr280085139540HLA-B39:10SPKGETMRI0.12480.70151019
NTM-CTNNA2chr11132082041chr280085139540HLA-B39:09RHISPKGETM0.98980.6878717
NTM-CTNNA2chr11132082041chr280085139540HLA-B39:12RHISPKGETM0.98810.848717
NTM-CTNNA2chr11132082041chr280085139540HLA-B39:05RHISPKGETM0.96470.832717
NTM-CTNNA2chr11132082041chr280085139540HLA-B14:03RHISPKGETM0.95480.7851717
NTM-CTNNA2chr11132082041chr280085139540HLA-B39:12WRHISPKGETM0.9990.835617
NTM-CTNNA2chr11132082041chr280085139540HLA-C01:02ISPKGETM0.99750.8748917
NTM-CTNNA2chr11132082041chr280085139540HLA-C01:03ISPKGETM0.99680.896917
NTM-CTNNA2chr11132082041chr280085139540HLA-C03:04HISPKGETM0.99740.9863817
NTM-CTNNA2chr11132082041chr280085139540HLA-C03:03HISPKGETM0.99740.9863817
NTM-CTNNA2chr11132082041chr280085139540HLA-C03:02HISPKGETM0.99510.9636817
NTM-CTNNA2chr11132082041chr280085139540HLA-C03:67HISPKGETM0.99360.9795817
NTM-CTNNA2chr11132082041chr280085139540HLA-C03:05HISPKGETM0.98620.9322817
NTM-CTNNA2chr11132082041chr280085139540HLA-C03:17HISPKGETM0.98440.9603817
NTM-CTNNA2chr11132082041chr280085139540HLA-B15:11HISPKGETM0.97870.8678817
NTM-CTNNA2chr11132082041chr280085139540HLA-C12:02HISPKGETM0.97830.9393817
NTM-CTNNA2chr11132082041chr280085139540HLA-B15:08HISPKGETM0.97620.8606817
NTM-CTNNA2chr11132082041chr280085139540HLA-B35:43HISPKGETM0.97150.8612817
NTM-CTNNA2chr11132082041chr280085139540HLA-C01:02HISPKGETM0.96560.9011817
NTM-CTNNA2chr11132082041chr280085139540HLA-C16:04HISPKGETM0.96270.9553817
NTM-CTNNA2chr11132082041chr280085139540HLA-C01:03HISPKGETM0.94470.9082817
NTM-CTNNA2chr11132082041chr280085139540HLA-B35:11HISPKGETM0.9410.8892817
NTM-CTNNA2chr11132082041chr280085139540HLA-C03:06HISPKGETM0.89650.9872817
NTM-CTNNA2chr11132082041chr280085139540HLA-B07:13HISPKGETM0.85960.7241817
NTM-CTNNA2chr11132082041chr280085139540HLA-C16:01HISPKGETM0.73390.9596817
NTM-CTNNA2chr11132082041chr280085139540HLA-B15:73HISPKGETM0.73090.8972817
NTM-CTNNA2chr11132082041chr280085139540HLA-B08:12HISPKGETM0.7250.5892817
NTM-CTNNA2chr11132082041chr280085139540HLA-B15:30HISPKGETM0.64290.7999817
NTM-CTNNA2chr11132082041chr280085139540HLA-C02:02HISPKGETM0.60440.9588817
NTM-CTNNA2chr11132082041chr280085139540HLA-C02:10HISPKGETM0.60440.9588817
NTM-CTNNA2chr11132082041chr280085139540HLA-B35:13HISPKGETM0.58550.936817
NTM-CTNNA2chr11132082041chr280085139540HLA-B78:02SPKGETMRI0.42320.56341019
NTM-CTNNA2chr11132082041chr280085139540HLA-C08:01HISPKGETM0.27930.974817
NTM-CTNNA2chr11132082041chr280085139540HLA-B35:09HISPKGETM0.23460.9744817
NTM-CTNNA2chr11132082041chr280085139540HLA-B67:01SPKGETMRI0.17370.50711019
NTM-CTNNA2chr11132082041chr280085139540HLA-C17:01HISPKGETM0.07770.8996817
NTM-CTNNA2chr11132082041chr280085139540HLA-B39:31RHISPKGETM0.99040.8446717
NTM-CTNNA2chr11132082041chr280085139540HLA-B39:02RHISPKGETM0.98990.8846717
NTM-CTNNA2chr11132082041chr280085139540HLA-B38:05RHISPKGETM0.96270.9106717
NTM-CTNNA2chr11132082041chr280085139540HLA-B39:11RHISPKGETM0.84380.7212717
NTM-CTNNA2chr11132082041chr280085139540HLA-B15:09RHISPKGETM0.78060.7356717

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Potential FusionNeoAntigen Information of NTM-CTNNA2 in HLA II

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

check button Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).
Fusion geneHchrHbpTgeneTchrTbpHLA IIFusionNeoAntigen peptideNeoantigen start (at BP 13)Neoantigen end (at BP 13)

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Fusion breakpoint peptide structures of NTM-CTNNA2

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
10535WRHISPKGETMRIANTMCTNNA2chr11132082041chr280085139540

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of NTM-CTNNA2

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-B14:023BVN10535WRHISPKGETMRIA-7.9962-8.1096
HLA-B14:023BVN10535WRHISPKGETMRIA-5.70842-6.74372
HLA-B52:013W3910535WRHISPKGETMRIA-6.83737-6.95077
HLA-B52:013W3910535WRHISPKGETMRIA-4.4836-5.5189
HLA-A11:014UQ210535WRHISPKGETMRIA-10.0067-10.1201
HLA-A11:014UQ210535WRHISPKGETMRIA-9.03915-10.0745
HLA-A24:025HGA10535WRHISPKGETMRIA-6.56204-6.67544
HLA-A24:025HGA10535WRHISPKGETMRIA-5.42271-6.45801
HLA-B44:053DX810535WRHISPKGETMRIA-7.85648-8.89178
HLA-B44:053DX810535WRHISPKGETMRIA-5.3978-5.5112
HLA-A02:016TDR10535WRHISPKGETMRIA-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of NTM-CTNNA2

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
NTM-CTNNA2chr11132082041chr2800851391019SPKGETMRICTCCCAAAGGTGAGACGATGCGGATCG
NTM-CTNNA2chr11132082041chr280085139617WRHISPKGETMGGAGACACATCTCTCCCAAAGGTGAGACGATGC
NTM-CTNNA2chr11132082041chr280085139717RHISPKGETMGACACATCTCTCCCAAAGGTGAGACGATGC
NTM-CTNNA2chr11132082041chr280085139817HISPKGETMACATCTCTCCCAAAGGTGAGACGATGC
NTM-CTNNA2chr11132082041chr280085139917ISPKGETMTCTCTCCCAAAGGTGAGACGATGC

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

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Information of the samples that have these potential fusion neoantigens of NTM-CTNNA2

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
SARCNTM-CTNNA2chr11132082041ENST00000374784chr280085139ENST00000361291TCGA-SI-A71O-01A

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Potential target of CAR-T therapy development for NTM-CTNNA2

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 NTM-CTNNA2

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 NTM-CTNNA2

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