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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:TNNT3-COL1A1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: TNNT3-COL1A1
FusionPDB ID: 92776
FusionGDB2.0 ID: 92776
HgeneTgene
Gene symbol

TNNT3

COL1A1

Gene ID

7140

1277

Gene nametroponin T3, fast skeletal typecollagen type I alpha 1 chain
SynonymsDA2B2|TNTF|beta-TnTFCAFYD|EDSARTH1|EDSC|OI1|OI2|OI3|OI4
Cytomap

11p15.5

17q21.33

Type of geneprotein-codingprotein-coding
Descriptiontroponin T, fast skeletal muscletroponin T type 3 (skeletal, fast)collagen alpha-1(I) chainalpha-1 type I collagenalpha1(I) procollagencollagen alpha 1 chain type Icollagen alpha-1(I) chain preproproteincollagen of skin, tendon and bone, alpha-1 chaincollagen, type I, alpha 1pro-alpha-1 collagen type 1type I pro
Modification date2020031320200322
UniProtAcc.

P02452

Main function of 5'-partner protein: FUNCTION: Type I collagen is a member of group I collagen (fibrillar forming collagen).
Ensembl transtripts involved in fusion geneENST idsENST00000493234, ENST00000278317, 
ENST00000360603, ENST00000381548, 
ENST00000381549, ENST00000381558, 
ENST00000381561, ENST00000381579, 
ENST00000381589, ENST00000397301, 
ENST00000397304, ENST00000446240, 
ENST00000225964, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score2 X 2 X 2=844 X 105 X 13=60060
# samples 280
** MAII scorelog2(2/8*10)=1.32192809488736log2(80/60060*10)=-6.23026066466979
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: TNNT3 [Title/Abstract] AND COL1A1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: TNNT3 [Title/Abstract] AND COL1A1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)TNNT3(1956115)-COL1A1(48275355), # samples:1
Anticipated loss of major functional domain due to fusion event.TNNT3-COL1A1 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.
TNNT3-COL1A1 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
HgeneTNNT3

GO:0003009

skeletal muscle contraction

17194691

HgeneTNNT3

GO:0006942

regulation of striated muscle contraction

17194691

HgeneTNNT3

GO:0043462

regulation of ATPase activity

17194691

TgeneCOL1A1

GO:0010718

positive regulation of epithelial to mesenchymal transition

20018240

TgeneCOL1A1

GO:0030335

positive regulation of cell migration

20018240

TgeneCOL1A1

GO:0034504

protein localization to nucleus

20018240

TgeneCOL1A1

GO:0045893

positive regulation of transcription, DNA-templated

20018240

TgeneCOL1A1

GO:0090263

positive regulation of canonical Wnt signaling pathway

20018240



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/chr11:1956115/chr17:48275355)
- 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 TNNT3 (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 COL1A1 (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)
ENST00000278317TNNT3chr111956115+ENST00000225964COL1A1chr1748275355-685584339056832975
ENST00000360603TNNT3chr111956115+ENST00000225964COL1A1chr1748275355-683081838806807975
ENST00000381561TNNT3chr111956115+ENST00000225964COL1A1chr1748275355-685784539076834975
ENST00000381549TNNT3chr111956115+ENST00000225964COL1A1chr1748275355-682481238746801975
ENST00000381548TNNT3chr111956115+ENST00000225964COL1A1chr1748275355-685484239046831975
ENST00000381579TNNT3chr111956115+ENST00000225964COL1A1chr1748275355-668767537376664975
ENST00000381589TNNT3chr111956115+ENST00000225964COL1A1chr1748275355-670569337556682975
ENST00000381558TNNT3chr111956115+ENST00000225964COL1A1chr1748275355-689187939416868975
ENST00000397301TNNT3chr111956115+ENST00000225964COL1A1chr1748275355-667766537276654975
ENST00000446240TNNT3chr111956115+ENST00000225964COL1A1chr1748275355-657956736296556975
ENST00000397304TNNT3chr111956115+ENST00000225964COL1A1chr1748275355-657956736296556975

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
ENST00000278317ENST00000225964TNNT3chr111956115+COL1A1chr1748275355-0.618450460.38154948
ENST00000360603ENST00000225964TNNT3chr111956115+COL1A1chr1748275355-0.60433950.3956605
ENST00000381561ENST00000225964TNNT3chr111956115+COL1A1chr1748275355-0.606194440.39380562
ENST00000381549ENST00000225964TNNT3chr111956115+COL1A1chr1748275355-0.61291040.38708964
ENST00000381548ENST00000225964TNNT3chr111956115+COL1A1chr1748275355-0.609439250.39056075
ENST00000381579ENST00000225964TNNT3chr111956115+COL1A1chr1748275355-0.570574050.42942593
ENST00000381589ENST00000225964TNNT3chr111956115+COL1A1chr1748275355-0.558287740.4417123
ENST00000381558ENST00000225964TNNT3chr111956115+COL1A1chr1748275355-0.64248140.35751864
ENST00000397301ENST00000225964TNNT3chr111956115+COL1A1chr1748275355-0.52977310.47022688
ENST00000446240ENST00000225964TNNT3chr111956115+COL1A1chr1748275355-0.52714450.47285554
ENST00000397304ENST00000225964TNNT3chr111956115+COL1A1chr1748275355-0.52714450.47285554

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 TNNT3-COL1A1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
TNNT3chr111956115COL1A1chr1748275355567119VGARGPAGDRGETGPAGPPGAPGAPG
TNNT3chr111956115COL1A1chr1748275355567155SGDRGETGAPGAEGSPGRDGSPGAKG
TNNT3chr111956115COL1A1chr174827535556720PGSAGAPGKDGLNGLPGPIGPPGPRG
TNNT3chr111956115COL1A1chr1748275355567222GPQGIAGQRGVVGLPGQRGERGFPGL
TNNT3chr111956115COL1A1chr1748275355567251SGNAGPPGPPGPAGKEGGKGPRGETG
TNNT3chr111956115COL1A1chr174827535556729DGLNGLPGPIGPPGPRGRTGDAGPVG
TNNT3chr111956115COL1A1chr1748275355567353PGDAGAKGDAGPPGPAGPAGPPGPIG
TNNT3chr111956115COL1A1chr1748275355567356AGAKGDAGPPGPAGPAGPPGPIGDRG
TNNT3chr111956115COL1A1chr1748275355567429GVRGLTGPIGPPGPAGAPGDKGDAGA
TNNT3chr111956115COL1A1chr1748275355567522GDLGAPGPSGARGLPGPAGPPGEAGK
TNNT3chr111956115COL1A1chr174827535556783TGEQGDRGIKGHRGFSGLQGPPGPPG
TNNT3chr111956115COL1A1chr174827535556787GDRGIKGHRGFSGLQGPPGPPGPAGP
TNNT3chr111956115COL1A1chr174827535556789RGIKGHRGFSGLQGPPGPPGPAGPTG
TNNT3chr111956115COL1A1chr1748275355665119VGARGPAGDRGETGPAGPPGAPGAPG
TNNT3chr111956115COL1A1chr1748275355665155SGDRGETGAPGAEGSPGRDGSPGAKG
TNNT3chr111956115COL1A1chr174827535566520PGSAGAPGKDGLNGLPGPIGPPGPRG
TNNT3chr111956115COL1A1chr1748275355665222GPQGIAGQRGVVGLPGQRGERGFPGL
TNNT3chr111956115COL1A1chr1748275355665251SGNAGPPGPPGPAGKEGGKGPRGETG
TNNT3chr111956115COL1A1chr174827535566529DGLNGLPGPIGPPGPRGRTGDAGPVG
TNNT3chr111956115COL1A1chr1748275355665353PGDAGAKGDAGPPGPAGPAGPPGPIG
TNNT3chr111956115COL1A1chr1748275355665356AGAKGDAGPPGPAGPAGPPGPIGDRG
TNNT3chr111956115COL1A1chr1748275355665429GVRGLTGPIGPPGPAGAPGDKGDAGA
TNNT3chr111956115COL1A1chr1748275355665522GDLGAPGPSGARGLPGPAGPPGEAGK
TNNT3chr111956115COL1A1chr174827535566583TGEQGDRGIKGHRGFSGLQGPPGPPG
TNNT3chr111956115COL1A1chr174827535566587GDRGIKGHRGFSGLQGPPGPPGPAGP
TNNT3chr111956115COL1A1chr174827535566589RGIKGHRGFSGLQGPPGPPGPAGPTG
TNNT3chr111956115COL1A1chr1748275355675119VGARGPAGDRGETGPAGPPGAPGAPG
TNNT3chr111956115COL1A1chr1748275355675155SGDRGETGAPGAEGSPGRDGSPGAKG
TNNT3chr111956115COL1A1chr174827535567520PGSAGAPGKDGLNGLPGPIGPPGPRG
TNNT3chr111956115COL1A1chr1748275355675222GPQGIAGQRGVVGLPGQRGERGFPGL
TNNT3chr111956115COL1A1chr1748275355675251SGNAGPPGPPGPAGKEGGKGPRGETG
TNNT3chr111956115COL1A1chr174827535567529DGLNGLPGPIGPPGPRGRTGDAGPVG
TNNT3chr111956115COL1A1chr1748275355675353PGDAGAKGDAGPPGPAGPAGPPGPIG
TNNT3chr111956115COL1A1chr1748275355675356AGAKGDAGPPGPAGPAGPPGPIGDRG
TNNT3chr111956115COL1A1chr1748275355675429GVRGLTGPIGPPGPAGAPGDKGDAGA
TNNT3chr111956115COL1A1chr1748275355675522GDLGAPGPSGARGLPGPAGPPGEAGK
TNNT3chr111956115COL1A1chr174827535567583TGEQGDRGIKGHRGFSGLQGPPGPPG
TNNT3chr111956115COL1A1chr174827535567587GDRGIKGHRGFSGLQGPPGPPGPAGP
TNNT3chr111956115COL1A1chr174827535567589RGIKGHRGFSGLQGPPGPPGPAGPTG
TNNT3chr111956115COL1A1chr1748275355693119VGARGPAGDRGETGPAGPPGAPGAPG
TNNT3chr111956115COL1A1chr1748275355693155SGDRGETGAPGAEGSPGRDGSPGAKG
TNNT3chr111956115COL1A1chr174827535569320PGSAGAPGKDGLNGLPGPIGPPGPRG
TNNT3chr111956115COL1A1chr1748275355693222GPQGIAGQRGVVGLPGQRGERGFPGL
TNNT3chr111956115COL1A1chr1748275355693251SGNAGPPGPPGPAGKEGGKGPRGETG
TNNT3chr111956115COL1A1chr174827535569329DGLNGLPGPIGPPGPRGRTGDAGPVG
TNNT3chr111956115COL1A1chr1748275355693353PGDAGAKGDAGPPGPAGPAGPPGPIG
TNNT3chr111956115COL1A1chr1748275355693356AGAKGDAGPPGPAGPAGPPGPIGDRG
TNNT3chr111956115COL1A1chr1748275355693429GVRGLTGPIGPPGPAGAPGDKGDAGA
TNNT3chr111956115COL1A1chr1748275355693522GDLGAPGPSGARGLPGPAGPPGEAGK
TNNT3chr111956115COL1A1chr174827535569383TGEQGDRGIKGHRGFSGLQGPPGPPG
TNNT3chr111956115COL1A1chr174827535569387GDRGIKGHRGFSGLQGPPGPPGPAGP
TNNT3chr111956115COL1A1chr174827535569389RGIKGHRGFSGLQGPPGPPGPAGPTG
TNNT3chr111956115COL1A1chr1748275355812119VGARGPAGDRGETGPAGPPGAPGAPG
TNNT3chr111956115COL1A1chr1748275355812155SGDRGETGAPGAEGSPGRDGSPGAKG
TNNT3chr111956115COL1A1chr174827535581220PGSAGAPGKDGLNGLPGPIGPPGPRG
TNNT3chr111956115COL1A1chr1748275355812222GPQGIAGQRGVVGLPGQRGERGFPGL
TNNT3chr111956115COL1A1chr1748275355812251SGNAGPPGPPGPAGKEGGKGPRGETG
TNNT3chr111956115COL1A1chr174827535581229DGLNGLPGPIGPPGPRGRTGDAGPVG
TNNT3chr111956115COL1A1chr1748275355812353PGDAGAKGDAGPPGPAGPAGPPGPIG
TNNT3chr111956115COL1A1chr1748275355812356AGAKGDAGPPGPAGPAGPPGPIGDRG
TNNT3chr111956115COL1A1chr1748275355812429GVRGLTGPIGPPGPAGAPGDKGDAGA
TNNT3chr111956115COL1A1chr1748275355812522GDLGAPGPSGARGLPGPAGPPGEAGK
TNNT3chr111956115COL1A1chr174827535581283TGEQGDRGIKGHRGFSGLQGPPGPPG
TNNT3chr111956115COL1A1chr174827535581287GDRGIKGHRGFSGLQGPPGPPGPAGP
TNNT3chr111956115COL1A1chr174827535581289RGIKGHRGFSGLQGPPGPPGPAGPTG
TNNT3chr111956115COL1A1chr1748275355818119VGARGPAGDRGETGPAGPPGAPGAPG
TNNT3chr111956115COL1A1chr1748275355818155SGDRGETGAPGAEGSPGRDGSPGAKG
TNNT3chr111956115COL1A1chr174827535581820PGSAGAPGKDGLNGLPGPIGPPGPRG
TNNT3chr111956115COL1A1chr1748275355818222GPQGIAGQRGVVGLPGQRGERGFPGL
TNNT3chr111956115COL1A1chr1748275355818251SGNAGPPGPPGPAGKEGGKGPRGETG
TNNT3chr111956115COL1A1chr174827535581829DGLNGLPGPIGPPGPRGRTGDAGPVG
TNNT3chr111956115COL1A1chr1748275355818353PGDAGAKGDAGPPGPAGPAGPPGPIG
TNNT3chr111956115COL1A1chr1748275355818356AGAKGDAGPPGPAGPAGPPGPIGDRG
TNNT3chr111956115COL1A1chr1748275355818429GVRGLTGPIGPPGPAGAPGDKGDAGA
TNNT3chr111956115COL1A1chr1748275355818522GDLGAPGPSGARGLPGPAGPPGEAGK
TNNT3chr111956115COL1A1chr174827535581883TGEQGDRGIKGHRGFSGLQGPPGPPG
TNNT3chr111956115COL1A1chr174827535581887GDRGIKGHRGFSGLQGPPGPPGPAGP
TNNT3chr111956115COL1A1chr174827535581889RGIKGHRGFSGLQGPPGPPGPAGPTG
TNNT3chr111956115COL1A1chr1748275355842119VGARGPAGDRGETGPAGPPGAPGAPG
TNNT3chr111956115COL1A1chr1748275355842155SGDRGETGAPGAEGSPGRDGSPGAKG
TNNT3chr111956115COL1A1chr174827535584220PGSAGAPGKDGLNGLPGPIGPPGPRG
TNNT3chr111956115COL1A1chr1748275355842222GPQGIAGQRGVVGLPGQRGERGFPGL
TNNT3chr111956115COL1A1chr1748275355842251SGNAGPPGPPGPAGKEGGKGPRGETG
TNNT3chr111956115COL1A1chr174827535584229DGLNGLPGPIGPPGPRGRTGDAGPVG
TNNT3chr111956115COL1A1chr1748275355842353PGDAGAKGDAGPPGPAGPAGPPGPIG
TNNT3chr111956115COL1A1chr1748275355842356AGAKGDAGPPGPAGPAGPPGPIGDRG
TNNT3chr111956115COL1A1chr1748275355842429GVRGLTGPIGPPGPAGAPGDKGDAGA
TNNT3chr111956115COL1A1chr1748275355842522GDLGAPGPSGARGLPGPAGPPGEAGK
TNNT3chr111956115COL1A1chr174827535584283TGEQGDRGIKGHRGFSGLQGPPGPPG
TNNT3chr111956115COL1A1chr174827535584287GDRGIKGHRGFSGLQGPPGPPGPAGP
TNNT3chr111956115COL1A1chr174827535584289RGIKGHRGFSGLQGPPGPPGPAGPTG
TNNT3chr111956115COL1A1chr1748275355843119VGARGPAGDRGETGPAGPPGAPGAPG
TNNT3chr111956115COL1A1chr1748275355843155SGDRGETGAPGAEGSPGRDGSPGAKG
TNNT3chr111956115COL1A1chr174827535584320PGSAGAPGKDGLNGLPGPIGPPGPRG
TNNT3chr111956115COL1A1chr1748275355843222GPQGIAGQRGVVGLPGQRGERGFPGL
TNNT3chr111956115COL1A1chr1748275355843251SGNAGPPGPPGPAGKEGGKGPRGETG
TNNT3chr111956115COL1A1chr174827535584329DGLNGLPGPIGPPGPRGRTGDAGPVG
TNNT3chr111956115COL1A1chr1748275355843353PGDAGAKGDAGPPGPAGPAGPPGPIG
TNNT3chr111956115COL1A1chr1748275355843356AGAKGDAGPPGPAGPAGPPGPIGDRG
TNNT3chr111956115COL1A1chr1748275355843429GVRGLTGPIGPPGPAGAPGDKGDAGA
TNNT3chr111956115COL1A1chr1748275355843522GDLGAPGPSGARGLPGPAGPPGEAGK
TNNT3chr111956115COL1A1chr174827535584383TGEQGDRGIKGHRGFSGLQGPPGPPG
TNNT3chr111956115COL1A1chr174827535584387GDRGIKGHRGFSGLQGPPGPPGPAGP
TNNT3chr111956115COL1A1chr174827535584389RGIKGHRGFSGLQGPPGPPGPAGPTG
TNNT3chr111956115COL1A1chr1748275355845119VGARGPAGDRGETGPAGPPGAPGAPG
TNNT3chr111956115COL1A1chr1748275355845155SGDRGETGAPGAEGSPGRDGSPGAKG
TNNT3chr111956115COL1A1chr174827535584520PGSAGAPGKDGLNGLPGPIGPPGPRG
TNNT3chr111956115COL1A1chr1748275355845222GPQGIAGQRGVVGLPGQRGERGFPGL
TNNT3chr111956115COL1A1chr1748275355845251SGNAGPPGPPGPAGKEGGKGPRGETG
TNNT3chr111956115COL1A1chr174827535584529DGLNGLPGPIGPPGPRGRTGDAGPVG
TNNT3chr111956115COL1A1chr1748275355845353PGDAGAKGDAGPPGPAGPAGPPGPIG
TNNT3chr111956115COL1A1chr1748275355845356AGAKGDAGPPGPAGPAGPPGPIGDRG
TNNT3chr111956115COL1A1chr1748275355845429GVRGLTGPIGPPGPAGAPGDKGDAGA
TNNT3chr111956115COL1A1chr1748275355845522GDLGAPGPSGARGLPGPAGPPGEAGK
TNNT3chr111956115COL1A1chr174827535584583TGEQGDRGIKGHRGFSGLQGPPGPPG
TNNT3chr111956115COL1A1chr174827535584587GDRGIKGHRGFSGLQGPPGPPGPAGP
TNNT3chr111956115COL1A1chr174827535584589RGIKGHRGFSGLQGPPGPPGPAGPTG
TNNT3chr111956115COL1A1chr1748275355879119VGARGPAGDRGETGPAGPPGAPGAPG
TNNT3chr111956115COL1A1chr1748275355879155SGDRGETGAPGAEGSPGRDGSPGAKG
TNNT3chr111956115COL1A1chr174827535587920PGSAGAPGKDGLNGLPGPIGPPGPRG
TNNT3chr111956115COL1A1chr1748275355879222GPQGIAGQRGVVGLPGQRGERGFPGL
TNNT3chr111956115COL1A1chr1748275355879251SGNAGPPGPPGPAGKEGGKGPRGETG
TNNT3chr111956115COL1A1chr174827535587929DGLNGLPGPIGPPGPRGRTGDAGPVG
TNNT3chr111956115COL1A1chr1748275355879353PGDAGAKGDAGPPGPAGPAGPPGPIG
TNNT3chr111956115COL1A1chr1748275355879356AGAKGDAGPPGPAGPAGPPGPIGDRG
TNNT3chr111956115COL1A1chr1748275355879429GVRGLTGPIGPPGPAGAPGDKGDAGA
TNNT3chr111956115COL1A1chr1748275355879522GDLGAPGPSGARGLPGPAGPPGEAGK
TNNT3chr111956115COL1A1chr174827535587983TGEQGDRGIKGHRGFSGLQGPPGPPG
TNNT3chr111956115COL1A1chr174827535587987GDRGIKGHRGFSGLQGPPGPPGPAGP
TNNT3chr111956115COL1A1chr174827535587989RGIKGHRGFSGLQGPPGPPGPAGPTG

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Potential FusionNeoAntigen Information of TNNT3-COL1A1 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.
TNNT3-COL1A1_1956115_48275355.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)
TNNT3-COL1A1chr111956115chr1748275355843HLA-B07:05GPSGARGL0.99930.5441614
TNNT3-COL1A1chr111956115chr1748275355843HLA-B07:02GPSGARGL0.99910.5902614
TNNT3-COL1A1chr111956115chr1748275355843HLA-B07:05APGPSGARGL0.99810.5818414
TNNT3-COL1A1chr111956115chr1748275355843HLA-B07:02APGPSGARGL0.99790.6633414
TNNT3-COL1A1chr111956115chr1748275355843HLA-B81:01APGPSGARGL0.58570.542414
TNNT3-COL1A1chr111956115chr1748275355843HLA-B82:01APGPSGARGL0.42030.5569414
TNNT3-COL1A1chr111956115chr1748275355843HLA-B07:12APGPSGARGL0.9940.8141414
TNNT3-COL1A1chr111956115chr1748275355843HLA-B07:04APGPSGARGL0.90710.5583414
TNNT3-COL1A1chr111956115chr1748275355843HLA-B42:01APGPSGARGL0.57360.6194414
TNNT3-COL1A1chr111956115chr1748275355843HLA-B07:22GPSGARGL0.99910.5902614
TNNT3-COL1A1chr111956115chr1748275355843HLA-B07:22APGPSGARGL0.99790.6633414
TNNT3-COL1A1chr111956115chr1748275355843HLA-B82:02APGPSGARGL0.42030.5569414
TNNT3-COL1A1chr111956115chr1748275355843HLA-B67:01APGPSGARGL0.35690.8884414

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Potential FusionNeoAntigen Information of TNNT3-COL1A1 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 TNNT3-COL1A1

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
3037GPSGARGLPGPAGPTNNT3COL1A1chr111956115chr1748275355843

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of TNNT3-COL1A1

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-B14:023BVN3037GPSGARGLPGPAGP-7.9962-8.1096
HLA-B14:023BVN3037GPSGARGLPGPAGP-5.70842-6.74372
HLA-B52:013W393037GPSGARGLPGPAGP-6.83737-6.95077
HLA-B52:013W393037GPSGARGLPGPAGP-4.4836-5.5189
HLA-A11:014UQ23037GPSGARGLPGPAGP-10.0067-10.1201
HLA-A11:014UQ23037GPSGARGLPGPAGP-9.03915-10.0745
HLA-A24:025HGA3037GPSGARGLPGPAGP-6.56204-6.67544
HLA-A24:025HGA3037GPSGARGLPGPAGP-5.42271-6.45801
HLA-B44:053DX83037GPSGARGLPGPAGP-7.85648-8.89178
HLA-B44:053DX83037GPSGARGLPGPAGP-5.3978-5.5112
HLA-A02:016TDR3037GPSGARGLPGPAGP-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of TNNT3-COL1A1

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
TNNT3-COL1A1chr111956115chr1748275355414APGPSGARGLGAGAAGCTGAAACGCCAGAAATATGACAGT
TNNT3-COL1A1chr111956115chr1748275355614GPSGARGLCTGAAACGCCAGAAATATGACAGT

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 TNNT3-COL1A1

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
HNSCTNNT3-COL1A1chr111956115ENST00000278317chr1748275355ENST00000225964TCGA-CN-6017-01A

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Potential target of CAR-T therapy development for TNNT3-COL1A1

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 TNNT3-COL1A1

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 TNNT3-COL1A1

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
TgeneCOL1A1C0268358Osteogenesis imperfecta, dominant perinatal lethal38CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL1A1C0268362Osteogenesis imperfecta type III (disorder)17CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL1A1C0023931Lobstein Disease15CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL1A1C0268363Osteogenesis imperfecta type IV (disorder)12GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL1A1C0023890Liver Cirrhosis4CTD_human
TgeneCOL1A1C0239946Fibrosis, Liver4CTD_human
TgeneCOL1A1C4551623EHLERS-DANLOS SYNDROME, ARTHROCHALASIA TYPE, 14CTD_human;GENOMICS_ENGLAND
TgeneCOL1A1C4552122EHLERS-DANLOS SYNDROME, CLASSIC TYPE, 14GENOMICS_ENGLAND;UNIPROT
TgeneCOL1A1C0020497Cortical Congenital Hyperostosis3CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneCOL1A1C0023893Liver Cirrhosis, Experimental3CTD_human
TgeneCOL1A1C0268345EHLERS-DANLOS SYNDROME, ARTHROCHALASIA TYPE2ORPHANET
TgeneCOL1A1C0000786Spontaneous abortion1CTD_human
TgeneCOL1A1C0000822Abortion, Tubal1CTD_human
TgeneCOL1A1C0002949Aneurysm, Dissecting1CTD_human
TgeneCOL1A1C0003504Aortic Valve Insufficiency1CTD_human
TgeneCOL1A1C0004364Autoimmune Diseases1CTD_human
TgeneCOL1A1C0005398Cholestasis, Extrahepatic1CTD_human
TgeneCOL1A1C0005779Blood Coagulation Disorders1GENOMICS_ENGLAND
TgeneCOL1A1C0006663Calcinosis1CTD_human
TgeneCOL1A1C0008311Cholangitis1CTD_human
TgeneCOL1A1C0013720Ehlers-Danlos Syndrome1GENOMICS_ENGLAND
TgeneCOL1A1C0016059Fibrosis1CTD_human
TgeneCOL1A1C0018824Heart valve disease1CTD_human
TgeneCOL1A1C0020538Hypertensive disease1CTD_human
TgeneCOL1A1C0022548Keloid1CTD_human
TgeneCOL1A1C0027719Nephrosclerosis1CTD_human
TgeneCOL1A1C0027726Nephrotic Syndrome1CTD_human
TgeneCOL1A1C0029172Oral Submucous Fibrosis1CTD_human
TgeneCOL1A1C0029434Osteogenesis Imperfecta1CTD_human;GENOMICS_ENGLAND
TgeneCOL1A1C0149721Left Ventricular Hypertrophy1CTD_human
TgeneCOL1A1C0220679Ehlers-Danlos Syndrome, Autosomal Dominant, Type Unspecified1ORPHANET
TgeneCOL1A1C0263628Tumoral calcinosis1CTD_human
TgeneCOL1A1C0340643Dissection of aorta1CTD_human
TgeneCOL1A1C0521174Microcalcification1CTD_human
TgeneCOL1A1C1458140Bleeding tendency1GENOMICS_ENGLAND
TgeneCOL1A1C1619692Nephrogenic Fibrosing Dermopathy1CTD_human
TgeneCOL1A1C1623038Cirrhosis1CTD_human
TgeneCOL1A1C1846545Autoimmune Lymphoproliferative Syndrome Type 2B1GENOMICS_ENGLAND
TgeneCOL1A1C3830362Early Pregnancy Loss1CTD_human
TgeneCOL1A1C4277533Dissection, Blood Vessel1CTD_human
TgeneCOL1A1C4552766Miscarriage1CTD_human