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Fusion Protein:PTCH1-TPM1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PTCH1-TPM1
	FusionPDB ID: 69869
	FusionGDB2.0 ID: 69869
		Hgene	Tgene
	Gene symbol	PTCH1	TPM1
	Gene ID	5727	7168
	Gene name	patched 1	tropomyosin 1
	Synonyms	BCNS\|NBCCS\|PTC\|PTC1\|PTCH	C15orf13\|CMD1Y\|CMH3\|HEL-S-265\|HTM-alpha\|LVNC9\|TMSA
	Cytomap	9q22.32	15q22.2
	Type of gene	protein-coding	protein-coding
	Description	protein patched homolog 1	tropomyosin alpha-1 chaincardiomyopathy, hypertrophic 3epididymis secretory protein Li 265sarcomeric tropomyosin kappa
	Modification date	20200314	20200320
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000331920, ENST00000375274, ENST00000418258, ENST00000421141, ENST00000429896, ENST00000430669, ENST00000437951, ENST00000468211, ENST00000548379,	ENST00000267996, ENST00000317516, ENST00000334895, ENST00000357980, ENST00000403994, ENST00000404484, ENST00000559281, ENST00000559397, ENST00000559556, ENST00000560445, ENST00000560959, ENST00000288398, ENST00000358278,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	6 X 7 X 4=168	14 X 8 X 8=896
	# samples	7	16
	** MAII score	log2(7/168*10)=-1.26303440583379 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(16/896*10)=-2.48542682717024 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: PTCH1 [Title/Abstract] AND TPM1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PTCH1 [Title/Abstract] AND TPM1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PTCH1(98224138)-TPM1(63349184), # samples:1
Anticipated loss of major functional domain due to fusion event.	PTCH1-TPM1 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. PTCH1-TPM1 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. PTCH1-TPM1 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. PTCH1-TPM1 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. PTCH1-TPM1 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF. PTCH1-TPM1 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor 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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	PTCH1	GO:0010875	positive regulation of cholesterol efflux	21931618
Hgene	PTCH1	GO:0072659	protein localization to plasma membrane	11278759

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr9:98224138/chr15:63349184)
- 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.

Retention 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.

Fusion gene breakpoints across PTCH1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across TPM1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Amino Acid Sequences

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	Seq length (transcript)	BP loci (transcript)	Predicted start (transcript)	Predicted stop (transcript)	Seq length (amino acids)
ENST00000418258	PTCH1	chr9	98224138	-	ENST00000288398	TPM1	chr15	63349184	+	3622	2765	113	3379	1088
ENST00000418258	PTCH1	chr9	98224138	-	ENST00000358278	TPM1	chr15	63349184	+	4097	2765	113	3379	1088
ENST00000430669	PTCH1	chr9	98224138	-	ENST00000288398	TPM1	chr15	63349184	+	3948	3091	586	3705	1039
ENST00000430669	PTCH1	chr9	98224138	-	ENST00000358278	TPM1	chr15	63349184	+	4423	3091	586	3705	1039

DeepORF 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.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000418258	ENST00000288398	PTCH1	chr9	98224138	-	TPM1	chr15	63349184	+	0.001643465	0.9983565
ENST00000418258	ENST00000358278	PTCH1	chr9	98224138	-	TPM1	chr15	63349184	+	0.001151003	0.99884903
ENST00000430669	ENST00000288398	PTCH1	chr9	98224138	-	TPM1	chr15	63349184	+	0.001095271	0.9989047
ENST00000430669	ENST00000358278	PTCH1	chr9	98224138	-	TPM1	chr15	63349184	+	0.000761052	0.99923897

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 PTCH1-TPM1

+/-13 AA sequence from the breakpoints of the fusion protein sequences.

Hgene	Hchr	Hbp	Tgene	Tchr	Tbp	Length(fusion protein)	BP in fusion protein	Peptide
PTCH1	chr9	98224138	TPM1	chr15	63349184	2765	884	QTGSRDKPIDISQAEADVASLNRRIQ
PTCH1	chr9	98224138	TPM1	chr15	63349184	3091	835	QTGSRDKPIDISQAEADVASLNRRIQ

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Potential FusionNeoAntigen Information of PTCH1-TPM1 in HLA I

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.

PTCH1-TPM1_98224138_63349184.msa

Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA I	FusionNeoAntigen peptide	Binding score	Immunogenic score	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B35:03	QAEADVASL	0.6997	0.876	12	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B35:04	QAEADVASL	0.5225	0.982	12	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B35:02	QAEADVASL	0.5225	0.982	12	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B48:01	SQAEADVASL	0.9863	0.6264	11	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B39:13	SQAEADVASL	0.9521	0.9083	11	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-A02:21	SQAEADVASL	0.9126	0.7375	11	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B13:02	SQAEADVASL	0.8345	0.6568	11	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B13:01	SQAEADVASL	0.8201	0.9711	11	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-C08:15	QAEADVASL	0.9996	0.9691	12	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-C08:04	QAEADVASL	0.9519	0.9737	12	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-C08:13	QAEADVASL	0.9519	0.9737	12	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-C08:03	QAEADVASL	0.8336	0.9836	12	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B35:12	QAEADVASL	0.5225	0.982	12	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B39:08	SQAEADVASL	0.9795	0.8769	11	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B54:01	KPIDISQAEA	0.9685	0.5095	6	16
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B48:03	SQAEADVASL	0.9659	0.5191	11	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B39:05	SQAEADVASL	0.9426	0.9323	11	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-C08:02	QAEADVASL	0.9996	0.9691	12	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-C03:06	QAEADVASL	0.9338	0.9933	12	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-C08:01	QAEADVASL	0.8336	0.9836	12	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B35:13	QAEADVASL	0.6771	0.8801	12	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B35:09	QAEADVASL	0.5225	0.982	12	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B35:22	QAEADVASL	0.3918	0.503	12	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B15:73	SQAEADVASL	0.9973	0.8846	11	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B15:30	SQAEADVASL	0.9943	0.8216	11	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B39:02	SQAEADVASL	0.9767	0.9116	11	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B39:11	SQAEADVASL	0.9704	0.8758	11	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B40:12	SQAEADVASL	0.9659	0.5191	11	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-A02:14	SQAEADVASL	0.9157	0.5976	11	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-A02:06	SQAEADVASL	0.9126	0.7375	11	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B40:21	SQAEADVASL	0.8838	0.5549	11	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	HLA-B56:05	KPIDISQAEA	0.7756	0.5272	6	16

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Potential FusionNeoAntigen Information of PTCH1-TPM1 in HLA II

PTCH1-TPM1_98224138_63349184.msa

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA II	FusionNeoAntigen peptide	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB1-0467	DKPIDISQAEADVAS	5	20
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB1-0904	DKPIDISQAEADVAS	5	20
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB1-0906	DKPIDISQAEADVAS	5	20
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB1-0906	RDKPIDISQAEADVA	4	19
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB1-0908	DKPIDISQAEADVAS	5	20
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB1-0908	RDKPIDISQAEADVA	4	19
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB1-1410	DKPIDISQAEADVAS	5	20
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB4-0101	PIDISQAEADVASLN	7	22
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB4-0101	KPIDISQAEADVASL	6	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB4-0101	DKPIDISQAEADVAS	5	20
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB4-0103	PIDISQAEADVASLN	7	22
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB4-0103	KPIDISQAEADVASL	6	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB4-0103	DKPIDISQAEADVAS	5	20
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB4-0104	PIDISQAEADVASLN	7	22
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB4-0104	KPIDISQAEADVASL	6	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB4-0104	DKPIDISQAEADVAS	5	20
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB4-0106	PIDISQAEADVASLN	7	22
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB4-0106	KPIDISQAEADVASL	6	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB4-0106	DKPIDISQAEADVAS	5	20
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB4-0107	PIDISQAEADVASLN	7	22
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB4-0107	KPIDISQAEADVASL	6	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB4-0107	DKPIDISQAEADVAS	5	20
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB4-0108	PIDISQAEADVASLN	7	22
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB4-0108	KPIDISQAEADVASL	6	21
PTCH1-TPM1	chr9	98224138	chr15	63349184	2765	DRB4-0108	DKPIDISQAEADVAS	5	20

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Fusion breakpoint peptide structures of PTCH1-TPM1

3D 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 name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
4481	KPIDISQAEADVAS	PTCH1	TPM1	chr9	98224138	chr15	63349184	2765

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PTCH1-TPM1

Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.

HLA allele	PDB ID	File name	BPseq	Docking score	Glide score
HLA-B14:02	3BVN	4481	KPIDISQAEADVAS	-7.9962	-8.1096
HLA-B14:02	3BVN	4481	KPIDISQAEADVAS	-5.70842	-6.74372
HLA-B52:01	3W39	4481	KPIDISQAEADVAS	-6.83737	-6.95077
HLA-B52:01	3W39	4481	KPIDISQAEADVAS	-4.4836	-5.5189
HLA-A11:01	4UQ2	4481	KPIDISQAEADVAS	-10.0067	-10.1201
HLA-A11:01	4UQ2	4481	KPIDISQAEADVAS	-9.03915	-10.0745
HLA-A24:02	5HGA	4481	KPIDISQAEADVAS	-6.56204	-6.67544
HLA-A24:02	5HGA	4481	KPIDISQAEADVAS	-5.42271	-6.45801
HLA-B44:05	3DX8	4481	KPIDISQAEADVAS	-7.85648	-8.89178
HLA-B44:05	3DX8	4481	KPIDISQAEADVAS	-5.3978	-5.5112
HLA-A02:01	6TDR	4481	KPIDISQAEADVAS	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of PTCH1-TPM1

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide sequence	FusionNeoAntigen RNA sequence
PTCH1-TPM1	chr9	98224138	chr15	63349184	11	21	SQAEADVASL	AGCCAGGCTGAAGCCGACGTAGCTTCTCTG
PTCH1-TPM1	chr9	98224138	chr15	63349184	12	21	QAEADVASL	CAGGCTGAAGCCGACGTAGCTTCTCTG
PTCH1-TPM1	chr9	98224138	chr15	63349184	6	16	KPIDISQAEA	AAGCCCATCGACATCAGCCAGGCTGAAGCC

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide	FusionNEoAntigen RNA sequence
PTCH1-TPM1	chr9	98224138	chr15	63349184	4	19	RDKPIDISQAEADVA	CGCGATAAGCCCATCGACATCAGCCAGGCTGAAGCCGACGTAGCT
PTCH1-TPM1	chr9	98224138	chr15	63349184	5	20	DKPIDISQAEADVAS	GATAAGCCCATCGACATCAGCCAGGCTGAAGCCGACGTAGCTTCT
PTCH1-TPM1	chr9	98224138	chr15	63349184	6	21	KPIDISQAEADVASL	AAGCCCATCGACATCAGCCAGGCTGAAGCCGACGTAGCTTCTCTG
PTCH1-TPM1	chr9	98224138	chr15	63349184	7	22	PIDISQAEADVASLN	CCCATCGACATCAGCCAGGCTGAAGCCGACGTAGCTTCTCTGAAC

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Information of the samples that have these potential fusion neoantigens of PTCH1-TPM1

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 type	Fusion gene	Hchr	Hbp	Henst	Tchr	Tbp	Tenst	Sample
SARC	PTCH1-TPM1	chr9	98224138	ENST00000418258	chr15	63349184	ENST00000288398	TCGA-DX-A6B9-01A

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Potential target of CAR-T therapy development for PTCH1-TPM1

Predicted 3D structure. We used RoseTTAFold.

Retention 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'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000331920

101_121

901

2534.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000331920

437_457

901

2534.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000331920

473_493

901

2534.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000331920

502_522

901

2534.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000331920

548_568

901

2534.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000331920

578_598

901

2534.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000331920

749_769

901

2534.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000375274

101_121

900

1526.3333333333333

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000375274

437_457

900

1526.3333333333333

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000375274

473_493

900

1526.3333333333333

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000375274

502_522

900

1526.3333333333333

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000375274

548_568

900

1526.3333333333333

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000375274

578_598

900

1526.3333333333333

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000375274

749_769

900

1526.3333333333333

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000418258

101_121

750

2461.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000418258

437_457

750

2461.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000418258

473_493

750

2461.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000418258

502_522

750

2461.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000418258

548_568

750

2461.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000418258

578_598

750

2461.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000421141

101_121

750

2513.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000421141

437_457

750

2513.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000421141

473_493

750

2513.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000421141

502_522

750

2513.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000421141

548_568

750

2513.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000421141

578_598

750

2513.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000429896

101_121

750

2093.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000429896

437_457

750

2093.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000429896

473_493

750

2093.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000429896

502_522

750

2093.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000429896

548_568

750

2093.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000429896

578_598

750

2093.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000430669

101_121

835

1382.0

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000430669

437_457

835

1382.0

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000430669

473_493

835

1382.0

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000430669

502_522

835

1382.0

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000430669

548_568

835

1382.0

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000430669

578_598

835

1382.0

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000430669

749_769

835

1382.0

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000437951

101_121

835

2468.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000437951

437_457

835

2468.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000437951

473_493

835

2468.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000437951

502_522

835

2468.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000437951

548_568

835

2468.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000437951

578_598

835

2468.3333333333335

Transmembrane

Helical

Hgene

PTCH1

chr9:98224138

chr15:63349184

ENST00000437951

749_769

835

2468.3333333333335

Transmembrane

Helical

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.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

Top

Related Drugs to PTCH1-TPM1

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to PTCH1-TPM1

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source

	Fusion Gene and Fusion Protein Summary
	Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)
	Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)
	Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)
	Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)
	Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)
	Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)
	Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)
	Potential target of CAR-T therapy development
	Information on the samples that have these potential fusion neoantigens
	Fusion Protein Targeting Drugs - (Manual Curation)
	Fusion Protein Related diseases - (Manual Curation)