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Fusion Protein:PCTP-BRIP1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PCTP-BRIP1
	FusionPDB ID: 63541
	FusionGDB2.0 ID: 63541
		Hgene	Tgene
	Gene symbol	PCTP	BRIP1
	Gene ID	58488	83990
	Gene name	phosphatidylcholine transfer protein	BRCA1 interacting protein C-terminal helicase 1
	Synonyms	PC-TP\|STARD2	BACH1\|FANCJ\|OF
	Cytomap	17q22	17q23.2
	Type of gene	protein-coding	protein-coding
	Description	phosphatidylcholine transfer proteinSTART domain-containing protein 2StAR-related lipid transfer (START) domain containing 2stAR-related lipid transfer protein 2	Fanconi anemia group J proteinATP-dependent RNA helicase BRIP1BRCA1-associated C-terminal helicase 1BRCA1-binding helicase-like protein BACH1BRCA1/BRCA2-associated helicase 1
	Modification date	20200313	20200315
	UniProtAcc	.	Q9BX63 Main function of 5'-partner protein: FUNCTION: DNA-dependent ATPase and 5' to 3' DNA helicase required for the maintenance of chromosomal stability. Acts late in the Fanconi anemia pathway, after FANCD2 ubiquitination. Involved in the repair of DNA double-strand breaks by homologous recombination in a manner that depends on its association with BRCA1. {ECO:0000269\|PubMed:11301010, ECO:0000269\|PubMed:14983014, ECO:0000269\|PubMed:16116421, ECO:0000269\|PubMed:16153896}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000268896, ENST00000573500, ENST00000576183, ENST00000325214, ENST00000576221,	ENST00000583837, ENST00000259008, ENST00000577598,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	6 X 3 X 5=90	12 X 15 X 7=1260
	# samples	7	13
	** MAII score	log2(7/90*10)=-0.362570079384708 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(13/1260*10)=-3.27684020535882 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: PCTP [Title/Abstract] AND BRIP1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PCTP [Title/Abstract] AND BRIP1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PCTP(53828605)-BRIP1(59861785), # samples:1
Anticipated loss of major functional domain due to fusion event.	PCTP-BRIP1 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. PCTP-BRIP1 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. PCTP-BRIP1 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. PCTP-BRIP1 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)

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	PCTP	GO:0015914	phospholipid transport	12055623
Tgene	BRIP1	GO:0006357	regulation of transcription by RNA polymerase II	14504288

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr17:53828605/chr17:59861785)
- 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 PCTP (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 BRIP1 (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)
ENST00000573500	PCTP	chr17	53828605	+	ENST00000259008	BRIP1	chr17	59861785	-	4458	151	10	2427	805
ENST00000573500	PCTP	chr17	53828605	+	ENST00000577598	BRIP1	chr17	59861785	-	2647	151	10	1662	550
ENST00000268896	PCTP	chr17	53828605	+	ENST00000259008	BRIP1	chr17	59861785	-	4573	266	89	2542	817
ENST00000268896	PCTP	chr17	53828605	+	ENST00000577598	BRIP1	chr17	59861785	-	2762	266	89	1777	562
ENST00000576183	PCTP	chr17	53828605	+	ENST00000259008	BRIP1	chr17	59861785	-	4491	184	7	2460	817
ENST00000576183	PCTP	chr17	53828605	+	ENST00000577598	BRIP1	chr17	59861785	-	2680	184	7	1695	562

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
ENST00000573500	ENST00000259008	PCTP	chr17	53828605	+	BRIP1	chr17	59861785	-	0.000458302	0.99954176
ENST00000573500	ENST00000577598	PCTP	chr17	53828605	+	BRIP1	chr17	59861785	-	0.000565195	0.99943477
ENST00000268896	ENST00000259008	PCTP	chr17	53828605	+	BRIP1	chr17	59861785	-	0.000462182	0.9995378
ENST00000268896	ENST00000577598	PCTP	chr17	53828605	+	BRIP1	chr17	59861785	-	0.000589687	0.9994103
ENST00000576183	ENST00000259008	PCTP	chr17	53828605	+	BRIP1	chr17	59861785	-	0.000466956	0.99953306
ENST00000576183	ENST00000577598	PCTP	chr17	53828605	+	BRIP1	chr17	59861785	-	0.00059627	0.9994037

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 PCTP-BRIP1

+/-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
PCTP	chr17	53828605	BRIP1	chr17	59861785	151	47	ETSGISIYRLLDKGHFSAVLQKEEKI
PCTP	chr17	53828605	BRIP1	chr17	59861785	184	59	ETSGISIYRLLDKGHFSAVLQKEEKI
PCTP	chr17	53828605	BRIP1	chr17	59861785	266	59	ETSGISIYRLLDKGHFSAVLQKEEKI

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Potential FusionNeoAntigen Information of PCTP-BRIP1 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.

PCTP-BRIP1_53828605_59861785.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)
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-B27:05	YRLLDKGHF	0.9994	0.7987	7	16
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-B27:04	YRLLDKGHF	0.9994	0.5518	7	16
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-B14:01	DKGHFSAVL	0.9946	0.9064	11	20
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-B14:02	DKGHFSAVL	0.9946	0.9064	11	20
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:11	LLDKGHFSA	0.9806	0.6874	9	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:60	LLDKGHFSA	0.9805	0.6433	9	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:24	LLDKGHFSA	0.9798	0.6518	9	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:30	LLDKGHFSA	0.9798	0.6518	9	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:67	LLDKGHFSA	0.9798	0.6518	9	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:27	LLDKGHFSA	0.9664	0.779	9	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:38	LLDKGHFSA	0.9561	0.7599	9	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:13	LLDKGHFSA	0.9526	0.8221	9	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:35	LLDKGHFSA	0.9239	0.6609	9	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:19	LLDKGHFSA	0.9225	0.6528	9	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-B15:37	DKGHFSAVL	0.8587	0.5163	11	20
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:29	LLDKGHFSA	0.8449	0.6512	9	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:13	RLLDKGHFSA	0.9939	0.8312	8	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A30:08	KGHFSAVLQK	0.9911	0.5617	12	22
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:13	LLDKGHFSAV	0.9908	0.8664	9	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:27	RLLDKGHFSA	0.9905	0.7449	8	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:27	LLDKGHFSAV	0.9895	0.8105	9	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:11	LLDKGHFSAV	0.9867	0.73	9	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:38	LLDKGHFSAV	0.9733	0.789	9	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:20	RLLDKGHFSA	0.8404	0.5852	8	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-B39:06	YRLLDKGHFSA	0.9994	0.9634	7	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:22	RLLDKGHFSAV	0.9994	0.699	8	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:13	RLLDKGHFSAV	0.9994	0.8588	8	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:11	RLLDKGHFSAV	0.9992	0.6123	8	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:60	RLLDKGHFSAV	0.9992	0.6344	8	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:30	RLLDKGHFSAV	0.9991	0.5918	8	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:67	RLLDKGHFSAV	0.9991	0.5918	8	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:24	RLLDKGHFSAV	0.9991	0.5918	8	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:27	RLLDKGHFSAV	0.9989	0.7548	8	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:21	RLLDKGHFSAV	0.9987	0.6759	8	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:04	RLLDKGHFSAV	0.9986	0.9124	8	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:38	RLLDKGHFSAV	0.9983	0.8401	8	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:19	RLLDKGHFSAV	0.9971	0.6341	8	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:35	RLLDKGHFSAV	0.9709	0.5984	8	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:29	RLLDKGHFSAV	0.905	0.5873	8	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:20	RLLDKGHFSAV	0.885	0.6009	8	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-C07:05	YRLLDKGHF	0.9952	0.7968	7	16
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-C07:27	YRLLDKGHF	0.9849	0.8521	7	16
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:07	LLDKGHFSA	0.9801	0.6906	9	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-B27:03	YRLLDKGHF	0.9801	0.8061	7	16
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:01	LLDKGHFSA	0.9798	0.6518	9	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-C07:46	YRLLDKGHF	0.9458	0.6065	7	16
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-C07:67	YRLLDKGHF	0.8572	0.8187	7	16
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-C07:80	YRLLDKGHF	0.8572	0.8187	7	16
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-C07:10	YRLLDKGHF	0.855	0.8646	7	16
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-B14:03	DKGHFSAVL	0.5514	0.9068	11	20
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-C12:16	YRLLDKGHF	0.0412	0.9131	7	16
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:07	LLDKGHFSAV	0.9865	0.7296	9	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-B73:01	YRLLDKGHFSA	0.9999	0.9171	7	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:01	RLLDKGHFSAV	0.9991	0.5918	8	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:07	LLDKGHFSAVL	0.9538	0.5663	9	20
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-B27:08	YRLLDKGHF	0.9994	0.6429	7	16
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-B27:09	YRLLDKGHF	0.9951	0.7092	7	16
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-C07:02	YRLLDKGHF	0.8572	0.8187	7	16
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-B15:09	DKGHFSAVL	0.6796	0.8502	11	20
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A30:01	KGHFSAVLQK	0.9919	0.7143	12	22
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:03	RLLDKGHFSAV	0.9995	0.7266	8	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	HLA-A02:06	RLLDKGHFSAV	0.9987	0.6759	8	19

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Potential FusionNeoAntigen Information of PCTP-BRIP1 in HLA II

PCTP-BRIP1_53828605_59861785.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)
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	DRB1-0832	DKGHFSAVLQKEEKI	11	26
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	DRB1-0908	DKGHFSAVLQKEEKI	11	26
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	DRB1-1172	ISIYRLLDKGHFSAV	4	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	DRB1-1172	GISIYRLLDKGHFSA	3	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	DRB1-13100	GISIYRLLDKGHFSA	3	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	DRB1-13100	ISIYRLLDKGHFSAV	4	19
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	DRB1-1346	GISIYRLLDKGHFSA	3	18
PCTP-BRIP1	chr17	53828605	chr17	59861785	266	DRB1-1346	ISIYRLLDKGHFSAV	4	19

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Fusion breakpoint peptide structures of PCTP-BRIP1

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
4084	IYRLLDKGHFSAVL	PCTP	BRIP1	chr17	53828605	chr17	59861785	266

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PCTP-BRIP1

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	4084	IYRLLDKGHFSAVL	-7.15543	-7.26883
HLA-B14:02	3BVN	4084	IYRLLDKGHFSAVL	-4.77435	-5.80965
HLA-B52:01	3W39	4084	IYRLLDKGHFSAVL	-6.80875	-6.92215
HLA-B52:01	3W39	4084	IYRLLDKGHFSAVL	-4.20386	-5.23916
HLA-A11:01	4UQ2	4084	IYRLLDKGHFSAVL	-7.5194	-8.5547
HLA-A11:01	4UQ2	4084	IYRLLDKGHFSAVL	-6.9601	-7.0735
HLA-A24:02	5HGA	4084	IYRLLDKGHFSAVL	-7.52403	-7.63743
HLA-A24:02	5HGA	4084	IYRLLDKGHFSAVL	-5.82433	-6.85963
HLA-B27:05	6PYJ	4084	IYRLLDKGHFSAVL	-3.28285	-4.31815
HLA-B44:05	3DX8	4084	IYRLLDKGHFSAVL	-5.91172	-6.94702
HLA-B44:05	3DX8	4084	IYRLLDKGHFSAVL	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of PCTP-BRIP1

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
PCTP-BRIP1	chr17	53828605	chr17	59861785	11	20	DKGHFSAVL	GACAAGGGACATTTTTCTGCTGTTCTT
PCTP-BRIP1	chr17	53828605	chr17	59861785	12	22	KGHFSAVLQK	AAGGGACATTTTTCTGCTGTTCTTCAAAAA
PCTP-BRIP1	chr17	53828605	chr17	59861785	7	16	YRLLDKGHF	TACCGGCTGCTGGACAAGGGACATTTT
PCTP-BRIP1	chr17	53828605	chr17	59861785	7	18	YRLLDKGHFSA	TACCGGCTGCTGGACAAGGGACATTTTTCTGCT
PCTP-BRIP1	chr17	53828605	chr17	59861785	8	18	RLLDKGHFSA	CGGCTGCTGGACAAGGGACATTTTTCTGCT
PCTP-BRIP1	chr17	53828605	chr17	59861785	8	19	RLLDKGHFSAV	CGGCTGCTGGACAAGGGACATTTTTCTGCTGTT
PCTP-BRIP1	chr17	53828605	chr17	59861785	9	18	LLDKGHFSA	CTGCTGGACAAGGGACATTTTTCTGCT
PCTP-BRIP1	chr17	53828605	chr17	59861785	9	19	LLDKGHFSAV	CTGCTGGACAAGGGACATTTTTCTGCTGTT
PCTP-BRIP1	chr17	53828605	chr17	59861785	9	20	LLDKGHFSAVL	CTGCTGGACAAGGGACATTTTTCTGCTGTTCTT

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
PCTP-BRIP1	chr17	53828605	chr17	59861785	11	26	DKGHFSAVLQKEEKI	GACAAGGGACATTTTTCTGCTGTTCTTCAAAAAGAGGAAAAAATC
PCTP-BRIP1	chr17	53828605	chr17	59861785	3	18	GISIYRLLDKGHFSA	GGCATCAGCATCTACCGGCTGCTGGACAAGGGACATTTTTCTGCT
PCTP-BRIP1	chr17	53828605	chr17	59861785	4	19	ISIYRLLDKGHFSAV	ATCAGCATCTACCGGCTGCTGGACAAGGGACATTTTTCTGCTGTT

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Information of the samples that have these potential fusion neoantigens of PCTP-BRIP1

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	PCTP-BRIP1	chr17	53828605	ENST00000268896	chr17	59861785	ENST00000259008	TCGA-IE-A3OV-01A

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Potential target of CAR-T therapy development for PCTP-BRIP1

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

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

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Related Drugs to PCTP-BRIP1

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

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to PCTP-BRIP1

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)