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Fusion Protein:PMF1-RAB25

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PMF1-RAB25
	FusionPDB ID: 66628
	FusionGDB2.0 ID: 66628
		Hgene	Tgene
	Gene symbol	PMF1	RAB25
	Gene ID	100527963	57111
	Gene name	PMF1-BGLAP readthrough	RAB25, member RAS oncogene family
	Synonyms	PMF-1\|PMF1	CATX-8\|RAB11C
	Cytomap	1q22	1q22
	Type of gene	protein-coding	protein-coding
	Description	PMF1-BGLAP proteinpolyamine-modulated factor 1	ras-related protein Rab-25
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000368273, ENST00000368277, ENST00000368279, ENST00000565805, ENST00000567140,	ENST00000487325, ENST00000361084,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	2 X 1 X 2=4	3 X 3 X 3=27
	# samples	3	4
	** MAII score	log2(3/4*10)=2.90689059560852	log2(4/27*10)=0.567040592723894 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: PMF1 [Title/Abstract] AND RAB25 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PMF1 [Title/Abstract] AND RAB25 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PMF1(156182967)-RAB25(156038061), # samples:3 RAB25(156031234)-PMF1(156202111), # samples:2
Anticipated loss of major functional domain due to fusion event.	PMF1-RAB25 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. PMF1-RAB25 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. RAB25-PMF1 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF. RAB25-PMF1 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
Tgene	RAB25	GO:0008284	positive regulation of cell proliferation	15502842
Tgene	RAB25	GO:0031268	pseudopodium organization	17925226

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:156182967/chr1:156038061)
- 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 PMF1 (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 RAB25 (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)
ENST00000368279	PMF1	chr1	156182967	+	ENST00000361084	RAB25	chr1	156038061	+	804	184	23	586	187
ENST00000368273	PMF1	chr1	156182967	+	ENST00000361084	RAB25	chr1	156038061	+	791	171	10	573	187
ENST00000368277	PMF1	chr1	156182967	+	ENST00000361084	RAB25	chr1	156038061	+	790	170	9	572	187
ENST00000565805	PMF1	chr1	156182967	+	ENST00000361084	RAB25	chr1	156038061	+	790	170	9	572	187
ENST00000567140	PMF1	chr1	156182967	+	ENST00000361084	RAB25	chr1	156038061	+	790	170	9	572	187
ENST00000368279	PMF1	chr1	156182967	+	ENST00000361084	RAB25	chr1	156038060	+	804	184	23	586	187
ENST00000368273	PMF1	chr1	156182967	+	ENST00000361084	RAB25	chr1	156038060	+	791	171	10	573	187
ENST00000368277	PMF1	chr1	156182967	+	ENST00000361084	RAB25	chr1	156038060	+	790	170	9	572	187
ENST00000565805	PMF1	chr1	156182967	+	ENST00000361084	RAB25	chr1	156038060	+	790	170	9	572	187
ENST00000567140	PMF1	chr1	156182967	+	ENST00000361084	RAB25	chr1	156038060	+	790	170	9	572	187

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
ENST00000368279	ENST00000361084	PMF1	chr1	156182967	+	RAB25	chr1	156038061	+	0.004511745	0.9954882
ENST00000368273	ENST00000361084	PMF1	chr1	156182967	+	RAB25	chr1	156038061	+	0.004624514	0.9953755
ENST00000368277	ENST00000361084	PMF1	chr1	156182967	+	RAB25	chr1	156038061	+	0.004515127	0.99548495
ENST00000565805	ENST00000361084	PMF1	chr1	156182967	+	RAB25	chr1	156038061	+	0.004515127	0.99548495
ENST00000567140	ENST00000361084	PMF1	chr1	156182967	+	RAB25	chr1	156038061	+	0.004515127	0.99548495
ENST00000368279	ENST00000361084	PMF1	chr1	156182967	+	RAB25	chr1	156038060	+	0.004511745	0.9954882
ENST00000368273	ENST00000361084	PMF1	chr1	156182967	+	RAB25	chr1	156038060	+	0.004624514	0.9953755
ENST00000368277	ENST00000361084	PMF1	chr1	156182967	+	RAB25	chr1	156038060	+	0.004515127	0.99548495
ENST00000565805	ENST00000361084	PMF1	chr1	156182967	+	RAB25	chr1	156038060	+	0.004515127	0.99548495
ENST00000567140	ENST00000361084	PMF1	chr1	156182967	+	RAB25	chr1	156038060	+	0.004515127	0.99548495

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 PMF1-RAB25

+/-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
PMF1	chr1	156182967	RAB25	chr1	156038060	170	53	MVDTFLQKLVAAGRYYRGAVGALLVF
PMF1	chr1	156182967	RAB25	chr1	156038060	171	53	MVDTFLQKLVAAGRYYRGAVGALLVF
PMF1	chr1	156182967	RAB25	chr1	156038060	184	53	MVDTFLQKLVAAGRYYRGAVGALLVF
PMF1	chr1	156182967	RAB25	chr1	156038061	170	53	MVDTFLQKLVAAGRYYRGAVGALLVF
PMF1	chr1	156182967	RAB25	chr1	156038061	171	53	MVDTFLQKLVAAGRYYRGAVGALLVF
PMF1	chr1	156182967	RAB25	chr1	156038061	184	53	MVDTFLQKLVAAGRYYRGAVGALLVF

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Potential FusionNeoAntigen Information of PMF1-RAB25 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.

PMF1-RAB25_156182967_156038060.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)
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:01	KLVAAGRYY	0.991	0.9042	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:25	KLVAAGRYY	0.9866	0.9252	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-A74:09	LVAAGRYYR	0.9732	0.5167	8	17
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-A74:11	LVAAGRYYR	0.9732	0.5167	8	17
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-A74:03	LVAAGRYYR	0.9732	0.5167	8	17
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:02	KLVAAGRYY	0.9539	0.9315	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:03	KLVAAGRYY	0.3869	0.7921	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:01	LQKLVAAGRY	0.9997	0.7801	5	15
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-A74:03	KLVAAGRYYR	0.9931	0.5575	7	17
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-A74:09	KLVAAGRYYR	0.9931	0.5575	7	17
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-A74:11	KLVAAGRYYR	0.9931	0.5575	7	17
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-A31:02	KLVAAGRYYR	0.9172	0.5343	7	17
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B27:04	GRYYRGAVGAL	1	0.7527	12	23
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B27:07	GRYYRGAVGAL	0.9999	0.8004	12	23
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:01	LQKLVAAGRYY	0.9997	0.6769	5	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-A31:02	TFLQKLVAAGR	0.9814	0.8318	3	14
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:07	KLVAAGRYY	0.9772	0.6045	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:05	KLVAAGRYY	0.8054	0.8836	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:04	KLVAAGRYY	0.6576	0.9346	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B27:14	GRYYRGAVGA	0.9993	0.6753	12	22
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-A31:01	KLVAAGRYYR	0.994	0.5016	7	17
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:04	LQKLVAAGRY	0.9756	0.8127	5	15
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:27	KLVAAGRYY	0.9911	0.9142	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:33	KLVAAGRYY	0.991	0.9042	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:34	KLVAAGRYY	0.991	0.9042	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:125	KLVAAGRYY	0.991	0.9042	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:135	KLVAAGRYY	0.9908	0.9181	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:50	KLVAAGRYY	0.9893	0.921	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:39	KLVAAGRYY	0.9873	0.8589	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:12	KLVAAGRYY	0.987	0.8621	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:35	KLVAAGRYY	0.9778	0.8427	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:24	KLVAAGRYY	0.9736	0.9436	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-A74:01	LVAAGRYYR	0.9732	0.5167	8	17
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:20	KLVAAGRYY	0.7988	0.9249	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B35:28	KLVAAGRYY	0.7111	0.9347	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:54	KLVAAGRYY	0.3904	0.8568	7	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:33	LQKLVAAGRY	0.9997	0.7801	5	15
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:27	LQKLVAAGRY	0.9997	0.8264	5	15
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:34	LQKLVAAGRY	0.9997	0.7801	5	15
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:125	LQKLVAAGRY	0.9997	0.7801	5	15
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:135	LQKLVAAGRY	0.9997	0.805	5	15
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:50	LQKLVAAGRY	0.9996	0.8301	5	15
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:35	LQKLVAAGRY	0.9985	0.6875	5	15
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:12	LQKLVAAGRY	0.9954	0.815	5	15
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-A74:01	KLVAAGRYYR	0.9931	0.5575	7	17
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B27:06	GRYYRGAVGAL	1	0.7858	12	23
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B27:10	GRYYRGAVGAL	1	0.8389	12	23
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B27:08	GRYYRGAVGAL	1	0.7069	12	23
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B27:09	GRYYRGAVGAL	0.9999	0.7505	12	23
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:27	LQKLVAAGRYY	0.9997	0.7332	5	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:33	LQKLVAAGRYY	0.9997	0.6769	5	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:135	LQKLVAAGRYY	0.9997	0.7056	5	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:125	LQKLVAAGRYY	0.9997	0.6769	5	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:34	LQKLVAAGRYY	0.9997	0.6769	5	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:50	LQKLVAAGRYY	0.9995	0.7137	5	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:35	LQKLVAAGRYY	0.9991	0.6098	5	16
PMF1-RAB25	chr1	156182967	chr1	156038060	171	HLA-B15:12	LQKLVAAGRYY	0.9973	0.7073	5	16

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Potential FusionNeoAntigen Information of PMF1-RAB25 in HLA II

PMF1-RAB25_156182967_156038060.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)
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-0113	AGRYYRGAVGALLVF	11	26
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-0117	AGRYYRGAVGALLVF	11	26
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-0117	AAGRYYRGAVGALLV	10	25
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-0904	AAGRYYRGAVGALLV	10	25
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-0904	AGRYYRGAVGALLVF	11	26
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-0905	AGRYYRGAVGALLVF	11	26
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-0905	AAGRYYRGAVGALLV	10	25
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-0907	AAGRYYRGAVGALLV	10	25
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-0907	AGRYYRGAVGALLVF	11	26
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1102	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1102	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1102	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1114	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1114	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1116	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1116	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1116	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1120	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1120	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1121	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1121	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1121	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1121	TFLQKLVAAGRYYRG	3	18
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1136	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1136	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1136	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1148	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1148	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1159	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1159	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1165	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1165	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1165	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1168	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1168	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1170	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1170	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1186	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1186	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1301	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1301	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1301	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1302	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1302	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1308	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1308	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1315	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1315	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1315	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1316	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1316	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1317	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1317	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1317	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1319	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1319	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1319	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1320	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1320	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1320	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1322	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1322	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1322	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1323	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1323	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1327	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1327	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1327	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1327	TFLQKLVAAGRYYRG	3	18
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1329	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1329	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1334	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1334	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1335	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1335	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1335	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1339	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1339	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1341	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1341	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1351	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1351	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1351	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1352	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1352	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1352	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1353	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1353	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1353	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1357	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1357	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1357	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1359	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1359	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1359	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1361	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1361	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1361	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1361	TFLQKLVAAGRYYRG	3	18
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1364	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1364	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1364	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1368	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1368	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1368	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1369	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1369	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1369	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1370	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1370	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1371	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1371	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1371	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1371	TFLQKLVAAGRYYRG	3	18
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1372	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1372	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1373	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1373	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1374	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1374	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1376	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1376	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1378	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1378	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1378	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1379	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1379	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1379	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1380	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1380	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1380	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1383	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1383	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1383	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1384	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1384	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1387	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1387	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1387	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1391	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1391	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1391	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1392	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1392	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1392	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1396	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1396	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1397	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1397	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1398	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1398	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1398	QKLVAAGRYYRGAVG	6	21
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1399	LQKLVAAGRYYRGAV	5	20
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB1-1399	FLQKLVAAGRYYRGA	4	19
PMF1-RAB25	chr1	156182967	chr1	156038060	171	DRB5-0205	DTFLQKLVAAGRYYR	2	17

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Fusion breakpoint peptide structures of PMF1-RAB25

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
7354	QKLVAAGRYYRGAV	PMF1	RAB25	chr1	156182967	chr1	156038060	171

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PMF1-RAB25

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	7354	QKLVAAGRYYRGAV	-7.14368	-7.25548
HLA-B14:02	3BVN	7354	QKLVAAGRYYRGAV	-6.90724	-7.95034
HLA-B52:01	3W39	7354	QKLVAAGRYYRGAV	-7.67666	-8.71976
HLA-B52:01	3W39	7354	QKLVAAGRYYRGAV	-5.5221	-5.6339
HLA-A11:01	4UQ2	7354	QKLVAAGRYYRGAV	-8.37369	-9.41679
HLA-A11:01	4UQ2	7354	QKLVAAGRYYRGAV	-6.26273	-6.37453
HLA-A24:02	5HGA	7354	QKLVAAGRYYRGAV	-7.6158	-8.6589
HLA-A24:02	5HGA	7354	QKLVAAGRYYRGAV	-5.36701	-5.47881
HLA-B44:05	3DX8	7354	QKLVAAGRYYRGAV	-8.09865	-8.21045
HLA-B44:05	3DX8	7354	QKLVAAGRYYRGAV	-5.97829	-7.02139

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Vaccine Design for the FusionNeoAntigens of PMF1-RAB25

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
PMF1-RAB25	chr1	156182967	chr1	156038060	12	22	GRYYRGAVGA	CAGGTACTATCGTGGTGCAGTGGGGGCCCT
PMF1-RAB25	chr1	156182967	chr1	156038060	12	23	GRYYRGAVGAL	CAGGTACTATCGTGGTGCAGTGGGGGCCCTCCT
PMF1-RAB25	chr1	156182967	chr1	156038060	3	14	TFLQKLVAAGR	TTTTCTTCAGAAGCTGGTCGCCGCCGGCAGGTA
PMF1-RAB25	chr1	156182967	chr1	156038060	5	15	LQKLVAAGRY	TCAGAAGCTGGTCGCCGCCGGCAGGTACTA
PMF1-RAB25	chr1	156182967	chr1	156038060	5	16	LQKLVAAGRYY	TCAGAAGCTGGTCGCCGCCGGCAGGTACTATCG
PMF1-RAB25	chr1	156182967	chr1	156038060	7	16	KLVAAGRYY	GCTGGTCGCCGCCGGCAGGTACTATCG
PMF1-RAB25	chr1	156182967	chr1	156038060	7	17	KLVAAGRYYR	GCTGGTCGCCGCCGGCAGGTACTATCGTGG
PMF1-RAB25	chr1	156182967	chr1	156038060	8	17	LVAAGRYYR	GGTCGCCGCCGGCAGGTACTATCGTGG

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
PMF1-RAB25	chr1	156182967	chr1	156038060	10	25	AAGRYYRGAVGALLV	CGCCGGCAGGTACTATCGTGGTGCAGTGGGGGCCCTCCTGGTGTT
PMF1-RAB25	chr1	156182967	chr1	156038060	11	26	AGRYYRGAVGALLVF	CGGCAGGTACTATCGTGGTGCAGTGGGGGCCCTCCTGGTGTTTGA
PMF1-RAB25	chr1	156182967	chr1	156038060	2	17	DTFLQKLVAAGRYYR	CACTTTTCTTCAGAAGCTGGTCGCCGCCGGCAGGTACTATCGTGG
PMF1-RAB25	chr1	156182967	chr1	156038060	3	18	TFLQKLVAAGRYYRG	TTTTCTTCAGAAGCTGGTCGCCGCCGGCAGGTACTATCGTGGTGC
PMF1-RAB25	chr1	156182967	chr1	156038060	4	19	FLQKLVAAGRYYRGA	TCTTCAGAAGCTGGTCGCCGCCGGCAGGTACTATCGTGGTGCAGT
PMF1-RAB25	chr1	156182967	chr1	156038060	5	20	LQKLVAAGRYYRGAV	TCAGAAGCTGGTCGCCGCCGGCAGGTACTATCGTGGTGCAGTGGG
PMF1-RAB25	chr1	156182967	chr1	156038060	6	21	QKLVAAGRYYRGAVG	GAAGCTGGTCGCCGCCGGCAGGTACTATCGTGGTGCAGTGGGGGC

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Information of the samples that have these potential fusion neoantigens of PMF1-RAB25

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
CESC	PMF1-RAB25	chr1	156182967	ENST00000368273	chr1	156038060	ENST00000361084	TCGA-DS-A1OC

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Potential target of CAR-T therapy development for PMF1-RAB25

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 PMF1-RAB25

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 PMF1-RAB25

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)