Home

Download

Statistics

Examples

Help

Contact

Fusion Protein:PDE9A-ABCG1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PDE9A-ABCG1
	FusionPDB ID: 63815
	FusionGDB2.0 ID: 63815
		Hgene	Tgene
	Gene symbol	PDE9A	ABCG1
	Gene ID	5152	9619
	Gene name	phosphodiesterase 9A	ATP binding cassette subfamily G member 1
	Synonyms	HSPDE9A2	ABC8\|WHITE1
	Cytomap	21q22.3	21q22.3
	Type of gene	protein-coding	protein-coding
	Description	high affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9ACGMP-specific 3',5'-cyclic phosphodiesterase type 9phosphodiesterase PDE9A21	ATP-binding cassette sub-family G member 1ABC transporter 8ATP-binding cassette transporter 8ATP-binding cassette transporter member 1 of subfamily GATP-binding cassette, sub-family G (WHITE), member 1homolog of Drosophila whitewhite protein homolog
	Modification date	20200327	20200329
	UniProtAcc	.	P45844 Main function of 5'-partner protein: FUNCTION: Catalyzes the efflux of phospholipids such as sphingomyelin, cholesterol and its oxygenated derivatives like 7beta-hydroxycholesterol and this transport is coupled to hydrlysis of ATP (PubMed:17408620, PubMed:24576892). The lipid efflux is ALB-dependent (PubMed:16702602). Is an active component of the macrophage lipid export complex. Could also be involved in intracellular lipid transport processes. The role in cellular lipid homeostasis may not be limited to macrophages. Prevents cell death by transporting cytotoxic 7beta-hydroxycholesterol (PubMed:17408620). {ECO:0000269\|PubMed:16702602, ECO:0000269\|PubMed:17408620, ECO:0000269\|PubMed:24576892}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000470987, ENST00000291539, ENST00000328862, ENST00000335440, ENST00000335512, ENST00000349112, ENST00000380328, ENST00000398224, ENST00000398225, ENST00000398227, ENST00000398229, ENST00000398232, ENST00000398234, ENST00000398236, ENST00000539837,	ENST00000398457, ENST00000343687, ENST00000347800, ENST00000361802, ENST00000398449, ENST00000462050, ENST00000340588, ENST00000398437,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	11 X 7 X 6=462	9 X 5 X 8=360
	# samples	11	10
	** MAII score	log2(11/462*10)=-2.0703893278914 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(10/360*10)=-1.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: PDE9A [Title/Abstract] AND ABCG1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PDE9A [Title/Abstract] AND ABCG1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PDE9A(44073993)-ABCG1(43645781), # samples:3
Anticipated loss of major functional domain due to fusion event.	PDE9A-ABCG1 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. PDE9A-ABCG1 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. PDE9A-ABCG1 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. PDE9A-ABCG1 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. PDE9A-ABCG1 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF. PDE9A-ABCG1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. PDE9A-ABCG1 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF. PDE9A-ABCG1 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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	PDE9A	GO:0046068	cGMP metabolic process	9624146
Hgene	PDE9A	GO:0046069	cGMP catabolic process	25799991
Tgene	ABCG1	GO:0008203	cholesterol metabolic process	15994327
Tgene	ABCG1	GO:0033344	cholesterol efflux	15994327
Tgene	ABCG1	GO:0033993	response to lipid	16556852
Tgene	ABCG1	GO:0034436	glycoprotein transport	17293612
Tgene	ABCG1	GO:0042632	cholesterol homeostasis	15994327
Tgene	ABCG1	GO:0042987	amyloid precursor protein catabolic process	17293612
Tgene	ABCG1	GO:0050714	positive regulation of protein secretion	17293612
Tgene	ABCG1	GO:1902004	positive regulation of amyloid-beta formation	17293612

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr21:44073993/chr21:43645781)
- 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 PDE9A (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 ABCG1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Top

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)
ENST00000335512	PDE9A	chr21	44073993	+	ENST00000398457	ABCG1	chr21	43645781	+	2945	134	65	2092	675
ENST00000291539	PDE9A	chr21	44073993	+	ENST00000398457	ABCG1	chr21	43645781	+	2940	129	60	2087	675
ENST00000398236	PDE9A	chr21	44073993	+	ENST00000398457	ABCG1	chr21	43645781	+	2916	105	36	2063	675
ENST00000380328	PDE9A	chr21	44073993	+	ENST00000398457	ABCG1	chr21	43645781	+	2916	105	36	2063	675
ENST00000328862	PDE9A	chr21	44073993	+	ENST00000398457	ABCG1	chr21	43645781	+	2916	105	36	2063	675
ENST00000335440	PDE9A	chr21	44073993	+	ENST00000398457	ABCG1	chr21	43645781	+	2916	105	36	2063	675
ENST00000349112	PDE9A	chr21	44073993	+	ENST00000398457	ABCG1	chr21	43645781	+	2882	71	2	2029	675

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
ENST00000335512	ENST00000398457	PDE9A	chr21	44073993	+	ABCG1	chr21	43645781	+	0.003511086	0.9964889
ENST00000291539	ENST00000398457	PDE9A	chr21	44073993	+	ABCG1	chr21	43645781	+	0.003492022	0.99650794
ENST00000398236	ENST00000398457	PDE9A	chr21	44073993	+	ABCG1	chr21	43645781	+	0.003539002	0.996461
ENST00000380328	ENST00000398457	PDE9A	chr21	44073993	+	ABCG1	chr21	43645781	+	0.003539002	0.996461
ENST00000328862	ENST00000398457	PDE9A	chr21	44073993	+	ABCG1	chr21	43645781	+	0.003539002	0.996461
ENST00000335440	ENST00000398457	PDE9A	chr21	44073993	+	ABCG1	chr21	43645781	+	0.003539002	0.996461
ENST00000349112	ENST00000398457	PDE9A	chr21	44073993	+	ABCG1	chr21	43645781	+	0.003559277	0.9964407

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

Top

Fusion Protein Breakpoint Sequences for PDE9A-ABCG1

+/-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
PDE9A	chr21	44073993	ABCG1	chr21	43645781	105	23	KAIYLDIDGRIQKNASSYSAEMTEPK
PDE9A	chr21	44073993	ABCG1	chr21	43645781	129	23	KAIYLDIDGRIQKNASSYSAEMTEPK
PDE9A	chr21	44073993	ABCG1	chr21	43645781	134	23	KAIYLDIDGRIQKNASSYSAEMTEPK
PDE9A	chr21	44073993	ABCG1	chr21	43645781	71	23	KAIYLDIDGRIQKNASSYSAEMTEPK

Top

Potential FusionNeoAntigen Information of PDE9A-ABCG1 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.

PDE9A-ABCG1_44073993_43645781.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)
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:01	IQKNASSY	0.9999	0.5841	10	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:25	IQKNASSY	0.9953	0.5409	10	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:01	RIQKNASSY	0.9997	0.7595	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:25	RIQKNASSY	0.9966	0.7418	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B39:06	QKNASSYSA	0.9941	0.6774	11	20
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:02	RIQKNASSY	0.9868	0.7714	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:17	RIQKNASSY	0.9651	0.7282	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B27:05	GRIQKNASSY	0.9999	0.8297	8	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B27:04	GRIQKNASSY	0.9999	0.628	8	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:04	IQKNASSY	0.9989	0.5842	10	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:21	RIQKNASSY	0.9851	0.717	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:04	RIQKNASSY	0.9597	0.7743	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:05	RIQKNASSY	0.8201	0.6413	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:31	RIQKNASSY	0.7248	0.6546	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B27:03	GRIQKNASSY	0.9987	0.8482	8	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-C07:46	GRIQKNASSY	0.9791	0.7802	8	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:27	IQKNASSY	0.9999	0.6385	10	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:33	IQKNASSY	0.9999	0.5841	10	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:135	IQKNASSY	0.9999	0.6002	10	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:50	IQKNASSY	0.9999	0.6604	10	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:125	IQKNASSY	0.9999	0.5841	10	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:34	IQKNASSY	0.9999	0.5841	10	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:53	IQKNASSY	0.9997	0.5078	10	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:12	IQKNASSY	0.9988	0.5742	10	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B35:28	IQKNASSY	0.9014	0.6415	10	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B18:04	IQKNASSY	0.8712	0.6852	10	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B48:02	IQKNASSY	0.609	0.6045	10	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:27	RIQKNASSY	0.9997	0.7755	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:135	RIQKNASSY	0.9997	0.7521	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:33	RIQKNASSY	0.9997	0.7595	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:34	RIQKNASSY	0.9997	0.7595	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:125	RIQKNASSY	0.9997	0.7595	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:50	RIQKNASSY	0.9995	0.7105	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:11	RIQKNASSY	0.9992	0.6787	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:08	RIQKNASSY	0.999	0.6626	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:12	RIQKNASSY	0.9987	0.7319	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:24	RIQKNASSY	0.9985	0.7056	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:35	RIQKNASSY	0.9976	0.71	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:39	RIQKNASSY	0.9966	0.5781	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:53	RIQKNASSY	0.9938	0.6959	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:54	RIQKNASSY	0.8905	0.6774	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-A32:01	RIQKNASSY	0.8666	0.7194	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:20	RIQKNASSY	0.809	0.7482	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B35:28	RIQKNASSY	0.7513	0.7488	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-C03:02	RIQKNASSY	0.4189	0.9189	9	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B27:10	GRIQKNASSY	0.9999	0.7412	8	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B27:08	GRIQKNASSY	0.9998	0.6924	8	18
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	HLA-B15:54	GRIQKNASSY	0.9215	0.6823	8	18

Top

Potential FusionNeoAntigen Information of PDE9A-ABCG1 in HLA II

PDE9A-ABCG1_44073993_43645781.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)
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0301	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0301	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0301	IYLDIDGRIQKNASS	2	17
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0303	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0303	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0305	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0305	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0307	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0307	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0307	IYLDIDGRIQKNASS	2	17
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0310	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0313	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0313	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0313	IYLDIDGRIQKNASS	2	17
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0315	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0315	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0318	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0318	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0318	IYLDIDGRIQKNASS	2	17
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0320	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0320	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0322	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0322	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0322	IYLDIDGRIQKNASS	2	17
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0324	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0324	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0326	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0326	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0328	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0328	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0328	IYLDIDGRIQKNASS	2	17
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0330	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0330	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0330	IYLDIDGRIQKNASS	2	17
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0332	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0332	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0332	IYLDIDGRIQKNASS	2	17
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0334	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0334	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0334	IYLDIDGRIQKNASS	2	17
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0336	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0336	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0336	IYLDIDGRIQKNASS	2	17
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0340	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0340	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0342	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0344	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0344	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0344	IYLDIDGRIQKNASS	2	17
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0346	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0346	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0346	IYLDIDGRIQKNASS	2	17
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0348	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0348	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0348	IYLDIDGRIQKNASS	2	17
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0350	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0350	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0350	IYLDIDGRIQKNASS	2	17
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0352	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0352	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0352	IYLDIDGRIQKNASS	2	17
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0354	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0354	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-0354	IYLDIDGRIQKNASS	2	17
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-1107	AIYLDIDGRIQKNAS	1	16
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-1107	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-1107	IYLDIDGRIQKNASS	2	17
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB1-1525	KAIYLDIDGRIQKNA	0	15
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0201	DGRIQKNASSYSAEM	7	22
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0201	IDGRIQKNASSYSAE	6	21
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0201	DIDGRIQKNASSYSA	5	20
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0201	GRIQKNASSYSAEMT	8	23
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0202	DGRIQKNASSYSAEM	7	22
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0202	IDGRIQKNASSYSAE	6	21
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0204	DGRIQKNASSYSAEM	7	22
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0204	IDGRIQKNASSYSAE	6	21
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0204	DIDGRIQKNASSYSA	5	20
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0205	DGRIQKNASSYSAEM	7	22
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0205	IDGRIQKNASSYSAE	6	21
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0210	DGRIQKNASSYSAEM	7	22
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0210	IDGRIQKNASSYSAE	6	21
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0211	DGRIQKNASSYSAEM	7	22
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0211	IDGRIQKNASSYSAE	6	21
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0212	DGRIQKNASSYSAEM	7	22
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0212	IDGRIQKNASSYSAE	6	21
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0213	DGRIQKNASSYSAEM	7	22
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0214	DGRIQKNASSYSAEM	7	22
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0214	IDGRIQKNASSYSAE	6	21
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0214	DIDGRIQKNASSYSA	5	20
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0215	DGRIQKNASSYSAEM	7	22
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0215	IDGRIQKNASSYSAE	6	21
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0217	DGRIQKNASSYSAEM	7	22
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0217	IDGRIQKNASSYSAE	6	21
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0218	DGRIQKNASSYSAEM	7	22
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0218	IDGRIQKNASSYSAE	6	21
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0219	DGRIQKNASSYSAEM	7	22
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0220	DGRIQKNASSYSAEM	7	22
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0220	IDGRIQKNASSYSAE	6	21
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0222	DGRIQKNASSYSAEM	7	22
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0223	DGRIQKNASSYSAEM	7	22
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0223	IDGRIQKNASSYSAE	6	21
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0224	DGRIQKNASSYSAEM	7	22
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0224	IDGRIQKNASSYSAE	6	21
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0224	DIDGRIQKNASSYSA	5	20
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0224	GRIQKNASSYSAEMT	8	23
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0225	DGRIQKNASSYSAEM	7	22
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0225	IDGRIQKNASSYSAE	6	21
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0301	IDGRIQKNASSYSAE	6	21
PDE9A-ABCG1	chr21	44073993	chr21	43645781	129	DRB3-0301	DGRIQKNASSYSAEM	7	22

Top

Fusion breakpoint peptide structures of PDE9A-ABCG1

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
3624	IDGRIQKNASSYSA	PDE9A	ABCG1	chr21	44073993	chr21	43645781	129

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PDE9A-ABCG1

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	3624	IDGRIQKNASSYSA	-4.62424	-5.65954
HLA-B14:02	3BVN	3624	IDGRIQKNASSYSA	-4.1114	-4.2248
HLA-B52:01	3W39	3624	IDGRIQKNASSYSA	-6.8001	-6.9135
HLA-B52:01	3W39	3624	IDGRIQKNASSYSA	-6.46104	-7.49634
HLA-A24:02	5HGA	3624	IDGRIQKNASSYSA	-9.1447	-9.2581
HLA-A24:02	5HGA	3624	IDGRIQKNASSYSA	-6.01279	-7.04809
HLA-B44:05	3DX8	3624	IDGRIQKNASSYSA	-5.02862	-5.14202
HLA-B44:05	3DX8	3624	IDGRIQKNASSYSA	-4.60714	-5.64244

Top

Vaccine Design for the FusionNeoAntigens of PDE9A-ABCG1

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
PDE9A-ABCG1	chr21	44073993	chr21	43645781	10	18	IQKNASSY	ATTCAGAAGAATGCCAGCAGTTAC
PDE9A-ABCG1	chr21	44073993	chr21	43645781	11	20	QKNASSYSA	CAGAAGAATGCCAGCAGTTACTCTGCA
PDE9A-ABCG1	chr21	44073993	chr21	43645781	8	18	GRIQKNASSY	GGACGCATTCAGAAGAATGCCAGCAGTTAC
PDE9A-ABCG1	chr21	44073993	chr21	43645781	9	18	RIQKNASSY	CGCATTCAGAAGAATGCCAGCAGTTAC

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
PDE9A-ABCG1	chr21	44073993	chr21	43645781	0	15	KAIYLDIDGRIQKNA	AAGGCCATCTACCTGGACATCGATGGACGCATTCAGAAGAATGCC
PDE9A-ABCG1	chr21	44073993	chr21	43645781	1	16	AIYLDIDGRIQKNAS	GCCATCTACCTGGACATCGATGGACGCATTCAGAAGAATGCCAGC
PDE9A-ABCG1	chr21	44073993	chr21	43645781	2	17	IYLDIDGRIQKNASS	ATCTACCTGGACATCGATGGACGCATTCAGAAGAATGCCAGCAGT
PDE9A-ABCG1	chr21	44073993	chr21	43645781	5	20	DIDGRIQKNASSYSA	GACATCGATGGACGCATTCAGAAGAATGCCAGCAGTTACTCTGCA
PDE9A-ABCG1	chr21	44073993	chr21	43645781	6	21	IDGRIQKNASSYSAE	ATCGATGGACGCATTCAGAAGAATGCCAGCAGTTACTCTGCAGAG
PDE9A-ABCG1	chr21	44073993	chr21	43645781	7	22	DGRIQKNASSYSAEM	GATGGACGCATTCAGAAGAATGCCAGCAGTTACTCTGCAGAGATG
PDE9A-ABCG1	chr21	44073993	chr21	43645781	8	23	GRIQKNASSYSAEMT	GGACGCATTCAGAAGAATGCCAGCAGTTACTCTGCAGAGATGACG

Top

Information of the samples that have these potential fusion neoantigens of PDE9A-ABCG1

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
LUAD	PDE9A-ABCG1	chr21	44073993	ENST00000291539	chr21	43645781	ENST00000398457	TCGA-50-5941-01A

Top

Potential target of CAR-T therapy development for PDE9A-ABCG1

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

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000343687

427_445

678.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000343687

457_477

678.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000343687

507_525

678.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000343687

534_555

678.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000343687

568_586

678.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000343687

650_669

678.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000347800

427_445

664.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000347800

457_477

664.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000347800

507_525

664.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000347800

534_555

664.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000347800

568_586

664.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000347800

650_669

664.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000361802

427_445

679.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000361802

457_477

679.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000361802

507_525

679.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000361802

534_555

679.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000361802

568_586

679.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000361802

650_669

679.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000398449

427_445

667.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000398449

457_477

667.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000398449

507_525

667.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000398449

534_555

667.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000398449

568_586

667.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000398449

650_669

667.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000398457

427_445

669.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000398457

457_477

669.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000398457

507_525

669.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000398457

534_555

669.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000398457

568_586

669.0

Transmembrane

Helical

Tgene

ABCG1

chr21:44073993

chr21:43645781

ENST00000398457

650_669

669.0

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 PDE9A-ABCG1

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

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to PDE9A-ABCG1

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)