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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:PTDSS1-CPQ (FusionGDB2 ID:69887)

Fusion Gene Summary for PTDSS1-CPQ

Fusion gene summary

Fusion gene information	Fusion gene name: PTDSS1-CPQ
	Fusion gene ID: 69887
		Hgene	Tgene
	Gene symbol	PTDSS1	CPQ
	Gene ID	9791	10404
	Gene name	phosphatidylserine synthase 1	carboxypeptidase Q
	Synonyms	LMHD\|PSS1\|PSSA	LDP\|PGCP
	Cytomap	8q22.1	8q22.1
	Type of gene	protein-coding	protein-coding
	Description	phosphatidylserine synthase 1PSS-1ptdSer synthase 1serine-exchange enzyme I	carboxypeptidase QSer-Met dipeptidaseaminopeptidaseblood plasma glutamate carboxypeptidaselysosomal dipeptidase
	Modification date	20200313	20200313
	UniProtAcc	.	Q9Y646
	Ensembl transtripts involved in fusion gene	ENST00000455950, ENST00000517309, ENST00000518776, ENST00000522072,	ENST00000529551, ENST00000220763,
Fusion gene scores	* DoF score	5 X 5 X 4=100	16 X 14 X 11=2464
	# samples	5	19
	** MAII score	log2(5/100*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(19/2464*10)=-3.69693093236395 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: PTDSS1 [Title/Abstract] AND CPQ [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	PTDSS1(97285618)-CPQ(98155248), # samples:1
Anticipated loss of major functional domain due to fusion event.	PTDSS1-CPQ seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF. PTDSS1-CPQ seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. PTDSS1-CPQ 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
Tgene	CPQ	GO:0006508	proteolysis	10206990
Tgene	CPQ	GO:0043171	peptide catabolic process	10206990

Fusion gene breakpoints across PTDSS1 (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 CPQ (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	STAD	TCGA-IN-7808-01A	PTDSS1	chr8	97285618	+	CPQ	chr8	98155248	+

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Fusion Gene ORF analysis for PTDSS1-CPQ

Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
5CDS-intron	ENST00000455950	ENST00000529551	PTDSS1	chr8	97285618	+	CPQ	chr8	98155248	+
5CDS-intron	ENST00000517309	ENST00000529551	PTDSS1	chr8	97285618	+	CPQ	chr8	98155248	+
Frame-shift	ENST00000517309	ENST00000220763	PTDSS1	chr8	97285618	+	CPQ	chr8	98155248	+
In-frame	ENST00000455950	ENST00000220763	PTDSS1	chr8	97285618	+	CPQ	chr8	98155248	+
intron-3CDS	ENST00000518776	ENST00000220763	PTDSS1	chr8	97285618	+	CPQ	chr8	98155248	+
intron-3CDS	ENST00000522072	ENST00000220763	PTDSS1	chr8	97285618	+	CPQ	chr8	98155248	+
intron-intron	ENST00000518776	ENST00000529551	PTDSS1	chr8	97285618	+	CPQ	chr8	98155248	+
intron-intron	ENST00000522072	ENST00000529551	PTDSS1	chr8	97285618	+	CPQ	chr8	98155248	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

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)

ENST00000455950

PTDSS1

chr8

97285618

ENST00000220763

CPQ

chr8

98155248

881

399

562

170

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
ENST00000455950	ENST00000220763	PTDSS1	chr8	97285618	+	CPQ	chr8	98155248	+	0.001722601	0.9982774

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Fusion Genomic Features for PTDSS1-CPQ

FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.

Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	1-p	p (fusion gene breakpoint)
PTDSS1	chr8	97285618	+	CPQ	chr8	98155247	+	1.31E-05	0.9999869
PTDSS1	chr8	97285618	+	CPQ	chr8	98155247	+	1.31E-05	0.9999869

Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for PTDSS1-CPQ

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr8:97285618/chr8:98155248)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
.	CPQ Q9Y646
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.	FUNCTION: Carboxypeptidase that may play an important role in the hydrolysis of circulating peptides. Catalyzes the hydrolysis of dipeptides with unsubstituted terminals into amino acids. May play a role in the liberation of thyroxine hormone from its thyroglobulin (Tg) precursor.

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, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at
download page

* Minus value of BPloci means that the break pointn is located before the CDS.

- In-frame and retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

PTDSS1

chr8:97285618

chr8:98155248

ENST00000517309

2_35

474.0

Topological domain

Cytoplasmic

Hgene

PTDSS1

chr8:97285618

chr8:98155248

ENST00000517309

57_72

474.0

Topological domain

Lumenal

Hgene

PTDSS1

chr8:97285618

chr8:98155248

ENST00000517309

36_56

474.0

Transmembrane

Helical

Hgene

PTDSS1

chr8:97285618

chr8:98155248

ENST00000517309

73_93

474.0

Transmembrane

Helical

- In-frame and not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

PTDSS1

chr8:97285618

chr8:98155248

ENST00000517309

124_186

474.0

Topological domain

Lumenal

Hgene

PTDSS1

chr8:97285618

chr8:98155248

ENST00000517309

208_216

474.0

Topological domain

Cytoplasmic

Hgene

PTDSS1

chr8:97285618

chr8:98155248

ENST00000517309

238_286

474.0

Topological domain

Lumenal

Hgene

PTDSS1

chr8:97285618

chr8:98155248

ENST00000517309

308_319

474.0

Topological domain

Cytoplasmic

Hgene

PTDSS1

chr8:97285618

chr8:98155248

ENST00000517309

343_355

474.0

Topological domain

Lumenal

Hgene

PTDSS1

chr8:97285618

chr8:98155248

ENST00000517309

377_383

474.0

Topological domain

Cytoplasmic

Hgene

PTDSS1

chr8:97285618

chr8:98155248

ENST00000517309

405_473

474.0

Topological domain

Lumenal

Hgene

PTDSS1

chr8:97285618

chr8:98155248

ENST00000517309

94_102

474.0

Topological domain

Cytoplasmic

Hgene

PTDSS1

chr8:97285618

chr8:98155248

ENST00000517309

103_123

474.0

Transmembrane

Helical

Hgene

PTDSS1

chr8:97285618

chr8:98155248

ENST00000517309

187_207

474.0

Transmembrane

Helical

Hgene

PTDSS1

chr8:97285618

chr8:98155248

ENST00000517309

217_237

474.0

Transmembrane

Helical

Hgene

PTDSS1

chr8:97285618

chr8:98155248

ENST00000517309

287_307

474.0

Transmembrane

Helical

Hgene

PTDSS1

chr8:97285618

chr8:98155248

ENST00000517309

320_342

474.0

Transmembrane

Helical

Hgene

PTDSS1

chr8:97285618

chr8:98155248

ENST00000517309

356_376

474.0

Transmembrane

Helical

Hgene

PTDSS1

chr8:97285618

chr8:98155248

ENST00000517309

384_404

474.0

Transmembrane

Helical

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Fusion Gene Sequence for PTDSS1-CPQ

For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>69887_69887_1_PTDSS1-CPQ_PTDSS1_chr8_97285618_ENST00000455950_CPQ_chr8_98155248_ENST00000220763_length(transcript)=881nt_BP=399nt
CAGCCTTTGCTGGGCGCCAGACCCGGCTTTGCCGTCCGGCTATTAGCCTACTGTGGCTAGTCACCCCCGGGGTCCCGGCCTTCTCGGGCT
GGGGCCGCCGCCACCGCGGCAGGACGGGGAGGCGGGCCATGGCGTCCTGCGTGGGGAGCCGGACCCTAAGCAAGGATGATGTGAACTACA
AAATGCATTTCCGGATGATCAACGAGCAGCAAGTGGAGGACATCACCATTGACTTCTTCTACCGGCCGCATACCATCACCCTGCTCAGCT
TCACCATCGTCAGCCTCATGTACTTCGCCTTTACCAGGGATGACTCTGTTCCAGAAGACAACATCTGGAGAGGCATCCTCTCTGTTATTT
TCTTCTTTCTTATCATCAGTGTGTTAGCTTTCCCCAATGGAGCCAGTCTACTTGATGACTTATACAAGTATTTCTTCTTCCATCACTCCC
ACGGAGACACCATGACTGTCATGGATCCAAAGCAGATGAATGTTGCTGCTGCTGTTTGGGCTGTTGTTTCTTATGTTGTTGCAGACATGG
AAGAAATGCTGCCTAGGTCCTAGAAACAGTAAGAAAGAAACGTTTTCATGCTTCTGGCCAGGAATCCTGGGTCTGCAACTTTGGAAAACT
CCTCTTCACATAACAATTTCATCCAATTCATCTTCAAAGCACAACTCTATTTCATGCTTTCTGTTATTATCTTTCTTGATACTTTCCAAA
TTCTCTGATTCTAGAAAAAGGAATCATTCTCCCCTCCCTCCCACCACATAGAATCAACATATGGTAGGGATTACAGTGGGGGCATTTCTT

>69887_69887_1_PTDSS1-CPQ_PTDSS1_chr8_97285618_ENST00000455950_CPQ_chr8_98155248_ENST00000220763_length(amino acids)=170AA_BP=1
MWLVTPGVPAFSGWGRRHRGRTGRRAMASCVGSRTLSKDDVNYKMHFRMINEQQVEDITIDFFYRPHTITLLSFTIVSLMYFAFTRDDSV

--------------------------------------------------------------

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Fusion Gene PPI Analysis for PTDSS1-CPQ

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for PTDSS1-CPQ

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for PTDSS1-CPQ

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source