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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:GPATCH2L-COPE (FusionGDB2 ID:34099)

Fusion Gene Summary for GPATCH2L-COPE

Fusion gene summary

Fusion gene information	Fusion gene name: GPATCH2L-COPE
	Fusion gene ID: 34099
		Hgene	Tgene
	Gene symbol	GPATCH2L	COPE
	Gene ID	55668	11316
	Gene name	G-patch domain containing 2 like	COPI coat complex subunit epsilon
	Synonyms	C14orf118	epsilon-COP
	Cytomap	14q24.3	19p13.11
	Type of gene	protein-coding	protein-coding
	Description	G patch domain-containing protein 2-like	coatomer subunit epsiloncoatomer epsilon subunitcoatomer protein complex subunit epsilonepsilon coat protein
	Modification date	20200313	20200313
	UniProtAcc	Q9NWQ4	O14579
	Ensembl transtripts involved in fusion gene	ENST00000261530, ENST00000312858, ENST00000553588, ENST00000556663, ENST00000556675, ENST00000557207, ENST00000557263,	ENST00000262812, ENST00000349893, ENST00000351079, ENST00000598969, ENST00000600932,
Fusion gene scores	* DoF score	4 X 2 X 2=16	7 X 7 X 3=147
	# samples	4	7
	** MAII score	log2(4/16*10)=1.32192809488736 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(7/147*10)=-1.0703893278914 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: GPATCH2L [Title/Abstract] AND COPE [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	GPATCH2L(76644041)-COPE(19027596), # samples:1
Anticipated loss of major functional domain due to fusion event.

* 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

Fusion gene breakpoints across GPATCH2L (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 COPE (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
ChiTaRS5.0	N/A	DL059409	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+

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Fusion Gene ORF analysis for GPATCH2L-COPE

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
intron-intron	ENST00000261530	ENST00000262812	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000261530	ENST00000349893	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000261530	ENST00000351079	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000261530	ENST00000598969	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000261530	ENST00000600932	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000312858	ENST00000262812	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000312858	ENST00000349893	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000312858	ENST00000351079	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000312858	ENST00000598969	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000312858	ENST00000600932	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000553588	ENST00000262812	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000553588	ENST00000349893	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000553588	ENST00000351079	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000553588	ENST00000598969	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000553588	ENST00000600932	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000556663	ENST00000262812	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000556663	ENST00000349893	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000556663	ENST00000351079	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000556663	ENST00000598969	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000556663	ENST00000600932	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000556675	ENST00000262812	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000556675	ENST00000349893	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000556675	ENST00000351079	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000556675	ENST00000598969	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000556675	ENST00000600932	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000557207	ENST00000262812	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000557207	ENST00000349893	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000557207	ENST00000351079	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000557207	ENST00000598969	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000557207	ENST00000600932	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000557263	ENST00000262812	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000557263	ENST00000349893	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000557263	ENST00000351079	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000557263	ENST00000598969	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+
intron-intron	ENST00000557263	ENST00000600932	GPATCH2L	chr14	76644041	-	COPE	chr19	19027596	+

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)

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

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Fusion Genomic Features for GPATCH2L-COPE

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)

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 GPATCH2L-COPE

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:76644041/:19027596)
- 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
GPATCH2L Q9NWQ4	COPE O14579
	FUNCTION: The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. The coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. In mammals, the coatomer can only be recruited by membranes associated with ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors (By similarity). {ECO:0000250}.

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

- 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

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Fusion Gene Sequence for GPATCH2L-COPE

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.

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Fusion Gene PPI Analysis for GPATCH2L-COPE

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 GPATCH2L-COPE

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 GPATCH2L-COPE

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source