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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein Structure
	pLDDT scores
	Ramachandran Plot of Fusion Protein Structure
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:COPA-STAC2

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: COPA-STAC2
	FusionPDB ID: 18583
	FusionGDB2.0 ID: 18583
		Hgene	Tgene
	Gene symbol	COPA	STAC2
	Gene ID	1314	342667
	Gene name	COPI coat complex subunit alpha	SH3 and cysteine rich domain 2
	Synonyms	AILJK\|HEP-COP\|alpha-COP	24b2\|24b2/STAC2
	Cytomap	1q23.2	17q12
	Type of gene	protein-coding	protein-coding
	Description	coatomer subunit alphaalpha coat proteincoatomer protein complex subunit alphaproxeninxenin	SH3 and cysteine-rich domain-containing protein 2SRC homology 3 and cysteine-rich domain-containing protein 2
	Modification date	20200327	20200313
	UniProtAcc	P53621	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000241704, ENST00000368069,	ENST00000333461,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	14 X 15 X 6=1260	9 X 6 X 6=324
	# samples	15	12
	** MAII score	log2(15/1260*10)=-3.0703893278914 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(12/324*10)=-1.43295940727611 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: COPA [Title/Abstract] AND STAC2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	COPA(160312921)-STAC2(37374426), # samples:2 COPA(160312920)-STAC2(37374426), # samples:2
Anticipated loss of major functional domain due to fusion event.	COPA-STAC2 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. COPA-STAC2 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	COPA	GO:0030157	pancreatic juice secretion	1429581

Fusion gene breakpoints across COPA (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 STAC2 (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 Gene Sample Information

Fusion gene information from FusionGDB2.0.

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	PRAD	TCGA-CH-5745-01A	COPA	chr1	160312921	-	STAC2	chr17	37374426	-
ChimerDB4	PRAD	TCGA-CH-5745	COPA	chr1	160312920	-	STAC2	chr17	37374426	-
ChimerDB4	PRAD	TCGA-CH-5745	COPA	chr1	160312921	-	STAC2	chr17	37374426	-

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Fusion ORF Analysis

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)
ENST00000368069	COPA	chr1	160312921	-	ENST00000333461	STAC2	chr17	37374426	-	3020	118	1335	112	407
ENST00000241704	COPA	chr1	160312921	-	ENST00000333461	STAC2	chr17	37374426	-	3172	270	1487	264	407
ENST00000368069	COPA	chr1	160312920	-	ENST00000333461	STAC2	chr17	37374426	-	3020	118	1335	112	407
ENST00000241704	COPA	chr1	160312920	-	ENST00000333461	STAC2	chr17	37374426	-	3172	270	1487	264	407

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
ENST00000368069	ENST00000333461	COPA	chr1	160312921	-	STAC2	chr17	37374426	-	0.010516961	0.98948306
ENST00000241704	ENST00000333461	COPA	chr1	160312921	-	STAC2	chr17	37374426	-	0.010668333	0.9893317
ENST00000368069	ENST00000333461	COPA	chr1	160312920	-	STAC2	chr17	37374426	-	0.010516961	0.98948306
ENST00000241704	ENST00000333461	COPA	chr1	160312920	-	STAC2	chr17	37374426	-	0.010668333	0.9893317

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Fusion Amino Acid Sequences

For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>18583_18583_1_COPA-STAC2_COPA_chr1_160312920_ENST00000241704_STAC2_chr17_37374426_ENST00000333461_length(amino acids)=407AA_BP=1
MIPSLARSKVQAWARVSSGFPWLLSDLSQGVDWHQAPLLATADADEAVSILASAHAHADLVLLEAHVTLFLVPGEGLAAAPNILAWPHPL
HKISWEEANPVADLALPPVLVRVIHQHDPISRLQSQIIVLLGQKLVECNVGVHGPHILPQGGFGELLSRTLLLWSWPFTLCWGCEYWRCT
VTRPLLRAADAAFPILGQLIPLTQAPCRGLRGAAETGAVHQCQGGAIAQGLVDRVHLPTVPSGWGLFACGTDWWRLMHQERGTEVAAEGG
GRLAWALLVGDLLRAPEVDADFAHLTSQALFGVSYDELVAQLTRASSLEDMFLEAVQPHWFERCQGAWDWAWGGGWGSQAPVRGCGWWGG

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

>18583_18583_2_COPA-STAC2_COPA_chr1_160312920_ENST00000368069_STAC2_chr17_37374426_ENST00000333461_length(amino acids)=407AA_BP=1
MIPSLARSKVQAWARVSSGFPWLLSDLSQGVDWHQAPLLATADADEAVSILASAHAHADLVLLEAHVTLFLVPGEGLAAAPNILAWPHPL
HKISWEEANPVADLALPPVLVRVIHQHDPISRLQSQIIVLLGQKLVECNVGVHGPHILPQGGFGELLSRTLLLWSWPFTLCWGCEYWRCT
VTRPLLRAADAAFPILGQLIPLTQAPCRGLRGAAETGAVHQCQGGAIAQGLVDRVHLPTVPSGWGLFACGTDWWRLMHQERGTEVAAEGG
GRLAWALLVGDLLRAPEVDADFAHLTSQALFGVSYDELVAQLTRASSLEDMFLEAVQPHWFERCQGAWDWAWGGGWGSQAPVRGCGWWGG

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

>18583_18583_3_COPA-STAC2_COPA_chr1_160312921_ENST00000241704_STAC2_chr17_37374426_ENST00000333461_length(amino acids)=407AA_BP=1
MIPSLARSKVQAWARVSSGFPWLLSDLSQGVDWHQAPLLATADADEAVSILASAHAHADLVLLEAHVTLFLVPGEGLAAAPNILAWPHPL
HKISWEEANPVADLALPPVLVRVIHQHDPISRLQSQIIVLLGQKLVECNVGVHGPHILPQGGFGELLSRTLLLWSWPFTLCWGCEYWRCT
VTRPLLRAADAAFPILGQLIPLTQAPCRGLRGAAETGAVHQCQGGAIAQGLVDRVHLPTVPSGWGLFACGTDWWRLMHQERGTEVAAEGG
GRLAWALLVGDLLRAPEVDADFAHLTSQALFGVSYDELVAQLTRASSLEDMFLEAVQPHWFERCQGAWDWAWGGGWGSQAPVRGCGWWGG

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

>18583_18583_4_COPA-STAC2_COPA_chr1_160312921_ENST00000368069_STAC2_chr17_37374426_ENST00000333461_length(amino acids)=407AA_BP=1
MIPSLARSKVQAWARVSSGFPWLLSDLSQGVDWHQAPLLATADADEAVSILASAHAHADLVLLEAHVTLFLVPGEGLAAAPNILAWPHPL
HKISWEEANPVADLALPPVLVRVIHQHDPISRLQSQIIVLLGQKLVECNVGVHGPHILPQGGFGELLSRTLLLWSWPFTLCWGCEYWRCT
VTRPLLRAADAAFPILGQLIPLTQAPCRGLRGAAETGAVHQCQGGAIAQGLVDRVHLPTVPSGWGLFACGTDWWRLMHQERGTEVAAEGG
GRLAWALLVGDLLRAPEVDADFAHLTSQALFGVSYDELVAQLTRASSLEDMFLEAVQPHWFERCQGAWDWAWGGGWGSQAPVRGCGWWGG

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

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:160312921/chr17:37374426)
- 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
COPA P53621	.
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. 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 to 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}.; FUNCTION: Xenin stimulates exocrine pancreatic secretion. It inhibits pentagastrin-stimulated secretion of acid, to induce exocrine pancreatic secretion and to affect small and large intestinal motility. In the gut, xenin interacts with the neurotensin receptor.	FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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.

- 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

Tgene

STAC2

chr1:160312920

chr17:37374426

ENST00000333461

70_101

30.0

412.0

Compositional bias

Note=Pro-rich

Tgene

STAC2

chr1:160312921

chr17:37374426

ENST00000333461

70_101

30.0

412.0

Compositional bias

Note=Pro-rich

Tgene

STAC2

chr1:160312920

chr17:37374426

ENST00000333461

292_351

30.0

412.0

Domain

SH3 1

Tgene

STAC2

chr1:160312920

chr17:37374426

ENST00000333461

354_411

30.0

412.0

Domain

SH3 2

Tgene

STAC2

chr1:160312921

chr17:37374426

ENST00000333461

292_351

30.0

412.0

Domain

SH3 1

Tgene

STAC2

chr1:160312921

chr17:37374426

ENST00000333461

354_411

30.0

412.0

Domain

SH3 2

Tgene

STAC2

chr1:160312920

chr17:37374426

ENST00000333461

110_161

30.0

412.0

Zinc finger

Phorbol-ester/DAG-type

Tgene

STAC2

chr1:160312921

chr17:37374426

ENST00000333461

110_161

30.0

412.0

Zinc finger

Phorbol-ester/DAG-type

- 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

COPA

chr1:160312920

chr17:37374426

ENST00000241704

126_164

13.333333333333334

1225.0

Repeat

Note=WD 4

Hgene

COPA

chr1:160312920

chr17:37374426

ENST00000241704

195_234

13.333333333333334

1225.0

Repeat

Note=WD 5

Hgene

COPA

chr1:160312920

chr17:37374426

ENST00000241704

241_278

13.333333333333334

1225.0

Repeat

Note=WD 6

Hgene

COPA

chr1:160312920

chr17:37374426

ENST00000241704

282_319

13.333333333333334

1225.0

Repeat

Note=WD 7

Hgene

COPA

chr1:160312920

chr17:37374426

ENST00000241704

3_38

13.333333333333334

1225.0

Repeat

Note=WD 1

Hgene

COPA

chr1:160312920

chr17:37374426

ENST00000241704

42_80

13.333333333333334

1225.0

Repeat

Note=WD 2

Hgene

COPA

chr1:160312920

chr17:37374426

ENST00000241704

84_122

13.333333333333334

1225.0

Repeat

Note=WD 3

Hgene

COPA

chr1:160312920

chr17:37374426

ENST00000368069

126_164

13.333333333333334

1234.0

Repeat

Note=WD 4

Hgene

COPA

chr1:160312920

chr17:37374426

ENST00000368069

195_234

13.333333333333334

1234.0

Repeat

Note=WD 5

Hgene

COPA

chr1:160312920

chr17:37374426

ENST00000368069

241_278

13.333333333333334

1234.0

Repeat

Note=WD 6

Hgene

COPA

chr1:160312920

chr17:37374426

ENST00000368069

282_319

13.333333333333334

1234.0

Repeat

Note=WD 7

Hgene

COPA

chr1:160312920

chr17:37374426

ENST00000368069

3_38

13.333333333333334

1234.0

Repeat

Note=WD 1

Hgene

COPA

chr1:160312920

chr17:37374426

ENST00000368069

42_80

13.333333333333334

1234.0

Repeat

Note=WD 2

Hgene

COPA

chr1:160312920

chr17:37374426

ENST00000368069

84_122

13.333333333333334

1234.0

Repeat

Note=WD 3

Hgene

COPA

chr1:160312921

chr17:37374426

ENST00000241704

126_164

13.333333333333334

1225.0

Repeat

Note=WD 4

Hgene

COPA

chr1:160312921

chr17:37374426

ENST00000241704

195_234

13.333333333333334

1225.0

Repeat

Note=WD 5

Hgene

COPA

chr1:160312921

chr17:37374426

ENST00000241704

241_278

13.333333333333334

1225.0

Repeat

Note=WD 6

Hgene

COPA

chr1:160312921

chr17:37374426

ENST00000241704

282_319

13.333333333333334

1225.0

Repeat

Note=WD 7

Hgene

COPA

chr1:160312921

chr17:37374426

ENST00000241704

3_38

13.333333333333334

1225.0

Repeat

Note=WD 1

Hgene

COPA

chr1:160312921

chr17:37374426

ENST00000241704

42_80

13.333333333333334

1225.0

Repeat

Note=WD 2

Hgene

COPA

chr1:160312921

chr17:37374426

ENST00000241704

84_122

13.333333333333334

1225.0

Repeat

Note=WD 3

Hgene

COPA

chr1:160312921

chr17:37374426

ENST00000368069

126_164

13.333333333333334

1234.0

Repeat

Note=WD 4

Hgene

COPA

chr1:160312921

chr17:37374426

ENST00000368069

195_234

13.333333333333334

1234.0

Repeat

Note=WD 5

Hgene

COPA

chr1:160312921

chr17:37374426

ENST00000368069

241_278

13.333333333333334

1234.0

Repeat

Note=WD 6

Hgene

COPA

chr1:160312921

chr17:37374426

ENST00000368069

282_319

13.333333333333334

1234.0

Repeat

Note=WD 7

Hgene

COPA

chr1:160312921

chr17:37374426

ENST00000368069

3_38

13.333333333333334

1234.0

Repeat

Note=WD 1

Hgene

COPA

chr1:160312921

chr17:37374426

ENST00000368069

42_80

13.333333333333334

1234.0

Repeat

Note=WD 2

Hgene

COPA

chr1:160312921

chr17:37374426

ENST00000368069

84_122

13.333333333333334

1234.0

Repeat

Note=WD 3

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Fusion Protein Structures

PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

Fusion protein PDB link (fusion AA seq ID in FusionPDB)	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	AA seq	Len(AA seq)
PDB file >>>821_COPA_160312921_STAC2_37374426_ranked_0.pdb	COPA	160312920	160312921	ENST00000333461	STAC2	chr17	37374426	-	MIPSLARSKVQAWARVSSGFPWLLSDLSQGVDWHQAPLLATADADEAVSILASAHAHADLVLLEAHVTLFLVPGEGLAAAPNILAWPHPL HKISWEEANPVADLALPPVLVRVIHQHDPISRLQSQIIVLLGQKLVECNVGVHGPHILPQGGFGELLSRTLLLWSWPFTLCWGCEYWRCT VTRPLLRAADAAFPILGQLIPLTQAPCRGLRGAAETGAVHQCQGGAIAQGLVDRVHLPTVPSGWGLFACGTDWWRLMHQERGTEVAAEGG GRLAWALLVGDLLRAPEVDADFAHLTSQALFGVSYDELVAQLTRASSLEDMFLEAVQPHWFERCQGAWDWAWGGGWGSQAPVRGCGWWGG	407

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pLDDT score distribution

pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

COPA_pLDDT.png

STAC2_pLDDT.png

pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

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Ramachandran Plot of Fusion Protein Structure

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.

Fusion AA seq ID in FusionPDB and their Ramachandran plots

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Fusion Protein-Protein Interaction

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 from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
COPA
STAC2

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs to COPA-STAC2

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 COPA-STAC2

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