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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:PSMG2-SETMAR

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PSMG2-SETMAR
	FusionPDB ID: 69767
	FusionGDB2.0 ID: 69767
		Hgene	Tgene
	Gene symbol	PSMG2	SETMAR
	Gene ID	56984	6419
	Gene name	proteasome assembly chaperone 2	SET domain and mariner transposase fusion gene
	Synonyms	CLAST3\|HCCA3\|HsT1707\|MDS003\|PAC2\|TNFSF5IP1	METNASE\|Mar1
	Cytomap	18p11.21	3p26.1
	Type of gene	protein-coding	protein-coding
	Description	proteasome assembly chaperone 2CD40 ligand-activated specific transcript 3HDCMC29PHSPC260PAC-2hepatocellular carcinoma susceptibility proteinhepatocellular carcinoma-susceptibility protein 3likely ortholog of mouse CD40 ligand-activated specific tr	histone-lysine N-methyltransferase SETMARSET domain and mariner transposase fusion gene-containing proteinSET domain and mariner transposase fusion protein
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000317615, ENST00000585331, ENST00000590217, ENST00000589405,	ENST00000462115, ENST00000425863, ENST00000430981, ENST00000358065,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	4 X 4 X 4=64	2 X 3 X 2=12
	# samples	5	3
	** MAII score	log2(5/64*10)=-0.356143810225275 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(3/12*10)=1.32192809488736 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)	PubMed: PSMG2 [Title/Abstract] AND SETMAR [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PSMG2(12706720)-SETMAR(4354582), # samples:3
Anticipated loss of major functional domain due to fusion event.	PSMG2-SETMAR 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. PSMG2-SETMAR 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. PSMG2-SETMAR 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. PSMG2-SETMAR 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. PSMG2-SETMAR seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. PSMG2-SETMAR seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor 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	PSMG2	GO:0043248	proteasome assembly	16251969
Tgene	SETMAR	GO:0000729	DNA double-strand break processing	21491884
Tgene	SETMAR	GO:0000737	DNA catabolic process, endonucleolytic	20521842\|21491884
Tgene	SETMAR	GO:0006303	double-strand break repair via nonhomologous end joining	16332963
Tgene	SETMAR	GO:0010452	histone H3-K36 methylation	16332963
Tgene	SETMAR	GO:0051568	histone H3-K4 methylation	16332963
Tgene	SETMAR	GO:2000373	positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity	18790802
Tgene	SETMAR	GO:2001034	positive regulation of double-strand break repair via nonhomologous end joining	20620605\|21491884
Tgene	SETMAR	GO:2001251	negative regulation of chromosome organization	20620605

Fusion gene breakpoints across PSMG2 (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 SETMAR (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-ZG-A9L2-01A	PSMG2	chr18	12706720	-	SETMAR	chr3	4354582	+
ChimerDB4	PRAD	TCGA-ZG-A9L2-01A	PSMG2	chr18	12706720	+	SETMAR	chr3	4354582	+
ChimerDB4	PRAD	TCGA-ZG-A9L2	PSMG2	chr18	12706720	+	SETMAR	chr3	4354582	+
ChimerDB4	PRAD	TCGA-ZG-A9L2	PSMG2	chr18	12706720	+	SETMAR	chr3	4355351	+
ChimerDB4	PRAD	TCGA-ZG-A9L2	PSMG2	chr18	12706720	+	SETMAR	chr3	4357896	+

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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)
ENST00000585331	PSMG2	chr18	12706720	+	ENST00000430981	SETMAR	chr3	4354582	+	1713	208	199	1149	316
ENST00000317615	PSMG2	chr18	12706720	+	ENST00000430981	SETMAR	chr3	4354582	+	2416	911	902	1852	316
ENST00000590217	PSMG2	chr18	12706720	+	ENST00000430981	SETMAR	chr3	4354582	+	1819	314	305	1255	316
ENST00000585331	PSMG2	chr18	12706720	+	ENST00000430981	SETMAR	chr3	4355351	+	943	208	3	293	96
ENST00000317615	PSMG2	chr18	12706720	+	ENST00000430981	SETMAR	chr3	4355351	+	1646	911	376	996	206
ENST00000590217	PSMG2	chr18	12706720	+	ENST00000430981	SETMAR	chr3	4355351	+	1049	314	25	399	124

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
ENST00000585331	ENST00000430981	PSMG2	chr18	12706720	+	SETMAR	chr3	4354582	+	0.000370852	0.99962914
ENST00000317615	ENST00000430981	PSMG2	chr18	12706720	+	SETMAR	chr3	4354582	+	0.001102115	0.9988979
ENST00000590217	ENST00000430981	PSMG2	chr18	12706720	+	SETMAR	chr3	4354582	+	0.000354759	0.99964523
ENST00000585331	ENST00000430981	PSMG2	chr18	12706720	+	SETMAR	chr3	4355351	+	0.14623667	0.85376334
ENST00000317615	ENST00000430981	PSMG2	chr18	12706720	+	SETMAR	chr3	4355351	+	0.019982312	0.98001766
ENST00000590217	ENST00000430981	PSMG2	chr18	12706720	+	SETMAR	chr3	4355351	+	0.023018876	0.9769811

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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

>69767_69767_1_PSMG2-SETMAR_PSMG2_chr18_12706720_ENST00000317615_SETMAR_chr3_4354582_ENST00000430981_length(amino acids)=316AA_BP=1
MLKYTPDHVVGPGADIDPTQITFPGCICVKTPCLPGTCSCLRHGENYDDNSCLRDIGSGGKYAEPVFECNVLCRCSDHCRNRVVQKGLQF
HFQVFKTHKKGWGLRTLEFIPKGRFVCEYAGEVLGFSEVQRRIHLQTKSDSNYIIAIREHVYNGQVMETFVDPTYIGNIGRFLNHSCEPN
LLMIPVRIDSMVPKLALFAAKDIVPEEELSYDYSGRYLNLTVSEDKERLDHGKLRKPCYCGAKSCTAFLPFDSSLYCPVEKSNISCGNEK

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

>69767_69767_2_PSMG2-SETMAR_PSMG2_chr18_12706720_ENST00000317615_SETMAR_chr3_4355351_ENST00000430981_length(amino acids)=206AA_BP=179
MIVSARRSTSPRAPHPETSAHPIALLARVSESAAGPSSRPPGGLFPPSEPAVSWTGLKGPAPRDSKDPPAPREAPGSRASAFLLPSFLPG
PRLVPAGHPTATMFVPCGESAPDLAGFTLLMPAVSVGNVGQLAMDLIISTLNMSKIGYFYTDCLVPMVGNNPYATTEGNSTELSINAEES

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

>69767_69767_3_PSMG2-SETMAR_PSMG2_chr18_12706720_ENST00000585331_SETMAR_chr3_4354582_ENST00000430981_length(amino acids)=316AA_BP=1
MLKYTPDHVVGPGADIDPTQITFPGCICVKTPCLPGTCSCLRHGENYDDNSCLRDIGSGGKYAEPVFECNVLCRCSDHCRNRVVQKGLQF
HFQVFKTHKKGWGLRTLEFIPKGRFVCEYAGEVLGFSEVQRRIHLQTKSDSNYIIAIREHVYNGQVMETFVDPTYIGNIGRFLNHSCEPN
LLMIPVRIDSMVPKLALFAAKDIVPEEELSYDYSGRYLNLTVSEDKERLDHGKLRKPCYCGAKSCTAFLPFDSSLYCPVEKSNISCGNEK

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

>69767_69767_4_PSMG2-SETMAR_PSMG2_chr18_12706720_ENST00000585331_SETMAR_chr3_4355351_ENST00000430981_length(amino acids)=96AA_BP=69
MNTSLSTPIFRPAVSVGNVGQLAMDLIISTLNMSKIGYFYTDCLVPMVGNNPYATTEGNSTELSINAEESRTSVVEMRRNPACVAQPLLC

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

>69767_69767_5_PSMG2-SETMAR_PSMG2_chr18_12706720_ENST00000590217_SETMAR_chr3_4354582_ENST00000430981_length(amino acids)=316AA_BP=1
MLKYTPDHVVGPGADIDPTQITFPGCICVKTPCLPGTCSCLRHGENYDDNSCLRDIGSGGKYAEPVFECNVLCRCSDHCRNRVVQKGLQF
HFQVFKTHKKGWGLRTLEFIPKGRFVCEYAGEVLGFSEVQRRIHLQTKSDSNYIIAIREHVYNGQVMETFVDPTYIGNIGRFLNHSCEPN
LLMIPVRIDSMVPKLALFAAKDIVPEEELSYDYSGRYLNLTVSEDKERLDHGKLRKPCYCGAKSCTAFLPFDSSLYCPVEKSNISCGNEK

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

>69767_69767_6_PSMG2-SETMAR_PSMG2_chr18_12706720_ENST00000590217_SETMAR_chr3_4355351_ENST00000430981_length(amino acids)=124AA_BP=97
MLPSFLPGPRLVPAGHPTATMFVPCGESAPDLAGFTLLMPAVSVGNVGQLAMDLIISTLNMSKIGYFYTDCLVPMVGNNPYATTEGNSTE

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

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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/chr18:12706720/chr3:4354582)
- 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
.	.
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.	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

SETMAR

chr18:12706720

chr3:4354582

ENST00000358065

364_395

52.0

685.0

DNA binding

H-T-H motif

Tgene

SETMAR

chr18:12706720

chr3:4354582

ENST00000358065

428_448

52.0

685.0

DNA binding

Note=H-T-H motif

Tgene

SETMAR

chr18:12706720

chr3:4355351

ENST00000358065

364_395

685.0

DNA binding

H-T-H motif

Tgene

SETMAR

chr18:12706720

chr3:4355351

ENST00000358065

428_448

685.0

DNA binding

Note=H-T-H motif

Tgene

SETMAR

chr18:12706720

chr3:4354582

ENST00000358065

139_263

52.0

685.0

Domain

SET

Tgene

SETMAR

chr18:12706720

chr3:4354582

ENST00000358065

283_299

52.0

685.0

Domain

Post-SET

Tgene

SETMAR

chr18:12706720

chr3:4354582

ENST00000358065

73_136

52.0

685.0

Domain

Pre-SET

Tgene

SETMAR

chr18:12706720

chr3:4355351

ENST00000358065

139_263

685.0

Domain

SET

Tgene

SETMAR

chr18:12706720

chr3:4355351

ENST00000358065

283_299

685.0

Domain

Post-SET

Tgene

SETMAR

chr18:12706720

chr3:4355351

ENST00000358065

73_136

685.0

Domain

Pre-SET

Tgene

SETMAR

chr18:12706720

chr3:4354582

ENST00000358065

149_151

52.0

685.0

Region

Note=S-adenosyl-L-methionine binding

Tgene

SETMAR

chr18:12706720

chr3:4354582

ENST00000358065

223_224

52.0

685.0

Region

Note=S-adenosyl-L-methionine binding

Tgene

SETMAR

chr18:12706720

chr3:4354582

ENST00000358065

346_684

52.0

685.0

Region

Note=Mariner transposase Hsmar1

Tgene

SETMAR

chr18:12706720

chr3:4355351

ENST00000358065

149_151

685.0

Region

Note=S-adenosyl-L-methionine binding

Tgene

SETMAR

chr18:12706720

chr3:4355351

ENST00000358065

1_345

685.0

Region

Note=Histone-lysine N-methyltransferase

Tgene

SETMAR

chr18:12706720

chr3:4355351

ENST00000358065

223_224

685.0

Region

Note=S-adenosyl-L-methionine binding

Tgene

SETMAR

chr18:12706720

chr3:4355351

ENST00000358065

346_684

685.0

Region

Note=Mariner transposase Hsmar1

- 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

Tgene

SETMAR

chr18:12706720

chr3:4354582

ENST00000358065

1_345

52.0

685.0

Region

Note=Histone-lysine N-methyltransferase

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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 >>>581_PSMG2_12706720_SETMAR_4354582_ranked_0.pdb	PSMG2	12706720	12706720	ENST00000430981	SETMAR	chr3	4354582	+	MLKYTPDHVVGPGADIDPTQITFPGCICVKTPCLPGTCSCLRHGENYDDNSCLRDIGSGGKYAEPVFECNVLCRCSDHCRNRVVQKGLQF HFQVFKTHKKGWGLRTLEFIPKGRFVCEYAGEVLGFSEVQRRIHLQTKSDSNYIIAIREHVYNGQVMETFVDPTYIGNIGRFLNHSCEPN LLMIPVRIDSMVPKLALFAAKDIVPEEELSYDYSGRYLNLTVSEDKERLDHGKLRKPCYCGAKSCTAFLPFDSSLYCPVEKSNISCGNEK	316

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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.

PSMG2_pLDDT.png

SETMAR_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
PSMG2
SETMAR

- 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 PSMG2-SETMAR

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 PSMG2-SETMAR

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