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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:PPARA-ATXN10

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PPARA-ATXN10
	FusionPDB ID: 67313
	FusionGDB2.0 ID: 67313
		Hgene	Tgene
	Gene symbol	PPARA	ATXN10
	Gene ID	5465	25814
	Gene name	peroxisome proliferator activated receptor alpha	ataxin 10
	Synonyms	NR1C1\|PPAR\|PPARalpha\|hPPAR	E46L\|HUMEEP\|SCA10
	Cytomap	22q13.31	22q13.31
	Type of gene	protein-coding	protein-coding
	Description	peroxisome proliferator-activated receptor alphaPPAR-alphanuclear receptor subfamily 1 group C member 1peroxisome proliferative activated receptor, alphaperoxisome proliferator-activated nuclear receptor alpha variant 3	ataxin-10brain protein E46 homologspinocerebellar ataxia type 10 protein
	Modification date	20200329	20200313
	UniProtAcc	.	Q9UBB4
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000262735, ENST00000396000, ENST00000402126, ENST00000407236, ENST00000434345, ENST00000481567,	ENST00000402380, ENST00000498009, ENST00000252934, ENST00000381061,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	15 X 10 X 10=1500	24 X 19 X 12=5472
	# samples	18	28
	** MAII score	log2(18/1500*10)=-3.05889368905357 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(28/5472*10)=-4.28856949794093 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: PPARA [Title/Abstract] AND ATXN10 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PPARA(46594488)-ATXN10(46238871), # samples:2
Anticipated loss of major functional domain due to fusion event.	PPARA-ATXN10 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. PPARA-ATXN10 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	PPARA	GO:0000122	negative regulation of transcription by RNA polymerase II	9748239\|12700342
Hgene	PPARA	GO:0010565	regulation of cellular ketone metabolic process	19955185
Hgene	PPARA	GO:0010745	negative regulation of macrophage derived foam cell differentiation	19114110
Hgene	PPARA	GO:0010871	negative regulation of receptor biosynthetic process	12700342
Hgene	PPARA	GO:0010887	negative regulation of cholesterol storage	19114110
Hgene	PPARA	GO:0010891	negative regulation of sequestering of triglyceride	12700342
Hgene	PPARA	GO:0019217	regulation of fatty acid metabolic process	19955185
Hgene	PPARA	GO:0045820	negative regulation of glycolytic process	19955185
Hgene	PPARA	GO:0045893	positive regulation of transcription, DNA-templated	12955147
Hgene	PPARA	GO:0045944	positive regulation of transcription by RNA polymerase II	9748239\|19955185\|20837115
Hgene	PPARA	GO:0050728	negative regulation of inflammatory response	21636785
Hgene	PPARA	GO:1902894	negative regulation of pri-miRNA transcription by RNA polymerase II	21636785
Hgene	PPARA	GO:1903038	negative regulation of leukocyte cell-cell adhesion	21636785
Tgene	ATXN10	GO:0031175	neuron projection development	16498633

Fusion gene breakpoints across PPARA (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 ATXN10 (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	UCS	TCGA-N7-A4Y8-01A	PPARA	chr22	46594488	-	ATXN10	chr22	46238871	+
ChimerDB4	UCS	TCGA-N7-A4Y8	PPARA	chr22	46594488	+	ATXN10	chr22	46238871	+

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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)
ENST00000396000	PPARA	chr22	46594488	+	ENST00000381061	ATXN10	chr22	46238871	+	2297	473	256	663	135
ENST00000396000	PPARA	chr22	46594488	+	ENST00000252934	ATXN10	chr22	46238871	+	2300	473	256	663	135
ENST00000262735	PPARA	chr22	46594488	+	ENST00000381061	ATXN10	chr22	46238871	+	2214	390	173	580	135
ENST00000262735	PPARA	chr22	46594488	+	ENST00000252934	ATXN10	chr22	46238871	+	2217	390	173	580	135
ENST00000407236	PPARA	chr22	46594488	+	ENST00000381061	ATXN10	chr22	46238871	+	2245	421	204	611	135
ENST00000407236	PPARA	chr22	46594488	+	ENST00000252934	ATXN10	chr22	46238871	+	2248	421	204	611	135
ENST00000402126	PPARA	chr22	46594488	+	ENST00000381061	ATXN10	chr22	46238871	+	2160	336	119	526	135
ENST00000402126	PPARA	chr22	46594488	+	ENST00000252934	ATXN10	chr22	46238871	+	2163	336	119	526	135
ENST00000434345	PPARA	chr22	46594488	+	ENST00000381061	ATXN10	chr22	46238871	+	2032	208	0	398	132
ENST00000434345	PPARA	chr22	46594488	+	ENST00000252934	ATXN10	chr22	46238871	+	2035	208	0	398	132

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
ENST00000396000	ENST00000381061	PPARA	chr22	46594488	+	ATXN10	chr22	46238871	+	0.01218946	0.9878106
ENST00000396000	ENST00000252934	PPARA	chr22	46594488	+	ATXN10	chr22	46238871	+	0.012388225	0.98761183
ENST00000262735	ENST00000381061	PPARA	chr22	46594488	+	ATXN10	chr22	46238871	+	0.009995935	0.990004
ENST00000262735	ENST00000252934	PPARA	chr22	46594488	+	ATXN10	chr22	46238871	+	0.00989294	0.99010706
ENST00000407236	ENST00000381061	PPARA	chr22	46594488	+	ATXN10	chr22	46238871	+	0.01808411	0.98191595
ENST00000407236	ENST00000252934	PPARA	chr22	46594488	+	ATXN10	chr22	46238871	+	0.018245464	0.9817546
ENST00000402126	ENST00000381061	PPARA	chr22	46594488	+	ATXN10	chr22	46238871	+	0.008164416	0.9918356
ENST00000402126	ENST00000252934	PPARA	chr22	46594488	+	ATXN10	chr22	46238871	+	0.008166531	0.99183345
ENST00000434345	ENST00000381061	PPARA	chr22	46594488	+	ATXN10	chr22	46238871	+	0.010749036	0.989251
ENST00000434345	ENST00000252934	PPARA	chr22	46594488	+	ATXN10	chr22	46238871	+	0.01057703	0.989423

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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

>67313_67313_1_PPARA-ATXN10_PPARA_chr22_46594488_ENST00000262735_ATXN10_chr22_46238871_ENST00000252934_length(amino acids)=135AA_BP=72
MVAMVDTESPLCPLSPLEAGDLESPLSEEFLQEMGNIQEISQSIGEDSSGSFGFTEYQYLGSCPGSDGSVITVLTQWVIYAIRNLTEDNS

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

>67313_67313_2_PPARA-ATXN10_PPARA_chr22_46594488_ENST00000262735_ATXN10_chr22_46238871_ENST00000381061_length(amino acids)=135AA_BP=72
MVAMVDTESPLCPLSPLEAGDLESPLSEEFLQEMGNIQEISQSIGEDSSGSFGFTEYQYLGSCPGSDGSVITVLTQWVIYAIRNLTEDNS

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

>67313_67313_3_PPARA-ATXN10_PPARA_chr22_46594488_ENST00000396000_ATXN10_chr22_46238871_ENST00000252934_length(amino acids)=135AA_BP=72
MVAMVDTESPLCPLSPLEAGDLESPLSEEFLQEMGNIQEISQSIGEDSSGSFGFTEYQYLGSCPGSDGSVITVLTQWVIYAIRNLTEDNS

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

>67313_67313_4_PPARA-ATXN10_PPARA_chr22_46594488_ENST00000396000_ATXN10_chr22_46238871_ENST00000381061_length(amino acids)=135AA_BP=72
MVAMVDTESPLCPLSPLEAGDLESPLSEEFLQEMGNIQEISQSIGEDSSGSFGFTEYQYLGSCPGSDGSVITVLTQWVIYAIRNLTEDNS

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

>67313_67313_5_PPARA-ATXN10_PPARA_chr22_46594488_ENST00000402126_ATXN10_chr22_46238871_ENST00000252934_length(amino acids)=135AA_BP=72
MVAMVDTESPLCPLSPLEAGDLESPLSEEFLQEMGNIQEISQSIGEDSSGSFGFTEYQYLGSCPGSDGSVITVLTQWVIYAIRNLTEDNS

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

>67313_67313_6_PPARA-ATXN10_PPARA_chr22_46594488_ENST00000402126_ATXN10_chr22_46238871_ENST00000381061_length(amino acids)=135AA_BP=72
MVAMVDTESPLCPLSPLEAGDLESPLSEEFLQEMGNIQEISQSIGEDSSGSFGFTEYQYLGSCPGSDGSVITVLTQWVIYAIRNLTEDNS

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

>67313_67313_7_PPARA-ATXN10_PPARA_chr22_46594488_ENST00000407236_ATXN10_chr22_46238871_ENST00000252934_length(amino acids)=135AA_BP=72
MVAMVDTESPLCPLSPLEAGDLESPLSEEFLQEMGNIQEISQSIGEDSSGSFGFTEYQYLGSCPGSDGSVITVLTQWVIYAIRNLTEDNS

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

>67313_67313_8_PPARA-ATXN10_PPARA_chr22_46594488_ENST00000407236_ATXN10_chr22_46238871_ENST00000381061_length(amino acids)=135AA_BP=72
MVAMVDTESPLCPLSPLEAGDLESPLSEEFLQEMGNIQEISQSIGEDSSGSFGFTEYQYLGSCPGSDGSVITVLTQWVIYAIRNLTEDNS

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

>67313_67313_9_PPARA-ATXN10_PPARA_chr22_46594488_ENST00000434345_ATXN10_chr22_46238871_ENST00000252934_length(amino acids)=132AA_BP=69
MVDTESPLCPLSPLEAGDLESPLSEEFLQEMGNIQEISQSIGEDSSGSFGFTEYQYLGSCPGSDGSVITVLTQWVIYAIRNLTEDNSQNQ

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

>67313_67313_10_PPARA-ATXN10_PPARA_chr22_46594488_ENST00000434345_ATXN10_chr22_46238871_ENST00000381061_length(amino acids)=132AA_BP=69
MVDTESPLCPLSPLEAGDLESPLSEEFLQEMGNIQEISQSIGEDSSGSFGFTEYQYLGSCPGSDGSVITVLTQWVIYAIRNLTEDNSQNQ

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

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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/chr22:46594488/chr22:46238871)
- 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
.	ATXN10 Q9UBB4
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: Necessary for the survival of cerebellar neurons. Induces neuritogenesis by activating the Ras-MAP kinase pathway. May play a role in the maintenance of a critical intracellular glycosylation level and homeostasis. {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.

- 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

- 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

PPARA

chr22:46594488

chr22:46238871

ENST00000262735

99_173

69.33333333333333

469.0

DNA binding

Nuclear receptor

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000396000

99_173

69.33333333333333

469.0

DNA binding

Nuclear receptor

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000402126

99_173

69.33333333333333

469.0

DNA binding

Nuclear receptor

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000407236

99_173

69.33333333333333

469.0

DNA binding

Nuclear receptor

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000434345

99_173

69.33333333333333

188.33333333333334

DNA binding

Nuclear receptor

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000262735

239_466

69.33333333333333

469.0

Domain

NR LBD

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000396000

239_466

69.33333333333333

469.0

Domain

NR LBD

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000402126

239_466

69.33333333333333

469.0

Domain

NR LBD

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000407236

239_466

69.33333333333333

469.0

Domain

NR LBD

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000434345

239_466

69.33333333333333

188.33333333333334

Domain

NR LBD

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000262735

304_433

69.33333333333333

469.0

Region

Note=Required for heterodimerization with RXRA

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000396000

304_433

69.33333333333333

469.0

Region

Note=Required for heterodimerization with RXRA

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000402126

304_433

69.33333333333333

469.0

Region

Note=Required for heterodimerization with RXRA

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000407236

304_433

69.33333333333333

469.0

Region

Note=Required for heterodimerization with RXRA

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000434345

304_433

69.33333333333333

188.33333333333334

Region

Note=Required for heterodimerization with RXRA

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000262735

102_122

69.33333333333333

469.0

Zinc finger

NR C4-type

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000262735

139_161

69.33333333333333

469.0

Zinc finger

NR C4-type

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000396000

102_122

69.33333333333333

469.0

Zinc finger

NR C4-type

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000396000

139_161

69.33333333333333

469.0

Zinc finger

NR C4-type

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000402126

102_122

69.33333333333333

469.0

Zinc finger

NR C4-type

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000402126

139_161

69.33333333333333

469.0

Zinc finger

NR C4-type

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000407236

102_122

69.33333333333333

469.0

Zinc finger

NR C4-type

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000407236

139_161

69.33333333333333

469.0

Zinc finger

NR C4-type

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000434345

102_122

69.33333333333333

188.33333333333334

Zinc finger

NR C4-type

Hgene

PPARA

chr22:46594488

chr22:46238871

ENST00000434345

139_161

69.33333333333333

188.33333333333334

Zinc finger

NR C4-type

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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 >>>84_PPARA_46594488_ATXN10_46238871_ranked_0.pdb	PPARA	46594488	46594488	ENST00000252934	ATXN10	chr22	46238871	+	MVAMVDTESPLCPLSPLEAGDLESPLSEEFLQEMGNIQEISQSIGEDSSGSFGFTEYQYLGSCPGSDGSVITVLTQWVIYAIRNLTEDNS	135

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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.

PPARA_pLDDT.png

ATXN10_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
PPARA
ATXN10

- 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 PPARA-ATXN10

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 PPARA-ATXN10

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