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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:PRAME-ACO2 (FusionGDB2 ID:68378)

Fusion Gene Summary for PRAME-ACO2

check button Fusion gene summary
Fusion gene informationFusion gene name: PRAME-ACO2
Fusion gene ID: 68378
HgeneTgene
Gene symbol

PRAME

ACO2

Gene ID

23532

50

Gene namepreferentially expressed antigen in melanomaaconitase 2
SynonymsCT130|MAPE|OIP-4|OIP4ACONM|HEL-S-284|ICRD|OCA8|OPA9
Cytomap

22q11.22

22q13.2

Type of geneprotein-codingprotein-coding
Descriptionmelanoma antigen preferentially expressed in tumorsOpa-interacting protein OIP4cancer/testis antigen 130opa-interacting protein 4preferentially expressed antigen of melanomaaconitate hydratase, mitochondrialaconitase 2, mitochondrialcitrate hydro-lyaseepididymis secretory sperm binding protein Li 284mitochondrial aconitase
Modification date2020032020200313
UniProtAcc

PRAMEF6

Q99798

Ensembl transtripts involved in fusion geneENST00000398741, ENST00000398743, 
ENST00000402697, ENST00000405655, 
ENST00000406503, ENST00000543184, 
ENST00000424204, ENST00000485532, 
ENST00000539862, 		ENST00000466237, 
ENST00000216254, ENST00000396512, 
Fusion gene scores* DoF score3 X 3 X 2=1813 X 16 X 8=1664
# samples 318
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(18/1664*10)=-3.20858662181142
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PRAME [Title/Abstract] AND ACO2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPRAME(22899232)-ACO2(41903795), # samples:3
Anticipated loss of major functional domain due to fusion event.PRAME-ACO2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PRAME-ACO2 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
PRAME-ACO2 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgenePRAME

GO:0008284

positive regulation of cell proliferation

16179254

HgenePRAME

GO:0043066

negative regulation of apoptotic process

16179254

HgenePRAME

GO:0045596

negative regulation of cell differentiation

16179254

HgenePRAME

GO:0045892

negative regulation of transcription, DNA-templated

16179254

HgenePRAME

GO:0048387

negative regulation of retinoic acid receptor signaling pathway

16179254

TgeneACO2

GO:0006099

tricarboxylic acid cycle

9630632

TgeneACO2

GO:0006101

citrate metabolic process

9630632


check buttonFusion gene breakpoints across PRAME (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across ACO2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4SKCMTCGA-BF-A5EQ-01APRAMEchr22

22899232

-ACO2chr22

41903795

+


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Fusion Gene ORF analysis for PRAME-ACO2

check button 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.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5CDS-intronENST00000398741ENST00000466237PRAMEchr22

22899232

-ACO2chr22

41903795

+
5CDS-intronENST00000398743ENST00000466237PRAMEchr22

22899232

-ACO2chr22

41903795

+
5CDS-intronENST00000402697ENST00000466237PRAMEchr22

22899232

-ACO2chr22

41903795

+
5CDS-intronENST00000405655ENST00000466237PRAMEchr22

22899232

-ACO2chr22

41903795

+
5CDS-intronENST00000406503ENST00000466237PRAMEchr22

22899232

-ACO2chr22

41903795

+
5CDS-intronENST00000543184ENST00000466237PRAMEchr22

22899232

-ACO2chr22

41903795

+
Frame-shiftENST00000398741ENST00000216254PRAMEchr22

22899232

-ACO2chr22

41903795

+
Frame-shiftENST00000398741ENST00000396512PRAMEchr22

22899232

-ACO2chr22

41903795

+
Frame-shiftENST00000398743ENST00000216254PRAMEchr22

22899232

-ACO2chr22

41903795

+
Frame-shiftENST00000398743ENST00000396512PRAMEchr22

22899232

-ACO2chr22

41903795

+
Frame-shiftENST00000402697ENST00000216254PRAMEchr22

22899232

-ACO2chr22

41903795

+
Frame-shiftENST00000402697ENST00000396512PRAMEchr22

22899232

-ACO2chr22

41903795

+
Frame-shiftENST00000405655ENST00000216254PRAMEchr22

22899232

-ACO2chr22

41903795

+
Frame-shiftENST00000405655ENST00000396512PRAMEchr22

22899232

-ACO2chr22

41903795

+
Frame-shiftENST00000406503ENST00000216254PRAMEchr22

22899232

-ACO2chr22

41903795

+
Frame-shiftENST00000406503ENST00000396512PRAMEchr22

22899232

-ACO2chr22

41903795

+
Frame-shiftENST00000543184ENST00000216254PRAMEchr22

22899232

-ACO2chr22

41903795

+
Frame-shiftENST00000543184ENST00000396512PRAMEchr22

22899232

-ACO2chr22

41903795

+
intron-3CDSENST00000424204ENST00000216254PRAMEchr22

22899232

-ACO2chr22

41903795

+
intron-3CDSENST00000424204ENST00000396512PRAMEchr22

22899232

-ACO2chr22

41903795

+
intron-3CDSENST00000485532ENST00000216254PRAMEchr22

22899232

-ACO2chr22

41903795

+
intron-3CDSENST00000485532ENST00000396512PRAMEchr22

22899232

-ACO2chr22

41903795

+
intron-3CDSENST00000539862ENST00000216254PRAMEchr22

22899232

-ACO2chr22

41903795

+
intron-3CDSENST00000539862ENST00000396512PRAMEchr22

22899232

-ACO2chr22

41903795

+
intron-intronENST00000424204ENST00000466237PRAMEchr22

22899232

-ACO2chr22

41903795

+
intron-intronENST00000485532ENST00000466237PRAMEchr22

22899232

-ACO2chr22

41903795

+
intron-intronENST00000539862ENST00000466237PRAMEchr22

22899232

-ACO2chr22

41903795

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for PRAME-ACO2


check buttonFusionAI 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.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
PRAMEchr2222899231-ACO2chr2241903794+2.55E-091
PRAMEchr2222899231-ACO2chr2241903794+2.55E-091

check buttonDistribution 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.

check buttonDistribution 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.
genomic feature of top 1%

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Fusion Protein Features for PRAME-ACO2


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:22899232/:41903795)
- 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PRAME

PRAMEF6

ACO2

Q99798

476FUNCTION: Catalyzes the isomerization of citrate to isocitrate via cis-aconitate. {ECO:0000250|UniProtKB:P16276}.

check buttonRetention 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.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for PRAME-ACO2


check button 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 PRAME-ACO2


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for PRAME-ACO2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for PRAME-ACO2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource