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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:EPM2A-RPL5 (FusionGDB2 ID:HG7957TG6125)

Fusion Gene Summary for EPM2A-RPL5

check button Fusion gene summary
Fusion gene informationFusion gene name: EPM2A-RPL5
Fusion gene ID: hg7957tg6125
HgeneTgene
Gene symbol

EPM2A

RPL5

Gene ID

7957

6125

Gene nameEPM2A glucan phosphatase, laforinribosomal protein L5
SynonymsEPM2|MELFL5|MSTP030|PPP1R135|uL18
Cytomap('EPM2A')('RPL5')

6q24.3

1p22.1

Type of geneprotein-codingprotein-coding
DescriptionlaforinEPM2A, laforin glucan phosphataseLAFPTPaseepilepsy, progressive myoclonus type 2, Lafora disease (laforin)epilepsy, progressive myoclonus type 2A, Lafora disease (laforin)glucan phosphataseglycogen phosphataselafora PTPase60S ribosomal protein L5large ribosomal subunit protein uL18protein phosphatase 1, regulatory subunit 135
Modification date2020031320200313
UniProtAcc

O95278

.
Ensembl transtripts involved in fusion geneENST00000367519, ENST00000496228, 
Fusion gene scores* DoF score2 X 2 X 1=412 X 10 X 5=600
# samples 214
** MAII scorelog2(2/4*10)=2.32192809488736log2(14/600*10)=-2.09953567355091
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: EPM2A [Title/Abstract] AND RPL5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointEPM2A(145757503)-RPL5(93307421), # 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneRPL5

GO:0010628

positive regulation of gene expression

18560357

TgeneRPL5

GO:0045727

positive regulation of translation

16213212

TgeneRPL5

GO:1904667

negative regulation of ubiquitin protein ligase activity

18560357

TgeneRPL5

GO:2000059

negative regulation of ubiquitin-dependent protein catabolic process

18560357

TgeneRPL5

GO:2000435

negative regulation of protein neddylation

18560357



check button Fusion gene information
* 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


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Fusion Gene ORF analysis for EPM2A-RPL5

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

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 EPM2A-RPL5


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)


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Fusion Protein Features for EPM2A-RPL5


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/:145757503/:93307421)
- 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
EPM2A

O95278

.
FUNCTION: Plays an important role in preventing glycogen hyperphosphorylation and the formation of insoluble aggregates, via its activity as glycogen phosphatase, and by promoting the ubiquitination of proteins involved in glycogen metabolism via its interaction with the E3 ubiquitin ligase NHLRC1/malin. Shows strong phosphatase activity towards complex carbohydrates in vitro, avoiding glycogen hyperphosphorylation which is associated with reduced branching and formation of insoluble aggregates (PubMed:16901901, PubMed:23922729, PubMed:26231210, PubMed:25538239, PubMed:25544560). Dephosphorylates phosphotyrosine and synthetic substrates, such as para-nitrophenylphosphate (pNPP), and has low activity with phosphoserine and phosphothreonine substrates (in vitro) (PubMed:11001928, PubMed:11220751, PubMed:11739371, PubMed:14532330, PubMed:16971387, PubMed:18617530, PubMed:22036712, PubMed:23922729, PubMed:14722920). Has been shown to dephosphorylate MAPT (By similarity). Forms a complex with NHLRC1/malin and HSP70, which suppresses the cellular toxicity of misfolded proteins by promoting their degradation through the ubiquitin-proteasome system (UPS). Acts as a scaffold protein to facilitate PPP1R3C/PTG ubiquitination by NHLRC1/malin (PubMed:23922729). Also promotes proteasome-independent protein degradation through the macroautophagy pathway (PubMed:20453062). {ECO:0000250|UniProtKB:Q9WUA5, ECO:0000269|PubMed:11001928, ECO:0000269|PubMed:11220751, ECO:0000269|PubMed:11739371, ECO:0000269|PubMed:14532330, ECO:0000269|PubMed:14722920, ECO:0000269|PubMed:16901901, ECO:0000269|PubMed:16971387, ECO:0000269|PubMed:18070875, ECO:0000269|PubMed:18617530, ECO:0000269|PubMed:19036738, ECO:0000269|PubMed:20453062, ECO:0000269|PubMed:22036712, ECO:0000269|PubMed:23624058, ECO:0000269|PubMed:23922729, ECO:0000269|PubMed:25538239, ECO:0000269|PubMed:25544560, ECO:0000269|PubMed:26231210}.; FUNCTION: [Isoform 2]: does not bind to glycogen (PubMed:18617530). Lacks phosphatase activity and might function as a dominant-negative regulator for the phosphatase activity of isoform 1 and isoform 7 (PubMed:18617530, PubMed:22036712). {ECO:0000269|PubMed:18617530, ECO:0000269|PubMed:22036712}.; FUNCTION: [Isoform 7]: has phosphatase activity (in vitro). {ECO:0000269|PubMed:22036712}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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 EPM2A-RPL5


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 EPM2A-RPL5


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 EPM2A-RPL5


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 EPM2A-RPL5


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneEPM2AC0751783Lafora Disease19CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneEPM2AC0751776Atypical Inclusion-Body Disease1CTD_human
HgeneEPM2AC0751777Familial Progressive Myoclonic Epilepsy1CTD_human
HgeneEPM2AC0751778Myoclonic Epilepsies, Progressive1CTD_human
HgeneEPM2AC0751779Action Myoclonus-Renal Failure Syndrome1CTD_human
HgeneEPM2AC0751780Biotin-Responsive Encephalopathy1CTD_human
HgeneEPM2AC0751781Dentatorubral-Pallidoluysian Atrophy1CTD_human
HgeneEPM2AC0751782May-White Syndrome1CTD_human
TgeneC1260899Anemia, Diamond-Blackfan3GENOMICS_ENGLAND
TgeneC0575897Thumb deformity2GENOMICS_ENGLAND
TgeneC2931850Aase Smith syndrome 22CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0008925Cleft Palate1GENOMICS_ENGLAND
TgeneC0010093Corpus Luteum Cyst1CTD_human
TgeneC0029927Ovarian Cysts1CTD_human
TgeneC1961099Precursor T-Cell Lymphoblastic Leukemia-Lymphoma1CGI;CTD_human
TgeneC4228778Abnormality of radial ray1GENOMICS_ENGLAND