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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:R3HDM2-PLEKHA5 (FusionGDB2 ID:71086)

Fusion Gene Summary for R3HDM2-PLEKHA5

check button Fusion gene summary
Fusion gene informationFusion gene name: R3HDM2-PLEKHA5
Fusion gene ID: 71086
HgeneTgene
Gene symbol

R3HDM2

PLEKHA5

Gene ID

22864

54477

Gene nameR3H domain containing 2pleckstrin homology domain containing A5
SynonymsCAG6|PR01365PEPP-2|PEPP2
Cytomap

12q13.3

12p12.3

Type of geneprotein-codingprotein-coding
DescriptionR3H domain-containing protein 2pleckstrin homology domain-containing family A member 5PH domain-containing family A member 5phosphoinositol 3-phosphate-binding protein-2pleckstrin homology domain containing, family A member 5
Modification date2020032020200320
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000347140, ENST00000402412, 
ENST00000358907, ENST00000403821, 
ENST00000413953, ENST00000441731, 
ENST00000546843, 
ENST00000309364, 
ENST00000317589, ENST00000355397, 
ENST00000359180, ENST00000429027, 
ENST00000299275, ENST00000424268, 
ENST00000538714, ENST00000539256, 
ENST00000543806, ENST00000510738, 
ENST00000540972, 
Fusion gene scores* DoF score36 X 22 X 12=950424 X 16 X 15=5760
# samples 3830
** MAII scorelog2(38/9504*10)=-4.64446351246982
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(30/5760*10)=-4.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: R3HDM2 [Title/Abstract] AND PLEKHA5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointR3HDM2(57789532)-PLEKHA5(19406874), # 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

check buttonFusion gene breakpoints across R3HDM2 (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 PLEKHA5 (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
ChimerDB4LUADTCGA-86-7954-01AR3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+


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Fusion Gene ORF analysis for R3HDM2-PLEKHA5

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
5UTR-3CDSENST00000347140ENST00000309364R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-3CDSENST00000347140ENST00000317589R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-3CDSENST00000347140ENST00000355397R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-3CDSENST00000347140ENST00000359180R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-3CDSENST00000347140ENST00000429027R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-3CDSENST00000402412ENST00000309364R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-3CDSENST00000402412ENST00000317589R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-3CDSENST00000402412ENST00000355397R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-3CDSENST00000402412ENST00000359180R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-3CDSENST00000402412ENST00000429027R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-5UTRENST00000347140ENST00000299275R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-5UTRENST00000347140ENST00000424268R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-5UTRENST00000347140ENST00000538714R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-5UTRENST00000347140ENST00000539256R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-5UTRENST00000347140ENST00000543806R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-5UTRENST00000402412ENST00000299275R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-5UTRENST00000402412ENST00000424268R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-5UTRENST00000402412ENST00000538714R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-5UTRENST00000402412ENST00000539256R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-5UTRENST00000402412ENST00000543806R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-intronENST00000347140ENST00000510738R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-intronENST00000347140ENST00000540972R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-intronENST00000402412ENST00000510738R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
5UTR-intronENST00000402412ENST00000540972R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000358907ENST00000309364R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000358907ENST00000317589R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000358907ENST00000355397R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000358907ENST00000359180R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000358907ENST00000429027R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000403821ENST00000309364R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000403821ENST00000317589R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000403821ENST00000355397R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000403821ENST00000359180R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000403821ENST00000429027R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000413953ENST00000309364R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000413953ENST00000317589R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000413953ENST00000355397R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000413953ENST00000359180R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000413953ENST00000429027R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000441731ENST00000309364R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000441731ENST00000317589R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000441731ENST00000355397R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000441731ENST00000359180R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000441731ENST00000429027R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000546843ENST00000309364R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000546843ENST00000317589R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000546843ENST00000355397R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000546843ENST00000359180R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-3CDSENST00000546843ENST00000429027R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000358907ENST00000299275R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000358907ENST00000424268R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000358907ENST00000538714R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000358907ENST00000539256R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000358907ENST00000543806R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000403821ENST00000299275R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000403821ENST00000424268R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000403821ENST00000538714R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000403821ENST00000539256R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000403821ENST00000543806R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000413953ENST00000299275R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000413953ENST00000424268R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000413953ENST00000538714R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000413953ENST00000539256R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000413953ENST00000543806R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000441731ENST00000299275R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000441731ENST00000424268R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000441731ENST00000538714R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000441731ENST00000539256R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000441731ENST00000543806R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000546843ENST00000299275R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000546843ENST00000424268R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000546843ENST00000538714R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000546843ENST00000539256R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-5UTRENST00000546843ENST00000543806R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-intronENST00000358907ENST00000510738R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-intronENST00000358907ENST00000540972R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-intronENST00000403821ENST00000510738R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-intronENST00000403821ENST00000540972R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-intronENST00000413953ENST00000510738R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-intronENST00000413953ENST00000540972R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-intronENST00000441731ENST00000510738R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-intronENST00000441731ENST00000540972R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-intronENST00000546843ENST00000510738R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+
intron-intronENST00000546843ENST00000540972R3HDM2chr12

57789532

-PLEKHA5chr12

19406874

+

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 R3HDM2-PLEKHA5


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)
R3HDM2chr1257789531-PLEKHA5chr1219406873+1.92E-081
R3HDM2chr1257789531-PLEKHA5chr1219406873+1.92E-081

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 R3HDM2-PLEKHA5


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/:57789532/:19406874)
- 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
..
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}.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 R3HDM2-PLEKHA5


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 R3HDM2-PLEKHA5


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 R3HDM2-PLEKHA5


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 R3HDM2-PLEKHA5


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