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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:LRRC28-MEF2A (FusionGDB2 ID:49905)

Fusion Gene Summary for LRRC28-MEF2A

check button Fusion gene summary
Fusion gene informationFusion gene name: LRRC28-MEF2A
Fusion gene ID: 49905
HgeneTgene
Gene symbol

LRRC28

MEF2A

Gene ID

123355

4205

Gene nameleucine rich repeat containing 28myocyte enhancer factor 2A
Synonyms-ADCAD1|RSRFC4|RSRFC9|mef2
Cytomap

15q26.3

15q26.3

Type of geneprotein-codingprotein-coding
Descriptionleucine-rich repeat-containing protein 28myocyte-specific enhancer factor 2AMADS box transcription enhancer factor 2, polypeptide A (myocyte enhancer factor 2A)serum response factor-like protein 1
Modification date2020031320200313
UniProtAcc

Q86X40

Q02078

Ensembl transtripts involved in fusion geneENST00000442993, ENST00000301981, 
ENST00000447360, ENST00000559399, 
ENST00000331450, ENST00000422500, 
ENST00000558879, 		ENST00000354410, 
ENST00000453228, ENST00000338042, 
ENST00000449277, ENST00000557785, 
ENST00000557942, ENST00000558812, 
ENST00000558856, 
Fusion gene scores* DoF score8 X 8 X 3=19211 X 10 X 5=550
# samples 811
** MAII scorelog2(8/192*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/550*10)=-2.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LRRC28 [Title/Abstract] AND MEF2A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLRRC28(99874334)-MEF2A(100185766), # samples:2
MEF2A(100215663)-LRRC28(99892574), # samples:2
Anticipated loss of major functional domain due to fusion event.LRRC28-MEF2A seems lost the major protein functional domain in Tgene partner, which is a transcription 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneMEF2A

GO:0000122

negative regulation of transcription by RNA polymerase II

16484498

TgeneMEF2A

GO:0000165

MAPK cascade

9858528

TgeneMEF2A

GO:0006351

transcription, DNA-templated

16043483

TgeneMEF2A

GO:0010613

positive regulation of cardiac muscle hypertrophy

24161931

TgeneMEF2A

GO:0045944

positive regulation of transcription by RNA polymerase II

7760790|9858528|10748098|15466416|20590529|21468593

TgeneMEF2A

GO:0071277

cellular response to calcium ion

16484498


check buttonFusion gene breakpoints across LRRC28 (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 MEF2A (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
ChimerDB4BRCATCGA-BH-A0BP-01ALRRC28chr15

99874334

+MEF2Achr15

100185766

+


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Fusion Gene ORF analysis for LRRC28-MEF2A

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
3UTR-3CDSENST00000442993ENST00000354410LRRC28chr15

99874334

+MEF2Achr15

100185766

+
3UTR-3CDSENST00000442993ENST00000453228LRRC28chr15

99874334

+MEF2Achr15

100185766

+
3UTR-intronENST00000442993ENST00000338042LRRC28chr15

99874334

+MEF2Achr15

100185766

+
3UTR-intronENST00000442993ENST00000449277LRRC28chr15

99874334

+MEF2Achr15

100185766

+
3UTR-intronENST00000442993ENST00000557785LRRC28chr15

99874334

+MEF2Achr15

100185766

+
3UTR-intronENST00000442993ENST00000557942LRRC28chr15

99874334

+MEF2Achr15

100185766

+
3UTR-intronENST00000442993ENST00000558812LRRC28chr15

99874334

+MEF2Achr15

100185766

+
3UTR-intronENST00000442993ENST00000558856LRRC28chr15

99874334

+MEF2Achr15

100185766

+
5CDS-intronENST00000301981ENST00000338042LRRC28chr15

99874334

+MEF2Achr15

100185766

+
5CDS-intronENST00000301981ENST00000449277LRRC28chr15

99874334

+MEF2Achr15

100185766

+
5CDS-intronENST00000301981ENST00000557785LRRC28chr15

99874334

+MEF2Achr15

100185766

+
5CDS-intronENST00000301981ENST00000557942LRRC28chr15

99874334

+MEF2Achr15

100185766

+
5CDS-intronENST00000301981ENST00000558812LRRC28chr15

99874334

+MEF2Achr15

100185766

+
5CDS-intronENST00000301981ENST00000558856LRRC28chr15

99874334

+MEF2Achr15

100185766

+
5CDS-intronENST00000447360ENST00000338042LRRC28chr15

99874334

+MEF2Achr15

100185766

+
5CDS-intronENST00000447360ENST00000449277LRRC28chr15

99874334

+MEF2Achr15

100185766

+
5CDS-intronENST00000447360ENST00000557785LRRC28chr15

99874334

+MEF2Achr15

100185766

+
5CDS-intronENST00000447360ENST00000557942LRRC28chr15

99874334

+MEF2Achr15

100185766

+
5CDS-intronENST00000447360ENST00000558812LRRC28chr15

99874334

+MEF2Achr15

100185766

+
5CDS-intronENST00000447360ENST00000558856LRRC28chr15

99874334

+MEF2Achr15

100185766

+
5CDS-intronENST00000559399ENST00000338042LRRC28chr15

99874334

+MEF2Achr15

100185766

+
5CDS-intronENST00000559399ENST00000449277LRRC28chr15

99874334

+MEF2Achr15

100185766

+
5CDS-intronENST00000559399ENST00000557785LRRC28chr15

99874334

+MEF2Achr15

100185766

+
5CDS-intronENST00000559399ENST00000557942LRRC28chr15

99874334

+MEF2Achr15

100185766

+
5CDS-intronENST00000559399ENST00000558812LRRC28chr15

99874334

+MEF2Achr15

100185766

+
5CDS-intronENST00000559399ENST00000558856LRRC28chr15

99874334

+MEF2Achr15

100185766

+
Frame-shiftENST00000301981ENST00000354410LRRC28chr15

99874334

+MEF2Achr15

100185766

+
Frame-shiftENST00000301981ENST00000453228LRRC28chr15

99874334

+MEF2Achr15

100185766

+
Frame-shiftENST00000447360ENST00000354410LRRC28chr15

99874334

+MEF2Achr15

100185766

+
Frame-shiftENST00000447360ENST00000453228LRRC28chr15

99874334

+MEF2Achr15

100185766

+
Frame-shiftENST00000559399ENST00000354410LRRC28chr15

99874334

+MEF2Achr15

100185766

+
Frame-shiftENST00000559399ENST00000453228LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-3CDSENST00000331450ENST00000354410LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-3CDSENST00000331450ENST00000453228LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-3CDSENST00000422500ENST00000354410LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-3CDSENST00000422500ENST00000453228LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-3CDSENST00000558879ENST00000354410LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-3CDSENST00000558879ENST00000453228LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-intronENST00000331450ENST00000338042LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-intronENST00000331450ENST00000449277LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-intronENST00000331450ENST00000557785LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-intronENST00000331450ENST00000557942LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-intronENST00000331450ENST00000558812LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-intronENST00000331450ENST00000558856LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-intronENST00000422500ENST00000338042LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-intronENST00000422500ENST00000449277LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-intronENST00000422500ENST00000557785LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-intronENST00000422500ENST00000557942LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-intronENST00000422500ENST00000558812LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-intronENST00000422500ENST00000558856LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-intronENST00000558879ENST00000338042LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-intronENST00000558879ENST00000449277LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-intronENST00000558879ENST00000557785LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-intronENST00000558879ENST00000557942LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-intronENST00000558879ENST00000558812LRRC28chr15

99874334

+MEF2Achr15

100185766

+
intron-intronENST00000558879ENST00000558856LRRC28chr15

99874334

+MEF2Achr15

100185766

+

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 LRRC28-MEF2A


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)
LRRC28chr1599874335+MEF2Achr15100185765+0.0058223490.9941777
LRRC28chr1599874335+MEF2Achr15100185765+0.0058223490.9941777

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 LRRC28-MEF2A


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/:99874334/:100185766)
- 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
LRRC28

Q86X40

MEF2A

Q02078

FUNCTION: Transcriptional activator which binds specifically to the MEF2 element, 5'-YTA[AT](4)TAR-3', found in numerous muscle-specific genes. Also involved in the activation of numerous growth factor- and stress-induced genes. Mediates cellular functions not only in skeletal and cardiac muscle development, but also in neuronal differentiation and survival. Plays diverse roles in the control of cell growth, survival and apoptosis via p38 MAPK signaling in muscle-specific and/or growth factor-related transcription. In cerebellar granule neurons, phosphorylated and sumoylated MEF2A represses transcription of NUR77 promoting synaptic differentiation. Associates with chromatin to the ZNF16 promoter. {ECO:0000269|PubMed:11904443, ECO:0000269|PubMed:12691662, ECO:0000269|PubMed:15834131, ECO:0000269|PubMed:16371476, ECO:0000269|PubMed:16484498, ECO:0000269|PubMed:16563226, ECO:0000269|PubMed:21468593, ECO:0000269|PubMed:9858528}.

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 LRRC28-MEF2A


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 LRRC28-MEF2A


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 LRRC28-MEF2A


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 LRRC28-MEF2A


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