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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:MUC16-RARA (FusionGDB2 ID:55995)

Fusion Gene Summary for MUC16-RARA

check button Fusion gene summary
Fusion gene informationFusion gene name: MUC16-RARA
Fusion gene ID: 55995
HgeneTgene
Gene symbol

MUC16

RARA

Gene ID

94025

5914

Gene namemucin 16, cell surface associatedretinoic acid receptor alpha
SynonymsCA125NR1B1|RAR
Cytomap

19p13.2

17q21.2

Type of geneprotein-codingprotein-coding
Descriptionmucin-16CA125 ovarian cancer antigenmucin-16 long isoformmucin-16 short isoformovarian cancer-related tumor marker CA125ovarian carcinoma antigen CA125retinoic acid receptor alphaRAR-alphanuclear receptor subfamily 1 group B member 1nucleophosmin-retinoic acid receptor alpha fusion protein NPM-RAR long formretinoic acid nuclear receptor alpha variant 1retinoic acid nuclear receptor alpha variant 2
Modification date2020032920200327
UniProtAcc

Q8WXI7

P10276

Ensembl transtripts involved in fusion geneENST00000397910, ENST00000380951, 
ENST00000596956, 		ENST00000254066, 
ENST00000394089, ENST00000425707, 
ENST00000394081, ENST00000394086, 
ENST00000420042, 
Fusion gene scores* DoF score12 X 24 X 4=115229 X 39 X 17=19227
# samples 2155
** MAII scorelog2(21/1152*10)=-2.45567948377619
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(55/19227*10)=-5.12755824682814
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MUC16 [Title/Abstract] AND RARA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMUC16(9045564)-RARA(38487109), # samples:2
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
TgeneRARA

GO:0007165

signal transduction

2825025

TgeneRARA

GO:0030853

negative regulation of granulocyte differentiation

19917671

TgeneRARA

GO:0032689

negative regulation of interferon-gamma production

18416830

TgeneRARA

GO:0032720

negative regulation of tumor necrosis factor production

18416830

TgeneRARA

GO:0032736

positive regulation of interleukin-13 production

18416830

TgeneRARA

GO:0032753

positive regulation of interleukin-4 production

18416830

TgeneRARA

GO:0032754

positive regulation of interleukin-5 production

18416830

TgeneRARA

GO:0045630

positive regulation of T-helper 2 cell differentiation

18416830

TgeneRARA

GO:0045892

negative regulation of transcription, DNA-templated

20080953

TgeneRARA

GO:0045893

positive regulation of transcription, DNA-templated

18845237|19850744|20080953

TgeneRARA

GO:0045944

positive regulation of transcription by RNA polymerase II

19850744|21131358

TgeneRARA

GO:0071300

cellular response to retinoic acid

19917671

TgeneRARA

GO:0071391

cellular response to estrogen stimulus

20080953


check buttonFusion gene breakpoints across MUC16 (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 RARA (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
ChimerDB4OVTCGA-29-2428-01AMUC16chr19

9045564

-RARAchr17

38487109

+
ChimerDB4OVTCGA-29-2428MUC16chr19

9045563

-RARAchr17

38487108

+


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Fusion Gene ORF analysis for MUC16-RARA

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-5UTRENST00000397910ENST00000254066MUC16chr19

9045564

-RARAchr17

38487109

+
5CDS-5UTRENST00000397910ENST00000254066MUC16chr19

9045563

-RARAchr17

38487108

+
5CDS-5UTRENST00000397910ENST00000394089MUC16chr19

9045564

-RARAchr17

38487109

+
5CDS-5UTRENST00000397910ENST00000394089MUC16chr19

9045563

-RARAchr17

38487108

+
5CDS-5UTRENST00000397910ENST00000425707MUC16chr19

9045564

-RARAchr17

38487109

+
5CDS-5UTRENST00000397910ENST00000425707MUC16chr19

9045563

-RARAchr17

38487108

+
5CDS-intronENST00000397910ENST00000394081MUC16chr19

9045564

-RARAchr17

38487109

+
5CDS-intronENST00000397910ENST00000394081MUC16chr19

9045563

-RARAchr17

38487108

+
5CDS-intronENST00000397910ENST00000394086MUC16chr19

9045564

-RARAchr17

38487109

+
5CDS-intronENST00000397910ENST00000394086MUC16chr19

9045563

-RARAchr17

38487108

+
5CDS-intronENST00000397910ENST00000420042MUC16chr19

9045564

-RARAchr17

38487109

+
5CDS-intronENST00000397910ENST00000420042MUC16chr19

9045563

-RARAchr17

38487108

+
intron-5UTRENST00000380951ENST00000254066MUC16chr19

9045564

-RARAchr17

38487109

+
intron-5UTRENST00000380951ENST00000254066MUC16chr19

9045563

-RARAchr17

38487108

+
intron-5UTRENST00000380951ENST00000394089MUC16chr19

9045564

-RARAchr17

38487109

+
intron-5UTRENST00000380951ENST00000394089MUC16chr19

9045563

-RARAchr17

38487108

+
intron-5UTRENST00000380951ENST00000425707MUC16chr19

9045564

-RARAchr17

38487109

+
intron-5UTRENST00000380951ENST00000425707MUC16chr19

9045563

-RARAchr17

38487108

+
intron-5UTRENST00000596956ENST00000254066MUC16chr19

9045564

-RARAchr17

38487109

+
intron-5UTRENST00000596956ENST00000254066MUC16chr19

9045563

-RARAchr17

38487108

+
intron-5UTRENST00000596956ENST00000394089MUC16chr19

9045564

-RARAchr17

38487109

+
intron-5UTRENST00000596956ENST00000394089MUC16chr19

9045563

-RARAchr17

38487108

+
intron-5UTRENST00000596956ENST00000425707MUC16chr19

9045564

-RARAchr17

38487109

+
intron-5UTRENST00000596956ENST00000425707MUC16chr19

9045563

-RARAchr17

38487108

+
intron-intronENST00000380951ENST00000394081MUC16chr19

9045564

-RARAchr17

38487109

+
intron-intronENST00000380951ENST00000394081MUC16chr19

9045563

-RARAchr17

38487108

+
intron-intronENST00000380951ENST00000394086MUC16chr19

9045564

-RARAchr17

38487109

+
intron-intronENST00000380951ENST00000394086MUC16chr19

9045563

-RARAchr17

38487108

+
intron-intronENST00000380951ENST00000420042MUC16chr19

9045564

-RARAchr17

38487109

+
intron-intronENST00000380951ENST00000420042MUC16chr19

9045563

-RARAchr17

38487108

+
intron-intronENST00000596956ENST00000394081MUC16chr19

9045564

-RARAchr17

38487109

+
intron-intronENST00000596956ENST00000394081MUC16chr19

9045563

-RARAchr17

38487108

+
intron-intronENST00000596956ENST00000394086MUC16chr19

9045564

-RARAchr17

38487109

+
intron-intronENST00000596956ENST00000394086MUC16chr19

9045563

-RARAchr17

38487108

+
intron-intronENST00000596956ENST00000420042MUC16chr19

9045564

-RARAchr17

38487109

+
intron-intronENST00000596956ENST00000420042MUC16chr19

9045563

-RARAchr17

38487108

+

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 MUC16-RARA


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)

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 MUC16-RARA


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/:9045564/:38487109)
- 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
MUC16

Q8WXI7

RARA

P10276

FUNCTION: Thought to provide a protective, lubricating barrier against particles and infectious agents at mucosal surfaces. {ECO:0000250}.FUNCTION: Receptor for retinoic acid (PubMed:19850744, PubMed:16417524, PubMed:20215566). Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes (PubMed:28167758). The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5 (PubMed:28167758, PubMed:19398580). In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone deacetylation, chromatin condensation and transcriptional suppression (PubMed:16417524). On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation (PubMed:9267036, PubMed:19850744, PubMed:20215566). Formation of a complex with histone deacetylases might lead to inhibition of RARE DNA element binding and to transcriptional repression (PubMed:28167758). Transcriptional activation and RARE DNA element binding might be supported by the transcription factor KLF2 (PubMed:28167758). RARA plays an essential role in the regulation of retinoic acid-induced germ cell development during spermatogenesis (By similarity). Has a role in the survival of early spermatocytes at the beginning prophase of meiosis (By similarity). In Sertoli cells, may promote the survival and development of early meiotic prophase spermatocytes (By similarity). In concert with RARG, required for skeletal growth, matrix homeostasis and growth plate function (By similarity). Together with RXRA, positively regulates microRNA-10a expression, thereby inhibiting the GATA6/VCAM1 signaling response to pulsatile shear stress in vascular endothelial cells (PubMed:28167758). In association with HDAC3, HDAC5 and HDAC7 corepressors, plays a role in the repression of microRNA-10a and thereby promotes the inflammatory response (PubMed:28167758). {ECO:0000250|UniProtKB:P11416, ECO:0000269|PubMed:16417524, ECO:0000269|PubMed:19398580, ECO:0000269|PubMed:19850744, ECO:0000269|PubMed:20215566, ECO:0000269|PubMed:28167758, ECO:0000269|PubMed:9267036}.

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 MUC16-RARA


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 MUC16-RARA


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 MUC16-RARA


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 MUC16-RARA


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