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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:RARA-JUP (FusionGDB2 ID:71838)

Fusion Gene Summary for RARA-JUP

check button Fusion gene summary
Fusion gene informationFusion gene name: RARA-JUP
Fusion gene ID: 71838
HgeneTgene
Gene symbol

RARA

JUP

Gene ID

5914

3728

Gene nameretinoic acid receptor alphajunction plakoglobin
SynonymsNR1B1|RARCTNNG|DP3|DPIII|PDGB|PKGB
Cytomap

17q21.2

17q21.2

Type of geneprotein-codingprotein-coding
Descriptionretinoic 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 2junction plakoglobincatenin (cadherin-associated protein), gamma 80kDadesmoplakin IIIdesmoplakin-3
Modification date2020032720200313
UniProtAcc.

P14923

Ensembl transtripts involved in fusion geneENST00000254066, ENST00000394089, 
ENST00000425707, ENST00000394086, 
ENST00000394081, ENST00000420042, 
ENST00000540235, ENST00000393930, 
ENST00000393931, ENST00000310706, 
Fusion gene scores* DoF score47 X 22 X 8=827225 X 18 X 10=4500
# samples 7426
** MAII scorelog2(74/8272*10)=-3.48263900979862
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(26/4500*10)=-4.11334147307594
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

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

Most frequent breakpointRARA(38465538)-JUP(39923832), # samples:1
RARA(38487648)-JUP(39928114), # 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
HgeneRARA

GO:0007165

signal transduction

2825025

HgeneRARA

GO:0030853

negative regulation of granulocyte differentiation

19917671

HgeneRARA

GO:0032689

negative regulation of interferon-gamma production

18416830

HgeneRARA

GO:0032720

negative regulation of tumor necrosis factor production

18416830

HgeneRARA

GO:0032736

positive regulation of interleukin-13 production

18416830

HgeneRARA

GO:0032753

positive regulation of interleukin-4 production

18416830

HgeneRARA

GO:0032754

positive regulation of interleukin-5 production

18416830

HgeneRARA

GO:0045630

positive regulation of T-helper 2 cell differentiation

18416830

HgeneRARA

GO:0045892

negative regulation of transcription, DNA-templated

20080953

HgeneRARA

GO:0045893

positive regulation of transcription, DNA-templated

18845237|19850744|20080953

HgeneRARA

GO:0045944

positive regulation of transcription by RNA polymerase II

19850744|21131358

HgeneRARA

GO:0071300

cellular response to retinoic acid

19917671

HgeneRARA

GO:0071391

cellular response to estrogen stimulus

20080953

TgeneJUP

GO:0002159

desmosome assembly

22889254

TgeneJUP

GO:0042127

regulation of cell proliferation

17924338

TgeneJUP

GO:0042307

positive regulation of protein import into nucleus

10825188|14661054

TgeneJUP

GO:0050982

detection of mechanical stimulus

18937352

TgeneJUP

GO:0051091

positive regulation of DNA-binding transcription factor activity

14661054

TgeneJUP

GO:0071681

cellular response to indole-3-methanol

10868478

TgeneJUP

GO:0098609

cell-cell adhesion

18937352


check buttonFusion gene breakpoints across RARA (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 JUP (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
ChimerDB4STADTCGA-EQ-8122RARAchr17

38465538

+JUPchr17

39923832

-
ChimerDB4STADTCGA-RD-A7BTRARAchr17

38487648

+JUPchr17

39928114

-


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Fusion Gene ORF analysis for RARA-JUP

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-3CDSENST00000254066ENST00000540235RARAchr17

38465538

+JUPchr17

39923832

-
5UTR-3CDSENST00000254066ENST00000393930RARAchr17

38465538

+JUPchr17

39923832

-
5UTR-3CDSENST00000254066ENST00000393931RARAchr17

38465538

+JUPchr17

39923832

-
5UTR-3CDSENST00000254066ENST00000310706RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000394089ENST00000540235RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000394089ENST00000393930RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000394089ENST00000393931RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000394089ENST00000310706RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000425707ENST00000540235RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000425707ENST00000393930RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000425707ENST00000393931RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000425707ENST00000310706RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000394086ENST00000540235RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000394086ENST00000393930RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000394086ENST00000393931RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000394086ENST00000310706RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000394081ENST00000540235RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000394081ENST00000393930RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000394081ENST00000393931RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000394081ENST00000310706RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000420042ENST00000540235RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000420042ENST00000393930RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000420042ENST00000393931RARAchr17

38465538

+JUPchr17

39923832

-
intron-3CDSENST00000420042ENST00000310706RARAchr17

38465538

+JUPchr17

39923832

-
5CDS-intronENST00000254066ENST00000540235RARAchr17

38487648

+JUPchr17

39928114

-
5CDS-5UTRENST00000254066ENST00000393930RARAchr17

38487648

+JUPchr17

39928114

-
5CDS-5UTRENST00000254066ENST00000393931RARAchr17

38487648

+JUPchr17

39928114

-
5CDS-5UTRENST00000254066ENST00000310706RARAchr17

38487648

+JUPchr17

39928114

-
5CDS-intronENST00000394089ENST00000540235RARAchr17

38487648

+JUPchr17

39928114

-
5CDS-5UTRENST00000394089ENST00000393930RARAchr17

38487648

+JUPchr17

39928114

-
5CDS-5UTRENST00000394089ENST00000393931RARAchr17

38487648

+JUPchr17

39928114

-
5CDS-5UTRENST00000394089ENST00000310706RARAchr17

38487648

+JUPchr17

39928114

-
5CDS-intronENST00000425707ENST00000540235RARAchr17

38487648

+JUPchr17

39928114

-
5CDS-5UTRENST00000425707ENST00000393930RARAchr17

38487648

+JUPchr17

39928114

-
5CDS-5UTRENST00000425707ENST00000393931RARAchr17

38487648

+JUPchr17

39928114

-
5CDS-5UTRENST00000425707ENST00000310706RARAchr17

38487648

+JUPchr17

39928114

-
intron-intronENST00000394086ENST00000540235RARAchr17

38487648

+JUPchr17

39928114

-
intron-5UTRENST00000394086ENST00000393930RARAchr17

38487648

+JUPchr17

39928114

-
intron-5UTRENST00000394086ENST00000393931RARAchr17

38487648

+JUPchr17

39928114

-
intron-5UTRENST00000394086ENST00000310706RARAchr17

38487648

+JUPchr17

39928114

-
intron-intronENST00000394081ENST00000540235RARAchr17

38487648

+JUPchr17

39928114

-
intron-5UTRENST00000394081ENST00000393930RARAchr17

38487648

+JUPchr17

39928114

-
intron-5UTRENST00000394081ENST00000393931RARAchr17

38487648

+JUPchr17

39928114

-
intron-5UTRENST00000394081ENST00000310706RARAchr17

38487648

+JUPchr17

39928114

-
intron-intronENST00000420042ENST00000540235RARAchr17

38487648

+JUPchr17

39928114

-
intron-5UTRENST00000420042ENST00000393930RARAchr17

38487648

+JUPchr17

39928114

-
intron-5UTRENST00000420042ENST00000393931RARAchr17

38487648

+JUPchr17

39928114

-
intron-5UTRENST00000420042ENST00000310706RARAchr17

38487648

+JUPchr17

39928114

-

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 RARA-JUP


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.

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Fusion Protein Features for RARA-JUP


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

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

P14923

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Common junctional plaque protein. The membrane-associated plaques are architectural elements in an important strategic position to influence the arrangement and function of both the cytoskeleton and the cells within the tissue. The presence of plakoglobin in both the desmosomes and in the intermediate junctions suggests that it plays a central role in the structure and function of submembranous plaques. Acts as a substrate for VE-PTP and is required by it to stimulate VE-cadherin function in endothelial cells. Can replace beta-catenin in E-cadherin/catenin adhesion complexes which are proposed to couple cadherins to the actin cytoskeleton (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 RARA-JUP


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 RARA-JUP


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 RARA-JUP


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneJUPP14923DB01593ZincSmall moleculeApproved|Investigational
TgeneJUPP14923DB01593ZincSmall moleculeApproved|Investigational
TgeneJUPP14923DB01593ZincSmall moleculeApproved|Investigational
TgeneJUPP14923DB14487Zinc acetateSmall moleculeApproved|Investigational
TgeneJUPP14923DB14487Zinc acetateSmall moleculeApproved|Investigational
TgeneJUPP14923DB14487Zinc acetateSmall moleculeApproved|Investigational

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Related Diseases for RARA-JUP


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRARAC0023487Acute Promyelocytic Leukemia24CTD_human;ORPHANET
HgeneRARAC0036341Schizophrenia3PSYGENET
HgeneRARAC0006142Malignant neoplasm of breast1CTD_human
HgeneRARAC0009363Congenital ocular coloboma (disorder)1GENOMICS_ENGLAND
HgeneRARAC0010701Phyllodes Tumor1CTD_human
HgeneRARAC0085183Neoplasms, Second Primary1CTD_human
HgeneRARAC0086696Neoplasms, Therapy-Associated1CTD_human
HgeneRARAC0149940Sciatic Neuropathy1CTD_human
HgeneRARAC0154748Lesion of Sciatic Nerve1CTD_human
HgeneRARAC0206650Fibroadenoma1CTD_human
HgeneRARAC0242013Sciatic Neuritis1CTD_human
HgeneRARAC0525045Mood Disorders1PSYGENET
HgeneRARAC0600066Malignant Cystosarcoma Phyllodes1CTD_human
HgeneRARAC0678222Breast Carcinoma1CTD_human
HgeneRARAC0751924Neuralgia-Neuritis, Sciatic Nerve1CTD_human
HgeneRARAC0751925Sciatic Nerve Palsy1CTD_human
HgeneRARAC0877578Treatment related secondary malignancy1CTD_human
HgeneRARAC1257931Mammary Neoplasms, Human1CTD_human
HgeneRARAC1458155Mammary Neoplasms1CTD_human
HgeneRARAC2239176Liver carcinoma1CTD_human
HgeneRARAC4704874Mammary Carcinoma, Human1CTD_human
TgeneJUPC1832600Naxos disease5CTD_human;GENOMICS_ENGLAND
TgeneJUPC1969081Arrhythmogenic Right Ventricular Dysplasia, Familial, 124CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneJUPC0023895Liver diseases1CTD_human
TgeneJUPC0033578Prostatic Neoplasms1CTD_human
TgeneJUPC0086565Liver Dysfunction1CTD_human
TgeneJUPC0232347No-Reflow Phenomenon1CTD_human
TgeneJUPC0376358Malignant neoplasm of prostate1CTD_human
TgeneJUPC1864826Epidermolysis bullosa, lethal acantholytic1ORPHANET
TgeneJUPC2713615Slow-Flow Phenomenon1CTD_human