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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-LTBP1 (FusionGDB2 ID:HG5914TG4052)

Fusion Gene Summary for RARA-LTBP1

check button Fusion gene summary
Fusion gene informationFusion gene name: RARA-LTBP1
Fusion gene ID: hg5914tg4052
HgeneTgene
Gene symbol

RARA

LTBP1

Gene ID

5914

4052

Gene nameretinoic acid receptor alphalatent transforming growth factor beta binding protein 1
SynonymsNR1B1|RAR-
Cytomap('RARA')('LTBP1')

17q21.2

2p22.3

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 2latent-transforming growth factor beta-binding protein 1LTBP-1TGF-beta1-BP-1transforming growth factor beta-1-binding protein 1
Modification date2020032720200329
UniProtAcc

P10276

Q14766

Ensembl transtripts involved in fusion geneENST00000394089, ENST00000425707, 
ENST00000254066, ENST00000394081, 
ENST00000394086, ENST00000420042, 
Fusion gene scores* DoF score47 X 22 X 8=827213 X 14 X 6=1092
# samples 7414
** MAII scorelog2(74/8272*10)=-3.48263900979862
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(14/1092*10)=-2.96347412397489
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RARA [Title/Abstract] AND LTBP1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRARA(38474700)-LTBP1(33447147), # 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
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

TgeneLTBP1

GO:0035583

sequestering of TGFbeta in extracellular matrix

2022183|8617200

TgeneLTBP1

GO:1901388

regulation of transforming growth factor beta activation

2022183|8617200



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
ChimerDB4UCECTCGA-AJ-A3QS-01ARARAchr17

38474700

-LTBP1chr2

33447147

+
ChimerDB4UCECTCGA-AJ-A3QS-01ARARAchr17

38474700

+LTBP1chr2

33447147

+


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Fusion Gene ORF analysis for RARA-LTBP1

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-3CDSENST00000394089ENST00000354476RARAchr17

38474700

+LTBP1chr2

33447147

+
5UTR-3CDSENST00000394089ENST00000390003RARAchr17

38474700

+LTBP1chr2

33447147

+
5UTR-3CDSENST00000394089ENST00000402934RARAchr17

38474700

+LTBP1chr2

33447147

+
5UTR-3CDSENST00000394089ENST00000404525RARAchr17

38474700

+LTBP1chr2

33447147

+
5UTR-3CDSENST00000394089ENST00000404816RARAchr17

38474700

+LTBP1chr2

33447147

+
5UTR-3CDSENST00000394089ENST00000407925RARAchr17

38474700

+LTBP1chr2

33447147

+
5UTR-3CDSENST00000394089ENST00000418533RARAchr17

38474700

+LTBP1chr2

33447147

+
5UTR-3CDSENST00000425707ENST00000354476RARAchr17

38474700

+LTBP1chr2

33447147

+
5UTR-3CDSENST00000425707ENST00000390003RARAchr17

38474700

+LTBP1chr2

33447147

+
5UTR-3CDSENST00000425707ENST00000402934RARAchr17

38474700

+LTBP1chr2

33447147

+
5UTR-3CDSENST00000425707ENST00000404525RARAchr17

38474700

+LTBP1chr2

33447147

+
5UTR-3CDSENST00000425707ENST00000404816RARAchr17

38474700

+LTBP1chr2

33447147

+
5UTR-3CDSENST00000425707ENST00000407925RARAchr17

38474700

+LTBP1chr2

33447147

+
5UTR-3CDSENST00000425707ENST00000418533RARAchr17

38474700

+LTBP1chr2

33447147

+
5UTR-intronENST00000394089ENST00000272273RARAchr17

38474700

+LTBP1chr2

33447147

+
5UTR-intronENST00000394089ENST00000498013RARAchr17

38474700

+LTBP1chr2

33447147

+
5UTR-intronENST00000425707ENST00000272273RARAchr17

38474700

+LTBP1chr2

33447147

+
5UTR-intronENST00000425707ENST00000498013RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000254066ENST00000354476RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000254066ENST00000390003RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000254066ENST00000402934RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000254066ENST00000404525RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000254066ENST00000404816RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000254066ENST00000407925RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000254066ENST00000418533RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000394081ENST00000354476RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000394081ENST00000390003RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000394081ENST00000402934RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000394081ENST00000404525RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000394081ENST00000404816RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000394081ENST00000407925RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000394081ENST00000418533RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000394086ENST00000354476RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000394086ENST00000390003RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000394086ENST00000402934RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000394086ENST00000404525RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000394086ENST00000404816RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000394086ENST00000407925RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000394086ENST00000418533RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000420042ENST00000354476RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000420042ENST00000390003RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000420042ENST00000402934RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000420042ENST00000404525RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000420042ENST00000404816RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000420042ENST00000407925RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-3CDSENST00000420042ENST00000418533RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-intronENST00000254066ENST00000272273RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-intronENST00000254066ENST00000498013RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-intronENST00000394081ENST00000272273RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-intronENST00000394081ENST00000498013RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-intronENST00000394086ENST00000272273RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-intronENST00000394086ENST00000498013RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-intronENST00000420042ENST00000272273RARAchr17

38474700

+LTBP1chr2

33447147

+
intron-intronENST00000420042ENST00000498013RARAchr17

38474700

+LTBP1chr2

33447147

+

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-LTBP1


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)
RARAchr1738474700+LTBP1chr233447146+0.021325890.97867405
RARAchr1738474700+LTBP1chr233447146+0.021325890.97867405


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 RARA-LTBP1


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/:38474700/:33447147)
- 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
RARA

P10276

LTBP1

Q14766

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}.FUNCTION: Key regulator of transforming growth factor beta (TGFB1, TGFB2 and TGFB3) that controls TGF-beta activation by maintaining it in a latent state during storage in extracellular space (PubMed:2022183, PubMed:8617200, PubMed:8939931). Associates specifically via disulfide bonds with the Latency-associated peptide (LAP), which is the regulatory chain of TGF-beta, and regulates integrin-dependent activation of TGF-beta (PubMed:8617200, PubMed:8939931, PubMed:15184403). Outcompeted by LRRC32/GARP for binding to LAP regulatory chain of TGF-beta (PubMed:22278742). {ECO:0000269|PubMed:15184403, ECO:0000269|PubMed:2022183, ECO:0000269|PubMed:22278742, ECO:0000269|PubMed:8617200, ECO:0000269|PubMed:8939931}.

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-LTBP1


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-LTBP1


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-LTBP1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneRARAP10276DB00210AdapaleneSmall moleculeApproved
HgeneRARAP10276DB00210AdapaleneSmall moleculeApproved
HgeneRARAP10276DB00459AcitretinAgonistSmall moleculeApproved
HgeneRARAP10276DB00459AcitretinAgonistSmall moleculeApproved
HgeneRARAP10276DB00982IsotretinoinOther/unknownSmall moleculeApproved
HgeneRARAP10276DB00982IsotretinoinOther/unknownSmall moleculeApproved
HgeneRARAP10276DB00523AlitretinoinAgonistSmall moleculeApproved|Investigational
HgeneRARAP10276DB00523AlitretinoinAgonistSmall moleculeApproved|Investigational
HgeneRARAP10276DB00799TazaroteneAgonistSmall moleculeApproved|Investigational
HgeneRARAP10276DB00799TazaroteneAgonistSmall moleculeApproved|Investigational
HgeneRARAP10276DB12808TrifaroteneAgonistSmall moleculeApproved|Investigational
HgeneRARAP10276DB12808TrifaroteneAgonistSmall moleculeApproved|Investigational
HgeneRARAP10276DB00755TretinoinSmall moleculeApproved|Investigational|Nutraceutical
HgeneRARAP10276DB00755TretinoinSmall moleculeApproved|Investigational|Nutraceutical

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Related Diseases for RARA-LTBP1


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
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneC0409959Osteoarthritis, Knee1CTD_human