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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 31596

FusionGeneSummary for RNF43_RARA

check button Fusion gene summary
Fusion gene informationFusion gene name: RNF43_RARA
Fusion gene ID: 31596
HgeneTgene
Gene symbol

RNF43

RARA

Gene ID

54894

5914

Gene namering finger protein 43retinoic acid receptor alpha
SynonymsRNF124|SSPCS|URCCNR1B1|RAR
Cytomap

17q22

17q21.2

Type of geneprotein-codingprotein-coding
DescriptionE3 ubiquitin-protein ligase RNF43RING-type E3 ubiquitin transferase RNF43retinoic 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 date2018052320180523
UniProtAcc

Q68DV7

P10276

Ensembl transtripts involved in fusion geneENST00000500597, ENST00000407977, 
ENST00000583753, ENST00000584437, 
ENST00000577716, ENST00000581868, 
ENST00000577625, ENST00000580014, 
ENST00000254066, ENST00000394089, 
ENST00000425707, ENST00000394086, 
ENST00000394081, ENST00000420042, 
Fusion gene scores* DoF score7 X 5 X 6=21018 X 16 X 10=2880
# samples 742
** MAII scorelog2(7/210*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(42/2880*10)=-2.77760757866355
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RNF43 [Title/Abstract] AND RARA [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
HgeneRNF43

GO:0006511

ubiquitin-dependent protein catabolic process

22895187

HgeneRNF43

GO:0016567

protein ubiquitination

22575959

HgeneRNF43

GO:0038018

Wnt receptor catabolic process

22895187

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

TgeneRARA

GO:0071300

cellular response to retinoic acid

19917671

TgeneRARA

GO:0071391

cellular response to estrogen stimulus

20080953


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVCOADTCGA-CM-6167-01ARNF43chr17

56492687

-RARAchr17

38487109

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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-5UTRENST00000500597ENST00000254066RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-5UTRENST00000500597ENST00000394089RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-5UTRENST00000500597ENST00000425707RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-intronENST00000500597ENST00000394086RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-intronENST00000500597ENST00000394081RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-intronENST00000500597ENST00000420042RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-5UTRENST00000407977ENST00000254066RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-5UTRENST00000407977ENST00000394089RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-5UTRENST00000407977ENST00000425707RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-intronENST00000407977ENST00000394086RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-intronENST00000407977ENST00000394081RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-intronENST00000407977ENST00000420042RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-5UTRENST00000583753ENST00000254066RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-5UTRENST00000583753ENST00000394089RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-5UTRENST00000583753ENST00000425707RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-intronENST00000583753ENST00000394086RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-intronENST00000583753ENST00000394081RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-intronENST00000583753ENST00000420042RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-5UTRENST00000584437ENST00000254066RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-5UTRENST00000584437ENST00000394089RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-5UTRENST00000584437ENST00000425707RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-intronENST00000584437ENST00000394086RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-intronENST00000584437ENST00000394081RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-intronENST00000584437ENST00000420042RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-5UTRENST00000577716ENST00000254066RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-5UTRENST00000577716ENST00000394089RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-5UTRENST00000577716ENST00000425707RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-intronENST00000577716ENST00000394086RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-intronENST00000577716ENST00000394081RNF43chr17

56492687

-RARAchr17

38487109

+
5CDS-intronENST00000577716ENST00000420042RNF43chr17

56492687

-RARAchr17

38487109

+
intron-5UTRENST00000581868ENST00000254066RNF43chr17

56492687

-RARAchr17

38487109

+
intron-5UTRENST00000581868ENST00000394089RNF43chr17

56492687

-RARAchr17

38487109

+
intron-5UTRENST00000581868ENST00000425707RNF43chr17

56492687

-RARAchr17

38487109

+
intron-intronENST00000581868ENST00000394086RNF43chr17

56492687

-RARAchr17

38487109

+
intron-intronENST00000581868ENST00000394081RNF43chr17

56492687

-RARAchr17

38487109

+
intron-intronENST00000581868ENST00000420042RNF43chr17

56492687

-RARAchr17

38487109

+
intron-5UTRENST00000577625ENST00000254066RNF43chr17

56492687

-RARAchr17

38487109

+
intron-5UTRENST00000577625ENST00000394089RNF43chr17

56492687

-RARAchr17

38487109

+
intron-5UTRENST00000577625ENST00000425707RNF43chr17

56492687

-RARAchr17

38487109

+
intron-intronENST00000577625ENST00000394086RNF43chr17

56492687

-RARAchr17

38487109

+
intron-intronENST00000577625ENST00000394081RNF43chr17

56492687

-RARAchr17

38487109

+
intron-intronENST00000577625ENST00000420042RNF43chr17

56492687

-RARAchr17

38487109

+
intron-5UTRENST00000580014ENST00000254066RNF43chr17

56492687

-RARAchr17

38487109

+
intron-5UTRENST00000580014ENST00000394089RNF43chr17

56492687

-RARAchr17

38487109

+
intron-5UTRENST00000580014ENST00000425707RNF43chr17

56492687

-RARAchr17

38487109

+
intron-intronENST00000580014ENST00000394086RNF43chr17

56492687

-RARAchr17

38487109

+
intron-intronENST00000580014ENST00000394081RNF43chr17

56492687

-RARAchr17

38487109

+
intron-intronENST00000580014ENST00000420042RNF43chr17

56492687

-RARAchr17

38487109

+

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FusionProtFeatures for RNF43_RARA


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RNF43

Q68DV7

RARA

P10276

E3 ubiquitin-protein ligase that acts as a negativeregulator of the Wnt signaling pathway by mediating theubiquitination, endocytosis and subsequent degradation of Wntreceptor complex components Frizzled. Acts on both canonical andnon-canonical Wnt signaling pathway. Acts as a tumor suppressor inthe intestinal stem cell zone by inhibiting the Wnt signalingpathway, thereby resticting the size of the intestinal stem cellzone. {ECO:0000269|PubMed:18313049, ECO:0000269|PubMed:22575959,ECO:0000269|PubMed:22895187}. Receptor for retinoic acid. Retinoic acid receptors bindas heterodimers to their target response elements in response totheir ligands, all-trans or 9-cis retinoic acid, and regulate geneexpression in various biological processes. The RXR/RARheterodimers bind to the retinoic acid response elements (RARE)composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In theabsence of ligand, the RXR-RAR heterodimers associate with amultiprotein complex containing transcription corepressors thatinduce histone acetylation, chromatin condensation andtranscriptional suppression. On ligand binding, the corepressorsdissociate from the receptors and associate with the coactivatorsleading to transcriptional activation. RARA plays an essentialrole in the regulation of retinoic acid-induced germ celldevelopment during spermatogenesis. Has a role in the survival ofearly spermatocytes at the beginning prophase of meiosis. InSertoli cells, may promote the survival and development of earlymeiotic prophase spermatocytes. In concert with RARG, required forskeletal growth, matrix homeostasis and growth plate function (Bysimilarity). {ECO:0000250|UniProtKB:P11416,ECO:0000269|PubMed:16417524, ECO:0000269|PubMed:19850744,ECO:0000269|PubMed:20215566}.

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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FusionGeneSequence for RNF43_RARA


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for RNF43_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
RNF43AKAP8L, KDM5B, UBE2D1, UBE2D2, UBE2D3, UBE2D4, UBE2E1, UBE2E3, UBE2N, HECW1, TP53, SFPQ, NONO, RSPO1, RNF43, DVL2, TCF7L2, FZD5, MYADM, CSNK1E, CSNK2A1RARANRBF2, ZBTB16, MECR, RXRG, RXRB, NCOA6, GADD45G, GADD45A, NRIP1, KAT2B, HDAC3, HDAC4, TDG, PML, TRIP4, KDM5A, RXRA, POU2F1, NCOR2, NR0B2, BAG1, TADA3, NCOR1, NKX2-1, TRIM24, IRX4, SP1, NPAS2, CLOCK, ARNTL, NR2E3, CCND3, NCOA2, SRC, AJUBA, LIMD1, WTIP, SKI, HR, PIN1, SUV39H1, PSMC5, EP300, PARP1, MED6, TOP2B, SAP130, HNRNPU, RFC4, NPM1, MRTO4, SNRNP40, MED1, NCOA1, HMGA1, RUVBL1, RUNX1, SIAH1, RARA, HDAC2, NCOA3, CREBBP, LRIF1, KLF5, SMARCD3, ARID1A, SPI1, PRDX6, NR1H2, ITGB1BP2, MED25, MAPK6, FOXO1, MAPK1, TRIM32, PHF8, TNIP1, HACE1, SQSTM1, UBQLN1, ARID5A, UBE3A, PRAM1, FAS, PRAME, TBL1XR1, SUZ12, EZH2, USP7, TMEM54, MMS19, AKT1, FN1, WWOX, E2F1, MBD3, MTA2, CBX5, CEBPA, HDAC1, NSD1, TEKT4, SNW1, SIRT1, ACTN4, SRF, MDM2, ZNF131, RARG, RARB, TRIM25


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


Top

RelatedDrugs for RNF43_RARA


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneRARAP10276DB00210AdapaleneRetinoic acid receptor alphasmall moleculeapproved
TgeneRARAP10276DB00459AcitretinRetinoic acid receptor alphasmall moleculeapproved
TgeneRARAP10276DB00982IsotretinoinRetinoic acid receptor alphasmall moleculeapproved
TgeneRARAP10276DB00523AlitretinoinRetinoic acid receptor alphasmall moleculeapproved|investigational
TgeneRARAP10276DB00799TazaroteneRetinoic acid receptor alphasmall moleculeapproved|investigational
TgeneRARAP10276DB00755TretinoinRetinoic acid receptor alphasmall moleculeapproved|investigational|nutraceutical

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RelatedDiseases for RNF43_RARA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRNF43C0009404Colorectal Neoplasms1CTD_human
HgeneRNF43C0014170Endometrial Neoplasms1CTD_human
HgeneRNF43C0023897Liver Diseases, Parasitic1CTD_human
HgeneRNF43C0038356Stomach Neoplasms1CTD_human
HgeneRNF43C0206698Cholangiocarcinoma1CTD_human
TgeneRARAC0023487Acute Promyelocytic Leukemia22CTD_human;HPO;ORPHANET
TgeneRARAC0036341Schizophrenia3PSYGENET
TgeneRARAC0005586Bipolar Disorder1PSYGENET
TgeneRARAC0010701Phyllodes Tumor1CTD_human
TgeneRARAC0085183Neoplasms, Second Primary1CTD_human
TgeneRARAC0149940Sciatic Neuropathy1CTD_human
TgeneRARAC0206650Fibroadenoma1CTD_human
TgeneRARAC0525045Mood Disorders1PSYGENET
TgeneRARAC1458155Mammary Neoplasms1CTD_human
TgeneRARAC2239176Liver carcinoma1CTD_human