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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: 35759

FusionGeneSummary for SPOP_RARA

check button Fusion gene summary
Fusion gene informationFusion gene name: SPOP_RARA
Fusion gene ID: 35759
HgeneTgene
Gene symbol

SPOP

RARA

Gene ID

8405

5914

Gene namespeckle type BTB/POZ proteinretinoic acid receptor alpha
SynonymsBTBD32|TEF2NR1B1|RAR
Cytomap

17q21.33

17q21.2

Type of geneprotein-codingprotein-coding
Descriptionspeckle-type POZ proteinHIB homolog 1roadkill homolog 1retinoic 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

O43791

P10276

Ensembl transtripts involved in fusion geneENST00000393328, ENST00000393331, 
ENST00000347630, ENST00000504102, 
ENST00000503676, ENST00000513080, 
ENST00000254066, ENST00000394089, 
ENST00000425707, ENST00000394086, 
ENST00000394081, ENST00000420042, 
Fusion gene scores* DoF score20 X 8 X 13=208018 X 16 X 10=2880
# samples 2242
** MAII scorelog2(22/2080*10)=-3.24100809950379
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: SPOP [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
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
TCGARVBRCATCGA-LD-A9QF-01ASPOPchr17

47755295

-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
5UTR-5UTRENST00000393328ENST00000254066SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-5UTRENST00000393328ENST00000394089SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-5UTRENST00000393328ENST00000425707SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-intronENST00000393328ENST00000394086SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-intronENST00000393328ENST00000394081SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-intronENST00000393328ENST00000420042SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-5UTRENST00000393331ENST00000254066SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-5UTRENST00000393331ENST00000394089SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-5UTRENST00000393331ENST00000425707SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-intronENST00000393331ENST00000394086SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-intronENST00000393331ENST00000394081SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-intronENST00000393331ENST00000420042SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-5UTRENST00000347630ENST00000254066SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-5UTRENST00000347630ENST00000394089SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-5UTRENST00000347630ENST00000425707SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-intronENST00000347630ENST00000394086SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-intronENST00000347630ENST00000394081SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-intronENST00000347630ENST00000420042SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-5UTRENST00000504102ENST00000254066SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-5UTRENST00000504102ENST00000394089SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-5UTRENST00000504102ENST00000425707SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-intronENST00000504102ENST00000394086SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-intronENST00000504102ENST00000394081SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-intronENST00000504102ENST00000420042SPOPchr17

47755295

-RARAchr17

38487109

+
intron-5UTRENST00000503676ENST00000254066SPOPchr17

47755295

-RARAchr17

38487109

+
intron-5UTRENST00000503676ENST00000394089SPOPchr17

47755295

-RARAchr17

38487109

+
intron-5UTRENST00000503676ENST00000425707SPOPchr17

47755295

-RARAchr17

38487109

+
intron-intronENST00000503676ENST00000394086SPOPchr17

47755295

-RARAchr17

38487109

+
intron-intronENST00000503676ENST00000394081SPOPchr17

47755295

-RARAchr17

38487109

+
intron-intronENST00000503676ENST00000420042SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-5UTRENST00000513080ENST00000254066SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-5UTRENST00000513080ENST00000394089SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-5UTRENST00000513080ENST00000425707SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-intronENST00000513080ENST00000394086SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-intronENST00000513080ENST00000394081SPOPchr17

47755295

-RARAchr17

38487109

+
5UTR-intronENST00000513080ENST00000420042SPOPchr17

47755295

-RARAchr17

38487109

+

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FusionProtFeatures for SPOP_RARA


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

O43791

RARA

P10276

Component of a cullin-RING-based BCR (BTB-CUL3-RBX1) E3ubiquitin-protein ligase complex that mediates the ubiquitinationof target proteins, leading most often to their proteasomaldegradation. In complex with CUL3, involved in ubiquitination andproteasomal degradation of BRMS1, DAXX, PDX1/IPF1, GLI2 and GLI3.In complex with CUL3, involved in ubiquitination of H2AFY andBMI1; this does not lead to their proteasomal degradation.Inhibits transcriptional activation of PDX1/IPF1 targets, such asinsulin, by promoting PDX1/IPF1 degradation. The cullin-RING-basedBCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex containinghomodimeric SPOP has higher ubiquitin ligase activity than thecomplex that contains the heterodimer formed by SPOP and SPOPL.{ECO:0000269|PubMed:14528312, ECO:0000269|PubMed:15897469,ECO:0000269|PubMed:16524876, ECO:0000269|PubMed:19818708,ECO:0000269|PubMed:22085717, ECO:0000269|PubMed:22632832}. 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 SPOP_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 SPOP_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
SPOPZBTB16, DPPA2, RXRB, DDIT3, RTN3, MYD88, SIRT2, DOK2, KPNA6, GDI1, PIP5K1B, TRAF1, TRAF6, AR, BMI1, NCOA3, CUL3, ESR1, DAXX, SPOP, PIP4K2B, UBE2E3, FADD, PIAS1, GIT2, SRRM1, ATM, GLI2, DEK, BRMS1, NUP50, RTN4, GCC1, ERG, ERF, PGR, GLI3, UBE2D1, UBE2D2, NANOG, PTEN, DUSP7, EGLN2, RFWD2, SOST, ARIH1, MSRB3, BRD4, BRD3, BRD2RARANRBF2, 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


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RelatedDrugs for SPOP_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 SPOP_RARA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSPOPC0014170Endometrial Neoplasms1CTD_human
HgeneSPOPC0033578Prostatic Neoplasms1CTD_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