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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: 39186

FusionGeneSummary for TPCN2_RARA

check button Fusion gene summary
Fusion gene informationFusion gene name: TPCN2_RARA
Fusion gene ID: 39186
HgeneTgene
Gene symbol

TPCN2

RARA

Gene ID

219931

5914

Gene nametwo pore segment channel 2retinoic acid receptor alpha
SynonymsSHEP10|TPC2NR1B1|RAR
Cytomap

11q13.3

17q21.2

Type of geneprotein-codingprotein-coding
Descriptiontwo pore calcium channel protein 2voltage-dependent calcium channel protein TPC2retinoic 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 date2018052220180523
UniProtAcc

Q8NHX9

P10276

Ensembl transtripts involved in fusion geneENST00000294309, ENST00000542467, 
ENST00000442692, 
ENST00000254066, 
ENST00000394089, ENST00000425707, 
ENST00000394086, ENST00000394081, 
ENST00000420042, 
Fusion gene scores* DoF score9 X 8 X 6=43218 X 16 X 10=2880
# samples 942
** MAII scorelog2(9/432*10)=-2.26303440583379
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: TPCN2 [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
HgeneTPCN2

GO:0006874

cellular calcium ion homeostasis

19387438

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
TCGALDBRCATCGA-EW-A1IW-01ATPCN2chr11

68830458

+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-5UTRENST00000294309ENST00000254066TPCN2chr11

68830458

+RARAchr17

38487109

+
5CDS-5UTRENST00000294309ENST00000394089TPCN2chr11

68830458

+RARAchr17

38487109

+
5CDS-5UTRENST00000294309ENST00000425707TPCN2chr11

68830458

+RARAchr17

38487109

+
5CDS-intronENST00000294309ENST00000394086TPCN2chr11

68830458

+RARAchr17

38487109

+
5CDS-intronENST00000294309ENST00000394081TPCN2chr11

68830458

+RARAchr17

38487109

+
5CDS-intronENST00000294309ENST00000420042TPCN2chr11

68830458

+RARAchr17

38487109

+
5CDS-5UTRENST00000542467ENST00000254066TPCN2chr11

68830458

+RARAchr17

38487109

+
5CDS-5UTRENST00000542467ENST00000394089TPCN2chr11

68830458

+RARAchr17

38487109

+
5CDS-5UTRENST00000542467ENST00000425707TPCN2chr11

68830458

+RARAchr17

38487109

+
5CDS-intronENST00000542467ENST00000394086TPCN2chr11

68830458

+RARAchr17

38487109

+
5CDS-intronENST00000542467ENST00000394081TPCN2chr11

68830458

+RARAchr17

38487109

+
5CDS-intronENST00000542467ENST00000420042TPCN2chr11

68830458

+RARAchr17

38487109

+
3UTR-5UTRENST00000442692ENST00000254066TPCN2chr11

68830458

+RARAchr17

38487109

+
3UTR-5UTRENST00000442692ENST00000394089TPCN2chr11

68830458

+RARAchr17

38487109

+
3UTR-5UTRENST00000442692ENST00000425707TPCN2chr11

68830458

+RARAchr17

38487109

+
3UTR-intronENST00000442692ENST00000394086TPCN2chr11

68830458

+RARAchr17

38487109

+
3UTR-intronENST00000442692ENST00000394081TPCN2chr11

68830458

+RARAchr17

38487109

+
3UTR-intronENST00000442692ENST00000420042TPCN2chr11

68830458

+RARAchr17

38487109

+

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FusionProtFeatures for TPCN2_RARA


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
TPCN2

Q8NHX9

RARA

P10276

Nicotinic acid adenine dinucleotide phosphate (NAADP)receptor that may function as one of the major voltage-gatedCa(2+) channels (VDCC) across the lysosomal membrane. May beinvolved in smooth muscle contraction.{ECO:0000269|PubMed:19387438, ECO:0000269|PubMed:19620632}. 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 TPCN2_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 TPCN2_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
TPCN2ANKRD27, AGBL5, USP32, DENND6A, TRAPPC8, WDR44, PTPRA, CLCN3, FBXO10, ARRB2, RRAGB, PI4K2A, RELT, AP3B1, WDR11, TSR3, PCDH9, DIP2A, RAB6B, ZRANB3, AP3D1, CD320, DDX11L8, VAMP3, CERK, OCRL, AP3S1, APPL1, HK3, MAP2K7, DAGLB, B4GALT5, TMEM56, RNF149, LRP10, VAMP2, ACP2, SNX17, PTPRD, BMPR1A, STX6, TRAPPC5, EHD4, CSNK1G3, NDFIP1, FGFR1, NOMO3, UXS1, EBP, ZDHHC18, NOMO1, TRIM25RARANRBF2, 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 TPCN2_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 TPCN2_RARA


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