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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: 32438

FusionGeneSummary for RXRA_KCNT2

check button Fusion gene summary
Fusion gene informationFusion gene name: RXRA_KCNT2
Fusion gene ID: 32438
HgeneTgene
Gene symbol

RXRA

KCNT2

Gene ID

6256

343450

Gene nameretinoid X receptor alphapotassium sodium-activated channel subfamily T member 2
SynonymsNR2B1EIEE57|KCa4.2|SLICK|SLO2.1
Cytomap

9q34.2

1q31.3

Type of geneprotein-codingprotein-coding
Descriptionretinoic acid receptor RXR-alphanuclear receptor subfamily 2 group B member 1retinoid X nuclear receptor alphapotassium channel subfamily T member 2potassium channel, subfamily T, member 2sequence like an intermediate conductance potassium channel subunitsodium and chloride-activated ATP-sensitive potassium channel Slo2.1sodium-and chloride-activated ATP-sens
Modification date2018052220180523
UniProtAcc

P19793

Q6UVM3

Ensembl transtripts involved in fusion geneENST00000481739, ENST00000356384, 
ENST00000540193, 		ENST00000367433, 
ENST00000498426, ENST00000367431, 
ENST00000609185, ENST00000451324, 
ENST00000294725, 
Fusion gene scores* DoF score7 X 4 X 4=1125 X 4 X 4=80
# samples 85
** MAII scorelog2(8/112*10)=-0.485426827170242
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/80*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RXRA [Title/Abstract] AND KCNT2 [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
HgeneRXRA

GO:0000122

negative regulation of transcription by RNA polymerase II

17426122

HgeneRXRA

GO:0019048

modulation by virus of host morphology or physiology

11915042

HgeneRXRA

GO:0035357

peroxisome proliferator activated receptor signaling pathway

10195690

HgeneRXRA

GO:0045944

positive regulation of transcription by RNA polymerase II

12037571|20219900

HgeneRXRA

GO:0051289

protein homotetramerization

7831303


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
TCGARVLIHCTCGA-2Y-A9H0-01ARXRAchr9

137218505

+KCNT2chr1

196461471

-
* 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
Frame-shiftENST00000481739ENST00000367433RXRAchr9

137218505

+KCNT2chr1

196461471

-
5CDS-intronENST00000481739ENST00000498426RXRAchr9

137218505

+KCNT2chr1

196461471

-
5CDS-intronENST00000481739ENST00000367431RXRAchr9

137218505

+KCNT2chr1

196461471

-
5CDS-intronENST00000481739ENST00000609185RXRAchr9

137218505

+KCNT2chr1

196461471

-
5CDS-5UTRENST00000481739ENST00000451324RXRAchr9

137218505

+KCNT2chr1

196461471

-
5CDS-5UTRENST00000481739ENST00000294725RXRAchr9

137218505

+KCNT2chr1

196461471

-
intron-3CDSENST00000356384ENST00000367433RXRAchr9

137218505

+KCNT2chr1

196461471

-
intron-intronENST00000356384ENST00000498426RXRAchr9

137218505

+KCNT2chr1

196461471

-
intron-intronENST00000356384ENST00000367431RXRAchr9

137218505

+KCNT2chr1

196461471

-
intron-intronENST00000356384ENST00000609185RXRAchr9

137218505

+KCNT2chr1

196461471

-
intron-5UTRENST00000356384ENST00000451324RXRAchr9

137218505

+KCNT2chr1

196461471

-
intron-5UTRENST00000356384ENST00000294725RXRAchr9

137218505

+KCNT2chr1

196461471

-
intron-3CDSENST00000540193ENST00000367433RXRAchr9

137218505

+KCNT2chr1

196461471

-
intron-intronENST00000540193ENST00000498426RXRAchr9

137218505

+KCNT2chr1

196461471

-
intron-intronENST00000540193ENST00000367431RXRAchr9

137218505

+KCNT2chr1

196461471

-
intron-intronENST00000540193ENST00000609185RXRAchr9

137218505

+KCNT2chr1

196461471

-
intron-5UTRENST00000540193ENST00000451324RXRAchr9

137218505

+KCNT2chr1

196461471

-
intron-5UTRENST00000540193ENST00000294725RXRAchr9

137218505

+KCNT2chr1

196461471

-

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FusionProtFeatures for RXRA_KCNT2


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

P19793

KCNT2

Q6UVM3

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 RAR/RXRheterodimers bind to the retinoic acid response elements (RARE)composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The highaffinity ligand for RXRs is 9-cis retinoic acid. RXRA serves as acommon heterodimeric partner for a number of nuclear receptors. Inthe absence 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. The RXRA/PPARA heterodimeris required for PPARA transcriptional activity on fatty acidoxidation genes such as ACOX1 and the P450 system genes.{ECO:0000269|PubMed:10195690, ECO:0000269|PubMed:11162439,ECO:0000269|PubMed:11915042, ECO:0000269|PubMed:20215566}. Outward rectifying potassium channel. Produces rapidlyactivating outward rectifier K(+) currents. Activated by highintracellular sodium and chloride levels. Channel activity isinhibited by ATP and by inhalation anesthetics, such as isoflurane(By similarity). Inhibited upon stimulation of G-protein coupledreceptors, such as CHRM1 and GRIA1. {ECO:0000250,ECO:0000269|PubMed:14684870, ECO:0000269|PubMed:16687497}.

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 RXRA_KCNT2


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 RXRA_KCNT2


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
RXRABRD8, NRBF2, CTNNB1, NCOA6, GADD45G, GADD45A, DNTTIP2, RNF8, NR4A1, HDAC3, HDAC4, TDG, THRB, PML, UBQLN4, TMPRSS3, RARA, POU2F1, NCOA3, MYOD1, NRIP1, NR0B2, EDF1, CTSL, TADA3, BCL3, NR1H2, NR1H4, NFKBIB, RELA, NFKB1, TBP, POU2F2, NR2F6, PPARA, NR1H3, TRIM24, PPARGC1A, SP1, PPARG, ITGB3BP, NPAS2, CLOCK, ARNTL, THRA, NR1I3, NCOA2, NR2E3, VDR, MED24, FUS, SNW1, NCOA1, IGFBP3, NCOR2, TAF1B, MED1, POLR2A, SMARCA4, RARB, GRIP1, NCOR1, SRC, CTCF, MAPK3, MAPK1, RARG, PPARD, NR1I2, KIF1A, NR4A2, MED25, GSK3B, CSNK2B, CASP2, TK1, PLK1, RPS6KA6, SMN1, PSMC5, ROBO4, TRIM32, EP300, BHLHE40, BHLHE41, ARID5A, RAD54L2, JAZF1, SMAD2, PRKD2, CHD9, STAT1, GK, NR3C2, ACVR1B, NCOA4, ALOX15B, NSD1, CNOT1, UBE2I, RXRA, TRIP4, SMARCD3, SRF, ZBTB16, KLF5, DNMT3L, TRAF2, PIK3R1, RXRG, TRIM25, SMARCB1KCNT2ZNRF4, SLC17A2, IL17RC, PCDHA3, PCDHB16, TNFRSF10A, IL4R, FAM189B


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 RXRA_KCNT2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneRXRAP19793DB00210AdapaleneRetinoic acid receptor RXR-alphasmall moleculeapproved
HgeneRXRAP19793DB00459AcitretinRetinoic acid receptor RXR-alphasmall moleculeapproved
HgeneRXRAP19793DB00307BexaroteneRetinoic acid receptor RXR-alphasmall moleculeapproved|investigational
HgeneRXRAP19793DB00412RosiglitazoneRetinoic acid receptor RXR-alphasmall moleculeapproved|investigational
HgeneRXRAP19793DB00523AlitretinoinRetinoic acid receptor RXR-alphasmall moleculeapproved|investigational
HgeneRXRAP19793DB01393BezafibrateRetinoic acid receptor RXR-alphasmall moleculeapproved|investigational
HgeneRXRAP19793DB00755TretinoinRetinoic acid receptor RXR-alphasmall moleculeapproved|investigational|nutraceutical
HgeneRXRAP19793DB00749EtodolacRetinoic acid receptor RXR-alphasmall moleculeapproved|investigational|vet_approved
HgeneRXRAP19793DB01436AlfacalcidolRetinoic acid receptor RXR-alphasmall moleculeapproved|nutraceutical

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RelatedDiseases for RXRA_KCNT2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRXRAC0033578Prostatic Neoplasms1CTD_human
HgeneRXRAC0040136Thyroid Neoplasm1CTD_human
HgeneRXRAC0149940Sciatic Neuropathy1CTD_human
HgeneRXRAC0345967Malignant mesothelioma1CTD_human
HgeneRXRAC1862939AMYOTROPHIC LATERAL SCLEROSIS 11CTD_human