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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: 38950

FusionGeneSummary for TNPO3_RCAN1

check button Fusion gene summary
Fusion gene informationFusion gene name: TNPO3_RCAN1
Fusion gene ID: 38950
HgeneTgene
Gene symbol

TNPO3

RCAN1

Gene ID

23534

1827

Gene nametransportin 3regulator of calcineurin 1
SynonymsIPO12|LGMD1F|MTR10A|TRN-SR|TRN-SR2|TRNSRADAPT78|CSP1|DSC1|DSCR1|MCIP1|RCN1
Cytomap

7q32.1

21q22.12

Type of geneprotein-codingprotein-coding
Descriptiontransportin-3imp12importin 12limb girdle muscular dystrophy 1F (autosomal dominant)transportin-SRcalcipressin-1Down syndrome candidate region 1Down syndrome critical region gene 1calcium and oxidant-inducible mRNAmodulatory calcineurin-interacting protein 1myocyte-enriched calcineurin-interacting protein 1near DSCR proline-rich protein
Modification date2018052320180523
UniProtAcc

Q9Y5L0

P53805

Ensembl transtripts involved in fusion geneENST00000393245, ENST00000265388, 
ENST00000482320, ENST00000471234, 
ENST00000471166, 
ENST00000487990, 
ENST00000399272, ENST00000489903, 
ENST00000313806, ENST00000443408, 
ENST00000482533, ENST00000481448, 
ENST00000381132, ENST00000381135, 
ENST00000492600, 
Fusion gene scores* DoF score5 X 4 X 4=805 X 3 X 4=60
# samples 56
** MAII scorelog2(5/80*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(6/60*10)=0
Context

PubMed: TNPO3 [Title/Abstract] AND RCAN1 [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

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-AR-A1AI-01ATNPO3chr7

128614922

-RCAN1chr21

35896008

-
* 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-5UTRENST00000393245ENST00000487990TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000393245ENST00000399272TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000393245ENST00000489903TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000393245ENST00000313806TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000393245ENST00000443408TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000393245ENST00000482533TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000393245ENST00000481448TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000393245ENST00000381132TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000393245ENST00000381135TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000393245ENST00000492600TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000265388ENST00000487990TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000265388ENST00000399272TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000265388ENST00000489903TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000265388ENST00000313806TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000265388ENST00000443408TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000265388ENST00000482533TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000265388ENST00000481448TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000265388ENST00000381132TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000265388ENST00000381135TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000265388ENST00000492600TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000482320ENST00000487990TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000482320ENST00000399272TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000482320ENST00000489903TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000482320ENST00000313806TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000482320ENST00000443408TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000482320ENST00000482533TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000482320ENST00000481448TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000482320ENST00000381132TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000482320ENST00000381135TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000482320ENST00000492600TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471234ENST00000487990TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471234ENST00000399272TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471234ENST00000489903TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471234ENST00000313806TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471234ENST00000443408TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471234ENST00000482533TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471234ENST00000481448TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471234ENST00000381132TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471234ENST00000381135TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471234ENST00000492600TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471166ENST00000487990TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471166ENST00000399272TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471166ENST00000489903TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471166ENST00000313806TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471166ENST00000443408TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471166ENST00000482533TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471166ENST00000481448TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471166ENST00000381132TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471166ENST00000381135TNPO3chr7

128614922

-RCAN1chr21

35896008

-
5CDS-5UTRENST00000471166ENST00000492600TNPO3chr7

128614922

-RCAN1chr21

35896008

-

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FusionProtFeatures for TNPO3_RCAN1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
TNPO3

Q9Y5L0

RCAN1

P53805

Seems to function in nuclear protein import as nucleartransport receptor. In vitro, mediates the nuclear import ofsplicing factor SR proteins RBM4, SFRS1 and SFRS2, by recognizingphosphorylated RS domains. {ECO:0000269|PubMed:10366588,ECO:0000269|PubMed:10713112, ECO:0000269|PubMed:11517331,ECO:0000269|PubMed:12628928}.

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 TNPO3_RCAN1


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 TNPO3_RCAN1


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
TNPO3C20orf24, PHLDA3, BRF2, USP19, ELAVL1, CHMP3, TNPO1, UBE3A, CA9, VCP, SMURF2, CFTR, SOX2, EGFR, CLK3, CLK2, ACTR3, ARPC2, FEN1, HNRNPH1, IPO9, PFDN6, PPP2CA, PPP3CA, ALDOA, ELAC2, PPP2R1A, TTLL12, NXF1, COMTD1, STX5, RSRP1, CD274, TMEM171, VSIG2, P2RY12, LUC7L, LYPD3, RP2, MICA, P2RX4, PTGER3, SCN2B, SCARA3, UNK, COL4A2, NTRK1, JAK3, RAD18, AK7, DUSP4, CD70, VIPR2, SIGLECL1, VASN, TMEM206, FZD10, HTR2C, ST6GAL1, ATP2B2, VSIG1, TNFRSF1A, P2RX5, BCAM, OPRM1, FCGRT, PTPRA, PTPRE, PTPRN, STOM, TRIM25RCAN1PPP3CA, STAT2, TOLLIP, IRAK1, TRAF6, HSP90AA1, BTRC, FBXW4, FBXW11, APP, FAM122A, PPP3CC, USP22, PPP3CB, GSK3A, PPP3R1, C6orf211, SRBD1, CST2, CST5, AMY1C, GSK3B, ZG16B, IGHA1, CLEC3A, 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 TNPO3_RCAN1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneRCAN1P53805DB00975DipyridamoleCalcipressin-1small moleculeapproved

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RelatedDiseases for TNPO3_RCAN1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTNPO3C1842062MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 1F1ORPHANET;UNIPROT
TgeneRCAN1C0003873Rheumatoid Arthritis1CTD_human
TgeneRCAN1C0013080Down Syndrome1CTD_human
TgeneRCAN1C0018798Congenital Heart Defects1CTD_human
TgeneRCAN1C0020179Huntington Disease1CTD_human
TgeneRCAN1C0376634Craniofacial Abnormalities1CTD_human