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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: 25022

FusionGeneSummary for NTRK3_LOXL2

check button Fusion gene summary
Fusion gene informationFusion gene name: NTRK3_LOXL2
Fusion gene ID: 25022
HgeneTgene
Gene symbol

NTRK3

LOXL2

Gene ID

4916

4017

Gene nameneurotrophic receptor tyrosine kinase 3lysyl oxidase like 2
SynonymsGP145-TrkC|TRKC|gp145(trkC)LOR|LOR2|WS9-14
Cytomap

15q25.3

8p21.3

Type of geneprotein-codingprotein-coding
DescriptionNT-3 growth factor receptorETS related protein-neurotrophic receptor tyrosine kinase fusion proteinETV6-NTRK3 fusionneurotrophic tyrosine kinase, receptor, type 3tyrosine kinase receptor Clysyl oxidase homolog 2lysyl oxidase related 2lysyl oxidase-like 2 delta e13lysyl oxidase-like 2 proteinlysyl oxidase-like protein 2lysyl oxidase-related protein 2lysyl oxidase-related protein WS9-14
Modification date2018052320180523
UniProtAcc

Q16288

Q9Y4K0

Ensembl transtripts involved in fusion geneENST00000394480, ENST00000557856, 
ENST00000357724, ENST00000355254, 
ENST00000360948, ENST00000542733, 
ENST00000558676, ENST00000317501, 
ENST00000558306, ENST00000540489, 
ENST00000389131, ENST00000518472, 
Fusion gene scores* DoF score7 X 7 X 3=1474 X 3 X 4=48
# samples 114
** MAII scorelog2(11/147*10)=-0.418312631311705
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NTRK3 [Title/Abstract] AND LOXL2 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotationTumor suppressor gene involved fusion gene, retained protein feature but frameshift.
DDR (DNA damage repair) gene involved fusion gene, in-frame but not retained their domain.
* 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
HgeneNTRK3

GO:0000187

activation of MAPK activity

23027130

HgeneNTRK3

GO:0001933

negative regulation of protein phosphorylation

23027130

HgeneNTRK3

GO:0007169

transmembrane receptor protein tyrosine kinase signaling pathway

23027130

HgeneNTRK3

GO:0008284

positive regulation of cell proliferation

23027130

HgeneNTRK3

GO:0010628

positive regulation of gene expression

23027130

HgeneNTRK3

GO:0030335

positive regulation of cell migration

23027130

HgeneNTRK3

GO:0032148

activation of protein kinase B activity

23027130

HgeneNTRK3

GO:0033138

positive regulation of peptidyl-serine phosphorylation

23027130

HgeneNTRK3

GO:0050927

positive regulation of positive chemotaxis

23027130

HgeneNTRK3

GO:0090630

activation of GTPase activity

23027130

HgeneNTRK3

GO:2000251

positive regulation of actin cytoskeleton reorganization

23027130

TgeneLOXL2

GO:0000122

negative regulation of transcription by RNA polymerase II

25959397

TgeneLOXL2

GO:0001837

epithelial to mesenchymal transition

16096638

TgeneLOXL2

GO:0006464

cellular protein modification process

23319596

TgeneLOXL2

GO:0018057

peptidyl-lysine oxidation

25959397|27735137

TgeneLOXL2

GO:0045892

negative regulation of transcription, DNA-templated

16096638

TgeneLOXL2

GO:0046688

response to copper ion

23319596


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
TCGALDLGGTCGA-FG-6692-01ANTRK3chr15

88799137

-LOXL2chr8

23191136

-
* 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-shiftENST00000394480ENST00000389131NTRK3chr15

88799137

-LOXL2chr8

23191136

-
5CDS-intronENST00000394480ENST00000518472NTRK3chr15

88799137

-LOXL2chr8

23191136

-
Frame-shiftENST00000557856ENST00000389131NTRK3chr15

88799137

-LOXL2chr8

23191136

-
5CDS-intronENST00000557856ENST00000518472NTRK3chr15

88799137

-LOXL2chr8

23191136

-
Frame-shiftENST00000357724ENST00000389131NTRK3chr15

88799137

-LOXL2chr8

23191136

-
5CDS-intronENST00000357724ENST00000518472NTRK3chr15

88799137

-LOXL2chr8

23191136

-
Frame-shiftENST00000355254ENST00000389131NTRK3chr15

88799137

-LOXL2chr8

23191136

-
5CDS-intronENST00000355254ENST00000518472NTRK3chr15

88799137

-LOXL2chr8

23191136

-
Frame-shiftENST00000360948ENST00000389131NTRK3chr15

88799137

-LOXL2chr8

23191136

-
5CDS-intronENST00000360948ENST00000518472NTRK3chr15

88799137

-LOXL2chr8

23191136

-
intron-3CDSENST00000542733ENST00000389131NTRK3chr15

88799137

-LOXL2chr8

23191136

-
intron-intronENST00000542733ENST00000518472NTRK3chr15

88799137

-LOXL2chr8

23191136

-
Frame-shiftENST00000558676ENST00000389131NTRK3chr15

88799137

-LOXL2chr8

23191136

-
5CDS-intronENST00000558676ENST00000518472NTRK3chr15

88799137

-LOXL2chr8

23191136

-
Frame-shiftENST00000317501ENST00000389131NTRK3chr15

88799137

-LOXL2chr8

23191136

-
5CDS-intronENST00000317501ENST00000518472NTRK3chr15

88799137

-LOXL2chr8

23191136

-
intron-3CDSENST00000558306ENST00000389131NTRK3chr15

88799137

-LOXL2chr8

23191136

-
intron-intronENST00000558306ENST00000518472NTRK3chr15

88799137

-LOXL2chr8

23191136

-
Frame-shiftENST00000540489ENST00000389131NTRK3chr15

88799137

-LOXL2chr8

23191136

-
5CDS-intronENST00000540489ENST00000518472NTRK3chr15

88799137

-LOXL2chr8

23191136

-

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FusionProtFeatures for NTRK3_LOXL2


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
NTRK3

Q16288

LOXL2

Q9Y4K0

Receptor tyrosine kinase involved in nervous system andprobably heart development. Upon binding of its ligandNTF3/neurotrophin-3, NTRK3 autophosphorylates and activatesdifferent signaling pathways, including the phosphatidylinositol3-kinase/AKT and the MAPK pathways, that control cell survival anddifferentiation. {ECO:0000269|PubMed:25196463}. Mediates the post-translational oxidative deamination oflysine residues on target proteins leading to the formation ofdeaminated lysine (allysine) (PubMed:27735137). Acts as atranscription corepressor and specifically mediates deamination oftrimethylated 'Lys-4' of histone H3 (H3K4me3), a specific tag forepigenetic transcriptional activation (PubMed:27735137). Shows noactivity against histone H3 when it is trimethylated on 'Lys-9'(H3K9me3) or 'Lys-27' (H3K27me3) or when 'Lys-4' is monomethylated(H3K4me1) or dimethylated (H3K4me2) (PubMed:27735137). Alsomediates deamination of methylated TAF10, a member of thetranscription factor IID (TFIID) complex, which induces release ofTAF10 from promoters, leading to inhibition of TFIID-dependenttranscription (PubMed:25959397). LOXL2-mediated deamination ofTAF10 results in transcriptional repression of genes required forembryonic stem cell pluripotency including POU5F1/OCT4, NANOG,KLF4 and SOX2 (By similarity). Involved in epithelial tomesenchymal transition (EMT) via interaction with SNAI1 andparticipates in repression of E-cadherin CDH1, probably bymediating deamination of histone H3 (PubMed:16096638,PubMed:27735137, PubMed:24414204). During EMT, involved with SNAI1in negatively regulating pericentromeric heterochromatintranscription (PubMed:24239292). SNAI1 recruits LOXL2 topericentromeric regions to oxidize histone H3 and represstranscription which leads to release of heterochromatin componentCBX5/HP1A, enabling chromatin reorganization and acquisition ofmesenchymal traits (PubMed:24239292). Interacts with theendoplasmic reticulum protein HSPA5 which activates the IRE1-XBP1pathway of the unfolded protein response, leading to expression ofseveral transcription factors involved in EMT and subsequent EMTinduction (PubMed:28332555). Involved in E-cadherin repressionfollowing hypoxia, a hallmark of EMT believed to amplify tumoraggressiveness, suggesting that it may play a role in tumorprogression (PubMed:20026874). When secreted into theextracellular matrix, promotes cross-linking of extracellularmatrix proteins by mediating oxidative deamination of peptidyllysine residues in precursors to fibrous collagen and elastin(PubMed:20306300). Acts as a regulator of sprouting angiogenesis,probably via collagen IV scaffolding (PubMed:21835952). Acts as aregulator of chondrocyte differentiation, probably by regulatingexpression of factors that control chondrocyte differentiation (Bysimilarity). {ECO:0000250|UniProtKB:P58022,ECO:0000269|PubMed:16096638, ECO:0000269|PubMed:20026874,ECO:0000269|PubMed:20306300, ECO:0000269|PubMed:21835952,ECO:0000269|PubMed:24239292, ECO:0000269|PubMed:24414204,ECO:0000269|PubMed:25959397, ECO:0000269|PubMed:27735137}.

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 NTRK3_LOXL2


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 NTRK3_LOXL2


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
NTRK3NTF3, FRS2, SHC1, PLCG1, SQSTM1, PTPN1, APP, HSP90AA1, IRAK3, TNK2, NTRK1, SH3BP4, PTPRS, MYADM, C1GALT1, GNB2, C6orf120, MTOR, LGALS1, PTCD2, TMEM11, PAG1, EFR3A, TBC1D24, GNB4, TMEM192, INTS7, DENND4A, FAM171A2, KIAA0391, EPHA2, ATP7B, CXCR4, ACAD10, HRAS, EHD4, RPTOR, HEATR6, SLC39A11LOXL2PDIA3, MTA1, MTA2, RBBP4, RBBP7, SIN3A, HDAC1, EZH2, HIST1H3A, KLK11, TAZ, KLK5, IDS, PLAUR, TMEM25, IL12RB1, TINAGL1, LYZL2, RBM14-RBM4, OS9, DEFA1, WNT7A, PSG8, ADAMTS4, SCGB2A2, INSL5, LRP1, IK, DEFA5, FBXO7, 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 NTRK3_LOXL2


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

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RelatedDiseases for NTRK3_LOXL2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneNTRK3C0036341Schizophrenia3PSYGENET
HgeneNTRK3C0041696Unipolar Depression2PSYGENET
HgeneNTRK3C1269683Major Depressive Disorder2PSYGENET
HgeneNTRK3C0014175Endometriosis1CTD_human
HgeneNTRK3C0017638Glioma1CTD_human
HgeneNTRK3C0038220Status Epilepticus1CTD_human
HgeneNTRK3C0525045Mood Disorders1PSYGENET
TgeneLOXL2C1458155Mammary Neoplasms2CTD_human
TgeneLOXL2C0007621Neoplastic Cell Transformation1CTD_human
TgeneLOXL2C0019163Hepatitis B1CTD_human
TgeneLOXL2C0019196Hepatitis C1CTD_human
TgeneLOXL2C0019202Hepatolenticular Degeneration1CTD_human
TgeneLOXL2C0023892Biliary cirrhosis1CTD_human
TgeneLOXL2C0023893Liver Cirrhosis, Experimental1CTD_human
TgeneLOXL2C0027626Neoplasm Invasiveness1CTD_human
TgeneLOXL2C0279626Squamous cell carcinoma of esophagus1CTD_human