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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:NTRK1-TPM3 (FusionGDB2 ID:60694)

Fusion Gene Summary for NTRK1-TPM3

check button Fusion gene summary
Fusion gene informationFusion gene name: NTRK1-TPM3
Fusion gene ID: 60694
HgeneTgene
Gene symbol

NTRK1

TPM3

Gene ID

4914

7170

Gene nameneurotrophic receptor tyrosine kinase 1tropomyosin 3
SynonymsMTC|TRK|TRK1|TRKA|Trk-A|p140-TrkACAPM1|CFTD|HEL-189|HEL-S-82p|NEM1|OK/SW-cl.5|TM-5|TM3|TM30|TM30nm|TM5|TPM3nu|TPMsk3|TRK|hscp30
Cytomap

1q23.1

1q21.3

Type of geneprotein-codingprotein-coding
Descriptionhigh affinity nerve growth factor receptorOncogene TRKTRK1-transforming tyrosine kinase proteingp140trkneurotrophic tyrosine kinase, receptor, type 1tropomyosin-related kinase Atyrosine kinase receptor Atropomyosin alpha-3 chainalpha-tropomyosin, slow skeletalcytoskeletal tropomyosin TM30epididymis luminal protein 189epididymis secretory sperm binding protein Li 82pheat-stable cytoskeletal protein 30 kDatropomyosin 3 nutropomyosin gammatropomyosi
Modification date2020031320200328
UniProtAcc.

P06753

Ensembl transtripts involved in fusion geneENST00000358660, ENST00000368196, 
ENST00000392302, ENST00000524377, 
ENST00000531606, 		ENST00000271850, 
ENST00000302206, ENST00000323144, 
ENST00000328159, ENST00000330188, 
ENST00000341372, ENST00000341485, 
ENST00000368530, ENST00000368531, 
ENST00000368533, ENST00000469717, 
Fusion gene scores* DoF score3 X 3 X 2=189 X 10 X 5=450
# samples 212
** MAII scorelog2(2/18*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(12/450*10)=-1.90689059560852
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NTRK1 [Title/Abstract] AND TPM3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTPM3(154142876)-NTRK1(156844363), # samples:4
Anticipated loss of major functional domain due to fusion event.TPM3-NTRK1 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
TPM3-NTRK1 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
TPM3-NTRK1 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
TPM3-NTRK1 seems lost the major protein functional domain in Tgene partner, which is a kinase due to the frame-shifted ORF.
* 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
HgeneNTRK1

GO:0006468

protein phosphorylation

15488758

HgeneNTRK1

GO:0008285

negative regulation of cell proliferation

15488758

HgeneNTRK1

GO:0010976

positive regulation of neuron projection development

15488758

HgeneNTRK1

GO:0018108

peptidyl-tyrosine phosphorylation

2927393

HgeneNTRK1

GO:0043547

positive regulation of GTPase activity

15488758

HgeneNTRK1

GO:0046579

positive regulation of Ras protein signal transduction

15488758

HgeneNTRK1

GO:0046777

protein autophosphorylation

15488758

HgeneNTRK1

GO:0048011

neurotrophin TRK receptor signaling pathway

15488758

HgeneNTRK1

GO:0051092

positive regulation of NF-kappaB transcription factor activity

15488758

HgeneNTRK1

GO:0070374

positive regulation of ERK1 and ERK2 cascade

15488758

HgeneNTRK1

GO:1904646

cellular response to amyloid-beta

11927634


check buttonFusion gene breakpoints across NTRK1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across TPM3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerKB3..NTRK1chr1

156843751

+TPM3chr1

154140416

-
ChimerKB3..NTRK1chr1

156844192

+TPM3chr1

154131524

-


Top

Fusion Gene ORF analysis for NTRK1-TPM3

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-intronENST00000358660ENST00000271850NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000358660ENST00000302206NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000358660ENST00000323144NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000358660ENST00000328159NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000358660ENST00000330188NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000358660ENST00000341372NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000358660ENST00000341485NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000358660ENST00000368530NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000358660ENST00000368531NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000358660ENST00000368533NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000358660ENST00000469717NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000368196ENST00000271850NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000368196ENST00000302206NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000368196ENST00000323144NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000368196ENST00000328159NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000368196ENST00000330188NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000368196ENST00000341372NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000368196ENST00000341485NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000368196ENST00000368530NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000368196ENST00000368531NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000368196ENST00000368533NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000368196ENST00000469717NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000392302ENST00000271850NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000392302ENST00000302206NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000392302ENST00000323144NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000392302ENST00000328159NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000392302ENST00000330188NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000392302ENST00000341372NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000392302ENST00000341485NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000392302ENST00000368530NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000392302ENST00000368531NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000392302ENST00000368533NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000392302ENST00000469717NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000524377ENST00000271850NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000524377ENST00000271850NTRK1chr1

156844192

+TPM3chr1

154131524

-
5CDS-intronENST00000524377ENST00000302206NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000524377ENST00000302206NTRK1chr1

156844192

+TPM3chr1

154131524

-
5CDS-intronENST00000524377ENST00000323144NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000524377ENST00000323144NTRK1chr1

156844192

+TPM3chr1

154131524

-
5CDS-intronENST00000524377ENST00000328159NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000524377ENST00000328159NTRK1chr1

156844192

+TPM3chr1

154131524

-
5CDS-intronENST00000524377ENST00000330188NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000524377ENST00000330188NTRK1chr1

156844192

+TPM3chr1

154131524

-
5CDS-intronENST00000524377ENST00000341372NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000524377ENST00000341372NTRK1chr1

156844192

+TPM3chr1

154131524

-
5CDS-intronENST00000524377ENST00000341485NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000524377ENST00000341485NTRK1chr1

156844192

+TPM3chr1

154131524

-
5CDS-intronENST00000524377ENST00000368530NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000524377ENST00000368530NTRK1chr1

156844192

+TPM3chr1

154131524

-
5CDS-intronENST00000524377ENST00000368531NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000524377ENST00000368531NTRK1chr1

156844192

+TPM3chr1

154131524

-
5CDS-intronENST00000524377ENST00000368533NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000524377ENST00000368533NTRK1chr1

156844192

+TPM3chr1

154131524

-
5CDS-intronENST00000524377ENST00000469717NTRK1chr1

156843751

+TPM3chr1

154140416

-
5CDS-intronENST00000524377ENST00000469717NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000358660ENST00000271850NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000358660ENST00000302206NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000358660ENST00000323144NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000358660ENST00000328159NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000358660ENST00000330188NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000358660ENST00000341372NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000358660ENST00000341485NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000358660ENST00000368530NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000358660ENST00000368531NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000358660ENST00000368533NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000358660ENST00000469717NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000368196ENST00000271850NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000368196ENST00000302206NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000368196ENST00000323144NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000368196ENST00000328159NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000368196ENST00000330188NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000368196ENST00000341372NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000368196ENST00000341485NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000368196ENST00000368530NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000368196ENST00000368531NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000368196ENST00000368533NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000368196ENST00000469717NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000392302ENST00000271850NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000392302ENST00000302206NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000392302ENST00000323144NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000392302ENST00000328159NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000392302ENST00000330188NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000392302ENST00000341372NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000392302ENST00000341485NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000392302ENST00000368530NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000392302ENST00000368531NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000392302ENST00000368533NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000392302ENST00000469717NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000531606ENST00000271850NTRK1chr1

156843751

+TPM3chr1

154140416

-
intron-intronENST00000531606ENST00000271850NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000531606ENST00000302206NTRK1chr1

156843751

+TPM3chr1

154140416

-
intron-intronENST00000531606ENST00000302206NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000531606ENST00000323144NTRK1chr1

156843751

+TPM3chr1

154140416

-
intron-intronENST00000531606ENST00000323144NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000531606ENST00000328159NTRK1chr1

156843751

+TPM3chr1

154140416

-
intron-intronENST00000531606ENST00000328159NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000531606ENST00000330188NTRK1chr1

156843751

+TPM3chr1

154140416

-
intron-intronENST00000531606ENST00000330188NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000531606ENST00000341372NTRK1chr1

156843751

+TPM3chr1

154140416

-
intron-intronENST00000531606ENST00000341372NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000531606ENST00000341485NTRK1chr1

156843751

+TPM3chr1

154140416

-
intron-intronENST00000531606ENST00000341485NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000531606ENST00000368530NTRK1chr1

156843751

+TPM3chr1

154140416

-
intron-intronENST00000531606ENST00000368530NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000531606ENST00000368531NTRK1chr1

156843751

+TPM3chr1

154140416

-
intron-intronENST00000531606ENST00000368531NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000531606ENST00000368533NTRK1chr1

156843751

+TPM3chr1

154140416

-
intron-intronENST00000531606ENST00000368533NTRK1chr1

156844192

+TPM3chr1

154131524

-
intron-intronENST00000531606ENST00000469717NTRK1chr1

156843751

+TPM3chr1

154140416

-
intron-intronENST00000531606ENST00000469717NTRK1chr1

156844192

+TPM3chr1

154131524

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

Top

Fusion Genomic Features for NTRK1-TPM3


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

Top

Fusion Protein Features for NTRK1-TPM3


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:154142876/:156844363)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.TPM3

P06753

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Binds to actin filaments in muscle and non-muscle cells. Plays a central role, in association with the troponin complex, in the calcium dependent regulation of vertebrate striated muscle contraction. Smooth muscle contraction is regulated by interaction with caldesmon. In non-muscle cells is implicated in stabilizing cytoskeleton actin filaments. {ECO:0000250|UniProtKB:P09493}.

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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Fusion Gene Sequence for NTRK1-TPM3


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for NTRK1-TPM3


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


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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Related Drugs for NTRK1-TPM3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for NTRK1-TPM3


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