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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in RPSMAP, MSBB, and Mayo

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Open reading frame (ORF) annotation in the exon skipping event

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Exon skipping events in the canonical protein sequence

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3'-UTR located exon skipping events lost miRNA binding sites

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SNVs in the skipped exons with depth of coverage

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AD stage-associated exon skipping events

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Correlation with RNA binding proteins (RBPs)

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Related drugs with this gene

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Related diseases with this gene

Gene summary for NTRK3

check button Gene summary
Gene informationGene symbol

NTRK3

Gene ID

4916

Gene nameneurotrophic receptor tyrosine kinase 3
SynonymsGP145-TrkC|TRKC|gp145(trkC)
Cytomap

15q25.3

Type of geneprotein-coding
DescriptionNT-3 growth factor receptorETS related protein-neurotrophic receptor tyrosine kinase fusion proteinETV6-NTRK3 fusionneurotrophic tyrosine kinase, receptor, type 3tyrosine kinase receptor C
Modification date20200313
UniProtAcc

A0A087WX31,

A0A0D9SFP6,

B7Z7U4,

H0YM90,

O95192,

O95193,

Q16288,

Q96CY4,

R4GMR8,

R4GN40,

R4GNH5,

X5D2R1,

X5D7M5,

X5DNW6,

X5DP84,

Context

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
NTRK3

GO:0000187

activation of MAPK activity

23027130

NTRK3

GO:0001933

negative regulation of protein phosphorylation

23027130

NTRK3

GO:0007169

transmembrane receptor protein tyrosine kinase signaling pathway

23027130

NTRK3

GO:0008284

positive regulation of cell proliferation

23027130

NTRK3

GO:0010628

positive regulation of gene expression

23027130

NTRK3

GO:0030335

positive regulation of cell migration

23027130

NTRK3

GO:0032148

activation of protein kinase B activity

23027130

NTRK3

GO:0033138

positive regulation of peptidyl-serine phosphorylation

23027130

NTRK3

GO:0050927

positive regulation of positive chemotaxis

23027130

NTRK3

GO:0090630

activation of GTPase activity

23027130

NTRK3

GO:2000251

positive regulation of actin cytoskeleton reorganization

23027130


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Gene structures and expression levels for NTRK3

check buttonSkipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

ENSG00000140538
check button Differentially expressed gene analysis across multiple brain tissues between AD and control.
Tissue typeDEG directionBase mean exp.log2FC(AD/control)P-valueAdj. p-value

check button Differentially expressed isoform analysis across multiple brain tissues between AD and control.
gencode gene structure
Tissue typeDEG directionENSTTranscript info.Base mean exp.log2FC(AD/control)P-valueAdjc. p-value
CBDOWNENST00000560201.1NTRK3-218:lncRNA:NTRK31.107493e+01-1.562181e+008.245094e-128.351086e-10
TCDOWNENST00000560201.1NTRK3-218:lncRNA:NTRK31.340072e+01-1.079936e+001.300579e-064.954374e-05
TCUPENST00000569588.1NTRK3-AS1-201:lncRNA:NTRK33.954766e+008.684418e-014.729090e-061.425942e-04

check button Landscape of isoform expressions across multiple brain tissues between AD and control.
gencode gene structure

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for NTRK3

check button Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).
boxplot

check button All exon skipping events in AD cohorts.
Exon skip IDchrExons involved in exon skippingSkipped exon
exon_skip_139335chr1587979345:87979463:87981226:87981360:88032857:8803304587981226:87981360
exon_skip_153807chr1587880270:87880428:87885694:87885735:87929191:8792943487885694:87885735
exon_skip_177210chr1587981226:87981360:88032857:88033045:88126271:8812636188032857:88033045
exon_skip_193232chr1588127162:88127226:88128711:88128734:88135101:8813539788128711:88128734
exon_skip_206433chr1587885694:87885735:87908489:87908563:87929191:8792943487908489:87908563
exon_skip_233987chr1587933012:87933184:87940623:87940753:88032857:8803304587940623:87940753
exon_skip_246972chr1588127162:88127226:88128711:88128734:88135101:8813521888128711:88128734
exon_skip_248584chr1587880270:87880428:87885694:87885735:87908489:8790856387885694:87885735
exon_skip_288076chr1587940623:87940753:88032857:88033045:88126271:8812636188032857:88033045
exon_skip_296459chr1588032857:88033045:88126271:88126373:88127162:8812719188126271:88126373

check button Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.
Exon skipping informationTissue typeAvg(PSIs) in ADAvg(PSIs) in controlDifference (PSI)Adj. p-value


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Open reading frame (ORF) annotation in the exon skipping event for NTRK3

check button Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000003609488794062387940753Frame-shift
ENST000006297658794062387940753Frame-shift
ENST000003609488812627188126373Frame-shift
ENST000006297658812627188126373Frame-shift
ENST000003609488788569487885735In-frame
ENST000006297658788569487885735In-frame
ENST000003609488803285788033045In-frame
ENST000006297658803285788033045In-frame
ENST000003609488812871188128734In-frame
ENST000006297658812871188128734In-frame

check button Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000003609488788569487885735In-frame
ENST000006297658788569487885735In-frame
ENST000003609488803285788033045In-frame
ENST000006297658803285788033045In-frame
ENST000003609488812871188128734In-frame
ENST000006297658812871188128734In-frame

check button Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000003609488794062387940753Frame-shift
ENST000006297658794062387940753Frame-shift
ENST000003609488788569487885735In-frame
ENST000006297658788569487885735In-frame
ENST000003609488803285788033045In-frame
ENST000006297658803285788033045In-frame
ENST000003609488812871188128734In-frame
ENST000006297658812871188128734In-frame

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Infer the effects of exon skipping event on protein functional features for NTRK3

p-ENSG00000140538_img4.png
boxplot

check button Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000003609483021839880328578803304517031890465528
ENST000006297652731839880328578803304514131600465528
ENST000003609483021839878856948788573524402480711724
ENST000006297652731839878856948788573521502190711724

check button Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000003609483021839880328578803304517031890465528
ENST000006297652731839880328578803304514131600465528
ENST000003609483021839878856948788573524402480711724
ENST000006297652731839878856948788573521502190711724

check button Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000003609483021839880328578803304517031890465528
ENST000006297652731839880328578803304514131600465528
ENST000003609483021839878856948788573524402480711724
ENST000006297652731839878856948788573521502190711724

check button Lost protein functional features of individual exon skipping events in ROSMAP.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q1628846552832839ChainID=PRO_0000016731;Note=NT-3 growth factor receptor
Q1628846552832839ChainID=PRO_0000016731;Note=NT-3 growth factor receptor
Q16288465528493493Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q6VNS1
Q16288465528493493Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q6VNS1
Q16288465528516516Modified residueNote=Phosphotyrosine%3B by autocatalysis;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25196463;Dbxref=PMID:25196463
Q16288465528516516Modified residueNote=Phosphotyrosine%3B by autocatalysis;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25196463;Dbxref=PMID:25196463
Q16288465528516516SiteNote=Interaction with SHC1;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q16288465528516516SiteNote=Interaction with SHC1;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q16288465528454839Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q16288465528454839Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q16288711724613839Alternative sequenceID=VSP_002926;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:7823156;Dbxref=PMID:7823156
Q16288711724613839Alternative sequenceID=VSP_002926;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:7823156;Dbxref=PMID:7823156
Q16288711724712725Alternative sequenceID=VSP_002927;Note=In isoform 3 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:7806211,ECO:0000303|PubMed:7823156;Dbxref=PMID:14702039,PMID:7806211,PMID:7823156
Q16288711724712725Alternative sequenceID=VSP_002927;Note=In isoform 3 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:7806211,ECO:0000303|PubMed:7823156;Dbxref=PMID:14702039,PMID:7806211,PMID:7823156
Q1628871172432839ChainID=PRO_0000016731;Note=NT-3 growth factor receptor
Q1628871172432839ChainID=PRO_0000016731;Note=NT-3 growth factor receptor
Q16288711724538839DomainNote=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159
Q16288711724538839DomainNote=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159
Q16288711724454839Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q16288711724454839Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255

check button Lost protein functional features of individual exon skipping events in MSBB.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q1628846552832839ChainID=PRO_0000016731;Note=NT-3 growth factor receptor
Q1628846552832839ChainID=PRO_0000016731;Note=NT-3 growth factor receptor
Q16288465528493493Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q6VNS1
Q16288465528493493Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q6VNS1
Q16288465528516516Modified residueNote=Phosphotyrosine%3B by autocatalysis;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25196463;Dbxref=PMID:25196463
Q16288465528516516Modified residueNote=Phosphotyrosine%3B by autocatalysis;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25196463;Dbxref=PMID:25196463
Q16288465528516516SiteNote=Interaction with SHC1;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q16288465528516516SiteNote=Interaction with SHC1;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q16288465528454839Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q16288465528454839Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q16288711724613839Alternative sequenceID=VSP_002926;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:7823156;Dbxref=PMID:7823156
Q16288711724613839Alternative sequenceID=VSP_002926;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:7823156;Dbxref=PMID:7823156
Q16288711724712725Alternative sequenceID=VSP_002927;Note=In isoform 3 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:7806211,ECO:0000303|PubMed:7823156;Dbxref=PMID:14702039,PMID:7806211,PMID:7823156
Q16288711724712725Alternative sequenceID=VSP_002927;Note=In isoform 3 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:7806211,ECO:0000303|PubMed:7823156;Dbxref=PMID:14702039,PMID:7806211,PMID:7823156
Q1628871172432839ChainID=PRO_0000016731;Note=NT-3 growth factor receptor
Q1628871172432839ChainID=PRO_0000016731;Note=NT-3 growth factor receptor
Q16288711724538839DomainNote=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159
Q16288711724538839DomainNote=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159
Q16288711724454839Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q16288711724454839Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255

check button Lost protein functional features of individual exon skipping events in Mayo.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q1628846552832839ChainID=PRO_0000016731;Note=NT-3 growth factor receptor
Q1628846552832839ChainID=PRO_0000016731;Note=NT-3 growth factor receptor
Q16288465528493493Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q6VNS1
Q16288465528493493Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q6VNS1
Q16288465528516516Modified residueNote=Phosphotyrosine%3B by autocatalysis;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25196463;Dbxref=PMID:25196463
Q16288465528516516Modified residueNote=Phosphotyrosine%3B by autocatalysis;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25196463;Dbxref=PMID:25196463
Q16288465528516516SiteNote=Interaction with SHC1;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q16288465528516516SiteNote=Interaction with SHC1;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q16288465528454839Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q16288465528454839Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q16288711724613839Alternative sequenceID=VSP_002926;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:7823156;Dbxref=PMID:7823156
Q16288711724613839Alternative sequenceID=VSP_002926;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:7823156;Dbxref=PMID:7823156
Q16288711724712725Alternative sequenceID=VSP_002927;Note=In isoform 3 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:7806211,ECO:0000303|PubMed:7823156;Dbxref=PMID:14702039,PMID:7806211,PMID:7823156
Q16288711724712725Alternative sequenceID=VSP_002927;Note=In isoform 3 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:7806211,ECO:0000303|PubMed:7823156;Dbxref=PMID:14702039,PMID:7806211,PMID:7823156
Q1628871172432839ChainID=PRO_0000016731;Note=NT-3 growth factor receptor
Q1628871172432839ChainID=PRO_0000016731;Note=NT-3 growth factor receptor
Q16288711724538839DomainNote=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159
Q16288711724538839DomainNote=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159
Q16288711724454839Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q16288711724454839Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255


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3'-UTR located exon skipping events that lost miRNA binding sites in NTRK3

check button 3'-UTR exon skipping evnets lost miRNA binding.
Tissue typeENSTExon skip startExon skip endmicroRNABinding site by TargetScanBinding type by TargetScanBdinding site by miRandaScore of miRandaEnergy by miRanda

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SNVs in the skipped exons for NTRK3

check button - Differential PSIs between mutated versus non-mutated samples.

check button - Depth of Coverage in the skipped exon of the mutated samples.

check button - Sashimi plot in the skipped exon of the mutated samples.

check button - Non-synonymous mutations located in the skipped exons.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange

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AD stage-associated exon skippint events for NTRK3

check button Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).
AD stage infoCohortTissueSE idCoefficient P-valueChromosomeStrandE1 startE1 endSkipped startSkipped endE2 startE2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NTRK3

check button sQTL information located at the skipped exons.
Tissue typeExon skip IDSNP idLocationP-valueFDR
HCCexon_skip_206433rs1435403chr15:878938387.160231e-044.501352e-02

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Correlation with RNA binding proteins (RBPs) for NTRK3

check button Correlated RBP and related information.
Tissue typeRBP nameExon skip IDCorrelation coeifficientP-value
IFGHNRNPDLexon_skip_139335-5.859062e-014.166212e-03
IFGHNRNPLexon_skip_139335-6.611966e-018.066312e-04

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RelatedDrugs for NTRK3

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
UniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
Q16288approved|investigationalDB12010Fostamatinibsmall moleculeQ16288

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RelatedDiseases for NTRK3

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource