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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for NTRK3 |
 Gene summary |
| Gene information | Gene symbol | NTRK3 | Gene ID | 4916 |
| Gene name | neurotrophic receptor tyrosine kinase 3 | |
| Synonyms | GP145-TrkC|TRKC|gp145(trkC) | |
| Cytomap | 15q25.3 | |
| Type of gene | protein-coding | |
| Description | NT-3 growth factor receptorETS related protein-neurotrophic receptor tyrosine kinase fusion proteinETV6-NTRK3 fusionneurotrophic tyrosine kinase, receptor, type 3tyrosine kinase receptor C | |
| Modification date | 20180523 | |
| UniProtAcc | Q16288 | |
| Context | PubMed: NTRK3 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed 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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Exon skipping events across known transcript of Ensembl for NTRK3 from UCSC genome browser |
| Skipped exons in TCGA and GTEx 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. |
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Gene isoform structures and expression levels for NTRK3 |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for NTRK3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_130464 | 15 | 88423500:88423659:88428924:88428966:88472421:88472665 | 88428924:88428966 | ENSG00000140538.12 | ENST00000357724.2,ENST00000360948.2 |
| exon_skip_130465 | 15 | 88459503:88459791:88468800:88468895:88472421:88472665 | 88468800:88468895 | ENSG00000140538.12 | ENST00000558576.1 |
| exon_skip_130468 | 15 | 88483853:88483984:88576087:88576276:88669501:88669592 | 88576087:88576276 | ENSG00000140538.12 | ENST00000557856.1,ENST00000542733.2,ENST00000558676.1,ENST00000357724.2,ENST00000355254.2,ENST00000394480.2,ENST00000360948.2 |
| exon_skip_130470 | 15 | 88522581:88522694:88524456:88524591:88576087:88576115 | 88524456:88524591 | ENSG00000140538.12 | ENST00000317501.3,ENST00000540489.2 |
| exon_skip_130472 | 15 | 88524456:88524591:88576087:88576276:88669501:88669592 | 88576087:88576276 | ENSG00000140538.12 | ENST00000317501.3,ENST00000540489.2 |
| exon_skip_130473 | 15 | 88576087:88576276:88669501:88669604:88670392:88670422 | 88669501:88669604 | ENSG00000140538.12 | ENST00000557856.1,ENST00000317501.3,ENST00000540489.2,ENST00000542733.2,ENST00000558676.1,ENST00000357724.2,ENST00000355254.2,ENST00000394480.2,ENST00000360948.2 |
| exon_skip_130474 | 15 | 88670392:88670457:88671941:88671965:88678331:88678628 | 88671941:88671965 | ENSG00000140538.12 | ENST00000317501.3,ENST00000540489.2,ENST00000542733.2,ENST00000355254.2,ENST00000394480.2,ENST00000360948.2 |
| exon_skip_130476 | 15 | 88680691:88680792:88690565:88690634:88726648:88726720 | 88690565:88690634 | ENSG00000140538.12 | ENST00000557856.1,ENST00000317501.3,ENST00000540489.2,ENST00000542733.2,ENST00000558676.1,ENST00000357724.2,ENST00000559188.1,ENST00000355254.2,ENST00000394480.2,ENST00000360948.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for NTRK3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_130464 | 15 | 88423500:88423659:88428924:88428966:88472421:88472665 | 88428924:88428966 | ENSG00000140538.12 | ENST00000360948.2,ENST00000357724.2 |
| exon_skip_130465 | 15 | 88459503:88459791:88468800:88468895:88472421:88472665 | 88468800:88468895 | ENSG00000140538.12 | ENST00000558576.1 |
| exon_skip_130468 | 15 | 88483853:88483984:88576087:88576276:88669501:88669592 | 88576087:88576276 | ENSG00000140538.12 | ENST00000394480.2,ENST00000557856.1,ENST00000360948.2,ENST00000357724.2,ENST00000355254.2,ENST00000542733.2,ENST00000558676.1 |
| exon_skip_130470 | 15 | 88522581:88522694:88524456:88524591:88576087:88576115 | 88524456:88524591 | ENSG00000140538.12 | ENST00000317501.3,ENST00000540489.2 |
| exon_skip_130472 | 15 | 88524456:88524591:88576087:88576276:88669501:88669592 | 88576087:88576276 | ENSG00000140538.12 | ENST00000317501.3,ENST00000540489.2 |
| exon_skip_130473 | 15 | 88576087:88576276:88669501:88669604:88670392:88670422 | 88669501:88669604 | ENSG00000140538.12 | ENST00000394480.2,ENST00000557856.1,ENST00000360948.2,ENST00000357724.2,ENST00000355254.2,ENST00000542733.2,ENST00000558676.1,ENST00000317501.3,ENST00000540489.2 |
| exon_skip_130474 | 15 | 88670392:88670457:88671941:88671965:88678331:88678628 | 88671941:88671965 | ENSG00000140538.12 | ENST00000394480.2,ENST00000360948.2,ENST00000355254.2,ENST00000542733.2,ENST00000317501.3,ENST00000540489.2 |
| exon_skip_130475 | 15 | 88670392:88670457:88678331:88678628:88679129:88679169 | 88678331:88678628 | ENSG00000140538.12 | ENST00000557856.1,ENST00000357724.2,ENST00000558676.1 |
| exon_skip_130476 | 15 | 88680691:88680792:88690565:88690634:88726648:88726720 | 88690565:88690634 | ENSG00000140538.12 | ENST00000394480.2,ENST00000557856.1,ENST00000360948.2,ENST00000357724.2,ENST00000355254.2,ENST00000542733.2,ENST00000558676.1,ENST00000317501.3,ENST00000540489.2,ENST00000559188.1 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for NTRK3 |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000360948 | 88669501 | 88669604 | Frame-shift |
| ENST00000360948 | 88428924 | 88428966 | In-frame |
| ENST00000360948 | 88576087 | 88576276 | In-frame |
| ENST00000360948 | 88671941 | 88671965 | In-frame |
| ENST00000360948 | 88690565 | 88690634 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000360948 | 88669501 | 88669604 | Frame-shift |
| ENST00000360948 | 88428924 | 88428966 | In-frame |
| ENST00000360948 | 88576087 | 88576276 | In-frame |
| ENST00000360948 | 88671941 | 88671965 | In-frame |
| ENST00000360948 | 88690565 | 88690634 | In-frame |
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Infer the effects of exon skipping event on protein functional features for NTRK3 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000360948 | 2843 | 839 | 88690565 | 88690634 | 558 | 626 | 132 | 154 |
| ENST00000360948 | 2843 | 839 | 88576087 | 88576276 | 1559 | 1747 | 465 | 528 |
| ENST00000360948 | 2843 | 839 | 88428924 | 88428966 | 2296 | 2337 | 711 | 725 |
| Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000360948 | 2843 | 839 | 88690565 | 88690634 | 558 | 626 | 132 | 154 |
| ENST00000360948 | 2843 | 839 | 88576087 | 88576276 | 1559 | 1747 | 465 | 528 |
| ENST00000360948 | 2843 | 839 | 88428924 | 88428966 | 2296 | 2337 | 711 | 725 |
| Lost protein functional features of individual exon skipping events in TCGA. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Q16288 | 132 | 154 | 32 | 839 | Chain | ID=PRO_0000016731;Note=NT-3 growth factor receptor |
| Q16288 | 132 | 154 | 133 | 133 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q16288 | 132 | 154 | 149 | 149 | Natural variant | ID=VAR_041471;Note=In a gastric adenocarcinoma sample%3B somatic mutation. T->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17344846;Dbxref=dbSNP:rs368222977,PMID:17344846 |
| Q16288 | 132 | 154 | 128 | 149 | Repeat | Note=LRR 2 |
| Q16288 | 132 | 154 | 32 | 429 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q16288 | 465 | 528 | 32 | 839 | Chain | ID=PRO_0000016731;Note=NT-3 growth factor receptor |
| Q16288 | 465 | 528 | 493 | 493 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q6VNS1 |
| Q16288 | 465 | 528 | 516 | 516 | Modified residue | Note=Phosphotyrosine%3B by autocatalysis;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25196463;Dbxref=PMID:25196463 |
| Q16288 | 465 | 528 | 516 | 516 | Site | Note=Interaction with SHC1;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q16288 | 465 | 528 | 454 | 839 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q16288 | 711 | 725 | 613 | 839 | Alternative sequence | ID=VSP_002926;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:7823156;Dbxref=PMID:7823156 |
| Q16288 | 711 | 725 | 712 | 725 | Alternative sequence | ID=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 |
| Q16288 | 711 | 725 | 32 | 839 | Chain | ID=PRO_0000016731;Note=NT-3 growth factor receptor |
| Q16288 | 711 | 725 | 538 | 839 | Domain | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| Q16288 | 711 | 725 | 454 | 839 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Lost protein functional features of individual exon skipping events in GTEx. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Q16288 | 132 | 154 | 32 | 839 | Chain | ID=PRO_0000016731;Note=NT-3 growth factor receptor |
| Q16288 | 132 | 154 | 133 | 133 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q16288 | 132 | 154 | 149 | 149 | Natural variant | ID=VAR_041471;Note=In a gastric adenocarcinoma sample%3B somatic mutation. T->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17344846;Dbxref=dbSNP:rs368222977,PMID:17344846 |
| Q16288 | 132 | 154 | 128 | 149 | Repeat | Note=LRR 2 |
| Q16288 | 132 | 154 | 32 | 429 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q16288 | 465 | 528 | 32 | 839 | Chain | ID=PRO_0000016731;Note=NT-3 growth factor receptor |
| Q16288 | 465 | 528 | 493 | 493 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q6VNS1 |
| Q16288 | 465 | 528 | 516 | 516 | Modified residue | Note=Phosphotyrosine%3B by autocatalysis;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25196463;Dbxref=PMID:25196463 |
| Q16288 | 465 | 528 | 516 | 516 | Site | Note=Interaction with SHC1;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q16288 | 465 | 528 | 454 | 839 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q16288 | 711 | 725 | 613 | 839 | Alternative sequence | ID=VSP_002926;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:7823156;Dbxref=PMID:7823156 |
| Q16288 | 711 | 725 | 712 | 725 | Alternative sequence | ID=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 |
| Q16288 | 711 | 725 | 32 | 839 | Chain | ID=PRO_0000016731;Note=NT-3 growth factor receptor |
| Q16288 | 711 | 725 | 538 | 839 | Domain | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| Q16288 | 711 | 725 | 454 | 839 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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SNVs in the skipped exons for NTRK3 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_130470 | 88524457 | 88524591 | 88524481 | 88524481 | Frame_Shift_Del | C | - | p.E566fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_130473 | 88669502 | 88669604 | 88669575 | 88669575 | Frame_Shift_Del | A | - | p.F441fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_130476 | 88690566 | 88690634 | 88690624 | 88690624 | Frame_Shift_Del | T | - | p.S136fs |
| BLCA | TCGA-DK-A3IT-01 | exon_skip_130468 exon_skip_130472 | 88576088 | 88576276 | 88576243 | 88576243 | Nonsense_Mutation | G | C | p.S477* |
| LUAD | TCGA-55-7576-01 | exon_skip_130473 | 88669502 | 88669604 | 88669511 | 88669511 | Nonsense_Mutation | C | A | p.G463* |
| COAD | TCGA-DM-A1D9-01 | exon_skip_130473 | 88669502 | 88669604 | 88669526 | 88669526 | Nonsense_Mutation | G | A | p.R458X |
| BRCA | TCGA-A8-A09N-01 | exon_skip_130474 | 88671942 | 88671965 | 88671941 | 88671941 | Splice_Site | C | A | e9+1 |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| MCC13_SKIN | 88428925 | 88428966 | 88428945 | 88428945 | Missense_Mutation | C | T | p.D719N |
| NCIH2172_LUNG | 88576088 | 88576276 | 88576107 | 88576107 | Missense_Mutation | G | T | p.N522K |
| SNU1196_BILIARY_TRACT | 88576088 | 88576276 | 88576120 | 88576120 | Missense_Mutation | C | T | p.R518H |
| LS411N_LARGE_INTESTINE | 88576088 | 88576276 | 88576153 | 88576153 | Missense_Mutation | C | T | p.R507H |
| HCC44_LUNG | 88576088 | 88576276 | 88576180 | 88576180 | Missense_Mutation | G | T | p.P498H |
| EW22_BONE | 88576088 | 88576276 | 88576199 | 88576199 | Missense_Mutation | A | T | p.S492T |
| RKO_LARGE_INTESTINE | 88576088 | 88576276 | 88576232 | 88576232 | Missense_Mutation | G | C | p.L481V |
| NCIH2171_LUNG | 88576088 | 88576276 | 88576256 | 88576256 | Missense_Mutation | C | A | p.G473C |
| NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 88576088 | 88576276 | 88576271 | 88576271 | Missense_Mutation | C | T | p.V468M |
| HEC251_ENDOMETRIUM | 88669502 | 88669604 | 88669522 | 88669522 | Missense_Mutation | C | A | p.R459L |
| CAL51_BREAST | 88669502 | 88669604 | 88669547 | 88669547 | Missense_Mutation | C | T | p.V451I |
| NCIH28_PLEURA | 88669502 | 88669604 | 88669547 | 88669547 | Missense_Mutation | C | T | p.V451I |
| NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 88671942 | 88671965 | 88671959 | 88671959 | Missense_Mutation | G | A | p.T404M |
| SNU1040_LARGE_INTESTINE | 88690566 | 88690634 | 88690598 | 88690598 | Nonsense_Mutation | C | T | p.W144* |
| SBC5_LUNG | 88428925 | 88428966 | 88428925 | 88428925 | Splice_Site | C | T | p.E725E |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NTRK3 |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
| exon_skip_130468 | 15 | 88483853:88483984:88576087:88576276:88669501:88669592 | 88576087:88576276 | ENST00000557856.1,ENST00000542733.2,ENST00000558676.1,ENST00000357724.2,ENST00000355254.2,ENST00000394480.2,ENST00000360948.2 | PRAD | rs2229910 | chr15:88576185 | G/C | 1.42e-05 |
| exon_skip_130472 | 15 | 88524456:88524591:88576087:88576276:88669501:88669592 | 88576087:88576276 | ENST00000317501.3,ENST00000540489.2 | PRAD | rs2229910 | chr15:88576185 | G/C | 1.42e-05 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NTRK3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NTRK3 |
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RelatedDrugs for NTRK3 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Q16288 | DB12010 | Fostamatinib | NT-3 growth factor receptor | small molecule | approved|investigational |
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RelatedDiseases for NTRK3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| NTRK3 | C0036341 | Schizophrenia | 3 | PSYGENET |
| NTRK3 | C0041696 | Unipolar Depression | 2 | PSYGENET |
| NTRK3 | C1269683 | Major Depressive Disorder | 2 | PSYGENET |
| NTRK3 | C0014175 | Endometriosis | 1 | CTD_human |
| NTRK3 | C0017638 | Glioma | 1 | CTD_human |
| NTRK3 | C0038220 | Status Epilepticus | 1 | CTD_human |
| NTRK3 | C0525045 | Mood Disorders | 1 | PSYGENET |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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