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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 PDGFRA |
 Gene summary |
| Gene information | Gene symbol | PDGFRA | Gene ID | 5156 |
| Gene name | platelet derived growth factor receptor alpha | |
| Synonyms | CD140A|PDGFR-2|PDGFR2 | |
| Cytomap | 4q12 | |
| Type of gene | protein-coding | |
| Description | platelet-derived growth factor receptor alphaCD140 antigen-like family member ACD140a antigenPDGF-R-alphaalpha-type platelet-derived growth factor receptorplatelet-derived growth factor receptor 2platelet-derived growth factor receptor, alpha polype | |
| Modification date | 20180523 | |
| UniProtAcc | P16234 | |
| Context | PubMed: PDGFRA [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 |
| PDGFRA | GO:0008284 | positive regulation of cell proliferation | 10806482 |
| PDGFRA | GO:0010544 | negative regulation of platelet activation | 8188664 |
| PDGFRA | GO:0018108 | peptidyl-tyrosine phosphorylation | 1646396|2536956|8188664 |
| PDGFRA | GO:0030335 | positive regulation of cell migration | 17470632 |
| PDGFRA | GO:0034614 | cellular response to reactive oxygen species | 24190966 |
| PDGFRA | GO:0038091 | positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway | 17470632 |
| PDGFRA | GO:0046777 | protein autophosphorylation | 1646396|2536956|8188664 |
| PDGFRA | GO:0048008 | platelet-derived growth factor receptor signaling pathway | 2536956|10806482 |
| PDGFRA | GO:0048146 | positive regulation of fibroblast proliferation | 10806482 |
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Exon skipping events across known transcript of Ensembl for PDGFRA 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 PDGFRA |
| 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 PDGFRA |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_423703 | 4 | 55124923:55124984:55127261:55127579:55129833:55130094 | 55127261:55127579 | ENSG00000134853.7 | ENST00000508170.1,ENST00000504461.1,ENST00000512522.1,ENST00000503856.1,ENST00000509490.1,ENST00000257290.5 |
| exon_skip_423704 | 4 | 55144528:55144682:55144985:55145138:55146482:55146649 | 55144985:55145138 | ENSG00000134853.7 | ENST00000509490.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PDGFRA |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_423703 | 4 | 55124923:55124984:55127261:55127579:55129833:55130094 | 55127261:55127579 | ENSG00000134853.7 | ENST00000257290.5,ENST00000508170.1,ENST00000509490.1,ENST00000503856.1,ENST00000504461.1,ENST00000512522.1 |
| exon_skip_423704 | 4 | 55144528:55144682:55144985:55145138:55146482:55146649 | 55144985:55145138 | ENSG00000134853.7 | ENST00000509490.1 |
| 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 PDGFRA |
| 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 |
| ENST00000257290 | 55127261 | 55127579 | 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 |
| ENST00000257290 | 55127261 | 55127579 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PDGFRA |
| 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 |
| ENST00000257290 | 6593 | 1089 | 55127261 | 55127579 | 381 | 698 | 16 | 122 |
| 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 |
| ENST00000257290 | 6593 | 1089 | 55127261 | 55127579 | 381 | 698 | 16 | 122 |
| 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 |
| P16234 | 16 | 122 | 24 | 1089 | Chain | ID=PRO_0000016760;Note=Platelet-derived growth factor receptor alpha |
| P16234 | 16 | 122 | 49 | 100 | Disulfide bond | Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00114 |
| P16234 | 16 | 122 | 24 | 113 | Domain | Note=Ig-like C2-type 1 |
| P16234 | 16 | 122 | 117 | 201 | Domain | Note=Ig-like C2-type 2 |
| P16234 | 16 | 122 | 42 | 42 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P16234 | 16 | 122 | 76 | 76 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P16234 | 16 | 122 | 103 | 103 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P16234 | 16 | 122 | 79 | 79 | Natural variant | ID=VAR_042032;Note=G->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17344846;Dbxref=dbSNP:rs36035373,PMID:17344846 |
| P16234 | 16 | 122 | 1 | 23 | Signal peptide | . |
| P16234 | 16 | 122 | 24 | 528 | Topological domain | Note=Extracellular;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 |
| P16234 | 16 | 122 | 24 | 1089 | Chain | ID=PRO_0000016760;Note=Platelet-derived growth factor receptor alpha |
| P16234 | 16 | 122 | 49 | 100 | Disulfide bond | Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00114 |
| P16234 | 16 | 122 | 24 | 113 | Domain | Note=Ig-like C2-type 1 |
| P16234 | 16 | 122 | 117 | 201 | Domain | Note=Ig-like C2-type 2 |
| P16234 | 16 | 122 | 42 | 42 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P16234 | 16 | 122 | 76 | 76 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P16234 | 16 | 122 | 103 | 103 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P16234 | 16 | 122 | 79 | 79 | Natural variant | ID=VAR_042032;Note=G->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17344846;Dbxref=dbSNP:rs36035373,PMID:17344846 |
| P16234 | 16 | 122 | 1 | 23 | Signal peptide | . |
| P16234 | 16 | 122 | 24 | 528 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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SNVs in the skipped exons for PDGFRA |
| - 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. |
PDGFRA_STAD_exon_skip_423703_psi_boxplot.png |
| - 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_423703 | 55127262 | 55127579 | 55127436 | 55127436 | Frame_Shift_Del | A | - | p.E75fs |
| BLCA | TCGA-4Z-AA7W-01 | exon_skip_423703 | 55127262 | 55127579 | 55127289 | 55127289 | Nonsense_Mutation | C | G | p.S26* |
| STAD | TCGA-VQ-A91Q-01 | exon_skip_423703 | 55127262 | 55127579 | 55127506 | 55127506 | Nonsense_Mutation | C | A | p.Y98* |
| STAD | TCGA-VQ-A91Q-01 | exon_skip_423703 | 55127262 | 55127579 | 55127506 | 55127506 | Nonsense_Mutation | C | A | p.Y98X |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-VQ-A91Q-01 |
| Cancer type: STAD | |
| ESID: exon_skip_423703 | |
| Skipped exon start: 55127262 | |
| Skipped exon end: 55127579 | |
| Mutation start: 55127506 | |
| Mutation end: 55127506 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: C | |
| Mutation seq: A | |
| AAchange: p.Y98X | |
| Sample: TCGA-VQ-A91Q-01 |
| Cancer type: STAD | |
| ESID: exon_skip_423703 | |
| Skipped exon start: 55127262 | |
| Skipped exon end: 55127579 | |
| Mutation start: 55127506 | |
| Mutation end: 55127506 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: C | |
| Mutation seq: A | |
| AAchange: p.Y98* | |
exon_skip_423703_STAD_TCGA-VQ-A91Q-01.png | |
| - 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 |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 55127262 | 55127579 | 55127409 | 55127409 | Frame_Shift_Del | G | - | p.S67fs |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 55127262 | 55127579 | 55127406 | 55127407 | Frame_Shift_Ins | - | C | p.ES65fs |
| COLO668_LUNG | 55127262 | 55127579 | 55127315 | 55127315 | Missense_Mutation | A | G | p.N35D |
| MFM223_BREAST | 55127262 | 55127579 | 55127352 | 55127352 | Missense_Mutation | T | A | p.L47Q |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 55127262 | 55127579 | 55127360 | 55127360 | Missense_Mutation | T | G | p.F50V |
| 22RV1_PROSTATE | 55127262 | 55127579 | 55127381 | 55127381 | Missense_Mutation | T | C | p.W57R |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 55127262 | 55127579 | 55127387 | 55127387 | Missense_Mutation | T | C | p.Y59H |
| HEC6_ENDOMETRIUM | 55127262 | 55127579 | 55127460 | 55127460 | Missense_Mutation | C | T | p.T83M |
| NCIH1568_LUNG | 55127262 | 55127579 | 55127495 | 55127495 | Missense_Mutation | A | T | p.T95S |
| EGI1_BILIARY_TRACT | 55127262 | 55127579 | 55127503 | 55127503 | Missense_Mutation | G | T | p.L97F |
| NCIH211_LUNG | 55127262 | 55127579 | 55127507 | 55127507 | Missense_Mutation | A | T | p.T99S |
| NCIH446_LUNG | 55127262 | 55127579 | 55127506 | 55127506 | Nonsense_Mutation | C | A | p.Y98* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PDGFRA |
| 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 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PDGFRA |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PDGFRA |
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RelatedDrugs for PDGFRA |
| 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 |
| P16234 | DB00619 | Imatinib | Platelet-derived growth factor receptor alpha | small molecule | approved | |
| P16234 | DB06589 | Pazopanib | Platelet-derived growth factor receptor alpha | small molecule | approved | |
| P16234 | DB08896 | Regorafenib | Platelet-derived growth factor receptor alpha | small molecule | approved | |
| P16234 | DB00102 | Becaplermin | Platelet-derived growth factor receptor alpha | biotech | approved|investigational | |
| P16234 | DB01268 | Sunitinib | Platelet-derived growth factor receptor alpha | small molecule | approved|investigational | |
| P16234 | DB06043 | Olaratumab | Platelet-derived growth factor receptor alpha | biotech | approved|investigational | |
| P16234 | DB06595 | Midostaurin | Platelet-derived growth factor receptor alpha | small molecule | approved|investigational | |
| P16234 | DB08901 | Ponatinib | Platelet-derived growth factor receptor alpha | small molecule | approved|investigational | |
| P16234 | DB12010 | Fostamatinib | Platelet-derived growth factor receptor alpha | small molecule | approved|investigational |
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RelatedDiseases for PDGFRA |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| PDGFRA | C0238198 | Gastrointestinal Stromal Tumors | 2 | CTD_human;HPO;ORPHANET;UNIPROT |
| PDGFRA | C0008925 | Cleft Palate | 1 | CTD_human |
| PDGFRA | C0015923 | Fetal Alcohol Syndrome | 1 | PSYGENET |
| PDGFRA | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
| PDGFRA | C0024115 | Lung diseases | 1 | CTD_human |
| PDGFRA | C0025149 | Medulloblastoma | 1 | CTD_human |
| PDGFRA | C0035238 | Congenital abnormality of respiratory system | 1 | CTD_human |
| PDGFRA | C0080178 | Spina Bifida | 1 | CTD_human |
| PDGFRA | C0206637 | Chondrosarcoma, Mesenchymal | 1 | CTD_human |
| PDGFRA | C0376634 | Craniofacial Abnormalities | 1 | CTD_human |
| PDGFRA | C1540912 | Hypereosinophilic syndrome | 1 | CTD_human |
| PDGFRA | C2985290 | Fetal Alcohol Spectrum Disorders | 1 | PSYGENET |
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