Protein:PDGFRA |
Protein Summary |
 Gene summary |
| Gene name: PDGFRA | ASpdb.0 ID: 5156 | Gene | 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 | 20240416 |
| UniProtAcc | P16234 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | PDGFRA | GO:0004672 | protein kinase activity | 24190966 |
| Gene | PDGFRA | GO:0004714 | transmembrane receptor protein tyrosine kinase activity | 1646396 |
| Gene | PDGFRA | GO:0005018 | platelet-derived growth factor alpha-receptor activity | 2536956|8188664|10806482 |
| Gene | PDGFRA | GO:0005021 | vascular endothelial growth factor receptor activity | 17470632 |
| Gene | PDGFRA | GO:0005654 | nucleoplasm | - |
| Gene | PDGFRA | GO:0005886 | plasma membrane | 2536956|2554309 |
| Gene | PDGFRA | GO:0008284 | positive regulation of cell population proliferation | 10806482 |
| Gene | PDGFRA | GO:0010544 | negative regulation of platelet activation | 8188664 |
| Gene | PDGFRA | GO:0018108 | peptidyl-tyrosine phosphorylation | 2536956|8188664 |
| Gene | PDGFRA | GO:0030054 | cell junction | - |
| Gene | PDGFRA | GO:0030335 | positive regulation of cell migration | 17470632 |
| Gene | PDGFRA | GO:0032991 | protein-containing complex | 24190966 |
| Gene | PDGFRA | GO:0034614 | cellular response to reactive oxygen species | 24190966 |
| Gene | PDGFRA | GO:0038091 | positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway | 17470632 |
| Gene | PDGFRA | GO:0042803 | protein homodimerization activity | 2542288 |
| Gene | PDGFRA | GO:0046777 | protein autophosphorylation | 2536956|8188664 |
| Gene | PDGFRA | GO:0048008 | platelet-derived growth factor receptor signaling pathway | 2536956|10806482 |
| Gene | PDGFRA | GO:0048146 | positive regulation of fibroblast proliferation | 10806482 |
| Gene | PDGFRA | GO:0048407 | platelet-derived growth factor binding | 2554309|8188664 |
AS Summary |
| Information of the canonical protein with experimentally identified structure from PDB (2023). |
| UniProt Acc | File name | PDB ID | Method | Resolution | Chain | Start | End |
| P16234-1 | P16234-1_6a32_A.pdb | 6A32 | X-ray | 1.87 | A | 554 | 973 |
| ASpdb's canonical and alternatively spliced isoform information. |
| accession_id | gene_name | canonical_id | alternative_id | canonical_length | alternative_length | canonical_start | canonical_end | type | originalSEQ | variationSEQ | alternative_start | alternative_end |
| P16234 | PDGFRA | P16234-1 | P16234-2 | 1089 | 218 | 210 | 218 | Substitution | ATSELDLEM | GTCIISFLL | 210 | 218 |
| P16234 | PDGFRA | P16234-1 | P16234-2 | 1089 | 218 | 219 | 1089 | Deletion | none | none | 218 | 218 |
| P16234 | PDGFRA | P16234-1 | P16234-3 | 1089 | 743 | 720 | 743 | Substitution | YVILSFENNGDYMDMKQADTTQYV | SGQGCLSSGTLQELSVDLQARGPC | 720 | 743 |
| P16234 | PDGFRA | P16234-1 | P16234-3 | 1089 | 743 | 744 | 1089 | Deletion | none | none | 743 | 743 |
| Multiple sequence alignment of our canonical and alternatively spliced PDGFRA |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of PDGFRA |
| UniProt-id | ENSG | ENST | ENSP |
| P16234-1 | ENSG00000134853.12 | ENST00000257290.10 | ENSP00000257290.5 |
| P16234-2 | ENSG00000134853.12 | ENST00000508170.5 | ENSP00000425648.1 |
| P16234-3 | ENSG00000134853.12 | ENST00000509490.5 | ENSP00000424218.1 |
| UniProt-id | NM ID | NP ID |
| P16234-1 | NM_001347829.1 | NP_001334758.1 |
| P16234-1 | NM_006206.5 | NP_006197.1 |
| P16234-1 | XM_005265743.1 | XP_005265800.1 |
| Amino acid sequences of our canonical and alternatively spliced PDGFRA |
| accession_id | Protein sequence |
| P16234-1 | MGTSHPAFLVLGCLLTGLSLILCQLSLPSILPNENEKVVQLNSSFSLRCFGESEVSWQYPMSEEESSDVEIRNEENNSGLFVTVLEVSSA SAAHTGLYTCYYNHTQTEENELEGRHIYIYVPDPDVAFVPLGMTDYLVIVEDDDSAIIPCRTTDPETPVTLHNSEGVVPASYDSRQGFNG TFTVGPYICEATVKGKKFQTIPFNVYALKATSELDLEMEALKTVYKSGETIVVTCAVFNNEVVDLQWTYPGEVKGKGITMLEEIKVPSIK LVYTLTVPEATVKDSGDYECAARQATREVKEMKKVTISVHEKGFIEIKPTFSQLEAVNLHEVKHFVVEVRAYPPPRISWLKNNLTLIENL TEITTDVEKIQEIRYRSKLKLIRAKEEDSGHYTIVAQNEDAVKSYTFELLTQVPSSILDLVDDHHGSTGGQTVRCTAEGTPLPDIEWMIC KDIKKCNNETSWTILANNVSNIITEIHSRDRSTVEGRVTFAKVEETIAVRCLAKNLLGAENRELKLVAPTLRSELTVAAAVLVLLVIVII SLIVLVVIWKQKPRYEIRWRVIESISPDGHEYIYVDPMQLPYDSRWEFPRDGLVLGRVLGSGAFGKVVEGTAYGLSRSQPVMKVAVKMLK PTARSSEKQALMSELKIMTHLGPHLNIVNLLGACTKSGPIYIITEYCFYGDLVNYLHKNRDSFLSHHPEKPKKELDIFGLNPADESTRSY VILSFENNGDYMDMKQADTTQYVPMLERKEVSKYSDIQRSLYDRPASYKKKSMLDSEVKNLLSDDNSEGLTLLDLLSFTYQVARGMEFLA SKNCVHRDLAARNVLLAQGKIVKICDFGLARDIMHDSNYVSKGSTFLPVKWMAPESIFDNLYTTLSDVWSYGILLWEIFSLGGTPYPGMM VDSTFYNKIKSGYRMAKPDHATSEVYEIMVKCWNSEPEKRPSFYHLSEIVENLLPGQYKKSYEKIHLDFLKSDHPAVARMRVDSDNAYIG VTYKNEEDKLKDWEGGLDEQRLSADSGYIIPLPDIDPVPEEEDLGKRNRHSSQTSEESAIETGSSSSTFIKREDETIEDIDMMDDIGIDS |
| P16234-2 | MGTSHPAFLVLGCLLTGLSLILCQLSLPSILPNENEKVVQLNSSFSLRCFGESEVSWQYPMSEEESSDVEIRNEENNSGLFVTVLEVSSA SAAHTGLYTCYYNHTQTEENELEGRHIYIYVPDPDVAFVPLGMTDYLVIVEDDDSAIIPCRTTDPETPVTLHNSEGVVPASYDSRQGFNG |
| P16234-3 | MGTSHPAFLVLGCLLTGLSLILCQLSLPSILPNENEKVVQLNSSFSLRCFGESEVSWQYPMSEEESSDVEIRNEENNSGLFVTVLEVSSA SAAHTGLYTCYYNHTQTEENELEGRHIYIYVPDPDVAFVPLGMTDYLVIVEDDDSAIIPCRTTDPETPVTLHNSEGVVPASYDSRQGFNG TFTVGPYICEATVKGKKFQTIPFNVYALKATSELDLEMEALKTVYKSGETIVVTCAVFNNEVVDLQWTYPGEVKGKGITMLEEIKVPSIK LVYTLTVPEATVKDSGDYECAARQATREVKEMKKVTISVHEKGFIEIKPTFSQLEAVNLHEVKHFVVEVRAYPPPRISWLKNNLTLIENL TEITTDVEKIQEIRYRSKLKLIRAKEEDSGHYTIVAQNEDAVKSYTFELLTQVPSSILDLVDDHHGSTGGQTVRCTAEGTPLPDIEWMIC KDIKKCNNETSWTILANNVSNIITEIHSRDRSTVEGRVTFAKVEETIAVRCLAKNLLGAENRELKLVAPTLRSELTVAAAVLVLLVIVII SLIVLVVIWKQKPRYEIRWRVIESISPDGHEYIYVDPMQLPYDSRWEFPRDGLVLGRVLGSGAFGKVVEGTAYGLSRSQPVMKVAVKMLK PTARSSEKQALMSELKIMTHLGPHLNIVNLLGACTKSGPIYIITEYCFYGDLVNYLHKNRDSFLSHHPEKPKKELDIFGLNPADESTRSS |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| PDGFRA (go to UniProt):P16234 |
| Retention analysis result of 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 * Minus value of BPloci means that the break pointn is located before the CDS. |
| - Retained protein feature among the 13 regional features. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| P16234 | Topological domain | 24 | 528 | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Substitution;Start=210;End=218 |
| P16234 | Topological domain | 24 | 528 | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Deletion;Start=219;End=1089 |
| P16234 | Transmembrane | 529 | 549 | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Deletion;Start=219;End=1089 |
| P16234 | Topological domain | 550 | 1089 | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Deletion;Start=219;End=1089 |
| P16234 | Topological domain | 550 | 1089 | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Substitution;Start=720;End=743 |
| P16234 | Topological domain | 550 | 1089 | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Deletion;Start=744;End=1089 |
| P16234 | Domain | 202 | 306 | Note=Ig-like C2-type 3 | Type=Substitution;Start=210;End=218 |
| P16234 | Domain | 202 | 306 | Note=Ig-like C2-type 3 | Type=Deletion;Start=219;End=1089 |
| P16234 | Domain | 319 | 410 | Note=Ig-like C2-type 4 | Type=Deletion;Start=219;End=1089 |
| P16234 | Domain | 414 | 517 | Note=Ig-like C2-type 5 | Type=Deletion;Start=219;End=1089 |
| P16234 | Domain | 593 | 954 | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 | Type=Deletion;Start=219;End=1089 |
| P16234 | Domain | 593 | 954 | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 | Type=Substitution;Start=720;End=743 |
| P16234 | Domain | 593 | 954 | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 | Type=Deletion;Start=744;End=1089 |
| P16234 | Region | 1018 | 1089 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=219;End=1089 |
| P16234 | Region | 1018 | 1089 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=744;End=1089 |
| P16234 | Compositional bias | 1029 | 1044 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=219;End=1089 |
| P16234 | Compositional bias | 1029 | 1044 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=744;End=1089 |
| P16234 | Compositional bias | 1045 | 1060 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=219;End=1089 |
| P16234 | Compositional bias | 1045 | 1060 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=744;End=1089 |
Gene Isoform Structures and Expression Levels for PDGFRA |
| Gene structures of our canonical and alternative spliced genes of PDGFRA * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Expression levels of gene isoforms across GTEx. |
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| Expression levels of gene isoforms across TCGA. |
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Protein Structures |
| PDB and CIF files of the predicted protein structures * Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| 3D view using mol* of P16234-1 |
| 3D view using mol* of P16234-2 |
| 3D view using mol* of P16234-3 |
pLDDT Score Distribution |
| pLDDT score distribution of the predicted protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
| pLDDT distribution across the protein length of P16234-1 |
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| pLDDT distribution across the protein length of P16234-2 |
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| pLDDT distribution across the protein length of P16234-3 |
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Ramachandran Plot of Protein Structures |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide. |
| Ramachandran plot of P16234-1 |
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| Ramachandran plot of P16234-2 |
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| Ramachandran plot of P16234-3 |
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Potential Active Site Information |
| The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite. |
| UniProt-id | Site score | Size | D score | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
| P16234-1 | 1.017 | 383 | 1.024 | 920.612 | 0.508 | 0.724 | 0.98 | 0.463 | 1.075 | 0.43 | 1.245 | 611,613,618,619,620,621,622,623,655,675,676,677,67 8,752,753,754,755,756,757,758,759,760,761,762,763, 764,765,766,767,768,775,778,779,782,783,784,785,78 6,827,828,829,831,833,957,960,961,962,964,965,968, 969,972,973,974 |
| P16234-2 | 0.637 | 30 | 0.594 | 75.803 | 0.659 | 0.598 | 0.935 | 0.455 | 0.859 | 0.529 | 0.924 | 54,55,56,73,74,75,76,80,81,82,83,103
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| P16234-3 | 0.997 | 118 | 1.048 | 426.692 | 0.672 | 0.635 | 0.781 | 0.409 | 0.838 | 0.488 | 1.236 | 597,599,607,625,627,644,658,672,674,675,676,677,67 8,679,680,681,684,685,687,688,689,690,702,703,704, 705,706,707,708,709,710,711 |
Protein Structure and Feature Comparision |
| Protein Structure Comparision Using Template Modeling Scores (TM-score). |
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| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green) |
| 3D view using mol* of P16234-1_P16234-1_6a32_A.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of P16234-1_6a32_A_P16234-2.pdb |
| 3D view using mol* of P16234-1_6a32_A_P16234-3.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of P16234-1_P16234-2.pdb |
| 3D view using mol* of P16234-1_P16234-3.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/P16234-1_vs_P16234-2.png |
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| ./stats/secondary_structure/figure/P16234-1_vs_P16234-3.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/P16234-1_vs_P16234-2.png |
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| ./stats/relative_asa/P16234-1_vs_P16234-3.png |
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Protein-Protein Interaction |
| Interactors from UniProt. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Interactors from STRING. |
| Gene name | Interactors |
Related Drugs to PDGFRA |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
| P16234 | PDGFRA | DB12010 | Fostamatinib | approved, investigational | inhibitor |
| P16234 | PDGFRA | DB10772 | Foreskin keratinocyte (neonatal) | approved | agonist |
| P16234 | PDGFRA | DB00102 | Becaplermin | approved, investigational | |
| P16234 | PDGFRA | DB06589 | Pazopanib | approved | inhibitor |
| P16234 | PDGFRA | DB06043 | Olaratumab | approved, investigational | antagonist |
| P16234 | PDGFRA | DB12147 | Erdafitinib | approved, investigational | substrate |
| P16234 | PDGFRA | DB06595 | Midostaurin | approved, investigational | antagonist, inhibitor |
| P16234 | PDGFRA | DB08901 | Ponatinib | approved, investigational | inhibitor |
| P16234 | PDGFRA | DB12742 | Amuvatinib | investigational | |
| P16234 | PDGFRA | DB11800 | Tivozanib | approved, investigational | inhibitor |
| P16234 | PDGFRA | DB14840 | Ripretinib | approved | inhibitor |
| P16234 | PDGFRA | DB01268 | Sunitinib | approved, investigational | inhibitor |
| P16234 | PDGFRA | DB09078 | Lenvatinib | approved, investigational | inhibitor |
| P16234 | PDGFRA | DB08896 | Regorafenib | approved | inhibitor |
| P16234 | PDGFRA | DB00619 | Imatinib | approved | antagonist |
| P16234 | PDGFRA | DB09079 | Nintedanib | approved | inhibitor |
| P16234 | PDGFRA | DB05146 | XL820 | investigational |
Related Diseases to PDGFRA |
| Previous studies relating to the alternative splicing of PDGFRA and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| PDGFRA | 8261442 | Developmentally regulated expression of two novel platelet-derived growth factor alpha-receptor transcripts in human teratocarcinoma cells. | Two novel platelet-derived growth factor (PDGF) alpha-receptor transcripts of 1.5 kilobases and 5.0 kilobases are expressed in the human teratocarcinoma cell line Tera-2 only while the cells are in an undifferentiated state. After retinoic acid-induced differentiation, expression of these mRNAs is completely shut off and instead, the cells express a single 6.4-kilobase mRNA species which is also expressed in many other cell types. The 1.5-kilobase mRNA initiates within intron 12, contains the correctly spliced exons 13, 14, 15, and 16, and contains a cryptic exon, designated teratocarcinoma cryptic exon, at the 3' end. Teratocarcinoma cryptic exon contains a functional polyadenylation signal. Exons 13 to 16 correspond to the first tyrosine kinase domain and to part of the interkinase domain of the PDGF alpha-receptor. Recently, a splice variant lacking exon 14 was identified. These results show that a combination of alternative promoter usage and alternative splicing of the human PDGF alpha-receptor gene occur in a developmentally regulated fashion. In vitro translation of the 1.5-kilobase mRNA generates protein products which can be specifically immunoprecipitated with a PDGF alpha-receptor-specific antibody. The significance of the expression of this transcript for the growth factor-independent proliferation of undifferentiated Tera-2 cells is unclear. Expression of PDGF alpha-receptor transcripts containing the cryptic exon may be useful as a marker for undifferentiated stem cells in human teratocarcinomas. | D018243 | Teratocarcinoma |
| PDGFRA | 8486649 | Identification of a soluble receptor for platelet-derived growth factor in cell-conditioned medium and human plasma. | We have discovered a soluble form of the platelet-derived growth factor (PDGF) alpha receptor, designated sPDGF-R alpha, that is produced by and secreted into the conditioned medium of the human osteosarcoma cell line, MG-63. Additionally, sPDGF-R alpha activity has been detected in normal human blood plasma and serum. We have achieved partial purification of this protein by column chromatography using three different affinity matrices: anti-PDGF-R alpha monoclonal antibody (mAb) 292.15-Sepharose, PDGF-BB-Sepharose, and wheat germ agglutinin-agarose. All three matrices have been shown to purify a 90-kDa protein that is recognized by mAbs specific for the PDGF-R alpha extracellular domain. sPDGF-R alpha is capable of binding PDGF ligand in solution and can compete with cell-associated PDGF receptors for ligand binding. We provide three pieces of data suggesting that the sPDGF-R alpha is generated by proteolytic clipping of the full-length PDGF-R alpha protein. First, the conditioned medium of an expression cell line transfected with a cDNA construct designed to produce only full-length PDGF-R alpha exhibits sPDGF-R alpha activity. Second, a truncated intracellular fragment of the PDGF-R alpha, presumably representing the intracellular counterpart of the clipped sPDGF-R alpha, can be immunoprecipitated from the MG-63 osteosarcoma cell extracts using antiserum raised against an intracellular portion of PDGF-R alpha. Finally, we have been unable to detect alternative splicing in the PDGF-R alpha transcript using reverse transcription-polymerase chain reaction. | D012516 | Osteosarcoma |
Clinically important variants in PDGFRA |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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