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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for PDGFRB |
 Gene summary |
| Gene information | Gene symbol | PDGFRB | Gene ID | 5159 |
| Gene name | platelet derived growth factor receptor beta | |
| Synonyms | CD140B|IBGC4|IMF1|JTK12|KOGS|PDGFR|PDGFR-1|PDGFR1|PENTT | |
| Cytomap | 5q32 | |
| Type of gene | protein-coding | |
| Description | platelet-derived growth factor receptor betaActivated tyrosine kinase PDGFRBCD140 antigen-like family member BNDEL1-PDGFRBPDGF-R-betaPDGFR-betabeta-type platelet-derived growth factor receptorplatelet-derived growth factor receptor 1platelet-deriv | |
| Modification date | 20200329 | |
| UniProtAcc | ||
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| PDGFRB | GO:0007165 | signal transduction | 10821867 |
| PDGFRB | GO:0010863 | positive regulation of phospholipase C activity | 1653029 |
| PDGFRB | GO:0018108 | peptidyl-tyrosine phosphorylation | 1653029|2536956|2850496 |
| PDGFRB | GO:0030335 | positive regulation of cell migration | 17470632 |
| PDGFRB | GO:0032516 | positive regulation of phosphoprotein phosphatase activity | 7691811 |
| PDGFRB | GO:0038091 | positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway | 17470632 |
| PDGFRB | GO:0043552 | positive regulation of phosphatidylinositol 3-kinase activity | 1314164 |
| PDGFRB | GO:0046777 | protein autophosphorylation | 1314164|2536956|2850496 |
| PDGFRB | GO:0048008 | platelet-derived growth factor receptor signaling pathway | 1314164|2536956 |
| PDGFRB | GO:0060326 | cell chemotaxis | 2554309|17991872 |
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Gene structures and expression levels for PDGFRB |
| Skipped 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. |
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ENSG00000113721
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| STG | UP | ENST00000261799.9 | PDGFRB-201:protein_coding:PDGFRB | 4.915401e+02 | 8.475474e-01 | 6.264348e-06 | 2.006182e-03 |
| STG | UP | ENST00000520229.1 | PDGFRB-206:retained_intron:PDGFRB | 9.825218e+00 | 8.776580e-01 | 9.469954e-04 | 3.727288e-02 |
| CB | DOWN | ENST00000520851.1 | PDGFRB-208:lncRNA:PDGFRB | 8.559972e+00 | -1.107207e+00 | 2.291754e-06 | 3.034678e-05 |
| TC | UP | ENST00000517957.1 | PDGFRB-204:protein_coding:PDGFRB | 1.952039e+00 | 1.255263e+00 | 6.910167e-05 | 1.205957e-03 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PDGFRB |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_118427 | chr5 | 150135828:150135878:150137008:150137053:150155397:150155627 | 150137008:150137053 |
| exon_skip_50854 | chr5 | 150135555:150135878:150137008:150137053:150155397:150155627 | 150137008:150137053 |
| exon_skip_56426 | chr5 | 150123042:150123201:150124250:150124360:150124727:150124831 | 150124250:150124360 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for PDGFRB |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000261799 | 150124250 | 150124360 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PDGFRB |
p-ENSG00000113721_img4.png |
| Loci of skipped exons in ROSMAP 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 |
| Loci of skipped exons in MSBB 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 |
| Loci of skipped exons in Mayo 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 |
| ENST00000261799 | 5734 | 1106 | 150124250 | 150124360 | 2383 | 2492 | 637 | 674 |
| 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 feature | Description of feature |
| 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 feature | Description of feature |
| 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 feature | Description of feature |
| P09619 | 637 | 674 | 337 | 1106 | Alternative sequence | ID=VSP_056009;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:18593464;Dbxref=PMID:18593464 |
| P09619 | 637 | 674 | 33 | 1106 | Chain | ID=PRO_0000016757;Note=Platelet-derived growth factor receptor beta |
| P09619 | 637 | 674 | 600 | 962 | Domain | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| P09619 | 637 | 674 | 658 | 658 | Natural variant | ID=VAR_069320;Note=In IBGC4%3B no effect on protein abundance%3B loss of PDGF beta receptor activity. L->P;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:23255827,ECO:0000269|PubMed:24065723,ECO:0000269|PubMed:26599395;Dbxre |
| P09619 | 637 | 674 | 660 | 660 | Natural variant | ID=VAR_069926;Note=In IMF1. P->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23731542;Dbxref=dbSNP:rs144050370,PMID:23731542 |
| P09619 | 637 | 674 | 665 | 665 | Natural variant | ID=VAR_075866;Note=In PENTT%3B gain of function in protein tyrosine kinase activity%3B shows ligand-independent constitutive signaling. V->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26279204;Dbxref=PMID:26279204 |
| P09619 | 637 | 674 | 554 | 1106 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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3'-UTR located exon skipping events that lost miRNA binding sites in PDGFRB |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for PDGFRB |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - 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 |
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AD stage-associated exon skippint events for PDGFRB |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PDGFRB |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for PDGFRB |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| IFG | RBM4 | exon_skip_50854 | 4.105651e-01 | 3.721570e-02 |
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RelatedDrugs for PDGFRB |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| P09619 | approved|investigational | DB00102 | Becaplermin | biotech | P09619 |
| P09619 | approved|investigational | DB00398 | Sorafenib | small molecule | P09619 |
| P09619 | approved | DB00619 | Imatinib | small molecule | P09619 |
| P09619 | approved|investigational | DB01254 | Dasatinib | small molecule | P09619 |
| P09619 | approved|investigational | DB01268 | Sunitinib | small molecule | P09619 |
| P09619 | approved | DB06589 | Pazopanib | small molecule | P09619 |
| P09619 | approved|investigational | DB06595 | Midostaurin | small molecule | P09619 |
| P09619 | approved | DB08896 | Regorafenib | small molecule | P09619 |
| P09619 | approved|investigational | DB12010 | Fostamatinib | small molecule | P09619 |
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RelatedDiseases for PDGFRB |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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