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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 PDK3 |
 Gene summary |
| Gene information | Gene symbol | PDK3 | Gene ID | 5165 |
| Gene name | pyruvate dehydrogenase kinase 3 | |
| Synonyms | CMTX6|GS1-358P8.4 | |
| Cytomap | Xp22.11 | |
| Type of gene | protein-coding | |
| Description | pyruvate dehydrogenase kinase, isozyme 3[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 3, mitochondrialpyruvate dehydrogenase kinase, isoenzyme 3pyruvate dehydrogenase, lipoamide, kinase isozyme 3, mitochondrial | |
| Modification date | 20180519 | |
| UniProtAcc | Q15120 | |
| Context | PubMed: PDK3 [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 |
| PDK3 | GO:0018105 | peptidyl-serine phosphorylation | 11486000 |
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Exon skipping events across known transcript of Ensembl for PDK3 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 PDK3 |
| 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 PDK3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_509679 | X | 24483572:24483678:24512858:24513000:24516945:24517017 | 24512858:24513000 | ENSG00000067992.8 | ENST00000441463.2 |
| exon_skip_509681 | X | 24523325:24523415:24537049:24537127:24544314:24544391 | 24537049:24537127 | ENSG00000067992.8 | ENST00000379162.4,ENST00000441463.2 |
| exon_skip_509683 | X | 24545690:24545792:24546192:24546303:24549773:24549887 | 24546192:24546303 | ENSG00000067992.8 | ENST00000379162.4,ENST00000441463.2 |
| exon_skip_509685 | X | 24546192:24546303:24549773:24549887:24552045:24552185 | 24549773:24549887 | ENSG00000067992.8 | ENST00000379162.4,ENST00000441463.2 |
| exon_skip_509686 | X | 24549773:24549887:24552045:24552185:24557250:24557954 | 24552045:24552185 | ENSG00000067992.8 | ENST00000441463.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PDK3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_509679 | X | 24483572:24483678:24512858:24513000:24516945:24517017 | 24512858:24513000 | ENSG00000067992.8 | ENST00000441463.2 |
| exon_skip_509683 | X | 24545690:24545792:24546192:24546303:24549773:24549887 | 24546192:24546303 | ENSG00000067992.8 | ENST00000379162.4,ENST00000441463.2 |
| exon_skip_509685 | X | 24546192:24546303:24549773:24549887:24552045:24552185 | 24549773:24549887 | ENSG00000067992.8 | ENST00000379162.4,ENST00000441463.2 |
| exon_skip_509686 | X | 24549773:24549887:24552045:24552185:24557250:24557954 | 24552045:24552185 | ENSG00000067992.8 | ENST00000441463.2 |
| 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 PDK3 |
| 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 |
| ENST00000379162 | 24537049 | 24537127 | In-frame |
| ENST00000379162 | 24546192 | 24546303 | In-frame |
| ENST00000379162 | 24549773 | 24549887 | 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 |
| ENST00000379162 | 24546192 | 24546303 | In-frame |
| ENST00000379162 | 24549773 | 24549887 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PDK3 |
| 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 |
| ENST00000379162 | 1826 | 406 | 24537049 | 24537127 | 831 | 908 | 198 | 224 |
| ENST00000379162 | 1826 | 406 | 24546192 | 24546303 | 1088 | 1198 | 284 | 321 |
| ENST00000379162 | 1826 | 406 | 24549773 | 24549887 | 1199 | 1312 | 321 | 359 |
| 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 |
| ENST00000379162 | 1826 | 406 | 24546192 | 24546303 | 1088 | 1198 | 284 | 321 |
| ENST00000379162 | 1826 | 406 | 24549773 | 24549887 | 1199 | 1312 | 321 | 359 |
| 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 |
| Q15120 | 198 | 224 | 218 | 224 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8O |
| Q15120 | 198 | 224 | 131 | 362 | Domain | Note=Histidine kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00107 |
| Q15120 | 198 | 224 | 193 | 212 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8O |
| Q15120 | 198 | 224 | 219 | 219 | Natural variant | ID=VAR_042297;Note=In a head %26 neck squamous cell carcinoma sample%3B somatic mutation. E->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17344846;Dbxref=PMID:17344846 |
| Q15120 | 284 | 321 | 278 | 287 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8O |
| Q15120 | 284 | 321 | 287 | 287 | Binding site | Note=ATP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15861126;Dbxref=PMID:15861126 |
| Q15120 | 284 | 321 | 131 | 362 | Domain | Note=Histidine kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00107 |
| Q15120 | 284 | 321 | 294 | 297 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8O |
| Q15120 | 284 | 321 | 298 | 301 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8O |
| Q15120 | 284 | 321 | 306 | 307 | Nucleotide binding | Note=ATP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15861126;Dbxref=PMID:15861126 |
| Q15120 | 284 | 321 | 303 | 305 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8O |
| Q15120 | 321 | 359 | 323 | 325 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8P |
| Q15120 | 321 | 359 | 341 | 347 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8O |
| Q15120 | 321 | 359 | 351 | 360 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8O |
| Q15120 | 321 | 359 | 131 | 362 | Domain | Note=Histidine kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00107 |
| Q15120 | 321 | 359 | 327 | 337 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8O |
| Q15120 | 321 | 359 | 334 | 334 | Natural variant | ID=VAR_070083;Note=Y->S;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23297365;Dbxref=PMID:23297365 |
| Q15120 | 321 | 359 | 323 | 328 | Nucleotide binding | Note=ATP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15861126;Dbxref=PMID:15861126 |
| Q15120 | 321 | 359 | 348 | 350 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8O |
| 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 |
| Q15120 | 284 | 321 | 278 | 287 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8O |
| Q15120 | 284 | 321 | 287 | 287 | Binding site | Note=ATP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15861126;Dbxref=PMID:15861126 |
| Q15120 | 284 | 321 | 131 | 362 | Domain | Note=Histidine kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00107 |
| Q15120 | 284 | 321 | 294 | 297 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8O |
| Q15120 | 284 | 321 | 298 | 301 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8O |
| Q15120 | 284 | 321 | 306 | 307 | Nucleotide binding | Note=ATP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15861126;Dbxref=PMID:15861126 |
| Q15120 | 284 | 321 | 303 | 305 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8O |
| Q15120 | 321 | 359 | 323 | 325 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8P |
| Q15120 | 321 | 359 | 341 | 347 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8O |
| Q15120 | 321 | 359 | 351 | 360 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8O |
| Q15120 | 321 | 359 | 131 | 362 | Domain | Note=Histidine kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00107 |
| Q15120 | 321 | 359 | 327 | 337 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8O |
| Q15120 | 321 | 359 | 334 | 334 | Natural variant | ID=VAR_070083;Note=Y->S;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23297365;Dbxref=PMID:23297365 |
| Q15120 | 321 | 359 | 323 | 328 | Nucleotide binding | Note=ATP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15861126;Dbxref=PMID:15861126 |
| Q15120 | 321 | 359 | 348 | 350 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1Y8O |
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SNVs in the skipped exons for PDK3 |
| - 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-A3A0-01 | exon_skip_509679 | 24512859 | 24513000 | 24512960 | 24512960 | Frame_Shift_Del | A | - | p.N70fs |
| LIHC | TCGA-BC-A112-01 | exon_skip_509686 | 24552046 | 24552185 | 24552079 | 24552080 | Frame_Shift_Ins | - | T | p.F371fs |
| UCEC | TCGA-BS-A0UF-01 | exon_skip_509679 | 24512859 | 24513000 | 24512886 | 24512886 | Nonsense_Mutation | C | A | p.S45* |
| UCEC | TCGA-AX-A063-01 | exon_skip_509683 | 24546193 | 24546303 | 24546223 | 24546223 | Nonsense_Mutation | C | T | p.R295* |
| ESCA | TCGA-ZR-A9CJ-01 | exon_skip_509686 | 24552046 | 24552185 | 24552067 | 24552067 | Nonsense_Mutation | G | T | p.E367* |
| ESCA | TCGA-ZR-A9CJ-01 | exon_skip_509686 | 24552046 | 24552185 | 24552067 | 24552067 | Nonsense_Mutation | G | T | p.E367X |
| LIHC | TCGA-G3-A7M6-01 | exon_skip_509679 | 24512859 | 24513000 | 24513001 | 24513001 | Splice_Site | G | C | . |
| - 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 |
| SNUC5_LARGE_INTESTINE | 24512859 | 24513000 | 24512936 | 24512936 | Missense_Mutation | A | G | p.R62G |
| ISHIKAWAHERAKLIO02ER_ENDOMETRIUM | 24512859 | 24513000 | 24512976 | 24512976 | Missense_Mutation | C | A | p.P75H |
| BB49HNC_UPPER_AERODIGESTIVE_TRACT | 24537050 | 24537127 | 24537110 | 24537110 | Missense_Mutation | A | C | p.E219A |
| HCC2998_LARGE_INTESTINE | 24546193 | 24546303 | 24546232 | 24546232 | Missense_Mutation | G | T | p.D298Y |
| MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 24546193 | 24546303 | 24546236 | 24546236 | Missense_Mutation | G | A | p.R299H |
| JHUEM7_ENDOMETRIUM | 24552046 | 24552185 | 24552071 | 24552071 | Missense_Mutation | G | T | p.R368I |
| KM12_LARGE_INTESTINE | 24552046 | 24552185 | 24552092 | 24552092 | Missense_Mutation | C | T | p.S375F |
| WM1552C_SKIN | 24552046 | 24552185 | 24552179 | 24552179 | Missense_Mutation | C | T | p.A404V |
| NCIH2009_LUNG | 24552046 | 24552185 | 24552053 | 24552053 | Nonsense_Mutation | C | G | p.S362* |
| FTC133_THYROID | 24537050 | 24537127 | 24537126 | 24537126 | Splice_Site | T | C | p.N224N |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PDK3 |
| 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 PDK3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PDK3 |
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RelatedDrugs for PDK3 |
| 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 |
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RelatedDiseases for PDK3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| PDK3 | C3806702 | CHARCOT-MARIE-TOOTH DISEASE, X-LINKED DOMINANT, 6 | 1 | ORPHANET;UNIPROT |
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