|
||||||
|
![]() | |
![]() | |
![]() | |
![]() | |
![]() | Open reading frame (ORF) annotation in the exon skipping event |
![]() | |
![]() | |
![]() | Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
![]() | Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
![]() | |
![]() |
Gene summary for PDCD10 |
Gene summary |
| Gene information | Gene symbol | PDCD10 | Gene ID | 11235 |
| Gene name | programmed cell death 10 | |
| Synonyms | CCM3|TFAR15 | |
| Cytomap | 3q26.1 | |
| Type of gene | protein-coding | |
| Description | programmed cell death protein 10TF-1 cell apoptosis-related protein 15apoptosis-related protein 15cerebral cavernous malformations 3 protein | |
| Modification date | 20180522 | |
| UniProtAcc | Q9BUL8 | |
| Context | PubMed: PDCD10 [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 |
| PDCD10 | GO:0008284 | positive regulation of cell proliferation | 17360971|23541896 |
| PDCD10 | GO:0030335 | positive regulation of cell migration | 23541896 |
| PDCD10 | GO:0032874 | positive regulation of stress-activated MAPK cascade | 22652780 |
| PDCD10 | GO:0042542 | response to hydrogen peroxide | 22291017 |
| PDCD10 | GO:0043066 | negative regulation of apoptotic process | 17360971 |
| PDCD10 | GO:0043406 | positive regulation of MAP kinase activity | 17360971 |
Top |
Exon skipping events across known transcript of Ensembl for PDCD10 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. |
![]() |
Top |
Gene isoform structures and expression levels for PDCD10 |
Expression levels of gene isoforms across TCGA. |
Expression levels of gene isoforms across GTEx. |
Top |
Exon skipping events with PSIs in TCGA for PDCD10 |
Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_389792 | 3 | 167402126:167402177:167405021:167405104:167405402:167405481 | 167405021:167405104 | ENSG00000114209.10 | ENST00000470131.1,ENST00000492396.1,ENST00000497056.2,ENST00000461494.1,ENST00000475915.2,ENST00000392750.2,ENST00000473645.2 |
| exon_skip_389797 | 3 | 167405025:167405104:167405402:167405481:167413383:167413510 | 167405402:167405481 | ENSG00000114209.10 | ENST00000470131.1,ENST00000492396.1,ENST00000497056.2,ENST00000461494.1,ENST00000475915.2,ENST00000392750.2,ENST00000473645.2,ENST00000487947.2,ENST00000471885.1 |
| exon_skip_389798 | 3 | 167414827:167414914:167415638:167415766:167422629:167422683 | 167415638:167415766 | ENSG00000114209.10 | ENST00000494502.2 |
| exon_skip_389799 | 3 | 167414827:167414914:167422629:167422683:167437849:167437886 | 167422629:167422683 | ENSG00000114209.10 | ENST00000470131.1,ENST00000497056.2,ENST00000462725.2,ENST00000461494.1,ENST00000475915.2,ENST00000392750.2,ENST00000479121.1,ENST00000492139.1,ENST00000473645.2,ENST00000483451.1,ENST00000487947.2,ENST00000464360.1,ENST00000471885.1 |
| exon_skip_389811 | 3 | 167422629:167422683:167437849:167438061:167443188:167443261 | 167437849:167438061 | ENSG00000114209.10 | ENST00000462725.2,ENST00000475915.2,ENST00000494502.2,ENST00000473645.2,ENST00000464360.1 |
| exon_skip_389812 | 3 | 167422629:167422683:167437849:167438061:167452593:167452620 | 167437849:167438061 | ENSG00000114209.10 | ENST00000481136.1,ENST00000497056.2 |
| exon_skip_389823 | 3 | 167437992:167438061:167443188:167443261:167452001:167452034 | 167443188:167443261 | ENSG00000114209.10 | ENST00000464360.1 |
| exon_skip_389825 | 3 | 167437992:167438061:167443188:167443261:167452219:167452305 | 167443188:167443261 | ENSG00000114209.10 | ENST00000462725.2 |
| exon_skip_389826 | 3 | 167437992:167438061:167443188:167443261:167452246:167452270 | 167443188:167443261 | ENSG00000114209.10 | ENST00000475915.2 |
| exon_skip_389828 | 3 | 167437992:167438061:167443188:167443261:167452593:167452620 | 167443188:167443261 | ENSG00000114209.10 | ENST00000494502.2,ENST00000473645.2 |
| exon_skip_389832 | 3 | 167437992:167438061:167452001:167452034:167452593:167452620 | 167452001:167452034 | ENSG00000114209.10 | ENST00000471885.1 |
| exon_skip_389836 | 3 | 167437992:167438061:167452001:167452133:167452593:167452620 | 167452001:167452133 | ENSG00000114209.10 | ENST00000470131.1 |
| exon_skip_389838 | 3 | 167437992:167438061:167452001:167452138:167452593:167452620 | 167452001:167452138 | ENSG00000114209.10 | ENST00000492139.1 |
| exon_skip_389843 | 3 | 167443188:167443261:167452001:167452133:167452593:167452620 | 167452001:167452133 | ENSG00000114209.10 | ENST00000464360.1 |
PSI values of skipped exons in TCGA. |
Top |
Exon skipping events with PSIs in GTEx for PDCD10 |
Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_389792 | 3 | 167402126:167402177:167405021:167405104:167405402:167405481 | 167405021:167405104 | ENSG00000114209.10 | ENST00000392750.2,ENST00000473645.2,ENST00000497056.2,ENST00000492396.1,ENST00000461494.1,ENST00000470131.1,ENST00000475915.2 |
| exon_skip_389797 | 3 | 167405025:167405104:167405402:167405481:167413383:167413510 | 167405402:167405481 | ENSG00000114209.10 | ENST00000392750.2,ENST00000473645.2,ENST00000497056.2,ENST00000492396.1,ENST00000461494.1,ENST00000470131.1,ENST00000475915.2,ENST00000487947.2,ENST00000471885.1 |
| exon_skip_389798 | 3 | 167414827:167414914:167415638:167415766:167422629:167422683 | 167415638:167415766 | ENSG00000114209.10 | ENST00000494502.2 |
| exon_skip_389799 | 3 | 167414827:167414914:167422629:167422683:167437849:167437886 | 167422629:167422683 | ENSG00000114209.10 | ENST00000392750.2,ENST00000473645.2,ENST00000497056.2,ENST00000461494.1,ENST00000470131.1,ENST00000475915.2,ENST00000487947.2,ENST00000471885.1,ENST00000479121.1,ENST00000462725.2,ENST00000492139.1,ENST00000483451.1,ENST00000464360.1 |
| exon_skip_389811 | 3 | 167422629:167422683:167437849:167438061:167443188:167443261 | 167437849:167438061 | ENSG00000114209.10 | ENST00000473645.2,ENST00000475915.2,ENST00000462725.2,ENST00000494502.2,ENST00000464360.1 |
| exon_skip_389812 | 3 | 167422629:167422683:167437849:167438061:167452593:167452620 | 167437849:167438061 | ENSG00000114209.10 | ENST00000497056.2,ENST00000481136.1 |
| exon_skip_389823 | 3 | 167437992:167438061:167443188:167443261:167452001:167452034 | 167443188:167443261 | ENSG00000114209.10 | ENST00000464360.1 |
| exon_skip_389825 | 3 | 167437992:167438061:167443188:167443261:167452219:167452305 | 167443188:167443261 | ENSG00000114209.10 | ENST00000462725.2 |
| exon_skip_389826 | 3 | 167437992:167438061:167443188:167443261:167452246:167452270 | 167443188:167443261 | ENSG00000114209.10 | ENST00000475915.2 |
| exon_skip_389828 | 3 | 167437992:167438061:167443188:167443261:167452593:167452620 | 167443188:167443261 | ENSG00000114209.10 | ENST00000473645.2,ENST00000494502.2 |
| exon_skip_389832 | 3 | 167437992:167438061:167452001:167452034:167452593:167452620 | 167452001:167452034 | ENSG00000114209.10 | ENST00000471885.1 |
| exon_skip_389836 | 3 | 167437992:167438061:167452001:167452133:167452593:167452620 | 167452001:167452133 | ENSG00000114209.10 | ENST00000470131.1 |
| exon_skip_389838 | 3 | 167437992:167438061:167452001:167452138:167452593:167452620 | 167452001:167452138 | ENSG00000114209.10 | ENST00000492139.1 |
| exon_skip_389843 | 3 | 167443188:167443261:167452001:167452133:167452593:167452620 | 167452001:167452133 | ENSG00000114209.10 | ENST00000464360.1 |
PSI values of skipped exons in GTEx. |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for PDCD10 |
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 |
| ENST00000473645 | 167437849 | 167438061 | 3UTR-3CDS |
| ENST00000497056 | 167437849 | 167438061 | 3UTR-3CDS |
| ENST00000473645 | 167443188 | 167443261 | 3UTR-3UTR |
| ENST00000470131 | 167452001 | 167452133 | 3UTR-3UTR |
| ENST00000392750 | 167405021 | 167405104 | Frame-shift |
| ENST00000461494 | 167405021 | 167405104 | Frame-shift |
| ENST00000470131 | 167405021 | 167405104 | Frame-shift |
| ENST00000473645 | 167405021 | 167405104 | Frame-shift |
| ENST00000497056 | 167405021 | 167405104 | Frame-shift |
| ENST00000392750 | 167405402 | 167405481 | Frame-shift |
| ENST00000461494 | 167405402 | 167405481 | Frame-shift |
| ENST00000470131 | 167405402 | 167405481 | Frame-shift |
| ENST00000473645 | 167405402 | 167405481 | Frame-shift |
| ENST00000497056 | 167405402 | 167405481 | Frame-shift |
| ENST00000392750 | 167422629 | 167422683 | In-frame |
| ENST00000461494 | 167422629 | 167422683 | In-frame |
| ENST00000470131 | 167422629 | 167422683 | In-frame |
| ENST00000473645 | 167422629 | 167422683 | In-frame |
| ENST00000497056 | 167422629 | 167422683 | 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 |
| ENST00000473645 | 167437849 | 167438061 | 3UTR-3CDS |
| ENST00000497056 | 167437849 | 167438061 | 3UTR-3CDS |
| ENST00000473645 | 167443188 | 167443261 | 3UTR-3UTR |
| ENST00000470131 | 167452001 | 167452133 | 3UTR-3UTR |
| ENST00000392750 | 167405021 | 167405104 | Frame-shift |
| ENST00000461494 | 167405021 | 167405104 | Frame-shift |
| ENST00000470131 | 167405021 | 167405104 | Frame-shift |
| ENST00000473645 | 167405021 | 167405104 | Frame-shift |
| ENST00000497056 | 167405021 | 167405104 | Frame-shift |
| ENST00000392750 | 167405402 | 167405481 | Frame-shift |
| ENST00000461494 | 167405402 | 167405481 | Frame-shift |
| ENST00000470131 | 167405402 | 167405481 | Frame-shift |
| ENST00000473645 | 167405402 | 167405481 | Frame-shift |
| ENST00000497056 | 167405402 | 167405481 | Frame-shift |
| ENST00000392750 | 167422629 | 167422683 | In-frame |
| ENST00000461494 | 167422629 | 167422683 | In-frame |
| ENST00000470131 | 167422629 | 167422683 | In-frame |
| ENST00000473645 | 167422629 | 167422683 | In-frame |
| ENST00000497056 | 167422629 | 167422683 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for PDCD10 |
Exon skipping at the protein sequence level and followed lost functional features.* Click on the image to enlarge it in a new window. |
![]() |
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 |
| ENST00000392750 | 2084 | 212 | 167422629 | 167422683 | 515 | 568 | 32 | 50 |
| ENST00000461494 | 951 | 212 | 167422629 | 167422683 | 326 | 379 | 32 | 50 |
| ENST00000470131 | 1043 | 212 | 167422629 | 167422683 | 432 | 485 | 32 | 50 |
| ENST00000473645 | 1377 | 212 | 167422629 | 167422683 | 420 | 473 | 32 | 50 |
| ENST00000497056 | 1293 | 212 | 167422629 | 167422683 | 338 | 391 | 32 | 50 |
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 |
| ENST00000392750 | 2084 | 212 | 167422629 | 167422683 | 515 | 568 | 32 | 50 |
| ENST00000461494 | 951 | 212 | 167422629 | 167422683 | 326 | 379 | 32 | 50 |
| ENST00000470131 | 1043 | 212 | 167422629 | 167422683 | 432 | 485 | 32 | 50 |
| ENST00000473645 | 1377 | 212 | 167422629 | 167422683 | 420 | 473 | 32 | 50 |
| ENST00000497056 | 1293 | 212 | 167422629 | 167422683 | 338 | 391 | 32 | 50 |
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 |
| Q9BUL8 | 32 | 50 | 1 | 212 | Chain | ID=PRO_0000187562;Note=Programmed cell death protein 10 |
| Q9BUL8 | 32 | 50 | 1 | 212 | Chain | ID=PRO_0000187562;Note=Programmed cell death protein 10 |
| Q9BUL8 | 32 | 50 | 1 | 212 | Chain | ID=PRO_0000187562;Note=Programmed cell death protein 10 |
| Q9BUL8 | 32 | 50 | 1 | 212 | Chain | ID=PRO_0000187562;Note=Programmed cell death protein 10 |
| Q9BUL8 | 32 | 50 | 1 | 212 | Chain | ID=PRO_0000187562;Note=Programmed cell death protein 10 |
| Q9BUL8 | 32 | 50 | 26 | 34 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
| Q9BUL8 | 32 | 50 | 26 | 34 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
| Q9BUL8 | 32 | 50 | 26 | 34 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
| Q9BUL8 | 32 | 50 | 26 | 34 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
| Q9BUL8 | 32 | 50 | 26 | 34 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
| Q9BUL8 | 32 | 50 | 38 | 54 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
| Q9BUL8 | 32 | 50 | 38 | 54 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
| Q9BUL8 | 32 | 50 | 38 | 54 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
| Q9BUL8 | 32 | 50 | 38 | 54 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
| Q9BUL8 | 32 | 50 | 38 | 54 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
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 |
| Q9BUL8 | 32 | 50 | 1 | 212 | Chain | ID=PRO_0000187562;Note=Programmed cell death protein 10 |
| Q9BUL8 | 32 | 50 | 1 | 212 | Chain | ID=PRO_0000187562;Note=Programmed cell death protein 10 |
| Q9BUL8 | 32 | 50 | 1 | 212 | Chain | ID=PRO_0000187562;Note=Programmed cell death protein 10 |
| Q9BUL8 | 32 | 50 | 1 | 212 | Chain | ID=PRO_0000187562;Note=Programmed cell death protein 10 |
| Q9BUL8 | 32 | 50 | 1 | 212 | Chain | ID=PRO_0000187562;Note=Programmed cell death protein 10 |
| Q9BUL8 | 32 | 50 | 26 | 34 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
| Q9BUL8 | 32 | 50 | 26 | 34 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
| Q9BUL8 | 32 | 50 | 26 | 34 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
| Q9BUL8 | 32 | 50 | 26 | 34 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
| Q9BUL8 | 32 | 50 | 26 | 34 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
| Q9BUL8 | 32 | 50 | 38 | 54 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
| Q9BUL8 | 32 | 50 | 38 | 54 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
| Q9BUL8 | 32 | 50 | 38 | 54 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
| Q9BUL8 | 32 | 50 | 38 | 54 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
| Q9BUL8 | 32 | 50 | 38 | 54 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH |
Top |
SNVs in the skipped exons for PDCD10 |
- Lollipop plot for presenting exon skipping associated SNVs.* Click on the image to enlarge it in a new window. |
- 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_389792 | 167405022 | 167405104 | 167405033 | 167405033 | Frame_Shift_Del | A | - | p.F182fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_389792 | 167405022 | 167405104 | 167405058 | 167405058 | Frame_Shift_Del | A | - | p.F174fs |
| LIHC | TCGA-DD-A3A1-01 | exon_skip_389792 | 167405022 | 167405104 | 167405062 | 167405062 | Frame_Shift_Del | T | - | p.S173fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_389811 exon_skip_389812 | 167437850 | 167438061 | 167437882 | 167437882 | Frame_Shift_Del | G | - | p.L22fs |
| SKCM | TCGA-FW-A3TU-06 | exon_skip_389792 | 167405022 | 167405104 | 167405098 | 167405098 | Nonsense_Mutation | C | A | p.E161* |
| LUSC | TCGA-66-2800-01 | exon_skip_389799 | 167422630 | 167422683 | 167422680 | 167422680 | Nonsense_Mutation | C | A | p.E34* |
| HNSC | TCGA-BA-4078-01 | exon_skip_389811 exon_skip_389812 | 167437850 | 167438061 | 167437849 | 167437849 | Splice_Site | C | T | p.E32_splice |
- Depth of coverage in the three exons composing exon skipping event |
- 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 |
| NCIH1694_LUNG | 167405403 | 167405481 | 167405431 | 167405435 | Frame_Shift_Del | AAGAC | - | p.VF148fs |
| NCIH1694_LUNG | 167405403 | 167405481 | 167405439 | 167405439 | Frame_Shift_Del | A | - | p.N147fs |
| NCIH1694_LUNG | 167405403 | 167405481 | 167405432 | 167405437 | In_Frame_Del | AGACAT | - | p.147_149NVF>I |
| JHU028_LUNG | 167405022 | 167405104 | 167405026 | 167405026 | Missense_Mutation | C | A | p.G185C |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 167405022 | 167405104 | 167405049 | 167405049 | Missense_Mutation | G | A | p.T177I |
| PEDS015T_SOFT_TISSUE | 167405022 | 167405104 | 167405101 | 167405101 | Missense_Mutation | G | C | p.L160V |
| SNU349_KIDNEY | 167405403 | 167405481 | 167405407 | 167405407 | Missense_Mutation | C | T | p.R157H |
| EW16_BONE | 167405403 | 167405481 | 167405420 | 167405420 | Missense_Mutation | G | T | p.Q153K |
| CCK81_LARGE_INTESTINE | 167422630 | 167422683 | 167422649 | 167422649 | Missense_Mutation | A | G | p.L44P |
| CAL12T_LUNG | 167422630 | 167422683 | 167422654 | 167422654 | Missense_Mutation | C | G | p.Q42H |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 167437850 | 167438061 | 167437878 | 167437878 | Missense_Mutation | T | A | p.Y23F |
| SNU81_LARGE_INTESTINE | 167405403 | 167405481 | 167405459 | 167405459 | Nonsense_Mutation | C | A | p.E140* |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PDCD10 |
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 |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PDCD10 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PDCD10 |
Top |
RelatedDrugs for PDCD10 |
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 |
Top |
RelatedDiseases for PDCD10 |
Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |