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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 PDCD5 |
Gene summary |
Gene information | Gene symbol | PDCD5 | Gene ID | 9141 |
Gene name | programmed cell death 5 | |
Synonyms | TFAR19 | |
Cytomap | 19q13.11 | |
Type of gene | protein-coding | |
Description | programmed cell death protein 5TF-1 cell apoptosis-related protein 19TF1 cell apoptosis-related gene 19TFAR19 novel apoptosis-related | |
Modification date | 20180523 | |
UniProtAcc | O14737 | |
Context | PubMed: PDCD5 [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 |
PDCD5 | GO:0010628 | positive regulation of gene expression | 24012345 |
PDCD5 | GO:0071560 | cellular response to transforming growth factor beta stimulus | 24012345 |
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Exon skipping events across known transcript of Ensembl for PDCD5 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 PDCD5 |
Expression levels of gene isoforms across TCGA. |
Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for PDCD5 |
Information of exkip skipping event in TCGA. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
exon_skip_304792 | 19 | 33073100:33073138:33075855:33075917:33076721:33076813 | 33075855:33075917 | ENSG00000105185.7 | ENST00000590247.2,ENST00000586035.1,ENST00000419343.3 |
exon_skip_304793 | 19 | 33073100:33073138:33075855:33075917:33077763:33077835 | 33075855:33075917 | ENSG00000105185.7 | ENST00000592786.1 |
exon_skip_304795 | 19 | 33073100:33073138:33075860:33075917:33076721:33076813 | 33075860:33075917 | ENSG00000105185.7 | ENST00000221784.4 |
exon_skip_304809 | 19 | 33075863:33075917:33076721:33076813:33077763:33077835 | 33076721:33076813 | ENSG00000105185.7 | ENST00000590247.2,ENST00000586035.1,ENST00000221784.4,ENST00000586316.1 |
exon_skip_304815 | 19 | 33075863:33075917:33077763:33077835:33078158:33078203 | 33077763:33077835 | ENSG00000105185.7 | ENST00000592786.1 |
exon_skip_304818 | 19 | 33076721:33076813:33077763:33077835:33078158:33078203 | 33077763:33077835 | ENSG00000105185.7 | ENST00000590247.2,ENST00000586035.1,ENST00000221784.4,ENST00000586316.1 |
PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PDCD5 |
Information of exkip skipping event in GTEx |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
exon_skip_304792 | 19 | 33073100:33073138:33075855:33075917:33076721:33076813 | 33075855:33075917 | ENSG00000105185.7 | ENST00000590247.2,ENST00000419343.3,ENST00000586035.1 |
exon_skip_304793 | 19 | 33073100:33073138:33075855:33075917:33077763:33077835 | 33075855:33075917 | ENSG00000105185.7 | ENST00000592786.1 |
exon_skip_304795 | 19 | 33073100:33073138:33075860:33075917:33076721:33076813 | 33075860:33075917 | ENSG00000105185.7 | ENST00000221784.4 |
exon_skip_304809 | 19 | 33075863:33075917:33076721:33076813:33077763:33077835 | 33076721:33076813 | ENSG00000105185.7 | ENST00000590247.2,ENST00000221784.4,ENST00000586035.1,ENST00000586316.1 |
exon_skip_304815 | 19 | 33075863:33075917:33077763:33077835:33078158:33078203 | 33077763:33077835 | ENSG00000105185.7 | ENST00000592786.1 |
exon_skip_304818 | 19 | 33076721:33076813:33077763:33077835:33078158:33078203 | 33077763:33077835 | ENSG00000105185.7 | ENST00000590247.2,ENST00000221784.4,ENST00000586035.1,ENST00000586316.1 |
PSI values of skipped exons in GTEx. |
* Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for PDCD5 |
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 |
ENST00000590247 | 33075855 | 33075917 | Frame-shift |
ENST00000590247 | 33076721 | 33076813 | Frame-shift |
ENST00000590247 | 33077763 | 33077835 | 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 |
ENST00000590247 | 33075855 | 33075917 | Frame-shift |
ENST00000590247 | 33076721 | 33076813 | Frame-shift |
ENST00000590247 | 33077763 | 33077835 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PDCD5 |
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 |
ENST00000590247 | 716 | 125 | 33077763 | 33077835 | 453 | 524 | 86 | 110 |
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 |
ENST00000590247 | 716 | 125 | 33077763 | 33077835 | 453 | 524 | 86 | 110 |
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 |
O14737 | 86 | 110 | 89 | 125 | Alternative sequence | ID=VSP_056203;Note=In isoform 2. EQGLIEILKKVSQQTEKTTTVKFNRRKVMDSDEDDDY->LDSLEELYCYLLYQNMASKGQLHLHWITEFLLTLRRNCWRE;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
O14737 | 86 | 110 | 100 | 102 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2K6B |
O14737 | 86 | 110 | 2 | 125 | Chain | ID=PRO_0000121545;Note=Programmed cell death protein 5 |
O14737 | 86 | 110 | 89 | 99 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CRU |
O14737 | 86 | 110 | 104 | 104 | Sequence conflict | Note=E->K;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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 |
O14737 | 86 | 110 | 89 | 125 | Alternative sequence | ID=VSP_056203;Note=In isoform 2. EQGLIEILKKVSQQTEKTTTVKFNRRKVMDSDEDDDY->LDSLEELYCYLLYQNMASKGQLHLHWITEFLLTLRRNCWRE;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
O14737 | 86 | 110 | 100 | 102 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2K6B |
O14737 | 86 | 110 | 2 | 125 | Chain | ID=PRO_0000121545;Note=Programmed cell death protein 5 |
O14737 | 86 | 110 | 89 | 99 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CRU |
O14737 | 86 | 110 | 104 | 104 | Sequence conflict | Note=E->K;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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SNVs in the skipped exons for PDCD5 |
- 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-G3-A3CJ-01 | exon_skip_304809 | 33076722 | 33076813 | 33076757 | 33076757 | Frame_Shift_Del | A | - | p.K68fs |
KIRP | TCGA-MH-A561-01 | exon_skip_304815 exon_skip_304818 | 33077764 | 33077835 | 33077794 | 33077794 | Frame_Shift_Del | A | - | p.K97fs |
KIRP | TCGA-MH-A561-01 | exon_skip_304815 exon_skip_304818 | 33077764 | 33077835 | 33077794 | 33077794 | Frame_Shift_Del | A | - | p.L96fs |
UCEC | TCGA-AX-A05S-01 | exon_skip_304815 exon_skip_304818 | 33077764 | 33077835 | 33077794 | 33077794 | Frame_Shift_Del | A | - | p.K97fs |
UCS | TCGA-NA-A5I1-01 | exon_skip_304815 exon_skip_304818 | 33077764 | 33077835 | 33077794 | 33077794 | Nonsense_Mutation | A | T | p.K97* |
UCS | TCGA-NA-A5I1-01 | exon_skip_304815 exon_skip_304818 | 33077764 | 33077835 | 33077794 | 33077794 | Nonsense_Mutation | A | T | p.K97X |
- 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 |
CAL39_VULVA | 33076722 | 33076813 | 33076737 | 33076737 | Missense_Mutation | T | G | p.L61R |
HEC1B_ENDOMETRIUM | 33077764 | 33077835 | 33077788 | 33077788 | Missense_Mutation | A | G | p.I95V |
HS274T_BREAST | 33077764 | 33077835 | 33077824 | 33077824 | Missense_Mutation | A | G | p.T107A |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PDCD5 |
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 PDCD5 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PDCD5 |
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RelatedDrugs for PDCD5 |
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 PDCD5 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |