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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 PDSS1 |
 Gene summary |
| Gene information | Gene symbol | PDSS1 | Gene ID | 23590 |
| Gene name | decaprenyl diphosphate synthase subunit 1 | |
| Synonyms | COQ1|COQ10D2|DPS|SPS|TPRT|TPT|TPT 1|hDPS1 | |
| Cytomap | 10p12.1 | |
| Type of gene | protein-coding | |
| Description | decaprenyl-diphosphate synthase subunit 1all-trans-decaprenyl-diphosphate synthase subunit 1coenzyme Q1 homologdecaprenyl pyrophosphate synthase subunit 1polyprenyl pyrophosphate synthetaseprenyl (decaprenyl) diphosphate synthase, subunit 1subunit 1 | |
| Modification date | 20180522 | |
| UniProtAcc | Q5T2R2 | |
| Context | PubMed: PDSS1 [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 |
| PDSS1 | GO:0006744 | ubiquinone biosynthetic process | 16262699 |
| PDSS1 | GO:0008299 | isoprenoid biosynthetic process | 16262699 |
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Exon skipping events across known transcript of Ensembl for PDSS1 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 PDSS1 |
| 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 PDSS1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_40205 | 10 | 26991090:26991123:26993605:26993670:26994214:26994323 | 26993605:26993670 | ENSG00000148459.11 | ENST00000376203.5,ENST00000376215.5 |
| exon_skip_40208 | 10 | 26993605:26993670:26994214:26994323:26998566:26998697 | 26994214:26994323 | ENSG00000148459.11 | ENST00000376203.5,ENST00000376215.5 |
| exon_skip_40213 | 10 | 26994236:26994323:26998566:26998697:27009063:27009288 | 26998566:26998697 | ENSG00000148459.11 | ENST00000473224.1 |
| exon_skip_40214 | 10 | 26994236:26994323:26998566:26998697:27009146:27009288 | 26998566:26998697 | ENSG00000148459.11 | ENST00000376203.5,ENST00000376215.5 |
| exon_skip_40218 | 10 | 27009271:27009288:27012734:27012846:27012942:27012948 | 27012734:27012846 | ENSG00000148459.11 | ENST00000473224.1,ENST00000491711.1,ENST00000376203.5,ENST00000376215.5 |
| exon_skip_40220 | 10 | 27024401:27024508:27029573:27029746:27031425:27031506 | 27029573:27029746 | ENSG00000148459.11 | ENST00000491711.1 |
| exon_skip_40223 | 10 | 27024394:27024508:27031425:27031506:27035261:27035470 | 27031425:27031506 | ENSG00000148459.11 | ENST00000376215.5,ENST00000470978.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PDSS1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_40205 | 10 | 26991090:26991123:26993605:26993670:26994214:26994323 | 26993605:26993670 | ENSG00000148459.11 | ENST00000376215.5,ENST00000376203.5 |
| exon_skip_40208 | 10 | 26993605:26993670:26994214:26994323:26998566:26998697 | 26994214:26994323 | ENSG00000148459.11 | ENST00000376215.5,ENST00000376203.5 |
| exon_skip_40213 | 10 | 26994236:26994323:26998566:26998697:27009063:27009288 | 26998566:26998697 | ENSG00000148459.11 | ENST00000473224.1 |
| exon_skip_40214 | 10 | 26994236:26994323:26998566:26998697:27009146:27009288 | 26998566:26998697 | ENSG00000148459.11 | ENST00000376215.5,ENST00000376203.5 |
| exon_skip_40218 | 10 | 27009271:27009288:27012734:27012846:27012942:27012948 | 27012734:27012846 | ENSG00000148459.11 | ENST00000376215.5,ENST00000376203.5,ENST00000473224.1,ENST00000491711.1 |
| exon_skip_40220 | 10 | 27024401:27024508:27029573:27029746:27031425:27031506 | 27029573:27029746 | ENSG00000148459.11 | ENST00000491711.1 |
| exon_skip_40223 | 10 | 27024394:27024508:27031425:27031506:27035261:27035470 | 27031425:27031506 | ENSG00000148459.11 | ENST00000376215.5,ENST00000470978.1 |
| 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 PDSS1 |
| 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 |
| ENST00000376215 | 26993605 | 26993670 | Frame-shift |
| ENST00000376215 | 26994214 | 26994323 | Frame-shift |
| ENST00000376215 | 26998566 | 26998697 | Frame-shift |
| ENST00000376215 | 27012734 | 27012846 | Frame-shift |
| ENST00000376215 | 27031425 | 27031506 | 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 |
| ENST00000376215 | 26993605 | 26993670 | Frame-shift |
| ENST00000376215 | 26994214 | 26994323 | Frame-shift |
| ENST00000376215 | 26998566 | 26998697 | Frame-shift |
| ENST00000376215 | 27012734 | 27012846 | Frame-shift |
| ENST00000376215 | 27031425 | 27031506 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PDSS1 |
| 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 |
| ENST00000376215 | 1643 | 415 | 27031425 | 27031506 | 1080 | 1160 | 342 | 369 |
| 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 |
| ENST00000376215 | 1643 | 415 | 27031425 | 27031506 | 1080 | 1160 | 342 | 369 |
| 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 |
| Q5T2R2 | 342 | 369 | 279 | 415 | Alternative sequence | ID=VSP_017101;Note=In isoform 2. SVLGCPDPVVHEIAYQYGKNVGIAFQLIDDVLDFTSCSDQMGKPTSADLKLGLATGPVLFACQQFPEMNAMIMRRFSLPGDVDRARQYVLQSDGVQQTTYLAQQYCHEAIREISKLRPSPERDALIQLSEIVLTRDK->FPRNECYDHATVQFAWRCRQSSTVCTTE;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed: |
| Q5T2R2 | 342 | 369 | 1 | 415 | Chain | ID=PRO_0000123975;Note=Decaprenyl-diphosphate synthase subunit 1 |
| 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 |
| Q5T2R2 | 342 | 369 | 279 | 415 | Alternative sequence | ID=VSP_017101;Note=In isoform 2. SVLGCPDPVVHEIAYQYGKNVGIAFQLIDDVLDFTSCSDQMGKPTSADLKLGLATGPVLFACQQFPEMNAMIMRRFSLPGDVDRARQYVLQSDGVQQTTYLAQQYCHEAIREISKLRPSPERDALIQLSEIVLTRDK->FPRNECYDHATVQFAWRCRQSSTVCTTE;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed: |
| Q5T2R2 | 342 | 369 | 1 | 415 | Chain | ID=PRO_0000123975;Note=Decaprenyl-diphosphate synthase subunit 1 |
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SNVs in the skipped exons for PDSS1 |
| - 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 |
| BLCA | TCGA-4Z-AA87-01 | exon_skip_40213 exon_skip_40214 | 26998567 | 26998697 | 26998639 | 26998639 | Nonsense_Mutation | C | T | p.R137* |
| LUAD | TCGA-55-7910-01 | exon_skip_40223 | 27031426 | 27031506 | 27031431 | 27031431 | Nonsense_Mutation | A | T | p.R281* |
| SKCM | TCGA-D9-A6EC-06 | exon_skip_40213 exon_skip_40214 | 26998567 | 26998697 | 26998699 | 26998699 | Splice_Site | T | G | . |
| - 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 |
| SNU1040_LARGE_INTESTINE | 26993606 | 26993670 | 26993615 | 26993615 | Missense_Mutation | A | G | p.I58V |
| SW48_LARGE_INTESTINE | 26998567 | 26998697 | 26998633 | 26998633 | Missense_Mutation | G | A | p.A135T |
| NCIH2172_LUNG | 27012735 | 27012846 | 27012744 | 27012744 | Missense_Mutation | G | T | p.A207S |
| NUGC3_STOMACH | 27012735 | 27012846 | 27012766 | 27012766 | Missense_Mutation | C | T | p.A214V |
| HT115_LARGE_INTESTINE | 27012735 | 27012846 | 27012787 | 27012787 | Missense_Mutation | G | A | p.R221Q |
| NCIH1355_LUNG | 27012735 | 27012846 | 27012831 | 27012831 | Missense_Mutation | G | A | p.E236K |
| HCC2450_LUNG | 27031426 | 27031506 | 27031484 | 27031484 | Missense_Mutation | G | A | p.R362K |
| HEC59_ENDOMETRIUM | 27031426 | 27031506 | 27031490 | 27031490 | Missense_Mutation | G | A | p.R364Q |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PDSS1 |
| 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 PDSS1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PDSS1 |
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RelatedDrugs for PDSS1 |
| 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 PDSS1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| PDSS1 | C3553354 | COENZYME Q10 DEFICIENCY, PRIMARY, 2 | 1 | ORPHANET;UNIPROT |
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