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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 PCSK4 |
 Gene summary |
| Gene information | Gene symbol | PCSK4 | Gene ID | 54760 |
| Gene name | proprotein convertase subtilisin/kexin type 4 | |
| Synonyms | PC4|SPC5 | |
| Cytomap | 19p13.3 | |
| Type of gene | protein-coding | |
| Description | proprotein convertase subtilisin/kexin type 4testicular tissue protein Li 135 | |
| Modification date | 20180519 | |
| UniProtAcc | Q6UW60 | |
| Context | PubMed: PCSK4 [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 |
| PCSK4 | GO:0016485 | protein processing | 16040806 |
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Exon skipping events across known transcript of Ensembl for PCSK4 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 PCSK4 |
| 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 PCSK4 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_312562 | 19 | 1482437:1482474:1482894:1483019:1483282:1483435 | 1482894:1483019 | ENSG00000115257.11 | ENST00000588195.1,ENST00000591303.1,ENST00000591201.1,ENST00000300954.5 |
| exon_skip_312563 | 19 | 1483648:1483766:1483836:1483940:1484025:1484126 | 1483836:1483940 | ENSG00000115257.11 | ENST00000588195.1,ENST00000591201.1,ENST00000300954.5,ENST00000441747.2 |
| exon_skip_312564 | 19 | 1483836:1483940:1484025:1484126:1486851:1486972 | 1484025:1484126 | ENSG00000115257.11 | ENST00000588195.1,ENST00000591201.1,ENST00000586616.1,ENST00000300954.5,ENST00000441747.2 |
| exon_skip_312565 | 19 | 1487216:1487312:1487601:1487690:1487783:1487860 | 1487601:1487690 | ENSG00000115257.11 | ENST00000300954.5 |
| exon_skip_312569 | 19 | 1488186:1488279:1489591:1489694:1489791:1489896 | 1489591:1489694 | ENSG00000115257.11 | ENST00000591687.1 |
| exon_skip_312570 | 19 | 1488186:1488279:1489791:1489896:1490156:1490334 | 1489791:1489896 | ENSG00000115257.11 | ENST00000588671.1,ENST00000588195.1,ENST00000300954.5 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PCSK4 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_312562 | 19 | 1482437:1482474:1482894:1483019:1483282:1483435 | 1482894:1483019 | ENSG00000115257.11 | ENST00000591201.1,ENST00000300954.5,ENST00000588195.1,ENST00000591303.1 |
| exon_skip_312563 | 19 | 1483648:1483766:1483836:1483940:1484025:1484126 | 1483836:1483940 | ENSG00000115257.11 | ENST00000591201.1,ENST00000441747.2,ENST00000300954.5,ENST00000588195.1 |
| exon_skip_312564 | 19 | 1483836:1483940:1484025:1484126:1486851:1486972 | 1484025:1484126 | ENSG00000115257.11 | ENST00000591201.1,ENST00000441747.2,ENST00000300954.5,ENST00000586616.1,ENST00000588195.1 |
| exon_skip_312565 | 19 | 1487216:1487312:1487601:1487690:1487783:1487860 | 1487601:1487690 | ENSG00000115257.11 | ENST00000300954.5 |
| exon_skip_312569 | 19 | 1488186:1488279:1489591:1489694:1489791:1489896 | 1489591:1489694 | ENSG00000115257.11 | ENST00000591687.1 |
| exon_skip_312570 | 19 | 1488186:1488279:1489791:1489896:1490156:1490334 | 1489791:1489896 | ENSG00000115257.11 | ENST00000300954.5,ENST00000588195.1,ENST00000588671.1 |
| exon_skip_312571 | 19 | 1488186:1488279:1489791:1489896:1490601:1490751 | 1489791:1489896 | ENSG00000115257.11 | ENST00000590057.1 |
| 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 PCSK4 |
| 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 |
| ENST00000300954 | 1482894 | 1483019 | Frame-shift |
| ENST00000300954 | 1483836 | 1483940 | Frame-shift |
| ENST00000300954 | 1484025 | 1484126 | Frame-shift |
| ENST00000300954 | 1487601 | 1487690 | Frame-shift |
| ENST00000300954 | 1489791 | 1489896 | 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 |
| ENST00000300954 | 1482894 | 1483019 | Frame-shift |
| ENST00000300954 | 1483836 | 1483940 | Frame-shift |
| ENST00000300954 | 1484025 | 1484126 | Frame-shift |
| ENST00000300954 | 1487601 | 1487690 | Frame-shift |
| ENST00000300954 | 1489791 | 1489896 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PCSK4 |
| 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 |
| ENST00000300954 | 2678 | 755 | 1489791 | 1489896 | 252 | 356 | 63 | 98 |
| 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 |
| ENST00000300954 | 2678 | 755 | 1489791 | 1489896 | 252 | 356 | 63 | 98 |
| 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 |
| Q6UW60 | 63 | 98 | 1 | 513 | Alternative sequence | ID=VSP_052097;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q6UW60 | 63 | 98 | 26 | 113 | Propeptide | ID=PRO_0000246778;Ontology_term=ECO:0000250,ECO:0000255;evidence=ECO:0000250|UniProtKB:P29121,ECO:0000255 |
| Q6UW60 | 63 | 98 | 66 | 66 | Sequence conflict | Note=P->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q6UW60 | 63 | 98 | 66 | 66 | Sequence conflict | Note=P->S;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 |
| Q6UW60 | 63 | 98 | 1 | 513 | Alternative sequence | ID=VSP_052097;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q6UW60 | 63 | 98 | 26 | 113 | Propeptide | ID=PRO_0000246778;Ontology_term=ECO:0000250,ECO:0000255;evidence=ECO:0000250|UniProtKB:P29121,ECO:0000255 |
| Q6UW60 | 63 | 98 | 66 | 66 | Sequence conflict | Note=P->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q6UW60 | 63 | 98 | 66 | 66 | Sequence conflict | Note=P->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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SNVs in the skipped exons for PCSK4 |
| - 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-A1EG-01 | exon_skip_312562 | 1482895 | 1483019 | 1482948 | 1482948 | Frame_Shift_Del | G | - | p.P548fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_312562 | 1482895 | 1483019 | 1482967 | 1482967 | Frame_Shift_Del | G | - | p.H542fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_312570 | 1489792 | 1489896 | 1489799 | 1489799 | Frame_Shift_Del | T | - | p.N96fs |
| KIRP | TCGA-BQ-5878-01 | exon_skip_312570 | 1489792 | 1489896 | 1489873 | 1489873 | Frame_Shift_Del | A | - | p.F71fs |
| COAD | TCGA-G4-6302-01 | exon_skip_312564 | 1484026 | 1484126 | 1484127 | 1484127 | Splice_Site | C | A | . |
| - 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 |
| SHP77_LUNG | 1484026 | 1484126 | 1484033 | 1484033 | Frame_Shift_Del | C | - | p.E388fs |
| HCT116_LARGE_INTESTINE | 1487602 | 1487690 | 1487625 | 1487626 | Frame_Shift_Ins | - | C | p.V220fs |
| SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 1482895 | 1483019 | 1482940 | 1482940 | Missense_Mutation | C | T | p.V551M |
| NCIH650_LUNG | 1483837 | 1483940 | 1483851 | 1483851 | Missense_Mutation | C | A | p.G420V |
| PANC1_PANCREAS | 1484026 | 1484126 | 1484045 | 1484045 | Missense_Mutation | C | T | p.A384T |
| SNU175_LARGE_INTESTINE | 1484026 | 1484126 | 1484054 | 1484054 | Missense_Mutation | C | T | p.G381S |
| HUH28_BILIARY_TRACT | 1484026 | 1484126 | 1484074 | 1484074 | Missense_Mutation | G | A | p.A374V |
| NCIH1105_LUNG | 1487602 | 1487690 | 1487659 | 1487659 | Missense_Mutation | C | A | p.A209S |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PCSK4 |
| 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 PCSK4 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PCSK4 |
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RelatedDrugs for PCSK4 |
| 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 PCSK4 |
| 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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