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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for PCSK6 |
 Gene summary |
| Gene information | Gene symbol | PCSK6 | Gene ID | 5046 |
| Gene name | proprotein convertase subtilisin/kexin type 6 | |
| Synonyms | PACE4|SPC4 | |
| Cytomap | 15q26.3 | |
| Type of gene | protein-coding | |
| Description | proprotein convertase subtilisin/kexin type 6paired basic amino acid cleaving enzyme 4paired basic amino acid cleaving system 4subtilisin-like proprotein convertase 4subtilisin/kexin-like protease PACE4 | |
| Modification date | 20200315 | |
| UniProtAcc | A0A024RCD0, A0A024RCE2, A0A087WY68, A0A087WZR0, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| PCSK6 | GO:0009100 | glycoprotein metabolic process | 8218226 |
| PCSK6 | GO:0016485 | protein processing | 8218226|9242664|9738469 |
| PCSK6 | GO:0016486 | peptide hormone processing | 9242664 |
| PCSK6 | GO:0032902 | nerve growth factor production | 8615794 |
| PCSK6 | GO:0032940 | secretion by cell | 8615794 |
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Gene structures and expression levels for PCSK6 |
| Skipped exons in the ROSMAP, MSBB, and Mayo 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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ENSG00000140479
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| PG | UP | ENST00000559499.1 | PCSK6-210:retained_intron:PCSK6 | 3.478225e+01 | 8.456880e-01 | 6.536520e-08 | 1.075265e-05 |
| PG | UP | ENST00000618548.4 | PCSK6-217:protein_coding:PCSK6 | 1.048639e+02 | 9.180236e-01 | 8.499683e-04 | 1.294636e-02 |
| PG | UP | ENST00000559417.1 | PCSK6-208:protein_coding:PCSK6 | 2.278493e+01 | 8.320242e-01 | 3.953097e-03 | 3.876664e-02 |
| CB | UP | ENST00000559417.1 | PCSK6-208:protein_coding:PCSK6 | 1.777319e+01 | 1.570023e+00 | 2.374322e-07 | 4.416191e-06 |
| TC | UP | ENST00000559417.1 | PCSK6-208:protein_coding:PCSK6 | 3.899849e+01 | 1.249601e+00 | 2.138950e-07 | 1.146627e-05 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PCSK6 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_104798 | chr15 | 101429987:101430063:101431320:101431463:101431990:101432079 | 101431320:101431463 |
| exon_skip_121786 | chr15 | 101366196:101366332:101370335:101370523:101382092:101382124 | 101370335:101370523 |
| exon_skip_128597 | chr15 | 101370335:101370523:101382092:101382209:101384322:101384425 | 101382092:101382209 |
| exon_skip_134473 | chr15 | 101427892:101427980:101429987:101430063:101431320:101431463 | 101429987:101430063 |
| exon_skip_141290 | chr15 | 101431990:101432100:101443556:101443660:101489374:101489435 | 101443556:101443660 |
| exon_skip_141543 | chr15 | 101326381:101326479:101331651:101331689:101331852:101331885 | 101331651:101331689 |
| exon_skip_146681 | chr15 | 101427892:101427980:101429987:101430063:101431990:101432100 | 101429987:101430063 |
| exon_skip_169021 | chr15 | 101346373:101347777:101364999:101365044:101366196:101366262 | 101364999:101365044 |
| exon_skip_24736 | chr15 | 101318319:101318422:101322520:101322607:101324850:101325042 | 101322520:101322607 |
| exon_skip_251459 | chr15 | 101318319:101318422:101322520:101322607:101324850:101325046 | 101322520:101322607 |
| exon_skip_266268 | chr15 | 101346742:101347777:101364999:101365044:101366196:101366262 | 101364999:101365044 |
| exon_skip_47697 | chr15 | 101429987:101430063:101431320:101431463:101431990:101432100 | 101431320:101431463 |
| exon_skip_57679 | chr15 | 101346742:101347777:101364999:101365044:101366196:101366332 | 101364999:101365044 |
| exon_skip_62231 | chr15 | 101393212:101393424:101398404:101398576:101427892:101427980 | 101398404:101398576 |
| exon_skip_68274 | chr15 | 101389464:101389564:101393212:101393424:101398404:101398576 | 101393212:101393424 |
| exon_skip_82491 | chr15 | 101305231:101305355:101307213:101307325:101313376:101313402 | 101307213:101307325 |
| exon_skip_83199 | chr15 | 101427892:101427980:101429987:101430063:101431990:101432079 | 101429987:101430063 |
| exon_skip_9349 | chr15 | 101429987:101430063:101431320:101431463:101431990:101432085 | 101431320:101431463 |
| exon_skip_96457 | chr15 | 101307291:101307325:101313376:101313505:101318319:101318422 | 101313376:101313505 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_47697 | Mayo_CB | 7.588889e-01 | 9.104478e-01 | -1.515589e-01 | 7.846903e-09 |
| exon_skip_104798 | Mayo_TC | 6.935366e-01 | 8.507895e-01 | -1.572529e-01 | 7.676183e-06 |
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Open reading frame (ORF) annotation in the exon skipping event for PCSK6 |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000611716 | 101307213 | 101307325 | Frame-shift |
| ENST00000611716 | 101313376 | 101313505 | Frame-shift |
| ENST00000611716 | 101382092 | 101382209 | Frame-shift |
| ENST00000611716 | 101398404 | 101398576 | Frame-shift |
| ENST00000611716 | 101331651 | 101331689 | In-frame |
| ENST00000611716 | 101393212 | 101393424 | In-frame |
| ENST00000611716 | 101431320 | 101431463 | In-frame |
| ENST00000611716 | 101443556 | 101443660 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000611716 | 101313376 | 101313505 | Frame-shift |
| ENST00000611716 | 101398404 | 101398576 | Frame-shift |
| ENST00000611716 | 101429987 | 101430063 | Frame-shift |
| ENST00000611716 | 101331651 | 101331689 | In-frame |
| ENST00000611716 | 101370335 | 101370523 | In-frame |
| ENST00000611716 | 101431320 | 101431463 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000611716 | 101313376 | 101313505 | Frame-shift |
| ENST00000611716 | 101322520 | 101322607 | Frame-shift |
| ENST00000611716 | 101382092 | 101382209 | Frame-shift |
| ENST00000611716 | 101398404 | 101398576 | Frame-shift |
| ENST00000611716 | 101331651 | 101331689 | In-frame |
| ENST00000611716 | 101370335 | 101370523 | In-frame |
| ENST00000611716 | 101393212 | 101393424 | In-frame |
| ENST00000611716 | 101431320 | 101431463 | In-frame |
| ENST00000611716 | 101443556 | 101443660 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PCSK6 |
p-ENSG00000140479_img4.png |
| Loci of skipped exons in ROSMAP 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 |
| ENST00000611716 | 4426 | 969 | 101443556 | 101443660 | 467 | 570 | 99 | 133 |
| ENST00000611716 | 4426 | 969 | 101431320 | 101431463 | 683 | 825 | 171 | 218 |
| ENST00000611716 | 4426 | 969 | 101393212 | 101393424 | 1166 | 1377 | 332 | 402 |
| ENST00000611716 | 4426 | 969 | 101331651 | 101331689 | 2208 | 2245 | 679 | 692 |
| Loci of skipped exons in MSBB 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 |
| ENST00000611716 | 4426 | 969 | 101431320 | 101431463 | 683 | 825 | 171 | 218 |
| ENST00000611716 | 4426 | 969 | 101370335 | 101370523 | 1702 | 1889 | 511 | 573 |
| ENST00000611716 | 4426 | 969 | 101331651 | 101331689 | 2208 | 2245 | 679 | 692 |
| Loci of skipped exons in Mayo 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 |
| ENST00000611716 | 4426 | 969 | 101443556 | 101443660 | 467 | 570 | 99 | 133 |
| ENST00000611716 | 4426 | 969 | 101431320 | 101431463 | 683 | 825 | 171 | 218 |
| ENST00000611716 | 4426 | 969 | 101393212 | 101393424 | 1166 | 1377 | 332 | 402 |
| ENST00000611716 | 4426 | 969 | 101370335 | 101370523 | 1702 | 1889 | 511 | 573 |
| ENST00000611716 | 4426 | 969 | 101331651 | 101331689 | 2208 | 2245 | 679 | 692 |
| Lost protein functional features of individual exon skipping events in ROSMAP. |
| 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 |
| P29122 | 99 | 133 | 1 | 167 | Alternative sequence | ID=VSP_005427;Note=In isoform PACE4D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8179631;Dbxref=PMID:8179631 |
| P29122 | 99 | 133 | 64 | 149 | Propeptide | ID=PRO_0000027110;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9738469;Dbxref=PMID:9738469 |
| P29122 | 171 | 218 | 205 | 205 | Active site | Note=Charge relay system;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P29122 | 171 | 218 | 150 | 969 | Chain | ID=PRO_0000027111;Note=Proprotein convertase subtilisin/kexin type 6 |
| P29122 | 171 | 218 | 200 | 487 | Domain | Note=Peptidase S8 |
| P29122 | 332 | 402 | 150 | 969 | Chain | ID=PRO_0000027111;Note=Proprotein convertase subtilisin/kexin type 6 |
| P29122 | 332 | 402 | 200 | 487 | Domain | Note=Peptidase S8 |
| P29122 | 679 | 692 | 472 | 969 | Alternative sequence | ID=VSP_005429;Note=In isoform PACE4B. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:1741956;Dbxref=PMID:1741956 |
| P29122 | 679 | 692 | 624 | 969 | Alternative sequence | ID=VSP_005431;Note=In isoform PACE4CS. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P29122 | 679 | 692 | 653 | 969 | Alternative sequence | ID=VSP_005433;Note=In isoform PACE4C. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8179631;Dbxref=PMID:8179631 |
| P29122 | 679 | 692 | 665 | 969 | Alternative sequence | ID=VSP_005435;Note=In isoform PACE4D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8179631;Dbxref=PMID:8179631 |
| P29122 | 679 | 692 | 680 | 693 | Alternative sequence | ID=VSP_005436;Note=In isoform PACE4A-II and isoform PACE4E-II. AQSTPGSANILQTS->G;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9192737;Dbxref=PMID:9192737 |
| P29122 | 679 | 692 | 150 | 969 | Chain | ID=PRO_0000027111;Note=Proprotein convertase subtilisin/kexin type 6 |
| P29122 | 679 | 692 | 692 | 739 | Repeat | Note=FU 1 |
| Lost protein functional features of individual exon skipping events in MSBB. |
| 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 |
| P29122 | 171 | 218 | 205 | 205 | Active site | Note=Charge relay system;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P29122 | 171 | 218 | 150 | 969 | Chain | ID=PRO_0000027111;Note=Proprotein convertase subtilisin/kexin type 6 |
| P29122 | 171 | 218 | 200 | 487 | Domain | Note=Peptidase S8 |
| P29122 | 511 | 573 | 472 | 969 | Alternative sequence | ID=VSP_005429;Note=In isoform PACE4B. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:1741956;Dbxref=PMID:1741956 |
| P29122 | 511 | 573 | 150 | 969 | Chain | ID=PRO_0000027111;Note=Proprotein convertase subtilisin/kexin type 6 |
| P29122 | 511 | 573 | 495 | 635 | Domain | Note=P/Homo B;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01173 |
| P29122 | 511 | 573 | 553 | 555 | Motif | Note=Cell attachment site;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P29122 | 679 | 692 | 472 | 969 | Alternative sequence | ID=VSP_005429;Note=In isoform PACE4B. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:1741956;Dbxref=PMID:1741956 |
| P29122 | 679 | 692 | 624 | 969 | Alternative sequence | ID=VSP_005431;Note=In isoform PACE4CS. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P29122 | 679 | 692 | 653 | 969 | Alternative sequence | ID=VSP_005433;Note=In isoform PACE4C. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8179631;Dbxref=PMID:8179631 |
| P29122 | 679 | 692 | 665 | 969 | Alternative sequence | ID=VSP_005435;Note=In isoform PACE4D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8179631;Dbxref=PMID:8179631 |
| P29122 | 679 | 692 | 680 | 693 | Alternative sequence | ID=VSP_005436;Note=In isoform PACE4A-II and isoform PACE4E-II. AQSTPGSANILQTS->G;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9192737;Dbxref=PMID:9192737 |
| P29122 | 679 | 692 | 150 | 969 | Chain | ID=PRO_0000027111;Note=Proprotein convertase subtilisin/kexin type 6 |
| P29122 | 679 | 692 | 692 | 739 | Repeat | Note=FU 1 |
| Lost protein functional features of individual exon skipping events in Mayo. |
| 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 |
| P29122 | 99 | 133 | 1 | 167 | Alternative sequence | ID=VSP_005427;Note=In isoform PACE4D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8179631;Dbxref=PMID:8179631 |
| P29122 | 99 | 133 | 64 | 149 | Propeptide | ID=PRO_0000027110;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9738469;Dbxref=PMID:9738469 |
| P29122 | 171 | 218 | 205 | 205 | Active site | Note=Charge relay system;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P29122 | 171 | 218 | 150 | 969 | Chain | ID=PRO_0000027111;Note=Proprotein convertase subtilisin/kexin type 6 |
| P29122 | 171 | 218 | 200 | 487 | Domain | Note=Peptidase S8 |
| P29122 | 332 | 402 | 150 | 969 | Chain | ID=PRO_0000027111;Note=Proprotein convertase subtilisin/kexin type 6 |
| P29122 | 332 | 402 | 200 | 487 | Domain | Note=Peptidase S8 |
| P29122 | 511 | 573 | 472 | 969 | Alternative sequence | ID=VSP_005429;Note=In isoform PACE4B. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:1741956;Dbxref=PMID:1741956 |
| P29122 | 511 | 573 | 150 | 969 | Chain | ID=PRO_0000027111;Note=Proprotein convertase subtilisin/kexin type 6 |
| P29122 | 511 | 573 | 495 | 635 | Domain | Note=P/Homo B;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01173 |
| P29122 | 511 | 573 | 553 | 555 | Motif | Note=Cell attachment site;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P29122 | 679 | 692 | 472 | 969 | Alternative sequence | ID=VSP_005429;Note=In isoform PACE4B. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:1741956;Dbxref=PMID:1741956 |
| P29122 | 679 | 692 | 624 | 969 | Alternative sequence | ID=VSP_005431;Note=In isoform PACE4CS. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P29122 | 679 | 692 | 653 | 969 | Alternative sequence | ID=VSP_005433;Note=In isoform PACE4C. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8179631;Dbxref=PMID:8179631 |
| P29122 | 679 | 692 | 665 | 969 | Alternative sequence | ID=VSP_005435;Note=In isoform PACE4D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8179631;Dbxref=PMID:8179631 |
| P29122 | 679 | 692 | 680 | 693 | Alternative sequence | ID=VSP_005436;Note=In isoform PACE4A-II and isoform PACE4E-II. AQSTPGSANILQTS->G;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9192737;Dbxref=PMID:9192737 |
| P29122 | 679 | 692 | 150 | 969 | Chain | ID=PRO_0000027111;Note=Proprotein convertase subtilisin/kexin type 6 |
| P29122 | 679 | 692 | 692 | 739 | Repeat | Note=FU 1 |
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3'-UTR located exon skipping events that lost miRNA binding sites in PCSK6 |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for PCSK6 |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - 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 |
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AD stage-associated exon skippint events for PCSK6 |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PCSK6 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for PCSK6 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | TARDBP | exon_skip_47697 | -4.597000e-01 | 4.166768e-09 |
| CB | CNOT4 | exon_skip_47697 | -4.927731e-01 | 1.990534e-10 |
| CB | PCBP1 | exon_skip_47697 | -4.292175e-01 | 5.232713e-08 |
| CB | PCBP4 | exon_skip_47697 | 5.714996e-01 | 3.307739e-14 |
| CB | TRA2A | exon_skip_47697 | -5.297378e-01 | 4.421827e-12 |
| CB | FUBP1 | exon_skip_47697 | -4.486875e-01 | 1.069829e-08 |
| CB | NUP42 | exon_skip_47697 | 4.903380e-01 | 2.518197e-10 |
| CB | PABPC4 | exon_skip_47697 | 4.158145e-01 | 1.474783e-07 |
| IFG | TARDBP | exon_skip_47697 | -5.418428e-01 | 5.146710e-03 |
| IFG | CNOT4 | exon_skip_47697 | -4.355499e-01 | 2.953764e-02 |
| IFG | RBM47 | exon_skip_47697 | -5.595670e-01 | 3.633032e-03 |
| IFG | TRA2A | exon_skip_47697 | -5.430073e-01 | 5.033158e-03 |
| IFG | PCBP2 | exon_skip_47697 | -5.911366e-01 | 1.859419e-03 |
| IFG | PABPC1 | exon_skip_47697 | -5.807685e-01 | 2.334110e-03 |
| TC | NOVA1 | exon_skip_104798 | 4.643201e-01 | 7.991053e-10 |
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RelatedDrugs for PCSK6 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for PCSK6 |
| 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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