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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 CPNE1 |
 Gene summary |
| Gene information | Gene symbol | CPNE1 | Gene ID | 8904 |
| Gene name | copine 1 | |
| Synonyms | COPN1|CPN1 | |
| Cytomap | 20q11.22 | |
| Type of gene | protein-coding | |
| Description | copine-1chromobindin 17copine I | |
| Modification date | 20200320 | |
| UniProtAcc | A6PVH9, B0QZ18, E7ENH5, E7EV27, F2Z2V0, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| CPNE1 | GO:0043392 | negative regulation of DNA binding | 18212740 |
| CPNE1 | GO:0045666 | positive regulation of neuron differentiation | 23263657 |
| CPNE1 | GO:0051897 | positive regulation of protein kinase B signaling | 23263657 |
| CPNE1 | GO:1990138 | neuron projection extension | 23263657 |
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Gene structures and expression levels for CPNE1 |
| 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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ENSG00000214078
| 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 |
| CB | UP | ENST00000437100.5 | CPNE1-215:protein_coding:CPNE1 | 6.789131e+01 | 9.934566e-01 | 2.496183e-07 | 4.599741e-06 |
| CB | DOWN | ENST00000397442.5 | CPNE1-203:protein_coding:CPNE1 | 2.614823e+01 | -1.159161e+00 | 7.347539e-07 | 1.152257e-05 |
| CB | UP | ENST00000458038.5 | CPNE1-220:protein_coding:CPNE1 | 1.712178e+01 | 1.297208e+00 | 6.027218e-06 | 6.865065e-05 |
| CB | UP | ENST00000416778.5 | CPNE1-210:protein_coding:CPNE1 | 3.235302e+01 | 1.277120e+00 | 1.092713e-03 | 5.565016e-03 |
| CB | DOWN | ENST00000397443.6 | CPNE1-204:protein_coding:CPNE1 | 8.790428e+00 | -4.133288e+00 | 9.422467e-03 | 3.311766e-02 |
| 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 CPNE1 |
| 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_134608 | chr20 | 35631945:35632025:35632163:35632234:35632311:35632385 | 35632163:35632234 |
| exon_skip_159964 | chr20 | 35626767:35626803:35627280:35627413:35630439:35630456 | 35627280:35627413 |
| exon_skip_178548 | chr20 | 35630439:35630490:35630741:35630795:35630901:35631034 | 35630741:35630795 |
| exon_skip_237710 | chr20 | 35632795:35632923:35655202:35655344:35658930:35658982 | 35655202:35655344 |
| exon_skip_239017 | chr20 | 35630439:35630490:35630741:35630795:35630901:35630961 | 35630741:35630795 |
| exon_skip_291352 | chr20 | 35626735:35626826:35627280:35627413:35630439:35630456 | 35627280:35627413 |
| exon_skip_39225 | chr20 | 35627285:35627413:35630439:35630490:35630741:35630795 | 35630439:35630490 |
| exon_skip_56354 | chr20 | 35626567:35626800:35627280:35627413:35630439:35630456 | 35627280:35627413 |
| exon_skip_75936 | chr20 | 35631945:35632025:35632163:35632248:35632311:35632385 | 35632163:35632248 |
| exon_skip_81528 | chr20 | 35626735:35626803:35627280:35627413:35630439:35630456 | 35627280:35627413 |
| 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_134608 | Mayo_CB | 4.743902e-01 | 6.081818e-01 | -1.337916e-01 | 1.328854e-08 |
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Open reading frame (ORF) annotation in the exon skipping event for CPNE1 |
| 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 |
| ENST00000352393 | 35655202 | 35655344 | 3UTR-3UTR |
| ENST00000352393 | 35627280 | 35627413 | Frame-shift |
| ENST00000352393 | 35630741 | 35630795 | Frame-shift |
| ENST00000352393 | 35632163 | 35632234 | 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 |
| ENST00000352393 | 35655202 | 35655344 | 3UTR-3UTR |
| ENST00000352393 | 35627280 | 35627413 | Frame-shift |
| ENST00000352393 | 35630741 | 35630795 | Frame-shift |
| ENST00000352393 | 35632163 | 35632234 | 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 |
| ENST00000352393 | 35655202 | 35655344 | 3UTR-3UTR |
| ENST00000352393 | 35627280 | 35627413 | Frame-shift |
| ENST00000352393 | 35630439 | 35630490 | Frame-shift |
| ENST00000352393 | 35630741 | 35630795 | Frame-shift |
| ENST00000352393 | 35632163 | 35632234 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CPNE1 |
p-ENSG00000214078_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 |
| ENST00000352393 | 2164 | 537 | 35632163 | 35632234 | 708 | 778 | 128 | 151 |
| 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 |
| ENST00000352393 | 2164 | 537 | 35632163 | 35632234 | 708 | 778 | 128 | 151 |
| 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 |
| ENST00000352393 | 2164 | 537 | 35632163 | 35632234 | 708 | 778 | 128 | 151 |
| 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 |
| Q99829 | 128 | 151 | 1 | 537 | Chain | ID=PRO_0000144834;Note=Copine-1 |
| Q99829 | 128 | 151 | 144 | 228 | Domain | Note=C2 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00041 |
| 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 |
| Q99829 | 128 | 151 | 1 | 537 | Chain | ID=PRO_0000144834;Note=Copine-1 |
| Q99829 | 128 | 151 | 144 | 228 | Domain | Note=C2 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00041 |
| 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 |
| Q99829 | 128 | 151 | 1 | 537 | Chain | ID=PRO_0000144834;Note=Copine-1 |
| Q99829 | 128 | 151 | 144 | 228 | Domain | Note=C2 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00041 |
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3'-UTR located exon skipping events that lost miRNA binding sites in CPNE1 |
| 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 |
| Mayo | ENST00000352393 | 35655202 | 35655344 | hsa-miR-942-5p | chr20:35655251-35655258 | 8mer-1a | chr20:35655237-35655258 | 175.00 | -27.45 |
| Mayo | ENST00000352393 | 35655202 | 35655344 | hsa-miR-4488 | chr20:35655226-35655233 | 8mer-1a | chr20:35655216-35655233 | 147.00 | -18.79 |
| Mayo | ENST00000352393 | 35655202 | 35655344 | hsa-miR-1908-5p | chr20:35655278-35655285 | 8mer-1a | chr20:35655262-35655285 | 154.00 | -26.53 |
| Mayo | ENST00000352393 | 35655202 | 35655344 | hsa-miR-1237-5p | chr20:35655226-35655233 | 8mer-1a | chr20:35655216-35655233 | 147.00 | -18.79 |
| Mayo | ENST00000352393 | 35655202 | 35655344 | hsa-miR-4697-5p | chr20:35655226-35655233 | 8mer-1a | chr20:35655216-35655233 | 147.00 | -18.79 |
| Mayo | ENST00000352393 | 35655202 | 35655344 | hsa-miR-378j | chr20:35655246-35655253 | 8mer-1a | chr20:35655237-35655258 | 175.00 | -27.45 |
| Mayo | ENST00000352393 | 35655202 | 35655344 | hsa-miR-6787-5p | chr20:35655278-35655285 | 8mer-1a | chr20:35655262-35655285 | 154.00 | -26.53 |
| Mayo | ENST00000352393 | 35655202 | 35655344 | hsa-miR-6788-3p | chr20:35655260-35655267 | 8mer-1a | chr20:35655247-35655267 | 165.00 | -24.80 |
| Mayo | ENST00000352393 | 35655202 | 35655344 | hsa-miR-7974 | chr20:35655314-35655321 | 8mer-1a | chr20:35655314-35655338 | 158.00 | -17.99 |
| Mayo | ENST00000352393 | 35655202 | 35655344 | hsa-miR-3191-5p | chr20:35655249-35655256 | 8mer-1a | chr20:35655237-35655258 | 175.00 | -27.45 |
| Mayo | ENST00000352393 | 35655202 | 35655344 | hsa-miR-150-5p | chr20:35655289-35655296 | 8mer-1a | chr20:35655289-35655310 | 158.00 | -19.75 |
| Mayo | ENST00000352393 | 35655202 | 35655344 | hsa-miR-518c-5p | chr20:35655248-35655255 | 8mer-1a | chr20:35655237-35655258 | 175.00 | -27.45 |
| Mayo | ENST00000352393 | 35655202 | 35655344 | hsa-miR-663a | chr20:35655278-35655285 | 8mer-1a | chr20:35655262-35655285 | 154.00 | -26.53 |
| Mayo | ENST00000352393 | 35655202 | 35655344 | hsa-miR-10396b-5p | chr20:35655278-35655285 | 8mer-1a | chr20:35655262-35655285 | 154.00 | -26.53 |
| Mayo | ENST00000352393 | 35655202 | 35655344 | hsa-miR-6839-5p | chr20:35655246-35655253 | 8mer-1a | chr20:35655237-35655258 | 175.00 | -27.45 |
| MSBB | ENST00000352393 | 35655202 | 35655344 | hsa-miR-942-5p | chr20:35655251-35655258 | 8mer-1a | chr20:35655237-35655258 | 175.00 | -27.45 |
| MSBB | ENST00000352393 | 35655202 | 35655344 | hsa-miR-4488 | chr20:35655226-35655233 | 8mer-1a | chr20:35655216-35655233 | 147.00 | -18.79 |
| MSBB | ENST00000352393 | 35655202 | 35655344 | hsa-miR-1908-5p | chr20:35655278-35655285 | 8mer-1a | chr20:35655262-35655285 | 154.00 | -26.53 |
| MSBB | ENST00000352393 | 35655202 | 35655344 | hsa-miR-1237-5p | chr20:35655226-35655233 | 8mer-1a | chr20:35655216-35655233 | 147.00 | -18.79 |
| MSBB | ENST00000352393 | 35655202 | 35655344 | hsa-miR-4697-5p | chr20:35655226-35655233 | 8mer-1a | chr20:35655216-35655233 | 147.00 | -18.79 |
| MSBB | ENST00000352393 | 35655202 | 35655344 | hsa-miR-378j | chr20:35655246-35655253 | 8mer-1a | chr20:35655237-35655258 | 175.00 | -27.45 |
| MSBB | ENST00000352393 | 35655202 | 35655344 | hsa-miR-6787-5p | chr20:35655278-35655285 | 8mer-1a | chr20:35655262-35655285 | 154.00 | -26.53 |
| MSBB | ENST00000352393 | 35655202 | 35655344 | hsa-miR-6788-3p | chr20:35655260-35655267 | 8mer-1a | chr20:35655247-35655267 | 165.00 | -24.80 |
| MSBB | ENST00000352393 | 35655202 | 35655344 | hsa-miR-7974 | chr20:35655314-35655321 | 8mer-1a | chr20:35655314-35655338 | 158.00 | -17.99 |
| MSBB | ENST00000352393 | 35655202 | 35655344 | hsa-miR-3191-5p | chr20:35655249-35655256 | 8mer-1a | chr20:35655237-35655258 | 175.00 | -27.45 |
| MSBB | ENST00000352393 | 35655202 | 35655344 | hsa-miR-150-5p | chr20:35655289-35655296 | 8mer-1a | chr20:35655289-35655310 | 158.00 | -19.75 |
| MSBB | ENST00000352393 | 35655202 | 35655344 | hsa-miR-518c-5p | chr20:35655248-35655255 | 8mer-1a | chr20:35655237-35655258 | 175.00 | -27.45 |
| MSBB | ENST00000352393 | 35655202 | 35655344 | hsa-miR-663a | chr20:35655278-35655285 | 8mer-1a | chr20:35655262-35655285 | 154.00 | -26.53 |
| MSBB | ENST00000352393 | 35655202 | 35655344 | hsa-miR-10396b-5p | chr20:35655278-35655285 | 8mer-1a | chr20:35655262-35655285 | 154.00 | -26.53 |
| MSBB | ENST00000352393 | 35655202 | 35655344 | hsa-miR-6839-5p | chr20:35655246-35655253 | 8mer-1a | chr20:35655237-35655258 | 175.00 | -27.45 |
| ROSMAP | ENST00000352393 | 35655202 | 35655344 | hsa-miR-942-5p | chr20:35655251-35655258 | 8mer-1a | chr20:35655237-35655258 | 175.00 | -27.45 |
| ROSMAP | ENST00000352393 | 35655202 | 35655344 | hsa-miR-4488 | chr20:35655226-35655233 | 8mer-1a | chr20:35655216-35655233 | 147.00 | -18.79 |
| ROSMAP | ENST00000352393 | 35655202 | 35655344 | hsa-miR-1908-5p | chr20:35655278-35655285 | 8mer-1a | chr20:35655262-35655285 | 154.00 | -26.53 |
| ROSMAP | ENST00000352393 | 35655202 | 35655344 | hsa-miR-1237-5p | chr20:35655226-35655233 | 8mer-1a | chr20:35655216-35655233 | 147.00 | -18.79 |
| ROSMAP | ENST00000352393 | 35655202 | 35655344 | hsa-miR-4697-5p | chr20:35655226-35655233 | 8mer-1a | chr20:35655216-35655233 | 147.00 | -18.79 |
| ROSMAP | ENST00000352393 | 35655202 | 35655344 | hsa-miR-378j | chr20:35655246-35655253 | 8mer-1a | chr20:35655237-35655258 | 175.00 | -27.45 |
| ROSMAP | ENST00000352393 | 35655202 | 35655344 | hsa-miR-6787-5p | chr20:35655278-35655285 | 8mer-1a | chr20:35655262-35655285 | 154.00 | -26.53 |
| ROSMAP | ENST00000352393 | 35655202 | 35655344 | hsa-miR-6788-3p | chr20:35655260-35655267 | 8mer-1a | chr20:35655247-35655267 | 165.00 | -24.80 |
| ROSMAP | ENST00000352393 | 35655202 | 35655344 | hsa-miR-7974 | chr20:35655314-35655321 | 8mer-1a | chr20:35655314-35655338 | 158.00 | -17.99 |
| ROSMAP | ENST00000352393 | 35655202 | 35655344 | hsa-miR-3191-5p | chr20:35655249-35655256 | 8mer-1a | chr20:35655237-35655258 | 175.00 | -27.45 |
| ROSMAP | ENST00000352393 | 35655202 | 35655344 | hsa-miR-150-5p | chr20:35655289-35655296 | 8mer-1a | chr20:35655289-35655310 | 158.00 | -19.75 |
| ROSMAP | ENST00000352393 | 35655202 | 35655344 | hsa-miR-518c-5p | chr20:35655248-35655255 | 8mer-1a | chr20:35655237-35655258 | 175.00 | -27.45 |
| ROSMAP | ENST00000352393 | 35655202 | 35655344 | hsa-miR-663a | chr20:35655278-35655285 | 8mer-1a | chr20:35655262-35655285 | 154.00 | -26.53 |
| ROSMAP | ENST00000352393 | 35655202 | 35655344 | hsa-miR-10396b-5p | chr20:35655278-35655285 | 8mer-1a | chr20:35655262-35655285 | 154.00 | -26.53 |
| ROSMAP | ENST00000352393 | 35655202 | 35655344 | hsa-miR-6839-5p | chr20:35655246-35655253 | 8mer-1a | chr20:35655237-35655258 | 175.00 | -27.45 |
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SNVs in the skipped exons for CPNE1 |
| - 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 CPNE1 |
| 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 CPNE1 |
| 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 CPNE1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | RBM6 | exon_skip_159964 | -4.178864e-01 | 4.237650e-08 |
| CB | PCBP4 | exon_skip_159964 | 4.479295e-01 | 3.214051e-09 |
| CB | DAZAP1 | exon_skip_134608 | -5.342410e-01 | 4.095196e-13 |
| CB | TRA2A | exon_skip_134608 | -5.646650e-01 | 9.027834e-15 |
| CB | HNRNPAB | exon_skip_134608 | -4.151656e-01 | 5.287767e-08 |
| PG | RBM3 | exon_skip_134608 | 4.214611e-01 | 4.274254e-08 |
| PG | NOVA1 | exon_skip_134608 | 4.007228e-01 | 2.175583e-07 |
| TC | KHDRBS2 | exon_skip_134608 | 4.896639e-01 | 5.744876e-11 |
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RelatedDrugs for CPNE1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Q99829 | approved | DB00277 | Theophylline | small molecule | Q99829 |
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RelatedDiseases for CPNE1 |
| 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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