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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 CACNA1D |
 Gene summary |
| Gene information | Gene symbol | CACNA1D | Gene ID | 776 |
| Gene name | calcium voltage-gated channel subunit alpha1 D | |
| Synonyms | CACH3|CACN4|CACNL1A2|CCHL1A2|Cav1.3|PASNA|SANDD | |
| Cytomap | 3p21.1 | |
| Type of gene | protein-coding | |
| Description | voltage-dependent L-type calcium channel subunit alpha-1Dcalcium channel, L type, alpha-1 polypeptidecalcium channel, neuroendocrine/brain-type, alpha 1 subunitcalcium channel, voltage-dependent, L type, alpha 1D subunitvoltage-gated calcium channel a | |
| Modification date | 20200313 | |
| UniProtAcc | A0A1B0GTN0, A0A1B0GTP8, A0A1B0GU49, A0A1B0GUB6, | |
| Context | - 27379157(Do Copy Number Changes in CACNA2D2, CACNA2D3, and CACNA1D Constitute a Predisposing Risk Factor for Alzheimer's Disease? 27379157) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| CACNA1D | GO:0006816 | calcium ion transport | 11160515 |
| CACNA1D | GO:0051928 | positive regulation of calcium ion transport | 1309651 |
| CACNA1D | GO:0070509 | calcium ion import | 1309651 |
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Gene structures and expression levels for CACNA1D |
| 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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ENSG00000157388
| 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 | DOWN | ENST00000636480.1 | CACNA1D-210:retained_intron:CACNA1D | 4.983443e+00 | -9.664064e-01 | 4.465903e-03 | 4.223722e-02 |
| CB | DOWN | ENST00000498251.2 | CACNA1D-207:lncRNA:CACNA1D | 3.327596e+01 | -1.397321e+00 | 4.315327e-11 | 3.140566e-09 |
| CB | UP | ENST00000636570.1 | CACNA1D-211:protein_coding:CACNA1D | 1.638623e+00 | 4.005767e+00 | 1.376595e-02 | 4.499216e-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 CACNA1D |
| 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_107392 | chr3 | 53732016:53732082:53732818:53732962:53735374:53735503 | 53732818:53732962 |
| exon_skip_125277 | chr3 | 53762551:53762634:53769973:53770017:53770424:53770552 | 53769973:53770017 |
| exon_skip_13013 | chr3 | 53753572:53753682:53762551:53762634:53770424:53770552 | 53762551:53762634 |
| exon_skip_143409 | chr3 | 53666401:53666535:53673713:53673816:53702641:53702810 | 53673713:53673816 |
| exon_skip_153 | chr3 | 53718305:53718388:53718682:53718741:53719755:53719781 | 53718682:53718741 |
| exon_skip_174054 | chr3 | 53718301:53718388:53718682:53718741:53719755:53719781 | 53718682:53718741 |
| exon_skip_199814 | chr3 | 53801264:53801425:53802147:53802173:53803423:53803572 | 53802147:53802173 |
| exon_skip_202212 | chr3 | 53731077:53731146:53732016:53732082:53735374:53735503 | 53732016:53732082 |
| exon_skip_208487 | chr3 | 53753572:53753682:53761998:53762081:53770424:53770552 | 53761998:53762081 |
| exon_skip_212657 | chr3 | 53753652:53753682:53762551:53762634:53769973:53770017 | 53762551:53762634 |
| exon_skip_228343 | chr3 | 53772833:53772898:53774587:53774678:53775886:53776030 | 53774587:53774678 |
| exon_skip_22995 | chr3 | 53761998:53762081:53769973:53770017:53770424:53770552 | 53769973:53770017 |
| exon_skip_272981 | chr3 | 53666401:53666535:53673023:53673126:53702641:53702810 | 53673023:53673126 |
| exon_skip_281054 | chr3 | 53749374:53749469:53751749:53751907:53753572:53753682 | 53751749:53751907 |
| exon_skip_282276 | chr3 | 53801314:53801425:53802147:53802173:53803423:53803572 | 53802147:53802173 |
| exon_skip_29551 | chr3 | 53781566:53781667:53786822:53786952:53790981:53791179 | 53786822:53786952 |
| exon_skip_68807 | chr3 | 53732016:53732082:53732815:53732962:53735374:53735503 | 53732815:53732962 |
| exon_skip_70276 | chr3 | 53753652:53753682:53761998:53762081:53769973:53770017 | 53761998:53762081 |
| exon_skip_74541 | chr3 | 53781566:53781667:53786822:53786952:53800249:53800344 | 53786822:53786952 |
| exon_skip_87724 | chr3 | 53801371:53801425:53802147:53802173:53803423:53803572 | 53802147:53802173 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for CACNA1D |
| 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 |
| ENST00000350061 | 53673023 | 53673126 | Frame-shift |
| ENST00000350061 | 53732815 | 53732962 | Frame-shift |
| ENST00000350061 | 53774587 | 53774678 | Frame-shift |
| ENST00000350061 | 53786822 | 53786952 | Frame-shift |
| ENST00000350061 | 53751749 | 53751907 | In-frame |
| ENST00000350061 | 53761998 | 53762081 | In-frame |
| ENST00000350061 | 53769973 | 53770017 | In-frame |
| ENST00000350061 | 53802147 | 53802173 | 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 |
| ENST00000350061 | 53673023 | 53673126 | Frame-shift |
| ENST00000350061 | 53732815 | 53732962 | Frame-shift |
| ENST00000350061 | 53774587 | 53774678 | Frame-shift |
| ENST00000350061 | 53769973 | 53770017 | In-frame |
| ENST00000350061 | 53802147 | 53802173 | 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 |
| ENST00000350061 | 53673023 | 53673126 | Frame-shift |
| ENST00000350061 | 53732815 | 53732962 | Frame-shift |
| ENST00000350061 | 53774587 | 53774678 | Frame-shift |
| ENST00000350061 | 53786822 | 53786952 | Frame-shift |
| ENST00000350061 | 53751749 | 53751907 | In-frame |
| ENST00000350061 | 53769973 | 53770017 | In-frame |
| ENST00000350061 | 53802147 | 53802173 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CACNA1D |
p-ENSG00000157388_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 |
| ENST00000350061 | 8073 | 2161 | 53751749 | 53751907 | 4029 | 4186 | 1172 | 1225 |
| ENST00000350061 | 8073 | 2161 | 53761998 | 53762081 | 4299 | 4381 | 1262 | 1290 |
| ENST00000350061 | 8073 | 2161 | 53769973 | 53770017 | 4383 | 4426 | 1290 | 1305 |
| 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 |
| ENST00000350061 | 8073 | 2161 | 53769973 | 53770017 | 4383 | 4426 | 1290 | 1305 |
| 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 |
| ENST00000350061 | 8073 | 2161 | 53751749 | 53751907 | 4029 | 4186 | 1172 | 1225 |
| ENST00000350061 | 8073 | 2161 | 53769973 | 53770017 | 4383 | 4426 | 1290 | 1305 |
| 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 |
| Q01668 | 1172 | 1225 | 1 | 2161 | Chain | ID=PRO_0000053933;Note=Voltage-dependent L-type calcium channel subunit alpha-1D |
| Q01668 | 1172 | 1225 | 1192 | 1467 | Repeat | Note=IV |
| Q01668 | 1172 | 1225 | 1149 | 1205 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q01668 | 1172 | 1225 | 1225 | 1239 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q01668 | 1172 | 1225 | 1206 | 1224 | Transmembrane | Note=Helical%3B Name%3DS1 of repeat IV;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q01668 | 1262 | 1290 | 1 | 2161 | Chain | ID=PRO_0000053933;Note=Voltage-dependent L-type calcium channel subunit alpha-1D |
| Q01668 | 1262 | 1290 | 1192 | 1467 | Repeat | Note=IV |
| Q01668 | 1262 | 1290 | 1289 | 1290 | Sequence conflict | Note=Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q01668 | 1262 | 1290 | 1260 | 1266 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q01668 | 1262 | 1290 | 1289 | 1313 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q01668 | 1262 | 1290 | 1267 | 1288 | Transmembrane | Note=Helical%3B Name%3DS3 of repeat IV;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q01668 | 1290 | 1305 | 1291 | 1305 | Alternative sequence | ID=VSP_046743;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:18482979;Dbxref=PMID:18482979 |
| Q01668 | 1290 | 1305 | 1 | 2161 | Chain | ID=PRO_0000053933;Note=Voltage-dependent L-type calcium channel subunit alpha-1D |
| Q01668 | 1290 | 1305 | 1192 | 1467 | Repeat | Note=IV |
| Q01668 | 1290 | 1305 | 1289 | 1290 | Sequence conflict | Note=Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q01668 | 1290 | 1305 | 1289 | 1313 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q01668 | 1290 | 1305 | 1291 | 1305 | Alternative sequence | ID=VSP_046743;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:18482979;Dbxref=PMID:18482979 |
| Q01668 | 1290 | 1305 | 1 | 2161 | Chain | ID=PRO_0000053933;Note=Voltage-dependent L-type calcium channel subunit alpha-1D |
| Q01668 | 1290 | 1305 | 1192 | 1467 | Repeat | Note=IV |
| Q01668 | 1290 | 1305 | 1289 | 1290 | Sequence conflict | Note=Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q01668 | 1290 | 1305 | 1289 | 1313 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q01668 | 1172 | 1225 | 1 | 2161 | Chain | ID=PRO_0000053933;Note=Voltage-dependent L-type calcium channel subunit alpha-1D |
| Q01668 | 1172 | 1225 | 1192 | 1467 | Repeat | Note=IV |
| Q01668 | 1172 | 1225 | 1149 | 1205 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q01668 | 1172 | 1225 | 1225 | 1239 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q01668 | 1172 | 1225 | 1206 | 1224 | Transmembrane | Note=Helical%3B Name%3DS1 of repeat IV;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q01668 | 1290 | 1305 | 1291 | 1305 | Alternative sequence | ID=VSP_046743;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:18482979;Dbxref=PMID:18482979 |
| Q01668 | 1290 | 1305 | 1 | 2161 | Chain | ID=PRO_0000053933;Note=Voltage-dependent L-type calcium channel subunit alpha-1D |
| Q01668 | 1290 | 1305 | 1192 | 1467 | Repeat | Note=IV |
| Q01668 | 1290 | 1305 | 1289 | 1290 | Sequence conflict | Note=Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q01668 | 1290 | 1305 | 1289 | 1313 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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3'-UTR located exon skipping events that lost miRNA binding sites in CACNA1D |
| 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 CACNA1D |
| - 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 CACNA1D |
| 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 CACNA1D |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| HCC | exon_skip_199814 | rs12487452 | chr3:53758384 | 7.615302e-05 | 7.247674e-03 |
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Correlation with RNA binding proteins (RBPs) for CACNA1D |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| IFG | SRSF9 | exon_skip_174054 | 5.188693e-01 | 1.906877e-02 |
| IFG | HNRNPF | exon_skip_174054 | 4.743611e-01 | 3.458497e-02 |
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RelatedDrugs for CACNA1D |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Q01668 | approved|investigational | DB00270 | Isradipine | small molecule | Q01668 |
| Q01668 | approved|investigational | DB00393 | Nimodipine | small molecule | Q01668 |
| Q01668 | approved | DB00401 | Nisoldipine | small molecule | Q01668 |
| Q01668 | approved|investigational | DB00568 | Cinnarizine | small molecule | Q01668 |
| Q01668 | approved|investigational | DB00622 | Nicardipine | small molecule | Q01668 |
| Q01668 | approved | DB00661 | Verapamil | small molecule | Q01668 |
| Q01668 | approved | DB00898 | Ethanol | small molecule | Q01668 |
| Q01668 | approved|investigational | DB01023 | Felodipine | small molecule | Q01668 |
| Q01668 | approved|investigational | DB01054 | Nitrendipine | small molecule | Q01668 |
| Q01668 | approved | DB01115 | Nifedipine | small molecule | Q01668 |
| Q01668 | approved | DB04855 | Dronedarone | small molecule | Q01668 |
| Q01668 | approved|investigational | DB04920 | Clevidipine | small molecule | Q01668 |
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RelatedDiseases for CACNA1D |
| 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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