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Open reading frame (ORF) annotation in the exon skipping event | |
3'-UTR located exon skipping events lost miRNA binding sites | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Gene summary for APOC1 |
Gene summary |
Gene information | Gene symbol | APOC1 | Gene ID | 341 |
Gene name | apolipoprotein C1 | |
Synonyms | Apo-CI|ApoC-I|apo-CIB|apoC-IB | |
Cytomap | 19q13.32 | |
Type of gene | protein-coding | |
Description | apolipoprotein C-I | |
Modification date | 20200313 | |
UniProtAcc | A0A024R0T8, | |
Context | - 20817608(APOE and Cholesterol Homeostasis in Alzheimer's Disease) |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
APOC1 | GO:0010900 | negative regulation of phosphatidylcholine catabolic process | 2302419 |
APOC1 | GO:0010916 | negative regulation of very-low-density lipoprotein particle clearance | 1917954 |
APOC1 | GO:0032375 | negative regulation of cholesterol transport | 10978346 |
APOC1 | GO:0033344 | cholesterol efflux | 11162594 |
APOC1 | GO:0033700 | phospholipid efflux | 11162594 |
APOC1 | GO:0034369 | plasma lipoprotein particle remodeling | 10978346 |
APOC1 | GO:0034382 | chylomicron remnant clearance | 4020294 |
APOC1 | GO:0045717 | negative regulation of fatty acid biosynthetic process | 15576844 |
APOC1 | GO:0045833 | negative regulation of lipid metabolic process | 182536 |
APOC1 | GO:0048261 | negative regulation of receptor-mediated endocytosis | 1917954 |
APOC1 | GO:0050995 | negative regulation of lipid catabolic process | 15576844 |
APOC1 | GO:0051005 | negative regulation of lipoprotein lipase activity | 15576844 |
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Gene structures and expression levels for APOC1 |
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. |
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. |
Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
PG | UP | ENST00000590334.5 | APOC1-206:nonsense_mediated_decay:APOC1 | 2.043511e+00 | 1.315107e+00 | 3.001730e-03 | 3.184359e-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 APOC1 |
Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
All exon skipping events in AD cohorts. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
exon_skip_120563 | chr19 | 44915098:44915217:44916190:44916325:44919173:44919209 | 44916190:44916325 |
exon_skip_170349 | chr19 | 44914869:44914949:44915098:44915217:44916190:44916325 | 44915098:44915217 |
exon_skip_185176 | chr19 | 44914872:44914949:44916190:44916470:44919173:44919234 | 44916190:44916470 |
exon_skip_240024 | chr19 | 44914872:44914949:44916190:44916325:44919173:44919343 | 44916190:44916325 |
exon_skip_269830 | chr19 | 44914872:44914949:44916190:44916325:44919173:44919234 | 44916190:44916325 |
exon_skip_28018 | chr19 | 44914872:44914949:44916190:44916470:44919173:44919343 | 44916190:44916470 |
exon_skip_45734 | chr19 | 44914869:44914949:44915098:44915217:44916190:44916322 | 44915098:44915217 |
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 APOC1 |
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 |
ENST00000588750 | 44916190 | 44916325 | Frame-shift |
ENST00000588802 | 44916190 | 44916325 | Frame-shift |
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 |
ENST00000588750 | 44916190 | 44916325 | Frame-shift |
ENST00000588802 | 44916190 | 44916325 | Frame-shift |
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 |
ENST00000588750 | 44916190 | 44916325 | Frame-shift |
ENST00000588802 | 44916190 | 44916325 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for APOC1 |
p-ENSG00000130208_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 |
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 |
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 |
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 |
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 |
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 |
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3'-UTR located exon skipping events that lost miRNA binding sites in APOC1 |
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 APOC1 |
- 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 APOC1 |
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 APOC1 |
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 APOC1 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for APOC1 |
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 APOC1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |