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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 ABCA1 |
 Gene summary |
| Gene information | Gene symbol | ABCA1 | Gene ID | 19 |
| Gene name | ATP binding cassette subfamily A member 1 | |
| Synonyms | ABC-1|ABC1|CERP|HDLCQTL13|HDLDT1|HPALP1|TGD | |
| Cytomap | 9q31.1 | |
| Type of gene | protein-coding | |
| Description | phospholipid-transporting ATPase ABCA1ATP-binding cassette sub-family A member 1ATP-binding cassette transporter A1ATP-binding cassette, sub-family A (ABC1), member 1cholesterol efflux regulatory proteinmembrane-bound | |
| Modification date | 20200313 | |
| UniProtAcc | ||
| Context | - 17510946(Association of Genetic Variants of ABCA1 With Alzheimer's Disease Risk) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| ABCA1 | GO:0007040 | lysosome organization | 15163665 |
| ABCA1 | GO:0008203 | cholesterol metabolic process | 14747463 |
| ABCA1 | GO:0016197 | endosomal transport | 14747463 |
| ABCA1 | GO:0033344 | cholesterol efflux | 10431236|11162594|16702602|23931754 |
| ABCA1 | GO:0033700 | phospholipid efflux | 10431236|11162594 |
| ABCA1 | GO:0042632 | cholesterol homeostasis | 10431236 |
| ABCA1 | GO:0045332 | phospholipid translocation | 24097981 |
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Gene structures and expression levels for ABCA1 |
| 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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ENSG00000165029
| 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 |
| 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 ABCA1 |
| 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_126442 | chr9 | 104786298:104786390:104786873:104786976:104787920:104788054 | 104786873:104786976 |
| exon_skip_180299 | chr9 | 104889102:104889195:104903614:104903771:104927935:104928139 | 104903614:104903771 |
| exon_skip_201592 | chr9 | 104803284:104803316:104804626:104804720:104806241:104806430 | 104804626:104804720 |
| exon_skip_256845 | chr9 | 104781006:104784455:104785396:104785639:104786298:104786390 | 104785396:104785639 |
| exon_skip_57222 | chr9 | 104883039:104883157:104884427:104884568:104889102:104889195 | 104884427:104884568 |
| 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 ABCA1 |
| 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 |
| ENST00000374736 | 104785396 | 104785639 | Frame-shift |
| ENST00000374736 | 104786873 | 104786976 | Frame-shift |
| ENST00000374736 | 104804626 | 104804720 | Frame-shift |
| ENST00000374736 | 104884427 | 104884568 | 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 |
| ENST00000374736 | 104785396 | 104785639 | Frame-shift |
| ENST00000374736 | 104786873 | 104786976 | Frame-shift |
| ENST00000374736 | 104804626 | 104804720 | Frame-shift |
| ENST00000374736 | 104884427 | 104884568 | 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 |
| ENST00000374736 | 104785396 | 104785639 | Frame-shift |
| ENST00000374736 | 104786873 | 104786976 | Frame-shift |
| ENST00000374736 | 104804626 | 104804720 | Frame-shift |
| ENST00000374736 | 104884427 | 104884568 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for ABCA1 |
p-ENSG00000165029_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 ABCA1 |
| 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 ABCA1 |
| - 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 ABCA1 |
| 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 ABCA1 |
| 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 ABCA1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for ABCA1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| O95477 | approved | DB01016 | Glyburide | small molecule | O95477 |
| O95477 | approved|investigational | DB01599 | Probucol | small molecule | O95477 |
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RelatedDiseases for ABCA1 |
| 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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