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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 LPAR1 |
Gene summary |
Gene information | Gene symbol | LPAR1 | Gene ID | 1902 |
Gene name | lysophosphatidic acid receptor 1 | |
Synonyms | EDG2|GPR26|Gpcr26|LPA1|Mrec1.3|VZG1|edg-2|rec.1.3|vzg-1 | |
Cytomap | 9q31.3 | |
Type of gene | protein-coding | |
Description | lysophosphatidic acid receptor 1LPA receptor 1LPA-1endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 2lysophosphatidic acid receptor Edg-2ventricular zone gene 1 | |
Modification date | 20200313 | |
UniProtAcc | ||
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
LPAR1 | GO:0007202 | activation of phospholipase C activity | 19306925 |
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Gene structures and expression levels for LPAR1 |
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 |
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 LPAR1 |
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_163559 | chr9 | 110941668:110942168:110972073:110972220:110973481:110973558 | 110972073:110972220 |
exon_skip_188060 | chr9 | 110941421:110942168:110945374:110945401:110972073:110972220 | 110945374:110945401 |
exon_skip_245980 | chr9 | 110972073:110972220:110973481:110973558:111036122:111036201 | 110973481:110973558 |
exon_skip_276259 | chr9 | 110972073:110972220:110973481:110973558:111038167:111038458 | 110973481:110973558 |
exon_skip_291381 | chr9 | 110941668:110942168:110972073:110972220:111037841:111038043 | 110972073:110972220 |
exon_skip_49176 | chr9 | 110972073:110972220:110973481:110973558:110999393:110999466 | 110973481:110973558 |
exon_skip_60756 | chr9 | 110874321:110875722:110941421:110942168:110972073:110972220 | 110941421:110942168 |
exon_skip_71639 | chr9 | 110972091:110972220:110973481:110973558:111038167:111038458 | 110973481:110973558 |
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 LPAR1 |
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 |
ENST00000358883 | 110972073 | 110972220 | 3UTR-3CDS |
ENST00000374430 | 110973481 | 110973558 | 3UTR-3UTR |
ENST00000358883 | 110941421 | 110942168 | Frame-shift |
ENST00000374430 | 110941421 | 110942168 | Frame-shift |
ENST00000374431 | 110941421 | 110942168 | 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 |
ENST00000358883 | 110972073 | 110972220 | 3UTR-3CDS |
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 |
ENST00000358883 | 110972073 | 110972220 | 3UTR-3CDS |
ENST00000374430 | 110972073 | 110972220 | 3UTR-3CDS |
ENST00000374431 | 110972073 | 110972220 | 3UTR-3CDS |
ENST00000374430 | 110973481 | 110973558 | 3UTR-3UTR |
ENST00000358883 | 110941421 | 110942168 | Frame-shift |
ENST00000374430 | 110941421 | 110942168 | Frame-shift |
ENST00000374431 | 110941421 | 110942168 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for LPAR1 |
p-ENSG00000198121_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 LPAR1 |
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 | ENST00000374430 | 110973481 | 110973558 | hsa-miR-3664-3p | chr9:110973500-110973507 | 8mer-1a | chr9:110973482-110973507 | 152.00 | -22.98 |
Mayo | ENST00000374430 | 110973481 | 110973558 | hsa-miR-6505-3p | chr9:110973505-110973512 | 8mer-1a | chr9:110973497-110973520 | 149.00 | -19.57 |
Mayo | ENST00000374430 | 110973481 | 110973558 | hsa-miR-6806-3p | chr9:110973535-110973542 | 8mer-1a | chr9:110973522-110973542 | 154.00 | -28.17 |
Mayo | ENST00000374430 | 110973481 | 110973558 | hsa-miR-3200-5p | chr9:110973517-110973524 | 8mer-1a | chr9:110973517-110973539 | 143.00 | -24.72 |
Mayo | ENST00000374430 | 110973481 | 110973558 | hsa-miR-3928-5p | chr9:110973535-110973542 | 8mer-1a | chr9:110973522-110973542 | 154.00 | -28.17 |
Mayo | ENST00000374430 | 110973481 | 110973558 | hsa-miR-29a-5p | chr9:110973544-110973551 | 8mer-1a | chr9:110973530-110973551 | 144.00 | -13.43 |
Mayo | ENST00000374430 | 110973481 | 110973558 | hsa-miR-1911-5p | chr9:110973513-110973520 | 8mer-1a | chr9:110973497-110973520 | 149.00 | -19.57 |
ROSMAP | ENST00000374430 | 110973481 | 110973558 | hsa-miR-3664-3p | chr9:110973500-110973507 | 8mer-1a | chr9:110973482-110973507 | 152.00 | -22.98 |
ROSMAP | ENST00000374430 | 110973481 | 110973558 | hsa-miR-6505-3p | chr9:110973505-110973512 | 8mer-1a | chr9:110973497-110973520 | 149.00 | -19.57 |
ROSMAP | ENST00000374430 | 110973481 | 110973558 | hsa-miR-6806-3p | chr9:110973535-110973542 | 8mer-1a | chr9:110973522-110973542 | 154.00 | -28.17 |
ROSMAP | ENST00000374430 | 110973481 | 110973558 | hsa-miR-3200-5p | chr9:110973517-110973524 | 8mer-1a | chr9:110973517-110973539 | 143.00 | -24.72 |
ROSMAP | ENST00000374430 | 110973481 | 110973558 | hsa-miR-3928-5p | chr9:110973535-110973542 | 8mer-1a | chr9:110973522-110973542 | 154.00 | -28.17 |
ROSMAP | ENST00000374430 | 110973481 | 110973558 | hsa-miR-29a-5p | chr9:110973544-110973551 | 8mer-1a | chr9:110973530-110973551 | 144.00 | -13.43 |
ROSMAP | ENST00000374430 | 110973481 | 110973558 | hsa-miR-1911-5p | chr9:110973513-110973520 | 8mer-1a | chr9:110973497-110973520 | 149.00 | -19.57 |
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SNVs in the skipped exons for LPAR1 |
- 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 LPAR1 |
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 |
ADstage | MSBB | IFG | exon_skip_294116 | 5.089899e-01 | 5.672878e-03 | chr9 | - | 110973481 | 110973558 | 111036122 | 111036201 | 111038167 | 111038458 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LPAR1 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
HCC | exon_skip_276259 | rs34615401 | chr9:110901241 | 7.160490e-04 | 4.501352e-02 |
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Correlation with RNA binding proteins (RBPs) for LPAR1 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for LPAR1 |
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 LPAR1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |