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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 LINGO2 |
Gene summary |
Gene information | Gene symbol | LINGO2 | Gene ID | 158038 |
Gene name | leucine rich repeat and Ig domain containing 2 | |
Synonyms | LERN3|LRRN6C | |
Cytomap | 9p21.2-p21.1 | |
Type of gene | protein-coding | |
Description | leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 2leucine rich repeat neuronal 6Cleucine-rich repeat neuronal protein 3leucine-rich repeat neuronal protein 6C | |
Modification date | 20200313 | |
UniProtAcc | B7ZMN0, Q7L985, | |
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
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Gene structures and expression levels for LINGO2 |
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 LINGO2 |
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_168068 | chr9 | 27948086:27950706:28012355:28012405:28295208:28295331 | 28012355:28012405 |
exon_skip_77159 | chr9 | 27948078:27950706:28012355:28012405:28295208:28295331 | 28012355:28012405 |
exon_skip_79019 | chr9 | 28295208:28295366:28372836:28372868:28475940:28476025 | 28372836:28372868 |
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 LINGO2 |
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 |
ENST00000379992 | 28012355 | 28012405 | 3UTR-3UTR |
ENST00000379992 | 28372836 | 28372868 | 3UTR-3UTR |
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 |
ENST00000379992 | 28012355 | 28012405 | 3UTR-3UTR |
ENST00000379992 | 28372836 | 28372868 | 3UTR-3UTR |
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 |
ENST00000379992 | 28012355 | 28012405 | 3UTR-3UTR |
ENST00000379992 | 28372836 | 28372868 | 3UTR-3UTR |
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Infer the effects of exon skipping event on protein functional features for LINGO2 |
p-ENSG00000174482_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 LINGO2 |
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 | ENST00000379992 | 28012355 | 28012405 | hsa-miR-4701-5p | chr9:28012370-28012377 | 8mer-1a | chr9:28012358-28012377 | 149.00 | -18.29 |
Mayo | ENST00000379992 | 28012355 | 28012405 | hsa-miR-3928-3p | chr9:28012389-28012396 | 8mer-1a | chr9:28012375-28012396 | 158.00 | -20.57 |
Mayo | ENST00000379992 | 28012355 | 28012405 | hsa-miR-588 | chr9:28012370-28012377 | 8mer-1a | chr9:28012358-28012377 | 149.00 | -18.29 |
MSBB | ENST00000379992 | 28012355 | 28012405 | hsa-miR-4701-5p | chr9:28012370-28012377 | 8mer-1a | chr9:28012358-28012377 | 149.00 | -18.29 |
MSBB | ENST00000379992 | 28012355 | 28012405 | hsa-miR-3928-3p | chr9:28012389-28012396 | 8mer-1a | chr9:28012375-28012396 | 158.00 | -20.57 |
MSBB | ENST00000379992 | 28012355 | 28012405 | hsa-miR-588 | chr9:28012370-28012377 | 8mer-1a | chr9:28012358-28012377 | 149.00 | -18.29 |
ROSMAP | ENST00000379992 | 28012355 | 28012405 | hsa-miR-4701-5p | chr9:28012370-28012377 | 8mer-1a | chr9:28012358-28012377 | 149.00 | -18.29 |
ROSMAP | ENST00000379992 | 28012355 | 28012405 | hsa-miR-3928-3p | chr9:28012389-28012396 | 8mer-1a | chr9:28012375-28012396 | 158.00 | -20.57 |
ROSMAP | ENST00000379992 | 28012355 | 28012405 | hsa-miR-588 | chr9:28012370-28012377 | 8mer-1a | chr9:28012358-28012377 | 149.00 | -18.29 |
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SNVs in the skipped exons for LINGO2 |
- 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 LINGO2 |
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 LINGO2 |
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 LINGO2 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for LINGO2 |
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 LINGO2 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |