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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 LRRC4C |
Gene summary |
Gene information | Gene symbol | LRRC4C | Gene ID | 57689 |
Gene name | leucine rich repeat containing 4C | |
Synonyms | NGL-1|NGL1 | |
Cytomap | 11p12 | |
Type of gene | protein-coding | |
Description | leucine-rich repeat-containing protein 4Cnetrin-G1 ligand | |
Modification date | 20200313 | |
UniProtAcc | E9PLP4, Q9HCJ2, | |
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
LRRC4C | GO:0050770 | regulation of axonogenesis | 14595443 |
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Gene structures and expression levels for LRRC4C |
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 |
STG | UP | ENST00000534577.1 | LRRC4C-206:lncRNA:LRRC4C | 1.350971e+01 | 1.066450e+00 | 2.969581e-04 | 2.050861e-02 |
CB | DOWN | ENST00000619527.4 | LRRC4C-207:protein_coding:LRRC4C | 4.041620e+01 | -8.887284e-01 | 4.503318e-04 | 2.636537e-03 |
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 LRRC4C |
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_123648 | chr11 | 40933635:40933723:41222797:41223008:41459431:41459652 | 41222797:41223008 |
exon_skip_188301 | chr11 | 40116170:40116334:40140801:40140853:40241519:40241598 | 40140801:40140853 |
exon_skip_194225 | chr11 | 40116170:40116334:40140801:40140853:40319628:40319721 | 40140801:40140853 |
exon_skip_217761 | chr11 | 40116170:40116334:40140801:40140853:40292193:40293130 | 40140801:40140853 |
exon_skip_249914 | chr11 | 40140801:40140853:40241519:40241598:40319628:40319721 | 40241519:40241598 |
exon_skip_90234 | chr11 | 40933639:40933723:41222797:41223008:41459431:41459652 | 41222797:41223008 |
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 LRRC4C |
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 |
ENST00000527150 | 40140801 | 40140853 | 3UTR-3UTR |
ENST00000528697 | 40140801 | 40140853 | 3UTR-3UTR |
ENST00000530763 | 40140801 | 40140853 | 3UTR-3UTR |
ENST00000619527 | 40140801 | 40140853 | 3UTR-3UTR |
ENST00000528697 | 40241519 | 40241598 | 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 |
ENST00000527150 | 40140801 | 40140853 | 3UTR-3UTR |
ENST00000528697 | 40140801 | 40140853 | 3UTR-3UTR |
ENST00000530763 | 40140801 | 40140853 | 3UTR-3UTR |
ENST00000619527 | 40140801 | 40140853 | 3UTR-3UTR |
ENST00000528697 | 40241519 | 40241598 | 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 |
ENST00000527150 | 40140801 | 40140853 | 3UTR-3UTR |
ENST00000528697 | 40140801 | 40140853 | 3UTR-3UTR |
ENST00000530763 | 40140801 | 40140853 | 3UTR-3UTR |
ENST00000619527 | 40140801 | 40140853 | 3UTR-3UTR |
ENST00000528697 | 40241519 | 40241598 | 3UTR-3UTR |
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Infer the effects of exon skipping event on protein functional features for LRRC4C |
p-ENSG00000148948_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 LRRC4C |
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 | ENST00000528697 | 40241519 | 40241598 | hsa-miR-4693-3p | chr11:40241581-40241588 | 8mer-1a | chr11:40241572-40241594 | 148.00 | -18.52 |
Mayo | ENST00000619527 | 40140801 | 40140853 | hsa-miR-24-2-5p | chr11:40140832-40140839 | 8mer-1a | chr11:40140824-40140846 | 159.00 | -19.98 |
Mayo | ENST00000528697 | 40241519 | 40241598 | hsa-miR-512-5p | chr11:40241550-40241557 | 8mer-1a | chr11:40241548-40241568 | 165.00 | -22.82 |
Mayo | ENST00000619527 | 40140801 | 40140853 | hsa-miR-4470 | chr11:40140844-40140851 | 8mer-1a | chr11:40140832-40140851 | 149.00 | -19.89 |
Mayo | ENST00000619527 | 40140801 | 40140853 | hsa-miR-24-1-5p | chr11:40140832-40140839 | 8mer-1a | chr11:40140824-40140846 | 159.00 | -19.98 |
MSBB | ENST00000528697 | 40241519 | 40241598 | hsa-miR-4693-3p | chr11:40241581-40241588 | 8mer-1a | chr11:40241572-40241594 | 148.00 | -18.52 |
MSBB | ENST00000619527 | 40140801 | 40140853 | hsa-miR-24-2-5p | chr11:40140832-40140839 | 8mer-1a | chr11:40140824-40140846 | 159.00 | -19.98 |
MSBB | ENST00000528697 | 40241519 | 40241598 | hsa-miR-512-5p | chr11:40241550-40241557 | 8mer-1a | chr11:40241548-40241568 | 165.00 | -22.82 |
MSBB | ENST00000619527 | 40140801 | 40140853 | hsa-miR-4470 | chr11:40140844-40140851 | 8mer-1a | chr11:40140832-40140851 | 149.00 | -19.89 |
MSBB | ENST00000619527 | 40140801 | 40140853 | hsa-miR-24-1-5p | chr11:40140832-40140839 | 8mer-1a | chr11:40140824-40140846 | 159.00 | -19.98 |
ROSMAP | ENST00000528697 | 40241519 | 40241598 | hsa-miR-4693-3p | chr11:40241581-40241588 | 8mer-1a | chr11:40241572-40241594 | 148.00 | -18.52 |
ROSMAP | ENST00000619527 | 40140801 | 40140853 | hsa-miR-24-2-5p | chr11:40140832-40140839 | 8mer-1a | chr11:40140824-40140846 | 159.00 | -19.98 |
ROSMAP | ENST00000528697 | 40241519 | 40241598 | hsa-miR-512-5p | chr11:40241550-40241557 | 8mer-1a | chr11:40241548-40241568 | 165.00 | -22.82 |
ROSMAP | ENST00000619527 | 40140801 | 40140853 | hsa-miR-4470 | chr11:40140844-40140851 | 8mer-1a | chr11:40140832-40140851 | 149.00 | -19.89 |
ROSMAP | ENST00000619527 | 40140801 | 40140853 | hsa-miR-24-1-5p | chr11:40140832-40140839 | 8mer-1a | chr11:40140824-40140846 | 159.00 | -19.98 |
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SNVs in the skipped exons for LRRC4C |
- 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 LRRC4C |
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 LRRC4C |
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 LRRC4C |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
IFG | ENOX1 | exon_skip_90344 | 4.231104e-01 | 4.976258e-02 |
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RelatedDrugs for LRRC4C |
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 LRRC4C |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |