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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 LGR5 |
 Gene summary |
| Gene information | Gene symbol | LGR5 | Gene ID | 8549 |
| Gene name | leucine rich repeat containing G protein-coupled receptor 5 | |
| Synonyms | FEX|GPR49|GPR67|GRP49|HG38 | |
| Cytomap | 12q21.1 | |
| Type of gene | protein-coding | |
| Description | leucine-rich repeat-containing G-protein coupled receptor 5G-protein coupled receptor 49G-protein coupled receptor 67G-protein coupled receptor HG38orphan G protein-coupled receptor HG38 | |
| Modification date | 20200329 | |
| UniProtAcc | A0A0A8K8C7, O75473, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| LGR5 | GO:0090263 | positive regulation of canonical Wnt signaling pathway | 21693646|22815884 |
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Gene structures and expression levels for LGR5 |
| 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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ENSG00000139292
| 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. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| TC | UP | ENST00000540815.2 | LGR5-203:protein_coding:LGR5 | 8.984422e+00 | 1.237021e+00 | 3.449416e-03 | 2.536283e-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 LGR5 |
| 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_132341 | chr12 | 71556619:71556690:71559586:71559654:71561781:71561852 | 71559586:71559654 |
| exon_skip_142763 | chr12 | 71580278:71580423:71582456:71582539:71583647:71583912 | 71582456:71582539 |
| exon_skip_164779 | chr12 | 71559586:71559654:71561781:71561852:71566404:71566475 | 71561781:71561852 |
| exon_skip_213152 | chr12 | 71571514:71571579:71572850:71572921:71577925:71577996 | 71572850:71572921 |
| exon_skip_3636 | chr12 | 71504614:71504685:71524406:71524477:71535115:71535186 | 71524406:71524477 |
| 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 LGR5 |
| 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 |
| ENST00000266674 | 71559586 | 71559654 | In-frame |
| ENST00000266674 | 71561781 | 71561852 | In-frame |
| ENST00000266674 | 71572850 | 71572921 | In-frame |
| 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 |
| ENST00000266674 | 71561781 | 71561852 | In-frame |
| ENST00000266674 | 71572850 | 71572921 | In-frame |
| 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 |
| ENST00000266674 | 71524406 | 71524477 | In-frame |
| ENST00000266674 | 71561781 | 71561852 | In-frame |
| ENST00000266674 | 71572850 | 71572921 | In-frame |
| ENST00000266674 | 71582456 | 71582539 | In-frame |
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Infer the effects of exon skipping event on protein functional features for LGR5 |
p-ENSG00000139292_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 |
| ENST00000266674 | 4628 | 907 | 71559586 | 71559654 | 1029 | 1096 | 239 | 261 |
| ENST00000266674 | 4628 | 907 | 71561781 | 71561852 | 1098 | 1168 | 262 | 285 |
| ENST00000266674 | 4628 | 907 | 71572850 | 71572921 | 1449 | 1519 | 379 | 402 |
| 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 |
| ENST00000266674 | 4628 | 907 | 71561781 | 71561852 | 1098 | 1168 | 262 | 285 |
| ENST00000266674 | 4628 | 907 | 71572850 | 71572921 | 1449 | 1519 | 379 | 402 |
| 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 |
| ENST00000266674 | 4628 | 907 | 71524406 | 71524477 | 597 | 667 | 95 | 118 |
| ENST00000266674 | 4628 | 907 | 71561781 | 71561852 | 1098 | 1168 | 262 | 285 |
| ENST00000266674 | 4628 | 907 | 71572850 | 71572921 | 1449 | 1519 | 379 | 402 |
| ENST00000266674 | 4628 | 907 | 71582456 | 71582539 | 1865 | 1947 | 518 | 545 |
| 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 |
| O75473 | 239 | 261 | 238 | 240 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 239 | 261 | 261 | 263 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 239 | 261 | 22 | 907 | Chain | ID=PRO_0000012794;Note=Leucine-rich repeat-containing G-protein coupled receptor 5 |
| O75473 | 239 | 261 | 252 | 254 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 239 | 261 | 235 | 256 | Repeat | Note=LRR 8 |
| O75473 | 239 | 261 | 258 | 279 | Repeat | Note=LRR 9 |
| O75473 | 239 | 261 | 22 | 561 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O75473 | 262 | 285 | 263 | 286 | Alternative sequence | ID=VSP_037746;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| O75473 | 262 | 285 | 261 | 263 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 262 | 285 | 285 | 287 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 262 | 285 | 22 | 907 | Chain | ID=PRO_0000012794;Note=Leucine-rich repeat-containing G-protein coupled receptor 5 |
| O75473 | 262 | 285 | 258 | 279 | Repeat | Note=LRR 9 |
| O75473 | 262 | 285 | 282 | 303 | Repeat | Note=LRR 10 |
| O75473 | 262 | 285 | 22 | 561 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O75473 | 262 | 285 | 274 | 279 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 379 | 402 | 380 | 385 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 379 | 402 | 401 | 408 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 379 | 402 | 22 | 907 | Chain | ID=PRO_0000012794;Note=Leucine-rich repeat-containing G-protein coupled receptor 5 |
| O75473 | 379 | 402 | 383 | 383 | Natural variant | ID=VAR_049411;Note=H->R;Dbxref=dbSNP:rs12303775 |
| O75473 | 379 | 402 | 375 | 396 | Repeat | Note=LRR 14 |
| O75473 | 379 | 402 | 399 | 420 | Repeat | Note=LRR 15 |
| O75473 | 379 | 402 | 22 | 561 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O75473 | 379 | 402 | 393 | 396 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KNG |
| 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 |
| O75473 | 262 | 285 | 263 | 286 | Alternative sequence | ID=VSP_037746;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| O75473 | 262 | 285 | 261 | 263 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 262 | 285 | 285 | 287 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 262 | 285 | 22 | 907 | Chain | ID=PRO_0000012794;Note=Leucine-rich repeat-containing G-protein coupled receptor 5 |
| O75473 | 262 | 285 | 258 | 279 | Repeat | Note=LRR 9 |
| O75473 | 262 | 285 | 282 | 303 | Repeat | Note=LRR 10 |
| O75473 | 262 | 285 | 22 | 561 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O75473 | 262 | 285 | 274 | 279 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 379 | 402 | 380 | 385 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 379 | 402 | 401 | 408 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 379 | 402 | 22 | 907 | Chain | ID=PRO_0000012794;Note=Leucine-rich repeat-containing G-protein coupled receptor 5 |
| O75473 | 379 | 402 | 383 | 383 | Natural variant | ID=VAR_049411;Note=H->R;Dbxref=dbSNP:rs12303775 |
| O75473 | 379 | 402 | 375 | 396 | Repeat | Note=LRR 14 |
| O75473 | 379 | 402 | 399 | 420 | Repeat | Note=LRR 15 |
| O75473 | 379 | 402 | 22 | 561 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O75473 | 379 | 402 | 393 | 396 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KNG |
| 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 |
| O75473 | 95 | 118 | 94 | 96 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KNG |
| O75473 | 95 | 118 | 118 | 120 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KNG |
| O75473 | 95 | 118 | 22 | 907 | Chain | ID=PRO_0000012794;Note=Leucine-rich repeat-containing G-protein coupled receptor 5 |
| O75473 | 95 | 118 | 91 | 112 | Repeat | Note=LRR 2 |
| O75473 | 95 | 118 | 115 | 136 | Repeat | Note=LRR 3 |
| O75473 | 95 | 118 | 22 | 561 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O75473 | 95 | 118 | 107 | 112 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KNG |
| O75473 | 262 | 285 | 263 | 286 | Alternative sequence | ID=VSP_037746;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| O75473 | 262 | 285 | 261 | 263 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 262 | 285 | 285 | 287 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 262 | 285 | 22 | 907 | Chain | ID=PRO_0000012794;Note=Leucine-rich repeat-containing G-protein coupled receptor 5 |
| O75473 | 262 | 285 | 258 | 279 | Repeat | Note=LRR 9 |
| O75473 | 262 | 285 | 282 | 303 | Repeat | Note=LRR 10 |
| O75473 | 262 | 285 | 22 | 561 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O75473 | 262 | 285 | 274 | 279 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 379 | 402 | 380 | 385 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 379 | 402 | 401 | 408 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 379 | 402 | 22 | 907 | Chain | ID=PRO_0000012794;Note=Leucine-rich repeat-containing G-protein coupled receptor 5 |
| O75473 | 379 | 402 | 383 | 383 | Natural variant | ID=VAR_049411;Note=H->R;Dbxref=dbSNP:rs12303775 |
| O75473 | 379 | 402 | 375 | 396 | Repeat | Note=LRR 14 |
| O75473 | 379 | 402 | 399 | 420 | Repeat | Note=LRR 15 |
| O75473 | 379 | 402 | 22 | 561 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O75473 | 379 | 402 | 393 | 396 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KNG |
| O75473 | 518 | 545 | 535 | 537 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 518 | 545 | 22 | 907 | Chain | ID=PRO_0000012794;Note=Leucine-rich repeat-containing G-protein coupled receptor 5 |
| O75473 | 518 | 545 | 479 | 541 | Disulfide bond | . |
| O75473 | 518 | 545 | 538 | 543 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
| O75473 | 518 | 545 | 22 | 561 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O75473 | 518 | 545 | 522 | 524 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4UFR |
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3'-UTR located exon skipping events that lost miRNA binding sites in LGR5 |
| 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 LGR5 |
| - 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 LGR5 |
| 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 LGR5 |
| 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 LGR5 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for LGR5 |
| 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 LGR5 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
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