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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 LSAMP |
 Gene summary |
| Gene information | Gene symbol | LSAMP | Gene ID | 4045 |
| Gene name | limbic system associated membrane protein | |
| Synonyms | IGLON3|LAMP | |
| Cytomap | 3q13.31 | |
| Type of gene | protein-coding | |
| Description | limbic system-associated membrane proteinIgLON family member 3 | |
| 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 |
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Gene structures and expression levels for LSAMP |
| 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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ENSG00000185565
| 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 |
| STG | UP | ENST00000333617.8 | LSAMP-201:protein_coding:LSAMP | 6.866039e+01 | 1.617817e+00 | 8.552652e-08 | 7.228755e-05 |
| CB | DOWN | ENST00000490351.1 | LSAMP-AS1-201:lncRNA:LSAMP | 1.133647e+00 | -8.424891e-01 | 7.737172e-04 | 4.166283e-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 LSAMP |
| 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_182547 | chr3 | 115816614:115816646:115834562:115834597:115841845:115841993 | 115834562:115834597 |
| exon_skip_210175 | chr3 | 115810276:115810414:115816614:115816646:115834562:115834597 | 115816614:115816646 |
| exon_skip_210223 | chr3 | 115842458:115842578:115852483:115852617:116019515:116019640 | 115852483:115852617 |
| exon_skip_240381 | chr3 | 115810381:115810414:115816614:115816646:115834562:115834597 | 115816614:115816646 |
| exon_skip_37250 | chr3 | 115852483:115852617:116019515:116019640:116086324:116086556 | 116019515:116019640 |
| exon_skip_46000 | chr3 | 116019515:116019640:116086324:116086556:116444877:116444955 | 116086324:116086556 |
| exon_skip_68467 | chr3 | 115810276:115810414:115814159:115814238:115816614:115816646 | 115814159:115814238 |
| 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 LSAMP |
| 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 |
| ENST00000490035 | 116086324 | 116086556 | Frame-shift |
| ENST00000490035 | 115852483 | 115852617 | 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 |
| 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 |
| ENST00000490035 | 116086324 | 116086556 | Frame-shift |
| ENST00000490035 | 116019515 | 116019640 | In-frame |
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Infer the effects of exon skipping event on protein functional features for LSAMP |
p-ENSG00000185565_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 |
| ENST00000490035 | 9463 | 338 | 115852483 | 115852617 | 1015 | 1148 | 171 | 216 |
| 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 |
| ENST00000490035 | 9463 | 338 | 116019515 | 116019640 | 889 | 1013 | 129 | 171 |
| 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 |
| Q13449 | 171 | 216 | 29 | 315 | Chain | ID=PRO_0000015102;Note=Limbic system-associated membrane protein |
| Q13449 | 171 | 216 | 153 | 197 | Disulfide bond | Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00114 |
| Q13449 | 171 | 216 | 132 | 214 | Domain | Note=Ig-like C2-type 2 |
| 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 |
| Q13449 | 129 | 171 | 29 | 315 | Chain | ID=PRO_0000015102;Note=Limbic system-associated membrane protein |
| Q13449 | 129 | 171 | 153 | 197 | Disulfide bond | Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00114 |
| Q13449 | 129 | 171 | 132 | 214 | Domain | Note=Ig-like C2-type 2 |
| Q13449 | 129 | 171 | 136 | 136 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q13449 | 129 | 171 | 148 | 148 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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3'-UTR located exon skipping events that lost miRNA binding sites in LSAMP |
| 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 LSAMP |
| - 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 LSAMP |
| 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 LSAMP |
| 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 LSAMP |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | PCBP1 | exon_skip_100994 | -5.235455e-01 | 1.687024e-12 |
| CB | HNRNPK | exon_skip_100994 | -4.253114e-01 | 2.541024e-08 |
| CB | PCBP2 | exon_skip_100994 | -4.945830e-01 | 3.977221e-11 |
| CB | KHSRP | exon_skip_100994 | -4.743179e-01 | 3.062839e-10 |
| FL | HNRNPK | exon_skip_100994 | -4.009324e-01 | 6.313324e-09 |
| FL | NOVA1 | exon_skip_100994 | -4.025970e-01 | 5.391562e-09 |
| HCC | SRSF5 | exon_skip_100994 | 4.060390e-01 | 3.518912e-12 |
| IFG | NUP42 | exon_skip_210175 | -4.305724e-01 | 2.218135e-02 |
| PG | HNRNPK | exon_skip_100994 | -4.104345e-01 | 2.042257e-08 |
| PG | PCBP2 | exon_skip_100994 | -4.055571e-01 | 3.106564e-08 |
| PG | NOVA1 | exon_skip_100994 | -5.252390e-01 | 1.180585e-13 |
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RelatedDrugs for LSAMP |
| 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 LSAMP |
| 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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