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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 L3MBTL2 |
 Gene summary |
| Gene information | Gene symbol | L3MBTL2 | Gene ID | 83746 |
| Gene name | L3MBTL histone methyl-lysine binding protein 2 | |
| Synonyms | H-l(3)mbt-l|L3MBT | |
| Cytomap | 22q13.2 | |
| Type of gene | protein-coding | |
| Description | lethal(3)malignant brain tumor-like protein 2H-l(3)mbt-like protein 2L(3)mbt-like protein 2L3MBTL2, polycomb repressive complex 1 subunitl(3)mbt-like 2 | |
| Modification date | 20200313 | |
| UniProtAcc | ||
| Context | - 30010129(The GWAS Risk Genes for Depression May Be Actively Involved in Alzheimer's Disease) |
| 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 L3MBTL2 |
| 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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ENSG00000100395
| 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 L3MBTL2 |
| 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_100709 | chr22 | 41205324:41205386:41206007:41206125:41209696:41209933 | 41206007:41206125 |
| exon_skip_10314 | chr22 | 41227089:41227323:41227575:41227679:41227804:41227869 | 41227575:41227679 |
| exon_skip_113911 | chr22 | 41224725:41224801:41224967:41225071:41225794:41225941 | 41224967:41225071 |
| exon_skip_131177 | chr22 | 41217123:41217202:41219419:41219536:41220734:41220868 | 41219419:41219536 |
| exon_skip_152547 | chr22 | 41209696:41209933:41213851:41214026:41216139:41216186 | 41213851:41214026 |
| exon_skip_18324 | chr22 | 41205324:41205386:41206007:41206125:41209696:41209815 | 41206007:41206125 |
| exon_skip_197864 | chr22 | 41227804:41227869:41229540:41229656:41230139:41230654 | 41229540:41229656 |
| exon_skip_203430 | chr22 | 41209840:41209933:41213893:41214026:41216139:41216262 | 41213893:41214026 |
| exon_skip_208481 | chr22 | 41217123:41217202:41219419:41219536:41220734:41220812 | 41219419:41219536 |
| exon_skip_212273 | chr22 | 41209839:41209933:41213893:41214026:41216139:41216262 | 41213893:41214026 |
| exon_skip_216869 | chr22 | 41205324:41205386:41209696:41209933:41213893:41214026 | 41209696:41209933 |
| exon_skip_221177 | chr22 | 41209696:41209933:41213851:41214026:41216139:41216262 | 41213851:41214026 |
| exon_skip_58849 | chr22 | 41209839:41209933:41213851:41214026:41216139:41216262 | 41213851:41214026 |
| exon_skip_68201 | chr22 | 41209840:41209933:41213851:41214026:41216139:41216262 | 41213851:41214026 |
| exon_skip_85405 | chr22 | 41209696:41209933:41213893:41214026:41216139:41216262 | 41213893:41214026 |
| exon_skip_91775 | chr22 | 41209696:41209933:41213893:41214026:41216139:41216186 | 41213893:41214026 |
| exon_skip_91827 | chr22 | 41205324:41205386:41206007:41206125:41209696:41209813 | 41206007:41206125 |
| 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 L3MBTL2 |
| 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 |
| ENST00000216237 | 41213893 | 41214026 | Frame-shift |
| ENST00000216237 | 41219419 | 41219536 | Frame-shift |
| ENST00000216237 | 41224967 | 41225071 | In-frame |
| ENST00000216237 | 41229540 | 41229656 | 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 |
| ENST00000216237 | 41209696 | 41209933 | Frame-shift |
| ENST00000216237 | 41213893 | 41214026 | Frame-shift |
| ENST00000216237 | 41219419 | 41219536 | Frame-shift |
| ENST00000216237 | 41229540 | 41229656 | 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 |
| ENST00000216237 | 41213893 | 41214026 | Frame-shift |
| ENST00000216237 | 41219419 | 41219536 | Frame-shift |
| ENST00000216237 | 41224967 | 41225071 | In-frame |
| ENST00000216237 | 41229540 | 41229656 | In-frame |
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Infer the effects of exon skipping event on protein functional features for L3MBTL2 |
p-ENSG00000100395_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 |
| ENST00000216237 | 3313 | 705 | 41224967 | 41225071 | 1411 | 1514 | 417 | 452 |
| ENST00000216237 | 3313 | 705 | 41229540 | 41229656 | 2048 | 2163 | 630 | 668 |
| 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 |
| ENST00000216237 | 3313 | 705 | 41229540 | 41229656 | 2048 | 2163 | 630 | 668 |
| 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 |
| ENST00000216237 | 3313 | 705 | 41224967 | 41225071 | 1411 | 1514 | 417 | 452 |
| ENST00000216237 | 3313 | 705 | 41229540 | 41229656 | 2048 | 2163 | 630 | 668 |
| 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 |
| Q969R5 | 417 | 452 | 420 | 422 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3F70 |
| Q969R5 | 417 | 452 | 433 | 438 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3F70 |
| Q969R5 | 417 | 452 | 441 | 453 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3F70 |
| Q969R5 | 417 | 452 | 1 | 705 | Chain | ID=PRO_0000084448;Note=Lethal(3)malignant brain tumor-like protein 2 |
| Q969R5 | 417 | 452 | 397 | 500 | Repeat | Note=MBT 3 |
| Q969R5 | 630 | 668 | 615 | 705 | Alternative sequence | ID=VSP_003905;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11682070;Dbxref=PMID:11682070 |
| Q969R5 | 630 | 668 | 618 | 705 | Alternative sequence | ID=VSP_003907;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q969R5 | 630 | 668 | 1 | 705 | Chain | ID=PRO_0000084448;Note=Lethal(3)malignant brain tumor-like protein 2 |
| Q969R5 | 630 | 668 | 647 | 647 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 |
| Q969R5 | 630 | 668 | 659 | 659 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 |
| 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 |
| Q969R5 | 630 | 668 | 615 | 705 | Alternative sequence | ID=VSP_003905;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11682070;Dbxref=PMID:11682070 |
| Q969R5 | 630 | 668 | 618 | 705 | Alternative sequence | ID=VSP_003907;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q969R5 | 630 | 668 | 1 | 705 | Chain | ID=PRO_0000084448;Note=Lethal(3)malignant brain tumor-like protein 2 |
| Q969R5 | 630 | 668 | 647 | 647 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 |
| Q969R5 | 630 | 668 | 659 | 659 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 |
| 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 |
| Q969R5 | 417 | 452 | 420 | 422 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3F70 |
| Q969R5 | 417 | 452 | 433 | 438 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3F70 |
| Q969R5 | 417 | 452 | 441 | 453 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3F70 |
| Q969R5 | 417 | 452 | 1 | 705 | Chain | ID=PRO_0000084448;Note=Lethal(3)malignant brain tumor-like protein 2 |
| Q969R5 | 417 | 452 | 397 | 500 | Repeat | Note=MBT 3 |
| Q969R5 | 630 | 668 | 615 | 705 | Alternative sequence | ID=VSP_003905;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11682070;Dbxref=PMID:11682070 |
| Q969R5 | 630 | 668 | 618 | 705 | Alternative sequence | ID=VSP_003907;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q969R5 | 630 | 668 | 1 | 705 | Chain | ID=PRO_0000084448;Note=Lethal(3)malignant brain tumor-like protein 2 |
| Q969R5 | 630 | 668 | 647 | 647 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 |
| Q969R5 | 630 | 668 | 659 | 659 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 |
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3'-UTR located exon skipping events that lost miRNA binding sites in L3MBTL2 |
| 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 L3MBTL2 |
| - 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 L3MBTL2 |
| 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 L3MBTL2 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| HCC | exon_skip_85405 | rs2281336 | chr22:41239200 | 1.295164e-06 | 2.058088e-04 |
| HCC | exon_skip_85405 | rs4820431 | chr22:41153917 | 1.835837e-06 | 2.823143e-04 |
| HCC | exon_skip_85405 | rs139453 | chr22:41214238 | 2.609938e-06 | 3.880355e-04 |
| HCC | exon_skip_85405 | rs1033611 | chr22:41162228 | 2.923018e-06 | 4.258984e-04 |
| HCC | exon_skip_85405 | rs139439 | chr22:41210026 | 2.923018e-06 | 4.258984e-04 |
| HCC | exon_skip_85405 | rs139474 | chr22:41223222 | 3.988410e-06 | 5.600629e-04 |
| HCC | exon_skip_85405 | rs2413637 | chr22:41145523 | 8.428565e-06 | 1.085204e-03 |
| HCC | exon_skip_85405 | rs139531 | chr22:41280172 | 9.503532e-05 | 8.734018e-03 |
| HCC | exon_skip_85405 | rs139452 | chr22:41214168 | 1.911035e-04 | 1.561520e-02 |
| PCC | exon_skip_85405 | rs139474 | chr22:41223222 | 1.088898e-04 | 1.846428e-02 |
| PCC | exon_skip_85405 | rs4820431 | chr22:41153917 | 1.097021e-04 | 1.851414e-02 |
| PCC | exon_skip_85405 | rs1033611 | chr22:41162228 | 1.097021e-04 | 1.851414e-02 |
| PCC | exon_skip_85405 | rs139439 | chr22:41210026 | 1.097021e-04 | 1.851414e-02 |
| PCC | exon_skip_85405 | rs139453 | chr22:41214238 | 1.274420e-04 | 2.082996e-02 |
| PCC | exon_skip_85405 | rs2281336 | chr22:41239200 | 1.655505e-04 | 2.564681e-02 |
| PCC | exon_skip_85405 | rs139452 | chr22:41214168 | 2.776232e-04 | 3.854586e-02 |
| PCC | exon_skip_85405 | rs2413637 | chr22:41145523 | 2.807818e-04 | 3.890834e-02 |
| DLPFC | exon_skip_85405 | rs139515 | chr22:41260129 | 6.843784e-05 | 6.090603e-03 |
| DLPFC | exon_skip_85405 | rs79546 | chr22:41206883 | 1.884691e-04 | 1.460902e-02 |
| DLPFC | exon_skip_85405 | rs2413637 | chr22:41145523 | 2.071074e-04 | 1.576120e-02 |
| DLPFC | exon_skip_85405 | rs2076578 | chr22:41173605 | 2.849863e-04 | 2.061714e-02 |
| DLPFC | exon_skip_85405 | rs139453 | chr22:41214238 | 4.073343e-04 | 2.746965e-02 |
| DLPFC | exon_skip_85405 | rs139452 | chr22:41214168 | 4.245302e-04 | 2.830930e-02 |
| DLPFC | exon_skip_85405 | rs1033611 | chr22:41162228 | 4.275497e-04 | 2.844253e-02 |
| DLPFC | exon_skip_85405 | rs139439 | chr22:41210026 | 4.275497e-04 | 2.844253e-02 |
| DLPFC | exon_skip_85405 | rs4820431 | chr22:41153917 | 4.324829e-04 | 2.872495e-02 |
| DLPFC | exon_skip_85405 | rs2281336 | chr22:41239200 | 4.929425e-04 | 3.197770e-02 |
| DLPFC | exon_skip_85405 | rs139531 | chr22:41280172 | 8.687179e-04 | 4.979864e-02 |
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Correlation with RNA binding proteins (RBPs) for L3MBTL2 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | PCBP4 | exon_skip_203430 | 4.347086e-01 | 2.193674e-08 |
| CB | TRA2A | exon_skip_203430 | -4.425187e-01 | 1.141779e-08 |
| IFG | RBM3 | exon_skip_85405 | 4.334502e-01 | 2.120913e-02 |
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RelatedDrugs for L3MBTL2 |
| 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 L3MBTL2 |
| 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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