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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 LDB2 |
 Gene summary |
| Gene information | Gene symbol | LDB2 | Gene ID | 9079 |
| Gene name | LIM domain binding 2 | |
| Synonyms | CLIM1|LDB-2|LDB1 | |
| Cytomap | 4p15.32 | |
| Type of gene | protein-coding | |
| Description | LIM domain-binding protein 2LIM binding domain 2LIM domain-binding factor CLIM1LIM domain-binding factor-2carboxyl-terminal LIM domain-binding protein 1 | |
| 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 LDB2 |
| 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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ENSG00000169744
| 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 |
| PG | DOWN | ENST00000510825.5 | LDB2-213:lncRNA:LDB2 | 6.687041e+00 | -1.070848e+00 | 2.769675e-04 | 5.787624e-03 |
| CB | UP | ENST00000478922.1 | PHLDB2-210:protein_coding:PHLDB2 | 1.928181e+00 | 1.657539e+00 | 1.138740e-03 | 5.766299e-03 |
| CB | UP | ENST00000412622.5 | PHLDB2-203:protein_coding:PHLDB2 | 2.919642e+00 | 2.700223e+00 | 2.914566e-03 | 1.260475e-02 |
| TC | UP | ENST00000393925.7 | PHLDB2-202:protein_coding:PHLDB2 | 9.541605e+01 | 1.894347e+00 | 6.051166e-11 | 1.263623e-08 |
| TC | UP | ENST00000431670.7 | PHLDB2-204:protein_coding:PHLDB2 | 5.267994e+01 | 5.263051e+00 | 1.807540e-10 | 3.229065e-08 |
| TC | UP | ENST00000478922.1 | PHLDB2-210:protein_coding:PHLDB2 | 1.085392e+01 | 3.041681e+00 | 1.933784e-10 | 3.419069e-08 |
| TC | UP | ENST00000477695.5 | PHLDB2-207:protein_coding:PHLDB2 | 8.630138e+00 | 1.745974e+00 | 2.879575e-09 | 3.163760e-07 |
| TC | UP | ENST00000412622.5 | PHLDB2-203:protein_coding:PHLDB2 | 3.043599e+01 | 3.232062e+00 | 5.587411e-06 | 1.625596e-04 |
| TC | UP | ENST00000498699.5 | PHLDB2-215:protein_coding:PHLDB2 | 6.055809e+00 | 5.045361e+00 | 2.269774e-05 | 4.940207e-04 |
| TC | UP | ENST00000481953.5 | PHLDB2-211:protein_coding:PHLDB2 | 2.846676e+01 | 1.613148e+00 | 3.820835e-04 | 4.656827e-03 |
| TC | UP | ENST00000638331.1 | PHLDB2-216:protein_coding:PHLDB2 | 3.022706e+00 | 2.505014e+00 | 1.089445e-03 | 1.057286e-02 |
| TC | UP | ENST00000393923.7 | PHLDB2-201:protein_coding:PHLDB2 | 4.623582e+00 | 3.615700e+00 | 5.000422e-03 | 3.354411e-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 LDB2 |
| 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_120654 | chr4 | 16595703:16595875:16674200:16674319:16759158:16759260 | 16674200:16674319 |
| exon_skip_120927 | chr4 | 16588710:16588832:16595703:16595875:16674200:16674319 | 16595703:16595875 |
| exon_skip_138472 | chr4 | 16512005:16512104:16585922:16586005:16588710:16588832 | 16585922:16586005 |
| exon_skip_151369 | chr4 | 16502042:16502873:16505840:16505982:16508535:16508683 | 16505840:16505982 |
| exon_skip_19362 | chr4 | 16512062:16512104:16585922:16586005:16588710:16588832 | 16585922:16586005 |
| exon_skip_23247 | chr4 | 16595703:16595875:16752407:16752458:16759158:16759260 | 16752407:16752458 |
| exon_skip_234649 | chr4 | 16585976:16586005:16588710:16588832:16595703:16595875 | 16588710:16588832 |
| exon_skip_249632 | chr4 | 16759158:16759260:16888674:16888758:16889241:16889302 | 16888674:16888758 |
| exon_skip_265831 | chr4 | 16595703:16595875:16759158:16759260:16898354:16898378 | 16759158:16759260 |
| exon_skip_290009 | chr4 | 16502143:16502873:16505840:16505982:16508535:16508683 | 16505840:16505982 |
| exon_skip_35404 | chr4 | 16508541:16508686:16511981:16512104:16585922:16586005 | 16511981:16512104 |
| exon_skip_53208 | chr4 | 16588710:16588832:16595703:16595875:16759158:16759260 | 16595703:16595875 |
| 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 LDB2 |
| 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 |
| ENST00000304523 | 16511981 | 16512104 | Frame-shift |
| ENST00000304523 | 16595703 | 16595875 | Frame-shift |
| ENST00000304523 | 16759158 | 16759260 | Frame-shift |
| ENST00000304523 | 16585922 | 16586005 | In-frame |
| ENST00000304523 | 16588710 | 16588832 | 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 |
| ENST00000304523 | 16595703 | 16595875 | Frame-shift |
| ENST00000304523 | 16759158 | 16759260 | Frame-shift |
| ENST00000304523 | 16585922 | 16586005 | 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 |
| ENST00000304523 | 16511981 | 16512104 | Frame-shift |
| ENST00000304523 | 16595703 | 16595875 | Frame-shift |
| ENST00000304523 | 16759158 | 16759260 | Frame-shift |
| ENST00000304523 | 16585922 | 16586005 | In-frame |
| ENST00000304523 | 16588710 | 16588832 | In-frame |
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Infer the effects of exon skipping event on protein functional features for LDB2 |
p-ENSG00000169744_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 |
| ENST00000304523 | 2565 | 373 | 16588710 | 16588832 | 733 | 854 | 136 | 176 |
| ENST00000304523 | 2565 | 373 | 16585922 | 16586005 | 856 | 938 | 177 | 204 |
| 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 |
| ENST00000304523 | 2565 | 373 | 16585922 | 16586005 | 856 | 938 | 177 | 204 |
| 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 |
| ENST00000304523 | 2565 | 373 | 16588710 | 16588832 | 733 | 854 | 136 | 176 |
| ENST00000304523 | 2565 | 373 | 16585922 | 16586005 | 856 | 938 | 177 | 204 |
| 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 |
| O43679 | 136 | 176 | 1 | 373 | Chain | ID=PRO_0000084387;Note=LIM domain-binding protein 2 |
| O43679 | 177 | 204 | 1 | 373 | Chain | ID=PRO_0000084387;Note=LIM domain-binding protein 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 |
| O43679 | 177 | 204 | 1 | 373 | Chain | ID=PRO_0000084387;Note=LIM domain-binding protein 2 |
| 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 |
| O43679 | 136 | 176 | 1 | 373 | Chain | ID=PRO_0000084387;Note=LIM domain-binding protein 2 |
| O43679 | 177 | 204 | 1 | 373 | Chain | ID=PRO_0000084387;Note=LIM domain-binding protein 2 |
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3'-UTR located exon skipping events that lost miRNA binding sites in LDB2 |
| 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 LDB2 |
| - 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 LDB2 |
| 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 |
| ADstage | MSBB | IFG | exon_skip_138472 | 4.283448e-01 | 2.295869e-02 | chr4 | - | 16512005 | 16512104 | 16585922 | 16586005 | 16588710 | 16588832 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LDB2 |
| 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 LDB2 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| IFG | PCBP4 | exon_skip_286514 | 4.382869e-01 | 2.841712e-02 |
| TC | KHDRBS2 | exon_skip_151369 | -4.874280e-01 | 2.193484e-10 |
| TC | KHDRBS3 | exon_skip_151369 | -4.118604e-01 | 1.487805e-07 |
| TC | NOVA1 | exon_skip_151369 | -4.827530e-01 | 3.443613e-10 |
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RelatedDrugs for LDB2 |
| 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 LDB2 |
| 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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