|
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 LMO3 |
Gene summary |
Gene information | Gene symbol | LMO3 | Gene ID | 55885 |
Gene name | LIM domain only 3 | |
Synonyms | RBTN3|RBTNL2|RHOM3|Rhom-3 | |
Cytomap | 12p12.3 | |
Type of gene | protein-coding | |
Description | LIM domain only protein 3LIM domain only 3 (rhombotin-like 2)neuronal-specific transcription factor DAT1rhombotin-3 | |
Modification date | 20200313 | |
UniProtAcc | A0A024RAT1, | |
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
LMO3 | GO:0035360 | positive regulation of peroxisome proliferator activated receptor signaling pathway | 23823477 |
LMO3 | GO:0070373 | negative regulation of ERK1 and ERK2 cascade | 23823477 |
LMO3 | GO:2000324 | positive regulation of glucocorticoid receptor signaling pathway | 23823477 |
Top |
Gene structures and expression levels for LMO3 |
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 |
PG | UP | ENST00000541589.5 | LMO3-226:nonsense_mediated_decay:LMO3 | 2.347375e+00 | 4.159982e+00 | 5.089339e-03 | 4.626561e-02 |
CB | DOWN | ENST00000616247.4 | LMO3-235:protein_coding:LMO3 | 5.425123e+02 | -1.324290e+00 | 2.248077e-03 | 1.014949e-02 |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for LMO3 |
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_137543 | chr12 | 16560506:16560538:16594137:16594334:16598792:16598967 | 16594137:16594334 |
exon_skip_142736 | chr12 | 16560506:16560538:16600655:16600868:16607936:16608000 | 16600655:16600868 |
exon_skip_151323 | chr12 | 16551318:16551327:16560413:16560538:16600655:16600868 | 16560413:16560538 |
exon_skip_1721 | chr12 | 16560506:16560538:16600714:16600868:16609734:16609824 | 16600714:16600868 |
exon_skip_175045 | chr12 | 16600714:16600868:16606066:16606132:16609734:16609824 | 16606066:16606132 |
exon_skip_193292 | chr12 | 16560506:16560538:16600601:16600868:16607936:16608000 | 16600601:16600868 |
exon_skip_193957 | chr12 | 16560506:16560538:16600655:16600868:16609734:16609824 | 16600655:16600868 |
exon_skip_195843 | chr12 | 16560506:16560538:16594137:16594261:16600655:16600868 | 16594137:16594261 |
exon_skip_19958 | chr12 | 16594252:16594334:16598792:16598967:16600655:16600666 | 16598792:16598967 |
exon_skip_202487 | chr12 | 16560506:16560538:16594137:16594261:16600655:16600666 | 16594137:16594261 |
exon_skip_225177 | chr12 | 16594252:16594334:16598792:16598967:16600655:16600868 | 16598792:16598967 |
exon_skip_230532 | chr12 | 16600714:16600868:16606066:16606132:16606339:16606440 | 16606066:16606132 |
exon_skip_26506 | chr12 | 16600714:16600868:16606066:16606132:16607936:16608104 | 16606066:16606132 |
exon_skip_289405 | chr12 | 16560506:16560538:16594137:16594261:16600714:16600721 | 16594137:16594261 |
exon_skip_35399 | chr12 | 16600714:16600868:16606066:16606132:16607936:16608000 | 16606066:16606132 |
exon_skip_72816 | chr12 | 16560506:16560538:16600714:16600868:16607936:16608000 | 16600714:16600868 |
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 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for LMO3 |
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 |
ENST00000354662 | 16600655 | 16600868 | 3UTR-3CDS |
ENST00000441439 | 16606066 | 16606132 | 3UTR-3UTR |
ENST00000534946 | 16606066 | 16606132 | 3UTR-3UTR |
ENST00000320122 | 16560413 | 16560538 | In-frame |
ENST00000354662 | 16560413 | 16560538 | In-frame |
ENST00000441439 | 16560413 | 16560538 | In-frame |
ENST00000447609 | 16560413 | 16560538 | In-frame |
ENST00000534946 | 16560413 | 16560538 | In-frame |
ENST00000535535 | 16560413 | 16560538 | In-frame |
ENST00000537304 | 16560413 | 16560538 | In-frame |
ENST00000540848 | 16560413 | 16560538 | In-frame |
ENST00000541846 | 16560413 | 16560538 | 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 |
ENST00000441439 | 16606066 | 16606132 | 3UTR-3UTR |
ENST00000534946 | 16606066 | 16606132 | 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 |
ENST00000354662 | 16600655 | 16600868 | 3UTR-3CDS |
ENST00000441439 | 16606066 | 16606132 | 3UTR-3UTR |
ENST00000534946 | 16606066 | 16606132 | 3UTR-3UTR |
Top |
Infer the effects of exon skipping event on protein functional features for LMO3 |
p-ENSG00000048540_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 |
ENST00000320122 | 3776 | 145 | 16560413 | 16560538 | 730 | 854 | 69 | 110 |
ENST00000354662 | 3591 | 145 | 16560413 | 16560538 | 494 | 618 | 69 | 110 |
ENST00000441439 | 3532 | 145 | 16560413 | 16560538 | 482 | 606 | 69 | 110 |
ENST00000447609 | 3382 | 145 | 16560413 | 16560538 | 333 | 457 | 69 | 110 |
ENST00000534946 | 1033 | 145 | 16560413 | 16560538 | 438 | 562 | 69 | 110 |
ENST00000535535 | 1505 | 145 | 16560413 | 16560538 | 418 | 542 | 69 | 110 |
ENST00000537304 | 1702 | 145 | 16560413 | 16560538 | 681 | 805 | 69 | 110 |
ENST00000540848 | 1591 | 145 | 16560413 | 16560538 | 320 | 444 | 69 | 110 |
ENST00000541846 | 590 | 145 | 16560413 | 16560538 | 302 | 426 | 69 | 110 |
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 |
Q8TAP4 | 69 | 110 | 50 | 69 | Alternative sequence | ID=VSP_045313;Note=In isoform 2. VGSTLYTKANLILCRRDYLR->HLKRCGSIYIHAAHTEIGICVTLEWPLPFVIIDFSQQITIAW;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q8TAP4 | 69 | 110 | 50 | 69 | Alternative sequence | ID=VSP_045313;Note=In isoform 2. VGSTLYTKANLILCRRDYLR->HLKRCGSIYIHAAHTEIGICVTLEWPLPFVIIDFSQQITIAW;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q8TAP4 | 69 | 110 | 50 | 69 | Alternative sequence | ID=VSP_045313;Note=In isoform 2. VGSTLYTKANLILCRRDYLR->HLKRCGSIYIHAAHTEIGICVTLEWPLPFVIIDFSQQITIAW;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q8TAP4 | 69 | 110 | 50 | 69 | Alternative sequence | ID=VSP_045313;Note=In isoform 2. VGSTLYTKANLILCRRDYLR->HLKRCGSIYIHAAHTEIGICVTLEWPLPFVIIDFSQQITIAW;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q8TAP4 | 69 | 110 | 50 | 69 | Alternative sequence | ID=VSP_045313;Note=In isoform 2. VGSTLYTKANLILCRRDYLR->HLKRCGSIYIHAAHTEIGICVTLEWPLPFVIIDFSQQITIAW;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q8TAP4 | 69 | 110 | 50 | 69 | Alternative sequence | ID=VSP_045313;Note=In isoform 2. VGSTLYTKANLILCRRDYLR->HLKRCGSIYIHAAHTEIGICVTLEWPLPFVIIDFSQQITIAW;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q8TAP4 | 69 | 110 | 50 | 69 | Alternative sequence | ID=VSP_045313;Note=In isoform 2. VGSTLYTKANLILCRRDYLR->HLKRCGSIYIHAAHTEIGICVTLEWPLPFVIIDFSQQITIAW;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q8TAP4 | 69 | 110 | 50 | 69 | Alternative sequence | ID=VSP_045313;Note=In isoform 2. VGSTLYTKANLILCRRDYLR->HLKRCGSIYIHAAHTEIGICVTLEWPLPFVIIDFSQQITIAW;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q8TAP4 | 69 | 110 | 50 | 69 | Alternative sequence | ID=VSP_045313;Note=In isoform 2. VGSTLYTKANLILCRRDYLR->HLKRCGSIYIHAAHTEIGICVTLEWPLPFVIIDFSQQITIAW;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q8TAP4 | 69 | 110 | 1 | 145 | Chain | ID=PRO_0000075817;Note=LIM domain only protein 3 |
Q8TAP4 | 69 | 110 | 1 | 145 | Chain | ID=PRO_0000075817;Note=LIM domain only protein 3 |
Q8TAP4 | 69 | 110 | 1 | 145 | Chain | ID=PRO_0000075817;Note=LIM domain only protein 3 |
Q8TAP4 | 69 | 110 | 1 | 145 | Chain | ID=PRO_0000075817;Note=LIM domain only protein 3 |
Q8TAP4 | 69 | 110 | 1 | 145 | Chain | ID=PRO_0000075817;Note=LIM domain only protein 3 |
Q8TAP4 | 69 | 110 | 1 | 145 | Chain | ID=PRO_0000075817;Note=LIM domain only protein 3 |
Q8TAP4 | 69 | 110 | 1 | 145 | Chain | ID=PRO_0000075817;Note=LIM domain only protein 3 |
Q8TAP4 | 69 | 110 | 1 | 145 | Chain | ID=PRO_0000075817;Note=LIM domain only protein 3 |
Q8TAP4 | 69 | 110 | 1 | 145 | Chain | ID=PRO_0000075817;Note=LIM domain only protein 3 |
Q8TAP4 | 69 | 110 | 11 | 73 | Domain | Note=LIM zinc-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
Q8TAP4 | 69 | 110 | 11 | 73 | Domain | Note=LIM zinc-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
Q8TAP4 | 69 | 110 | 11 | 73 | Domain | Note=LIM zinc-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
Q8TAP4 | 69 | 110 | 11 | 73 | Domain | Note=LIM zinc-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
Q8TAP4 | 69 | 110 | 11 | 73 | Domain | Note=LIM zinc-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
Q8TAP4 | 69 | 110 | 11 | 73 | Domain | Note=LIM zinc-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
Q8TAP4 | 69 | 110 | 11 | 73 | Domain | Note=LIM zinc-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
Q8TAP4 | 69 | 110 | 11 | 73 | Domain | Note=LIM zinc-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
Q8TAP4 | 69 | 110 | 11 | 73 | Domain | Note=LIM zinc-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
Q8TAP4 | 69 | 110 | 75 | 137 | Domain | Note=LIM zinc-binding 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
Q8TAP4 | 69 | 110 | 75 | 137 | Domain | Note=LIM zinc-binding 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
Q8TAP4 | 69 | 110 | 75 | 137 | Domain | Note=LIM zinc-binding 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
Q8TAP4 | 69 | 110 | 75 | 137 | Domain | Note=LIM zinc-binding 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
Q8TAP4 | 69 | 110 | 75 | 137 | Domain | Note=LIM zinc-binding 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
Q8TAP4 | 69 | 110 | 75 | 137 | Domain | Note=LIM zinc-binding 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
Q8TAP4 | 69 | 110 | 75 | 137 | Domain | Note=LIM zinc-binding 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
Q8TAP4 | 69 | 110 | 75 | 137 | Domain | Note=LIM zinc-binding 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
Q8TAP4 | 69 | 110 | 75 | 137 | Domain | Note=LIM zinc-binding 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
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 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in LMO3 |
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 | ENST00000534946 | 16606066 | 16606132 | hsa-miR-4724-5p | chr12:16606096-16606103 | 8mer-1a | chr12:16606089-16606111 | 163.00 | -23.58 |
MSBB | ENST00000534946 | 16606066 | 16606132 | hsa-miR-4724-5p | chr12:16606096-16606103 | 8mer-1a | chr12:16606089-16606111 | 163.00 | -23.58 |
ROSMAP | ENST00000534946 | 16606066 | 16606132 | hsa-miR-4724-5p | chr12:16606096-16606103 | 8mer-1a | chr12:16606089-16606111 | 163.00 | -23.58 |
Top |
SNVs in the skipped exons for LMO3 |
- 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 |
Top |
AD stage-associated exon skippint events for LMO3 |
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 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LMO3 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
Top |
Correlation with RNA binding proteins (RBPs) for LMO3 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
IFG | RBM5 | exon_skip_35399 | -4.000017e-01 | 4.756699e-02 |
IFG | RBM5 | exon_skip_175045 | 4.000014e-01 | 3.870330e-02 |
Top |
RelatedDrugs for LMO3 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for LMO3 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |