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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for LMO1 |
 Gene summary |
| Gene information | Gene symbol | LMO1 | Gene ID | 4004 |
| Gene name | LIM domain only 1 | |
| Synonyms | RBTN1|RHOM1|TTG1 | |
| Cytomap | 11p15.4 | |
| Type of gene | protein-coding | |
| Description | rhombotin-1LIM domain only 1 (rhombotin 1)LIM domain only protein 1LMO-1T-cell translocation gene 1T-cell translocation protein 1cysteine-rich protein TTG-1 | |
| Modification date | 20180519 | |
| UniProtAcc | P25800 | |
| Context | PubMed: LMO1 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| 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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Exon skipping events across known transcript of Ensembl for LMO1 from UCSC genome browser |
| Skipped exons in TCGA and GTEx 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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Gene isoform structures and expression levels for LMO1 |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for LMO1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_68592 | 11 | 8246025:8246268:8248400:8248647:8251837:8252051 | 8248400:8248647 | ENSG00000166407.9 | ENST00000524379.1 |
| exon_skip_68593 | 11 | 8246025:8246268:8248521:8248647:8251837:8252051 | 8248521:8248647 | ENSG00000166407.9 | ENST00000335790.3,ENST00000428101.2,ENST00000534484.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for LMO1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_68592 | 11 | 8246025:8246268:8248400:8248647:8251837:8252051 | 8248400:8248647 | ENSG00000166407.9 | ENST00000524379.1 |
| exon_skip_68593 | 11 | 8246025:8246268:8248521:8248647:8251837:8252051 | 8248521:8248647 | ENSG00000166407.9 | ENST00000335790.3,ENST00000428101.2,ENST00000534484.1 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for LMO1 |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000335790 | 8248521 | 8248647 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000335790 | 8248521 | 8248647 | In-frame |
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Infer the effects of exon skipping event on protein functional features for LMO1 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| Loci of skipped exons in TCGA 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 |
| ENST00000335790 | 1296 | 156 | 8248521 | 8248647 | 736 | 861 | 80 | 121 |
| Loci of skipped exons in GTEx 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 |
| ENST00000335790 | 1296 | 156 | 8248521 | 8248647 | 736 | 861 | 80 | 121 |
| Lost protein functional features of individual exon skipping events in TCGA. |
| 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 |
| P25800 | 80 | 121 | 1 | 156 | Chain | ID=PRO_0000075894;Note=Rhombotin-1 |
| P25800 | 80 | 121 | 24 | 83 | Domain | Note=LIM zinc-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
| P25800 | 80 | 121 | 88 | 147 | 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 GTEx. |
| 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 |
| P25800 | 80 | 121 | 1 | 156 | Chain | ID=PRO_0000075894;Note=Rhombotin-1 |
| P25800 | 80 | 121 | 24 | 83 | Domain | Note=LIM zinc-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
| P25800 | 80 | 121 | 88 | 147 | Domain | Note=LIM zinc-binding 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 |
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SNVs in the skipped exons for LMO1 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - 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 |
| GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 8248401 | 8248647 | 8248565 | 8248565 | Missense_Mutation | C | T | p.V108M |
| GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 8248522 | 8248647 | 8248565 | 8248565 | Missense_Mutation | C | T | p.V108M |
| UMUC5_URINARY_TRACT | 8248401 | 8248647 | 8248567 | 8248567 | Missense_Mutation | T | G | p.N107T |
| UMUC5_URINARY_TRACT | 8248522 | 8248647 | 8248567 | 8248567 | Missense_Mutation | T | G | p.N107T |
| HT115_LARGE_INTESTINE | 8248401 | 8248647 | 8248592 | 8248592 | Missense_Mutation | C | T | p.E99K |
| HT115_LARGE_INTESTINE | 8248522 | 8248647 | 8248592 | 8248592 | Missense_Mutation | C | T | p.E99K |
| OC316_OVARY | 8248401 | 8248647 | 8248522 | 8248522 | Splice_Site | C | T | p.R122K |
| OC316_OVARY | 8248522 | 8248647 | 8248522 | 8248522 | Splice_Site | C | T | p.R122K |
| OC314_OVARY | 8248401 | 8248647 | 8248522 | 8248522 | Splice_Site | C | T | p.R122K |
| OC314_OVARY | 8248522 | 8248647 | 8248522 | 8248522 | Splice_Site | C | T | p.R122K |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LMO1 |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LMO1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LMO1 |
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RelatedDrugs for LMO1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for LMO1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| LMO1 | C0023492 | Leukemia, T-Cell | 2 | CTD_human |
| LMO1 | C1961099 | Precursor T-Cell Lymphoblastic Leukemia-Lymphoma | 1 | CTD_human |
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