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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 LARS2 |
 Gene summary |
| Gene information | Gene symbol | LARS2 | Gene ID | 23395 |
| Gene name | leucyl-tRNA synthetase 2, mitochondrial | |
| Synonyms | HLASA|LEURS|PRLTS4|mtLeuRS | |
| Cytomap | 3p21.31 | |
| Type of gene | protein-coding | |
| Description | probable leucine--tRNA ligase, mitochondrialleucine tRNA ligase 2, mitochondrialleucine tRNA ligase 2, mitocondrialleucine translaseprobable leucyl-tRNA synthetase, mitochondrial | |
| Modification date | 20180523 | |
| UniProtAcc | Q15031 | |
| Context | PubMed: LARS2 [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 |
| LARS2 | GO:0006429 | leucyl-tRNA aminoacylation | 10684970 |
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Exon skipping events across known transcript of Ensembl for LARS2 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 LARS2 |
| 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 LARS2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_373660 | 3 | 45430110:45430172:45430524:45430598:45433074:45433140 | 45430524:45430598 | ENSG00000011376.5 | ENST00000430399.1 |
| exon_skip_373663 | 3 | 45435944:45436179:45441736:45441865:45458973:45459065 | 45441736:45441865 | ENSG00000011376.5 | ENST00000415258.1,ENST00000265537.3 |
| exon_skip_373664 | 3 | 45461160:45461221:45488382:45488472:45500234:45500378 | 45488382:45488472 | ENSG00000011376.5 | ENST00000414984.1,ENST00000415258.1,ENST00000265537.3 |
| exon_skip_373665 | 3 | 45488382:45488472:45500234:45500378:45515734:45515842 | 45500234:45500378 | ENSG00000011376.5 | ENST00000414984.1,ENST00000415258.1,ENST00000265537.3 |
| exon_skip_373666 | 3 | 45500234:45500378:45515734:45515842:45517959:45518119 | 45515734:45515842 | ENSG00000011376.5 | ENST00000414984.1,ENST00000415258.1,ENST00000265537.3 |
| exon_skip_373667 | 3 | 45530188:45530304:45533008:45533292:45537766:45537865 | 45533008:45533292 | ENSG00000011376.5 | ENST00000414984.1,ENST00000415258.1,ENST00000265537.3 |
| exon_skip_373669 | 3 | 45537766:45537865:45541933:45542071:45554626:45554727 | 45541933:45542071 | ENSG00000011376.5 | ENST00000414984.1,ENST00000415258.1,ENST00000265537.3 |
| exon_skip_373670 | 3 | 45542032:45542071:45554626:45554727:45557585:45557768 | 45554626:45554727 | ENSG00000011376.5 | ENST00000414984.1,ENST00000415258.1,ENST00000467936.1,ENST00000265537.3 |
| exon_skip_373671 | 3 | 45559454:45559564:45561184:45561282:45561710:45561788 | 45561184:45561282 | ENSG00000011376.5 | ENST00000485461.1 |
| exon_skip_373673 | 3 | 45559454:45559564:45561710:45561788:45565488:45565600 | 45561710:45561788 | ENSG00000011376.5 | ENST00000414984.1,ENST00000415258.1,ENST00000467936.1,ENST00000265537.3 |
| exon_skip_373675 | 3 | 45561710:45561788:45565488:45565600:45583320:45583448 | 45565488:45565600 | ENSG00000011376.5 | ENST00000414984.1,ENST00000415258.1,ENST00000265537.3,ENST00000485461.1 |
| exon_skip_373679 | 3 | 45565488:45565600:45583320:45583448:45588842:45588896 | 45583320:45583448 | ENSG00000011376.5 | ENST00000414984.1,ENST00000415258.1,ENST00000265537.3,ENST00000485461.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for LARS2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_373660 | 3 | 45430110:45430172:45430524:45430598:45433074:45433140 | 45430524:45430598 | ENSG00000011376.5 | ENST00000430399.1 |
| exon_skip_373664 | 3 | 45461160:45461221:45488382:45488472:45500234:45500378 | 45488382:45488472 | ENSG00000011376.5 | ENST00000265537.3,ENST00000415258.1,ENST00000414984.1 |
| exon_skip_373666 | 3 | 45500234:45500378:45515734:45515842:45517959:45518119 | 45515734:45515842 | ENSG00000011376.5 | ENST00000265537.3,ENST00000415258.1,ENST00000414984.1 |
| exon_skip_373667 | 3 | 45530188:45530304:45533008:45533292:45537766:45537865 | 45533008:45533292 | ENSG00000011376.5 | ENST00000265537.3,ENST00000415258.1,ENST00000414984.1 |
| exon_skip_373669 | 3 | 45537766:45537865:45541933:45542071:45554626:45554727 | 45541933:45542071 | ENSG00000011376.5 | ENST00000265537.3,ENST00000415258.1,ENST00000414984.1 |
| exon_skip_373670 | 3 | 45542032:45542071:45554626:45554727:45557585:45557768 | 45554626:45554727 | ENSG00000011376.5 | ENST00000265537.3,ENST00000415258.1,ENST00000414984.1,ENST00000467936.1 |
| exon_skip_373671 | 3 | 45559454:45559564:45561184:45561282:45561710:45561788 | 45561184:45561282 | ENSG00000011376.5 | ENST00000485461.1 |
| exon_skip_373673 | 3 | 45559454:45559564:45561710:45561788:45565488:45565600 | 45561710:45561788 | ENSG00000011376.5 | ENST00000265537.3,ENST00000415258.1,ENST00000414984.1,ENST00000467936.1 |
| exon_skip_373675 | 3 | 45561710:45561788:45565488:45565600:45583320:45583448 | 45565488:45565600 | ENSG00000011376.5 | ENST00000265537.3,ENST00000415258.1,ENST00000414984.1,ENST00000485461.1 |
| exon_skip_373679 | 3 | 45565488:45565600:45583320:45583448:45588842:45588896 | 45583320:45583448 | ENSG00000011376.5 | ENST00000265537.3,ENST00000415258.1,ENST00000414984.1,ENST00000485461.1 |
| 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 LARS2 |
| 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 |
| ENST00000265537 | 45533008 | 45533292 | Frame-shift |
| ENST00000415258 | 45533008 | 45533292 | Frame-shift |
| ENST00000265537 | 45554626 | 45554727 | Frame-shift |
| ENST00000415258 | 45554626 | 45554727 | Frame-shift |
| ENST00000265537 | 45565488 | 45565600 | Frame-shift |
| ENST00000415258 | 45565488 | 45565600 | Frame-shift |
| ENST00000265537 | 45583320 | 45583448 | Frame-shift |
| ENST00000415258 | 45583320 | 45583448 | Frame-shift |
| ENST00000265537 | 45441736 | 45441865 | In-frame |
| ENST00000415258 | 45441736 | 45441865 | In-frame |
| ENST00000265537 | 45488382 | 45488472 | In-frame |
| ENST00000415258 | 45488382 | 45488472 | In-frame |
| ENST00000265537 | 45500234 | 45500378 | In-frame |
| ENST00000415258 | 45500234 | 45500378 | In-frame |
| ENST00000265537 | 45515734 | 45515842 | In-frame |
| ENST00000415258 | 45515734 | 45515842 | In-frame |
| ENST00000265537 | 45541933 | 45542071 | In-frame |
| ENST00000415258 | 45541933 | 45542071 | In-frame |
| ENST00000265537 | 45561710 | 45561788 | In-frame |
| ENST00000415258 | 45561710 | 45561788 | 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 |
| ENST00000265537 | 45533008 | 45533292 | Frame-shift |
| ENST00000415258 | 45533008 | 45533292 | Frame-shift |
| ENST00000265537 | 45554626 | 45554727 | Frame-shift |
| ENST00000415258 | 45554626 | 45554727 | Frame-shift |
| ENST00000265537 | 45565488 | 45565600 | Frame-shift |
| ENST00000415258 | 45565488 | 45565600 | Frame-shift |
| ENST00000265537 | 45583320 | 45583448 | Frame-shift |
| ENST00000415258 | 45583320 | 45583448 | Frame-shift |
| ENST00000265537 | 45488382 | 45488472 | In-frame |
| ENST00000415258 | 45488382 | 45488472 | In-frame |
| ENST00000265537 | 45515734 | 45515842 | In-frame |
| ENST00000415258 | 45515734 | 45515842 | In-frame |
| ENST00000265537 | 45541933 | 45542071 | In-frame |
| ENST00000415258 | 45541933 | 45542071 | In-frame |
| ENST00000265537 | 45561710 | 45561788 | In-frame |
| ENST00000415258 | 45561710 | 45561788 | In-frame |
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Infer the effects of exon skipping event on protein functional features for LARS2 |
| 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 |
| ENST00000265537 | 4298 | 903 | 45441736 | 45441865 | 497 | 625 | 78 | 121 |
| ENST00000415258 | 4761 | 903 | 45441736 | 45441865 | 376 | 504 | 78 | 121 |
| ENST00000265537 | 4298 | 903 | 45488382 | 45488472 | 779 | 868 | 172 | 202 |
| ENST00000415258 | 4761 | 903 | 45488382 | 45488472 | 658 | 747 | 172 | 202 |
| ENST00000265537 | 4298 | 903 | 45500234 | 45500378 | 869 | 1012 | 202 | 250 |
| ENST00000415258 | 4761 | 903 | 45500234 | 45500378 | 748 | 891 | 202 | 250 |
| ENST00000265537 | 4298 | 903 | 45515734 | 45515842 | 1013 | 1120 | 250 | 286 |
| ENST00000415258 | 4761 | 903 | 45515734 | 45515842 | 892 | 999 | 250 | 286 |
| ENST00000265537 | 4298 | 903 | 45541933 | 45542071 | 1885 | 2022 | 541 | 586 |
| ENST00000415258 | 4761 | 903 | 45541933 | 45542071 | 1764 | 1901 | 541 | 586 |
| ENST00000265537 | 4298 | 903 | 45561710 | 45561788 | 2477 | 2554 | 738 | 764 |
| ENST00000415258 | 4761 | 903 | 45561710 | 45561788 | 2356 | 2433 | 738 | 764 |
| 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 |
| ENST00000265537 | 4298 | 903 | 45488382 | 45488472 | 779 | 868 | 172 | 202 |
| ENST00000415258 | 4761 | 903 | 45488382 | 45488472 | 658 | 747 | 172 | 202 |
| ENST00000265537 | 4298 | 903 | 45515734 | 45515842 | 1013 | 1120 | 250 | 286 |
| ENST00000415258 | 4761 | 903 | 45515734 | 45515842 | 892 | 999 | 250 | 286 |
| ENST00000265537 | 4298 | 903 | 45541933 | 45542071 | 1885 | 2022 | 541 | 586 |
| ENST00000415258 | 4761 | 903 | 45541933 | 45542071 | 1764 | 1901 | 541 | 586 |
| ENST00000265537 | 4298 | 903 | 45561710 | 45561788 | 2477 | 2554 | 738 | 764 |
| ENST00000415258 | 4761 | 903 | 45561710 | 45561788 | 2356 | 2433 | 738 | 764 |
| 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 |
| Q15031 | 78 | 121 | 92 | 102 | Motif | Note="HIGH" region |
| Q15031 | 78 | 121 | 92 | 102 | Motif | Note="HIGH" region |
| Q15031 | 202 | 250 | 236 | 236 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| Q15031 | 202 | 250 | 236 | 236 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| 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 |
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SNVs in the skipped exons for LARS2 |
| - 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 |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_373666 | 45515735 | 45515842 | 45515839 | 45515839 | Frame_Shift_Del | A | - | p.L285fs |
| UCEC | TCGA-AP-A05N-01 | exon_skip_373667 | 45533009 | 45533292 | 45533245 | 45533245 | Frame_Shift_Del | C | - | p.G492fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_373669 | 45541934 | 45542071 | 45541984 | 45541984 | Frame_Shift_Del | T | - | p.I558fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_373669 | 45541934 | 45542071 | 45542039 | 45542039 | Frame_Shift_Del | T | - | p.H576fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_373669 | 45541934 | 45542071 | 45542053 | 45542053 | Frame_Shift_Del | A | - | p.Q581fs |
| ESCA | TCGA-IG-A3YB-01 | exon_skip_373665 | 45500235 | 45500378 | 45500280 | 45500280 | Nonsense_Mutation | G | T | p.E218* |
| ESCA | TCGA-IG-A3YB-01 | exon_skip_373665 | 45500235 | 45500378 | 45500280 | 45500280 | Nonsense_Mutation | G | T | p.E218X |
| BLCA | TCGA-XF-AAMG-01 | exon_skip_373673 | 45561711 | 45561788 | 45561759 | 45561759 | Nonsense_Mutation | C | T | p.Q755* |
| BRCA | TCGA-BH-A0W7-01 | exon_skip_373673 | 45561711 | 45561788 | 45561759 | 45561759 | Nonsense_Mutation | C | T | p.Q755* |
| UCEC | TCGA-AP-A051-01 | exon_skip_373669 | 45541934 | 45542071 | 45541932 | 45541932 | Splice_Site | A | T | e13-2 |
| STAD | TCGA-BR-8372-01 | exon_skip_373670 | 45554627 | 45554727 | 45554625 | 45554625 | Splice_Site | A | C | . |
| STAD | TCGA-BR-8372-01 | exon_skip_373670 | 45554627 | 45554727 | 45554625 | 45554625 | Splice_Site | A | C | p.R587_splice |
| - 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 |
| AU565_BREAST | 45533009 | 45533292 | 45533168 | 45533169 | Frame_Shift_Del | TG | - | p.C467fs |
| NCIH630_LARGE_INTESTINE | 45541934 | 45542071 | 45542053 | 45542053 | Frame_Shift_Del | A | - | p.Q581fs |
| MESSA_SOFT_TISSUE | 45583321 | 45583448 | 45583374 | 45583375 | Frame_Shift_Ins | - | T | p.V820fs |
| RL952_ENDOMETRIUM | 45441737 | 45441865 | 45441827 | 45441827 | Missense_Mutation | G | A | p.D109N |
| MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 45441737 | 45441865 | 45441856 | 45441856 | Missense_Mutation | A | C | p.R118S |
| MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 45441737 | 45441865 | 45441856 | 45441856 | Missense_Mutation | A | C | p.R118S |
| NCIH1930_LUNG | 45500235 | 45500378 | 45500249 | 45500249 | Missense_Mutation | G | T | p.W207C |
| GP2D_LARGE_INTESTINE | 45533009 | 45533292 | 45533114 | 45533114 | Missense_Mutation | A | T | p.I449F |
| GP5D_LARGE_INTESTINE | 45533009 | 45533292 | 45533114 | 45533114 | Missense_Mutation | A | T | p.I449F |
| HEC59_ENDOMETRIUM | 45533009 | 45533292 | 45533130 | 45533130 | Missense_Mutation | A | G | p.Y454C |
| C75_LARGE_INTESTINE | 45533009 | 45533292 | 45533207 | 45533207 | Missense_Mutation | A | C | p.T480P |
| 2313287_STOMACH | 45533009 | 45533292 | 45533222 | 45533222 | Missense_Mutation | G | A | p.A485T |
| HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 45541934 | 45542071 | 45542057 | 45542058 | Missense_Mutation | AA | GT | p.M583L |
| HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 45541934 | 45542071 | 45542058 | 45542058 | Missense_Mutation | A | T | p.M583L |
| DU145_PROSTATE | 45554627 | 45554727 | 45554705 | 45554705 | Missense_Mutation | G | C | p.Q613H |
| KPNSI9S_AUTONOMIC_GANGLIA | 45554627 | 45554727 | 45554707 | 45554707 | Missense_Mutation | G | A | p.R614K |
| SQ1_LUNG | 45554627 | 45554727 | 45554707 | 45554707 | Missense_Mutation | G | A | p.R614K |
| HEC1A_ENDOMETRIUM | 45565489 | 45565600 | 45565504 | 45565504 | Missense_Mutation | G | A | p.V770I |
| HEC1_ENDOMETRIUM | 45565489 | 45565600 | 45565504 | 45565504 | Missense_Mutation | G | A | p.V770I |
| HEC1B_ENDOMETRIUM | 45565489 | 45565600 | 45565504 | 45565504 | Missense_Mutation | G | A | p.V770I |
| UACC812_BREAST | 45565489 | 45565600 | 45565533 | 45565533 | Missense_Mutation | T | A | p.D779E |
| BT474_BREAST | 45583321 | 45583448 | 45583365 | 45583365 | Missense_Mutation | G | T | p.D817Y |
| MDAPCA2B_PROSTATE | 45583321 | 45583448 | 45583435 | 45583435 | Missense_Mutation | A | G | p.Q840R |
| RO82W1_THYROID | 45441737 | 45441865 | 45441863 | 45441863 | Nonsense_Mutation | C | T | p.Q121* |
| SW48_LARGE_INTESTINE | 45500235 | 45500378 | 45500346 | 45500346 | Nonsense_Mutation | C | T | p.Q240* |
| SNU1040_LARGE_INTESTINE | 45583321 | 45583448 | 45583391 | 45583391 | Nonsense_Mutation | G | A | p.W825* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LARS2 |
| 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 LARS2 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LARS2 |
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RelatedDrugs for LARS2 |
| 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 LARS2 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| LARS2 | C3809105 | PERRAULT SYNDROME 4 | 2 | UNIPROT |
| LARS2 | C0005586 | Bipolar Disorder | 1 | PSYGENET |
| LARS2 | C0036341 | Schizophrenia | 1 | PSYGENET |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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