|
||||||
|
 | |
| |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
| |
|
Gene summary for LRPPRC |
 Gene summary |
| Gene information | Gene symbol | LRPPRC | Gene ID | 10128 |
| Gene name | leucine rich pentatricopeptide repeat containing | |
| Synonyms | CLONE-23970|GP130|LRP130|LSFC | |
| Cytomap | 2p21 | |
| Type of gene | protein-coding | |
| Description | leucine-rich PPR motif-containing protein, mitochondrial130 kDa leucine-rich proteinLRP 130leucine-rich PPR-motif containingmitochondrial leucine-rich PPR motif-containing protein | |
| Modification date | 20180522 | |
| UniProtAcc | P42704 | |
| Context | PubMed: LRPPRC [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 |
Top |
Exon skipping events across known transcript of Ensembl for LRPPRC 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. |
 |
Top |
Gene isoform structures and expression levels for LRPPRC |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for LRPPRC |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_338722 | 2 | 44116872:44117015:44117361:44117501:44121683:44121768 | 44117361:44117501 | ENSG00000138095.14 | ENST00000419884.1 |
| exon_skip_338731 | 2 | 44121683:44121768:44123772:44123847:44126357:44126423 | 44123772:44123847 | ENSG00000138095.14 | ENST00000463456.1,ENST00000260665.7,ENST00000419884.1 |
| exon_skip_338737 | 2 | 44126357:44126473:44126604:44126744:44128458:44128663 | 44126604:44126744 | ENSG00000138095.14 | ENST00000463456.1,ENST00000260665.7 |
| exon_skip_338738 | 2 | 44132830:44132919:44139570:44139697:44145163:44145272 | 44139570:44139697 | ENSG00000138095.14 | ENST00000260665.7 |
| exon_skip_338740 | 2 | 44139570:44139697:44145163:44145272:44145394:44145537 | 44145163:44145272 | ENSG00000138095.14 | ENST00000260665.7 |
| exon_skip_338745 | 2 | 44170825:44171033:44172470:44172556:44173251:44173382 | 44172470:44172556 | ENSG00000138095.14 | ENST00000260665.7 |
| exon_skip_338747 | 2 | 44173251:44173382:44174395:44174509:44174869:44174914 | 44174395:44174509 | ENSG00000138095.14 | ENST00000260665.7 |
| exon_skip_338748 | 2 | 44174395:44174509:44174869:44174914:44175260:44175338 | 44174869:44174914 | ENSG00000138095.14 | ENST00000260665.7 |
| exon_skip_338752 | 2 | 44203281:44203368:44204132:44204191:44204293:44204415 | 44204132:44204191 | ENSG00000138095.14 | ENST00000260665.7,ENST00000409659.1,ENST00000409946.1,ENST00000447246.1 |
| exon_skip_338753 | 2 | 44206964:44207087:44209376:44209573:44222937:44223117 | 44209376:44209573 | ENSG00000138095.14 | ENST00000409659.1,ENST00000409946.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for LRPPRC |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_338722 | 2 | 44116872:44117015:44117361:44117501:44121683:44121768 | 44117361:44117501 | ENSG00000138095.14 | ENST00000419884.1 |
| exon_skip_338731 | 2 | 44121683:44121768:44123772:44123847:44126357:44126423 | 44123772:44123847 | ENSG00000138095.14 | ENST00000260665.7,ENST00000419884.1,ENST00000463456.1 |
| exon_skip_338737 | 2 | 44126357:44126473:44126604:44126744:44128458:44128663 | 44126604:44126744 | ENSG00000138095.14 | ENST00000260665.7,ENST00000463456.1 |
| exon_skip_338738 | 2 | 44132830:44132919:44139570:44139697:44145163:44145272 | 44139570:44139697 | ENSG00000138095.14 | ENST00000260665.7 |
| exon_skip_338740 | 2 | 44139570:44139697:44145163:44145272:44145394:44145537 | 44145163:44145272 | ENSG00000138095.14 | ENST00000260665.7 |
| exon_skip_338745 | 2 | 44170825:44171033:44172470:44172556:44173251:44173382 | 44172470:44172556 | ENSG00000138095.14 | ENST00000260665.7 |
| exon_skip_338747 | 2 | 44173251:44173382:44174395:44174509:44174869:44174914 | 44174395:44174509 | ENSG00000138095.14 | ENST00000260665.7 |
| exon_skip_338748 | 2 | 44174395:44174509:44174869:44174914:44175260:44175338 | 44174869:44174914 | ENSG00000138095.14 | ENST00000260665.7 |
| exon_skip_338752 | 2 | 44203281:44203368:44204132:44204191:44204293:44204415 | 44204132:44204191 | ENSG00000138095.14 | ENST00000260665.7,ENST00000409946.1,ENST00000409659.1,ENST00000447246.1 |
| exon_skip_338753 | 2 | 44206964:44207087:44209376:44209573:44222937:44223117 | 44209376:44209573 | ENSG00000138095.14 | ENST00000409946.1,ENST00000409659.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for LRPPRC |
| 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 |
| ENST00000260665 | 44126604 | 44126744 | Frame-shift |
| ENST00000260665 | 44139570 | 44139697 | Frame-shift |
| ENST00000260665 | 44145163 | 44145272 | Frame-shift |
| ENST00000260665 | 44172470 | 44172556 | Frame-shift |
| ENST00000260665 | 44204132 | 44204191 | Frame-shift |
| ENST00000260665 | 44123772 | 44123847 | In-frame |
| ENST00000260665 | 44174395 | 44174509 | In-frame |
| ENST00000260665 | 44174869 | 44174914 | 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 |
| ENST00000260665 | 44126604 | 44126744 | Frame-shift |
| ENST00000260665 | 44139570 | 44139697 | Frame-shift |
| ENST00000260665 | 44145163 | 44145272 | Frame-shift |
| ENST00000260665 | 44172470 | 44172556 | Frame-shift |
| ENST00000260665 | 44204132 | 44204191 | Frame-shift |
| ENST00000260665 | 44123772 | 44123847 | In-frame |
| ENST00000260665 | 44174395 | 44174509 | In-frame |
| ENST00000260665 | 44174869 | 44174914 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for LRPPRC |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
 |
| 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 |
| ENST00000260665 | 6352 | 1394 | 44174869 | 44174914 | 1979 | 2023 | 640 | 655 |
| ENST00000260665 | 6352 | 1394 | 44174395 | 44174509 | 2024 | 2137 | 655 | 693 |
| ENST00000260665 | 6352 | 1394 | 44123772 | 44123847 | 3884 | 3958 | 1275 | 1300 |
| 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 |
| ENST00000260665 | 6352 | 1394 | 44174869 | 44174914 | 1979 | 2023 | 640 | 655 |
| ENST00000260665 | 6352 | 1394 | 44174395 | 44174509 | 2024 | 2137 | 655 | 693 |
| ENST00000260665 | 6352 | 1394 | 44123772 | 44123847 | 3884 | 3958 | 1275 | 1300 |
| 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 |
| P42704 | 640 | 655 | 60 | 1394 | Chain | ID=PRO_0000084467;Note=Leucine-rich PPR motif-containing protein%2C mitochondrial |
| P42704 | 640 | 655 | 648 | 648 | Sequence conflict | Note=S->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P42704 | 655 | 693 | 60 | 1394 | Chain | ID=PRO_0000084467;Note=Leucine-rich PPR motif-containing protein%2C mitochondrial |
| P42704 | 655 | 693 | 678 | 709 | Repeat | Note=PPR 9 |
| P42704 | 655 | 693 | 676 | 676 | Sequence conflict | Note=Q->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P42704 | 1275 | 1300 | 60 | 1394 | Chain | ID=PRO_0000084467;Note=Leucine-rich PPR motif-containing protein%2C mitochondrial |
| P42704 | 1275 | 1300 | 1121 | 1394 | Region | Note=RNA-binding |
| 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 |
| P42704 | 640 | 655 | 60 | 1394 | Chain | ID=PRO_0000084467;Note=Leucine-rich PPR motif-containing protein%2C mitochondrial |
| P42704 | 640 | 655 | 648 | 648 | Sequence conflict | Note=S->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P42704 | 655 | 693 | 60 | 1394 | Chain | ID=PRO_0000084467;Note=Leucine-rich PPR motif-containing protein%2C mitochondrial |
| P42704 | 655 | 693 | 678 | 709 | Repeat | Note=PPR 9 |
| P42704 | 655 | 693 | 676 | 676 | Sequence conflict | Note=Q->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P42704 | 1275 | 1300 | 60 | 1394 | Chain | ID=PRO_0000084467;Note=Leucine-rich PPR motif-containing protein%2C mitochondrial |
| P42704 | 1275 | 1300 | 1121 | 1394 | Region | Note=RNA-binding |
Top |
SNVs in the skipped exons for LRPPRC |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
 |
| - 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-G3-A3CJ-01 | exon_skip_338731 | 44123773 | 44123847 | 44123782 | 44123782 | Frame_Shift_Del | T | - | p.K1297fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_338738 | 44139571 | 44139697 | 44139682 | 44139682 | Frame_Shift_Del | A | - | p.F1055fs |
| ACC | TCGA-PK-A5HB-01 | exon_skip_338740 | 44145164 | 44145272 | 44145165 | 44145165 | Frame_Shift_Del | T | - | p.G1050fs |
| ESCA | TCGA-L5-A8NM-01 | exon_skip_338740 | 44145164 | 44145272 | 44145165 | 44145165 | Frame_Shift_Del | T | - | p.A1051fs |
| HNSC | TCGA-BA-4077-01 | exon_skip_338747 | 44174396 | 44174509 | 44174430 | 44174430 | Frame_Shift_Del | A | - | p.L682fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_338753 | 44209377 | 44209573 | 44209396 | 44209396 | Frame_Shift_Del | A | - | p.F109fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_338753 | 44209377 | 44209573 | 44209402 | 44209402 | Frame_Shift_Del | T | - | p.K107fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_338753 | 44209377 | 44209573 | 44209402 | 44209402 | Frame_Shift_Del | T | - | p.K107fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_338753 | 44209377 | 44209573 | 44209500 | 44209500 | Frame_Shift_Del | A | - | p.S76fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_338753 | 44209377 | 44209573 | 44209525 | 44209525 | Frame_Shift_Del | T | - | p.K66fs |
| UCEC | TCGA-B5-A0JY-01 | exon_skip_338753 | 44209377 | 44209573 | 44209440 | 44209440 | Nonsense_Mutation | G | A | p.R95* |
| BLCA | TCGA-2F-A9KT-01 | exon_skip_338753 | 44209377 | 44209573 | 44209479 | 44209479 | Nonsense_Mutation | G | A | p.Q82* |
| LUAD | TCGA-05-4430-01 | exon_skip_338752 | 44204133 | 44204191 | 44204192 | 44204192 | Splice_Site | C | T | p.V198_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 |
| TOV21G_OVARY | 44174396 | 44174509 | 44174416 | 44174417 | Frame_Shift_Del | AT | - | p.L687fs |
| EW11_BONE | 44123773 | 44123847 | 44123840 | 44123840 | Missense_Mutation | C | A | p.G1278V |
| SKOV3_OVARY | 44126605 | 44126744 | 44126658 | 44126658 | Missense_Mutation | G | A | p.A1219V |
| HEC108_ENDOMETRIUM | 44126605 | 44126744 | 44126668 | 44126668 | Missense_Mutation | A | G | p.F1216L |
| HCC2998_LARGE_INTESTINE | 44126605 | 44126744 | 44126712 | 44126712 | Missense_Mutation | T | A | p.E1201V |
| SNU1040_LARGE_INTESTINE | 44139571 | 44139697 | 44139589 | 44139589 | Missense_Mutation | G | A | p.A1086V |
| MRKNU1_BREAST | 44145164 | 44145272 | 44145212 | 44145212 | Missense_Mutation | C | A | p.D1034Y |
| OCIMY5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 44145164 | 44145272 | 44145238 | 44145238 | Missense_Mutation | G | C | p.S1025C |
| COLO320_LARGE_INTESTINE | 44172471 | 44172556 | 44172479 | 44172479 | Missense_Mutation | T | G | p.K763T |
| JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 44172471 | 44172556 | 44172552 | 44172552 | Missense_Mutation | G | A | p.R739C |
| NCIH1688_LUNG | 44174396 | 44174509 | 44174443 | 44174443 | Missense_Mutation | T | C | p.I678V |
| GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 44174396 | 44174509 | 44174473 | 44174473 | Missense_Mutation | G | T | p.L668I |
| HT1376_URINARY_TRACT | 44204133 | 44204191 | 44204149 | 44204149 | Missense_Mutation | C | G | p.D212H |
| HEC59_ENDOMETRIUM | 44209377 | 44209573 | 44209383 | 44209383 | Missense_Mutation | G | A | p.R114C |
| CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 44209377 | 44209573 | 44209434 | 44209434 | Missense_Mutation | T | C | p.T97A |
| EGI1_BILIARY_TRACT | 44209377 | 44209573 | 44209449 | 44209449 | Missense_Mutation | G | A | p.L92F |
| NCIH345_LUNG | 44209377 | 44209573 | 44209532 | 44209532 | Missense_Mutation | T | C | p.K64R |
| OVTOKO_OVARY | 44209377 | 44209573 | 44209535 | 44209535 | Missense_Mutation | G | A | p.A63V |
| SCLC22H_LUNG | 44209377 | 44209573 | 44209563 | 44209563 | Missense_Mutation | T | A | p.S54C |
| SCLC21H_LUNG | 44209377 | 44209573 | 44209563 | 44209563 | Missense_Mutation | T | A | p.S54C |
| ES7_BONE | 44209377 | 44209573 | 44209469 | 44209469 | Nonsense_Mutation | C | T | p.W85* |
| HCC2998_LARGE_INTESTINE | 44209377 | 44209573 | 44209530 | 44209530 | Nonsense_Mutation | C | A | p.E65* |
| HEC108_ENDOMETRIUM | 44172471 | 44172556 | 44172472 | 44172472 | Splice_Site | T | C | p.Q765Q |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LRPPRC |
| 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 |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LRPPRC |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LRPPRC |
Top |
RelatedDrugs for LRPPRC |
| 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 |
Top |
RelatedDiseases for LRPPRC |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| LRPPRC | C1857355 | Leigh syndrome , French Canadian type | 1 | CTD_human;ORPHANET;UNIPROT |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|