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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 LRRK1 |
 Gene summary |
| Gene information | Gene symbol | LRRK1 | Gene ID | 79705 |
| Gene name | leucine rich repeat kinase 1 | |
| Synonyms | RIPK6|Roco1 | |
| Cytomap | 15q26.3 | |
| Type of gene | protein-coding | |
| Description | leucine-rich repeat serine/threonine-protein kinase 1 | |
| Modification date | 20180519 | |
| UniProtAcc | Q38SD2 | |
| Context | PubMed: LRRK1 [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 LRRK1 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 LRRK1 |
| 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 LRRK1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_125347 | 15 | 101459549:101459656:101460235:101460460:101464715:101464934 | 101460235:101460460 | ENSG00000154237.8 | ENST00000534045.1 |
| exon_skip_125350 | 15 | 101464807:101464934:101514008:101514172:101523732:101523893 | 101514008:101514172 | ENSG00000154237.8 | ENST00000284395.5,ENST00000525284.1,ENST00000531270.1,ENST00000388948.3,ENST00000532029.2 |
| exon_skip_125354 | 15 | 101514008:101514172:101523732:101523904:101528838:101529018 | 101523732:101523904 | ENSG00000154237.8 | ENST00000525284.1,ENST00000531270.1,ENST00000388948.3,ENST00000532029.2 |
| exon_skip_125357 | 15 | 101552212:101552350:101554520:101554633:101555530:101555607 | 101554520:101554633 | ENSG00000154237.8 | ENST00000284395.5,ENST00000525284.1,ENST00000531270.1,ENST00000388948.3 |
| exon_skip_125359 | 15 | 101586185:101586357:101588698:101588862:101589848:101589988 | 101588698:101588862 | ENSG00000154237.8 | ENST00000284395.5,ENST00000525284.1,ENST00000388948.3 |
| exon_skip_125360 | 15 | 101601375:101601493:101602585:101602895:101605556:101606410 | 101602585:101602895 | ENSG00000154237.8 | ENST00000525284.1 |
| exon_skip_125361 | 15 | 101601375:101601493:101602778:101602895:101605556:101606410 | 101602778:101602895 | ENSG00000154237.8 | ENST00000284395.5,ENST00000531270.1,ENST00000388948.3,ENST00000526457.2 |
| exon_skip_125362 | 15 | 101605556:101606410:101606844:101606946:101608875:101609273 | 101606844:101606946 | ENSG00000154237.8 | ENST00000284395.5,ENST00000525284.1,ENST00000532145.1,ENST00000531270.1,ENST00000388948.3 |
| exon_skip_125363 | 15 | 101606844:101606946:101607444:101607592:101608875:101609049 | 101607444:101607592 | ENSG00000154237.8 | ENST00000526457.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for LRRK1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_125347 | 15 | 101459549:101459656:101460235:101460460:101464715:101464934 | 101460235:101460460 | ENSG00000154237.8 | ENST00000534045.1 |
| exon_skip_125350 | 15 | 101464807:101464934:101514008:101514172:101523732:101523893 | 101514008:101514172 | ENSG00000154237.8 | ENST00000388948.3,ENST00000284395.5,ENST00000532029.2,ENST00000525284.1,ENST00000531270.1 |
| exon_skip_125354 | 15 | 101514008:101514172:101523732:101523904:101528838:101529018 | 101523732:101523904 | ENSG00000154237.8 | ENST00000388948.3,ENST00000532029.2,ENST00000525284.1,ENST00000531270.1 |
| exon_skip_125357 | 15 | 101552212:101552350:101554520:101554633:101555530:101555607 | 101554520:101554633 | ENSG00000154237.8 | ENST00000388948.3,ENST00000284395.5,ENST00000525284.1,ENST00000531270.1 |
| exon_skip_125359 | 15 | 101586185:101586357:101588698:101588862:101589848:101589988 | 101588698:101588862 | ENSG00000154237.8 | ENST00000388948.3,ENST00000284395.5,ENST00000525284.1 |
| exon_skip_125360 | 15 | 101601375:101601493:101602585:101602895:101605556:101606410 | 101602585:101602895 | ENSG00000154237.8 | ENST00000525284.1 |
| exon_skip_125361 | 15 | 101601375:101601493:101602778:101602895:101605556:101606410 | 101602778:101602895 | ENSG00000154237.8 | ENST00000388948.3,ENST00000284395.5,ENST00000531270.1,ENST00000526457.2 |
| exon_skip_125362 | 15 | 101605556:101606410:101606844:101606946:101608875:101609273 | 101606844:101606946 | ENSG00000154237.8 | ENST00000388948.3,ENST00000284395.5,ENST00000525284.1,ENST00000531270.1,ENST00000532145.1 |
| exon_skip_125363 | 15 | 101606844:101606946:101607444:101607592:101608875:101609049 | 101607444:101607592 | ENSG00000154237.8 | ENST00000526457.2 |
| 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 LRRK1 |
| 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 |
| ENST00000388948 | 101514008 | 101514172 | Frame-shift |
| ENST00000388948 | 101523732 | 101523904 | Frame-shift |
| ENST00000388948 | 101554520 | 101554633 | Frame-shift |
| ENST00000388948 | 101588698 | 101588862 | Frame-shift |
| ENST00000388948 | 101602778 | 101602895 | In-frame |
| ENST00000388948 | 101606844 | 101606946 | 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 |
| ENST00000388948 | 101514008 | 101514172 | Frame-shift |
| ENST00000388948 | 101523732 | 101523904 | Frame-shift |
| ENST00000388948 | 101554520 | 101554633 | Frame-shift |
| ENST00000388948 | 101588698 | 101588862 | Frame-shift |
| ENST00000388948 | 101602778 | 101602895 | In-frame |
| ENST00000388948 | 101606844 | 101606946 | In-frame |
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Infer the effects of exon skipping event on protein functional features for LRRK1 |
| 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 |
| ENST00000388948 | 7688 | 2015 | 101602778 | 101602895 | 5157 | 5273 | 1599 | 1638 |
| ENST00000388948 | 7688 | 2015 | 101606844 | 101606946 | 6128 | 6229 | 1923 | 1956 |
| 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 |
| ENST00000388948 | 7688 | 2015 | 101602778 | 101602895 | 5157 | 5273 | 1599 | 1638 |
| ENST00000388948 | 7688 | 2015 | 101606844 | 101606946 | 6128 | 6229 | 1923 | 1956 |
| 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 |
| Q38SD2 | 1599 | 1638 | 265 | 2015 | Alternative sequence | ID=VSP_040120;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q38SD2 | 1599 | 1638 | 1 | 2015 | Chain | ID=PRO_0000233377;Note=Leucine-rich repeat serine/threonine-protein kinase 1 |
| Q38SD2 | 1923 | 1956 | 265 | 2015 | Alternative sequence | ID=VSP_040120;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q38SD2 | 1923 | 1956 | 1 | 2015 | Chain | ID=PRO_0000233377;Note=Leucine-rich repeat serine/threonine-protein kinase 1 |
| Q38SD2 | 1923 | 1956 | 1927 | 1927 | Natural variant | ID=VAR_040677;Note=D->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17344846;Dbxref=PMID:17344846 |
| Q38SD2 | 1923 | 1956 | 1938 | 1938 | Sequence conflict | Note=G->E;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q38SD2 | 1923 | 1956 | 1938 | 1938 | Sequence conflict | Note=G->E;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| 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 |
| Q38SD2 | 1599 | 1638 | 265 | 2015 | Alternative sequence | ID=VSP_040120;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q38SD2 | 1599 | 1638 | 1 | 2015 | Chain | ID=PRO_0000233377;Note=Leucine-rich repeat serine/threonine-protein kinase 1 |
| Q38SD2 | 1923 | 1956 | 265 | 2015 | Alternative sequence | ID=VSP_040120;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q38SD2 | 1923 | 1956 | 1 | 2015 | Chain | ID=PRO_0000233377;Note=Leucine-rich repeat serine/threonine-protein kinase 1 |
| Q38SD2 | 1923 | 1956 | 1927 | 1927 | Natural variant | ID=VAR_040677;Note=D->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17344846;Dbxref=PMID:17344846 |
| Q38SD2 | 1923 | 1956 | 1938 | 1938 | Sequence conflict | Note=G->E;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q38SD2 | 1923 | 1956 | 1938 | 1938 | Sequence conflict | Note=G->E;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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SNVs in the skipped exons for LRRK1 |
| - 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 |
| LGG | TCGA-HT-7680-01 | exon_skip_125350 | 101514009 | 101514172 | 101514014 | 101514014 | Frame_Shift_Del | G | - | p.G8fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_125362 | 101606845 | 101606946 | 101606898 | 101606898 | Frame_Shift_Del | G | - | p.R1938fs |
| STAD | TCGA-HU-A4GX-01 | exon_skip_125361 | 101602779 | 101602895 | 101602777 | 101602777 | Splice_Site | A | C | . |
| STAD | TCGA-HU-A4GX-01 | exon_skip_125361 | 101602779 | 101602895 | 101602777 | 101602777 | Splice_Site | A | C | p.D1600_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 |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 101588699 | 101588862 | 101588798 | 101588799 | Frame_Shift_Del | AA | - | p.K1079fs |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 101588699 | 101588862 | 101588796 | 101588797 | Frame_Shift_Ins | - | CC | p.K1079fs |
| MERO84_LUNG | 101514009 | 101514172 | 101514089 | 101514089 | Missense_Mutation | G | A | p.A60T |
| SNU1_STOMACH | 101514009 | 101514172 | 101514111 | 101514111 | Missense_Mutation | G | A | p.R67H |
| SKNSH_AUTONOMIC_GANGLIA | 101523733 | 101523904 | 101523754 | 101523754 | Missense_Mutation | G | A | p.A95T |
| SHSY5Y_AUTONOMIC_GANGLIA | 101523733 | 101523904 | 101523754 | 101523754 | Missense_Mutation | G | A | p.A95T |
| TC71_BONE | 101523733 | 101523904 | 101523763 | 101523763 | Missense_Mutation | G | T | p.G98W |
| SW684_SOFT_TISSUE | 101523733 | 101523904 | 101523828 | 101523829 | Missense_Mutation | GG | TA | p.D120N |
| NCIH1694_LUNG | 101523733 | 101523904 | 101523836 | 101523836 | Missense_Mutation | A | C | p.N122T |
| GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 101523733 | 101523904 | 101523857 | 101523857 | Missense_Mutation | A | G | p.Y129C |
| NCIH345_LUNG | 101523733 | 101523904 | 101523902 | 101523902 | Missense_Mutation | C | G | p.P144R |
| NCIH187_LUNG | 101588699 | 101588862 | 101588705 | 101588705 | Missense_Mutation | G | A | p.E1048K |
| TE9_OESOPHAGUS | 101588699 | 101588862 | 101588706 | 101588706 | Missense_Mutation | A | G | p.E1048G |
| HEC251_ENDOMETRIUM | 101588699 | 101588862 | 101588844 | 101588844 | Missense_Mutation | T | G | p.F1094C |
| DG75_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 101588699 | 101588862 | 101588852 | 101588852 | Missense_Mutation | G | T | p.G1097C |
| COLO684_ENDOMETRIUM | 101588699 | 101588862 | 101588855 | 101588855 | Missense_Mutation | T | A | p.Y1098N |
| COLO704_OVARY | 101588699 | 101588862 | 101588855 | 101588855 | Missense_Mutation | T | A | p.Y1098N |
| SNUC2A_LARGE_INTESTINE | 101602586 | 101602895 | 101602878 | 101602878 | Missense_Mutation | G | A | p.V1633M |
| SNUC2A_LARGE_INTESTINE | 101602779 | 101602895 | 101602878 | 101602878 | Missense_Mutation | G | A | p.V1633M |
| SNUC2B_LARGE_INTESTINE | 101602586 | 101602895 | 101602878 | 101602878 | Missense_Mutation | G | A | p.V1633M |
| SNUC2B_LARGE_INTESTINE | 101602779 | 101602895 | 101602878 | 101602878 | Missense_Mutation | G | A | p.V1633M |
| MG63_BONE | 101606845 | 101606946 | 101606910 | 101606910 | Missense_Mutation | T | C | p.I1945T |
| ME180_CERVIX | 101606845 | 101606946 | 101606903 | 101606903 | Nonsense_Mutation | C | T | p.R1943* |
| SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 101588699 | 101588862 | 101588700 | 101588700 | Splice_Site | T | - | p.L1046fs |
| HCT15_LARGE_INTESTINE | 101606845 | 101606946 | 101606846 | 101606846 | Splice_Site | C | T | p.R1924C |
| HRT18_LARGE_INTESTINE | 101606845 | 101606946 | 101606846 | 101606846 | Splice_Site | C | T | p.R1924C |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LRRK1 |
| 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 |
| exon_skip_125363 | 15 | 101606844:101606946:101607444:101607592:101608875:101609049 | 101607444:101607592 | ENST00000526457.2 | STAD | rs78439439 | chr15:101607450 | T/C | 1.26e-03 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LRRK1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LRRK1 |
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RelatedDrugs for LRRK1 |
| 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 LRRK1 |
| 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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