Lrrk2 (leucine-rich repeat kinase 2) - Rat Genome Database

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Gene: Lrrk2 (leucine-rich repeat kinase 2) Rattus norvegicus
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Symbol: Lrrk2
Name: leucine-rich repeat kinase 2
RGD ID: 1561168
Description: Predicted to enable several functions, including GTP binding activity; cytoskeletal protein binding activity; and protein serine/threonine kinase activity. Involved in several processes, including nervous system development; positive regulation of macromolecule metabolic process; and positive regulation of microglial cell activation. Located in several cellular components, including axon; dendrite; and perikaryon. Used to study neurodegenerative disease. Biomarker of diabetic neuropathy. Human ortholog(s) of this gene implicated in Crohn's disease; Parkinson's disease; Parkinson's disease 8; Parkinsonism; and cancer. Orthologous to human LRRK2 (leucine rich repeat kinase 2); PARTICIPATES IN Parkinson's disease pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: leucine-rich repeat serine/threonine-protein kinase 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Lrrk1em1SageLrrk2em1Sage   Lrrk2em1Sage  
Genetic Models: LE-Lrrk2em1Sage-/- LE-Lrrk2em1Sage LE-Lrrk1em1Sage-/-Lrrk2em1Sage-/- LE-Lrrk1em1SageLrrk2em1Sage
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27122,826,712 - 122,987,711 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7122,826,696 - 122,987,703 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7124,609,699 - 124,765,717 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.07126,835,567 - 126,991,586 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.07126,763,694 - 126,919,689 (+)NCBIRnor_WKY
Rnor_6.07132,857,311 - 133,018,549 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7132,857,628 - 133,018,584 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07132,531,591 - 132,694,226 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47130,105,902 - 130,267,747 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera7119,264,946 - 119,423,875 (+)NCBICelera
Cytogenetic Map7q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3-methyladenine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
arsenite(3-)  (ISO)
bafilomycin A1  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chlorpyrifos  (ISO)
cisplatin  (ISO)
clozapine  (ISO)
copper(II) sulfate  (ISO)
corticosterone  (ISO)
crocidolite asbestos  (ISO)
dimethylarsinic acid  (ISO)
dioxygen  (ISO)
dopamine  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fenamidone  (ISO)
folic acid  (ISO)
furan  (EXP)
gentamycin  (EXP)
GTP  (ISO)
hydrogen peroxide  (ISO)
lactacystin  (ISO)
lipopolysaccharide  (ISO)
luteolin  (ISO)
maneb  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
methapyrilene  (ISO)
methylarsonic acid  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nickel atom  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
pentanal  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
permethrin  (EXP)
pirinixic acid  (ISO)
resveratrol  (ISO)
rotenone  (EXP,ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
trovafloxacin  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
calcium-mediated signaling  (IBA,ISO)
cellular response to dopamine  (ISO)
cellular response to manganese ion  (ISO)
cellular response to organic cyclic compound  (IBA,IEP)
cellular response to oxidative stress  (ISO)
cellular response to starvation  (ISO)
determination of adult lifespan  (ISO)
endocytosis  (ISO)
endoplasmic reticulum organization  (IBA,ISO)
excitatory postsynaptic potential  (ISO,ISS)
exploration behavior  (ISO)
Golgi organization  (IBA,ISO)
GTP metabolic process  (ISO)
innate immune response  (IEA)
intracellular distribution of mitochondria  (ISO)
intracellular signal transduction  (ISO,ISS)
JNK cascade  (ISO)
locomotory exploration behavior  (ISO,ISS)
lysosome organization  (ISO)
MAPK cascade  (ISO)
mitochondrion localization  (ISO)
mitochondrion organization  (IBA,ISO)
negative regulation of autophagosome assembly  (IBA,ISO)
negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway  (ISO)
negative regulation of excitatory postsynaptic potential  (ISO)
negative regulation of GTPase activity  (ISO)
negative regulation of hydrogen peroxide-induced cell death  (ISO)
negative regulation of macroautophagy  (ISO)
negative regulation of neuron death  (ISO)
negative regulation of neuron projection development  (IMP)
negative regulation of peroxidase activity  (IEA)
negative regulation of protein binding  (ISO)
negative regulation of protein phosphorylation  (ISO,ISS)
negative regulation of protein processing  (ISO)
negative regulation of protein targeting to mitochondrion  (ISO)
negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation  (ISO)
neuromuscular junction development  (ISO)
neuron death  (ISO)
neuron projection arborization  (IMP)
neuron projection morphogenesis  (IBA,ISO,ISS)
olfactory bulb development  (ISO)
peptidyl-serine phosphorylation  (ISO)
peptidyl-threonine phosphorylation  (ISO)
phosphorylation  (ISO)
positive regulation of autophagy  (IBA,ISO)
positive regulation of canonical Wnt signaling pathway  (ISO)
positive regulation of dopamine receptor signaling pathway  (ISO)
positive regulation of histone deacetylase activity  (ISO)
positive regulation of MAP kinase activity  (ISO)
positive regulation of microglial cell activation  (IMP)
positive regulation of nitric-oxide synthase biosynthetic process  (IMP)
positive regulation of programmed cell death  (ISO)
positive regulation of proteasomal ubiquitin-dependent protein catabolic process  (ISO)
positive regulation of protein autoubiquitination  (ISO)
positive regulation of protein binding  (ISO)
positive regulation of protein kinase activity  (ISO)
positive regulation of protein phosphorylation  (ISO)
positive regulation of protein ubiquitination  (ISO)
positive regulation of synaptic vesicle endocytosis  (IMP)
positive regulation of tumor necrosis factor production  (IMP)
protein autophosphorylation  (ISO)
protein import into nucleus  (ISO)
protein localization  (ISO,ISS)
protein localization to endoplasmic reticulum exit site  (IBA,ISO)
protein phosphorylation  (IBA,ISO)
reactive oxygen species metabolic process  (ISO)
regulation of autophagy  (ISO)
regulation of branching morphogenesis of a nerve  (ISO)
regulation of CAMKK-AMPK signaling cascade  (ISO)
regulation of canonical Wnt signaling pathway  (IBA,ISO)
regulation of dendritic spine morphogenesis  (IBA,ISO,ISS)
regulation of dopamine receptor signaling pathway  (IBA,ISO,ISS)
regulation of ER to Golgi vesicle-mediated transport  (ISO)
regulation of gene expression  (ISO)
regulation of kidney size  (ISO)
regulation of locomotion  (ISO)
regulation of lysosomal lumen pH  (ISO)
regulation of membrane potential  (IBA,ISO)
regulation of mitochondrial depolarization  (ISO)
regulation of neuroblast proliferation  (ISO)
regulation of neuron death  (ISO)
regulation of neuron maturation  (ISO)
regulation of protein kinase A signaling  (ISO,ISS)
regulation of protein stability  (ISO)
regulation of retrograde transport, endosome to Golgi  (IBA,ISO)
regulation of synaptic transmission, glutamatergic  (ISO,ISS)
regulation of synaptic vesicle endocytosis  (ISO)
regulation of synaptic vesicle exocytosis  (ISO)
regulation of synaptic vesicle transport  (IBA,ISO)
response to oxidative stress  (ISO)
signal transduction  (IBA)
spermatogenesis  (IEP)
striatum development  (IEP)
tangential migration from the subventricular zone to the olfactory bulb  (ISO)
Wnt signalosome assembly  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Novel pathogenic LRRK2 p.Asn1437His substitution in familial Parkinson's disease. Aasly JO, etal., Mov Disord. 2010 Oct 15;25(13):2156-63.
2. Loss of leucine-rich repeat kinase 2 (LRRK2) in rats leads to progressive abnormal phenotypes in peripheral organs. Baptista MA, etal., PLoS One. 2013 Nov 14;8(11):e80705. doi: 10.1371/journal.pone.0080705. eCollection 2013.
3. Genes associated with Parkinson's disease: regulation of autophagy and beyond. Beilina A and Cookson MR, J Neurochem. 2015 Jul 30. doi: 10.1111/jnc.13266.
4. Localization of LRRK2 to membranous and vesicular structures in mammalian brain. Biskup S, etal., Ann Neurol. 2006 Nov;60(5):557-69.
5. Clinical and brain imaging characteristics in leucine-rich repeat kinase 2-associated PD and asymptomatic mutation carriers. Brockmann K, etal., Mov Disord. 2011 Oct 11. doi: 10.1002/mds.23991.
6. LRRK2 R1398H polymorphism is associated with decreased risk of Parkinson's disease in a Han Chinese population. Chen L, etal., Parkinsonism Relat Disord. 2011 May;17(4):291-2. Epub 2010 Dec 14.
7. Abrogation of a-synuclein-mediated dopaminergic neurodegeneration in LRRK2-deficient rats. Daher JP, etal., Proc Natl Acad Sci U S A. 2014 Jun 24;111(25):9289-94. doi: 10.1073/pnas.1403215111. Epub 2014 Jun 9.
8. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. Impaired intracellular trafficking defines early Parkinson's disease. Hunn BH, etal., Trends Neurosci. 2015 Mar;38(3):178-88. doi: 10.1016/j.tins.2014.12.009. Epub 2015 Jan 29.
10. Inhibitors of leucine-rich repeat kinase-2 protect against models of Parkinson's disease. Lee BD, etal., Nat Med. 2010 Sep;16(9):998-1000. Epub 2010 Aug 22.
11. Lrrk2 S1647T and BDNF V66M interact with environmental factors to increase risk of Parkinson's disease. Lin CH, etal., Parkinsonism Relat Disord. 2011 Feb;17(2):84-8. Epub 2010 Dec 16.
12. The kinase LRRK2 is a regulator of the transcription factor NFAT that modulates the severity of inflammatory bowel disease. Liu Z, etal., Nat Immunol. 2011 Oct 9. doi: 10.1038/ni.2113.
13. The familial Parkinsonism gene LRRK2 regulates neurite process morphology. MacLeod D, etal., Neuron. 2006 Nov 22;52(4):587-93.
14. Surfactant secretion in LRRK2 knock-out rats: changes in lamellar body morphology and rate of exocytosis. Miklavc P, etal., PLoS One. 2014 Jan 21;9(1):e84926. doi: 10.1371/journal.pone.0084926. eCollection 2014.
15. Lrrk2 and chronic inflammation are linked to pallido-ponto-nigral degeneration caused by the N279K tau mutation. Miklossy J, etal., Acta Neuropathol. 2007 Sep;114(3):243-54. Epub 2007 Jul 17.
16. LRRK2 inhibition attenuates microglial inflammatory responses. Moehle MS, etal., J Neurosci. 2012 Feb 1;32(5):1602-11. doi: 10.1523/JNEUROSCI.5601-11.2012.
17. Isolation and expression profiling of genes upregulated in bone marrow-derived mononuclear cells of rheumatoid arthritis patients. Nakamura N, etal., DNA Res. 2006 Aug 31;13(4):169-83.
18. Leucine-rich repeat kinase 2 (LRRK2)-deficient rats exhibit renal tubule injury and perturbations in metabolic and immunological homeostasis. Ness D, etal., PLoS One. 2013 Jun 14;8(6):e66164. doi: 10.1371/journal.pone.0066164. Print 2013.
19. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
20. Curcumin exposure induces expression of the Parkinson's disease-associated leucine-rich repeat kinase 2 (LRRK2) in rat mesencephalic cells. Ortiz-Ortiz MA, etal., Neurosci Lett. 2010 Jan 4;468(2):120-4. Epub 2009 Oct 30.
21. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
22. GOA pipeline RGD automated data pipeline
23. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
24. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
25. Comprehensive gene review and curation RGD comprehensive gene curation
26. Penetrance in Parkinson's disease related to the LRRK2 R1441G mutation in the Basque country (Spain). Ruiz-Martinez J, etal., Mov Disord. 2010 Oct 30;25(14):2340-5.
27. LRRK2 G2019S mutations are associated with an increased cancer risk in Parkinson disease. Saunders-Pullman R, etal., Mov Disord. 2010 Nov 15;25(15):2536-41.
28. Comprehensive mutational analysis of LRRK2 reveals variants supporting association with autosomal dominant Parkinson's disease. Seki N, etal., J Hum Genet. 2011 Sep;56(9):671-5. doi: 10.1038/jhg.2011.79. Epub 2011 Jul 28.
29. LRRK2 regulates synaptic vesicle endocytosis. Shin N, etal., Exp Cell Res. 2008 Jun 10;314(10):2055-65. doi: 10.1016/j.yexcr.2008.02.015. Epub 2008 Mar 5.
30. Differential gene expression in patients with amyotrophic lateral sclerosis. Shtilbans A, etal., Amyotroph Lateral Scler. 2011 Jul;12(4):250-6. Epub 2011 Mar 4.
31. High frequency and reduced penetrance of lRRK2 g2019S mutation among Parkinson's disease patients in Cantabria (Spain). Sierra M, etal., Mov Disord. 2011 Sep 27. doi: 10.1002/mds.23965.
32. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
33. LRRK2 G2019S mutation does not contribute to Parkinson's disease in South India. Vijayan B, etal., Neurol India. 2011 Mar-Apr;59(2):157-60.
34. Leucine-rich repeat kinase 2 is associated with the endoplasmic reticulum in dopaminergic neurons and accumulates in the core of Lewy bodies in Parkinson disease. Vitte J, etal., J Neuropathol Exp Neurol. 2010 Sep;69(9):959-72.
35. Developmental regulation of leucine-rich repeat kinase 1 and 2 expression in the brain and other rodent and human organs: Implications for Parkinson's disease. Westerlund M, etal., Neuroscience. 2008 Mar 18;152(2):429-36. doi: 10.1016/j.neuroscience.2007.10.062. Epub 2008 Jan 10.
36. Mitochondrial dysfunction driven by the LRRK2-mediated pathway is associated with loss of Purkinje cells and motor coordination deficits in diabetic rat model. Yang S, etal., Cell Death Dis. 2014 May 8;5:e1217. doi: 10.1038/cddis.2014.184.
37. Expression of leucine-rich-repeat-kinase 2 (LRRK2) during embryonic development. Zechel S, etal., Int J Dev Neurosci. 2010 Aug;28(5):391-9. doi: 10.1016/j.ijdevneu.2010.04.002. Epub 2010 Apr 18.
Additional References at PubMed
PMID:15726496   PMID:16269541   PMID:16321986   PMID:16352719   PMID:16771836   PMID:16980962   PMID:17200152   PMID:17260967   PMID:17341485   PMID:17442267   PMID:18230735   PMID:18397888  
PMID:18790059   PMID:19056867   PMID:19302196   PMID:19576176   PMID:19625296   PMID:19640926   PMID:19692353   PMID:19712061   PMID:19733152   PMID:20173330   PMID:20457918   PMID:20515039  
PMID:20659558   PMID:21048939   PMID:21073465   PMID:21159966   PMID:21168496   PMID:21307259   PMID:21362567   PMID:21370995   PMID:21390248   PMID:21696411   PMID:21850687   PMID:21857923  
PMID:22012985   PMID:22363216   PMID:22423108   PMID:22664934   PMID:22736029   PMID:22764206   PMID:22899650   PMID:22952686   PMID:23220480   PMID:23241358   PMID:23395371   PMID:23628791  
PMID:23886663   PMID:23916833   PMID:23949442   PMID:24167564   PMID:24211199   PMID:24275654   PMID:24403142   PMID:24427314   PMID:24464040   PMID:24510904   PMID:24576675   PMID:24591621  
PMID:24633735   PMID:24874075   PMID:24904275   PMID:25174649   PMID:25201882   PMID:25416817   PMID:25427558   PMID:25500533   PMID:25501810   PMID:25904107   PMID:25926623   PMID:26014385  
PMID:26078453   PMID:26365310   PMID:26384650   PMID:26744332   PMID:26824392   PMID:27013965   PMID:27169991   PMID:27357661   PMID:27631370   PMID:27798112   PMID:28720718   PMID:28751472  
PMID:28973664   PMID:29563162   PMID:30048803   PMID:30452424   PMID:30954703   PMID:31039583   PMID:32572455   PMID:32631998   PMID:33434630   PMID:33594532  


Genomics

Comparative Map Data
Lrrk2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27122,826,712 - 122,987,711 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7122,826,696 - 122,987,703 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7124,609,699 - 124,765,717 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.07126,835,567 - 126,991,586 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.07126,763,694 - 126,919,689 (+)NCBIRnor_WKY
Rnor_6.07132,857,311 - 133,018,549 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7132,857,628 - 133,018,584 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07132,531,591 - 132,694,226 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47130,105,902 - 130,267,747 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera7119,264,946 - 119,423,875 (+)NCBICelera
Cytogenetic Map7q35NCBI
LRRK2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381240,224,997 - 40,369,285 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1240,196,744 - 40,369,285 (+)EnsemblGRCh38hg38GRCh38
GRCh371240,618,799 - 40,763,087 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361238,905,081 - 39,049,354 (+)NCBINCBI36Build 36hg18NCBI36
Celera1239,422,059 - 39,566,110 (+)NCBICelera
Cytogenetic Map12q12NCBI
HuRef1237,646,624 - 37,790,676 (+)NCBIHuRef
CHM1_11240,584,126 - 40,728,194 (+)NCBICHM1_1
T2T-CHM13v2.01240,177,355 - 40,321,422 (+)NCBIT2T-CHM13v2.0
Lrrk2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391591,556,994 - 91,700,327 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1591,557,378 - 91,700,323 (+)EnsemblGRCm39 Ensembl
GRCm381591,672,791 - 91,816,124 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1591,673,175 - 91,816,120 (+)EnsemblGRCm38mm10GRCm38
MGSCv371591,503,655 - 91,646,555 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361591,501,048 - 91,643,302 (+)NCBIMGSCv36mm8
Celera1593,785,543 - 93,930,186 (+)NCBICelera
Cytogenetic Map15E3NCBI
Lrrk2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495550581,796 - 216,923 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495550584,324 - 216,923 (-)NCBIChiLan1.0ChiLan1.0
LRRK2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11249,205,930 - 49,350,462 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1249,205,930 - 49,350,462 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01248,343,621 - 48,488,337 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LRRK2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12713,282,824 - 13,420,917 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2713,283,756 - 13,420,870 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2733,032,944 - 33,171,543 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02713,454,479 - 13,594,189 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2713,454,985 - 13,594,935 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12713,240,908 - 13,387,064 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02713,302,124 - 13,442,060 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02733,159,660 - 33,299,460 (+)NCBIUU_Cfam_GSD_1.0
Lrrk2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494573,794,012 - 73,929,347 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936607626,991 - 761,123 (-)EnsemblSpeTri2.0
SpeTri2.0NW_004936607628,469 - 761,117 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LRRK2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl571,800,225 - 71,945,828 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1571,800,337 - 71,945,828 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2574,510,979 - 74,653,410 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LRRK2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11136,490,775 - 36,634,215 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1136,492,011 - 36,634,216 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037210,139,337 - 210,285,872 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lrrk2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624778108,761 - 279,230 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624778106,594 - 279,325 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lrrk2
1233 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:51
Count of miRNA genes:38
Interacting mature miRNAs:40
Transcripts:ENSRNOT00000005438
Prediction methods:Microtar, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)780221299124373579Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)780221299125221299Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)781737938126737938Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)783153392128153392Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)784257275129257275Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)784257275129257275Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)791412594129807172Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat
1582240Sffal1Serum free fatty acids level QTL 13.40.0021blood free fatty acid amount (VT:0001553)serum free fatty acids level (CMO:0000547)7116677010124049952Rat
631201Panci1Pancreas inflammation QTL 100.001pancreas integrity trait (VT:0010560)percentage of study population displaying chronic pancreatitis at a point in time (CMO:0001214)7116677189127103496Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat

Markers in Region
D7Rat6  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27122,935,432 - 122,935,679 (+)MAPPERmRatBN7.2
Rnor_6.07132,966,481 - 132,966,727NCBIRnor6.0
Rnor_5.07132,640,754 - 132,641,000UniSTSRnor5.0
RGSC_v3.47130,215,239 - 130,215,486RGDRGSC3.4
RGSC_v3.47130,215,240 - 130,215,486UniSTSRGSC3.4
RGSC_v3.17130,288,255 - 130,288,501RGD
Celera7119,372,086 - 119,372,332UniSTS
RH 3.4 Map7987.5RGD
RH 3.4 Map7987.5UniSTS
RH 2.0 Map7738.4RGD
SHRSP x BN Map772.5599RGD
Cytogenetic Map7q35UniSTS
RH138644  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27122,853,337 - 122,853,463 (+)MAPPERmRatBN7.2
Rnor_6.07132,884,280 - 132,884,405NCBIRnor6.0
Rnor_5.07132,558,585 - 132,558,710UniSTSRnor5.0
RGSC_v3.47130,133,139 - 130,133,264UniSTSRGSC3.4
Celera7119,291,420 - 119,291,545UniSTS
RH 3.4 Map7979.7UniSTS
Cytogenetic Map7q35UniSTS


Genetic Models
This gene Lrrk2 is modified in the following models/strains

Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 4 2 13 1 1 17 17 4 11 1
Low 1 39 52 38 6 38 7 10 57 18 37 7
Below cutoff 3 3 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000005438   ⟹   ENSRNOP00000005438
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7122,826,696 - 122,987,703 (+)Ensembl
Rnor_6.0 Ensembl7132,857,628 - 133,018,584 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000104823   ⟹   ENSRNOP00000087057
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7122,826,696 - 122,987,519 (+)Ensembl
RefSeq Acc Id: NM_001191789   ⟹   NP_001178718
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27122,826,748 - 122,987,255 (+)NCBI
Rnor_6.07132,857,708 - 133,018,086 (+)NCBI
Rnor_5.07132,531,591 - 132,694,226 (+)NCBI
Celera7119,264,946 - 119,423,875 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006242190   ⟹   XP_006242252
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27122,826,712 - 122,987,711 (+)NCBI
Rnor_6.07132,857,311 - 133,018,549 (+)NCBI
Rnor_5.07132,531,591 - 132,694,226 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008765689   ⟹   XP_008763911
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27122,826,712 - 122,987,711 (+)NCBI
Rnor_6.07132,857,311 - 133,018,549 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039078901   ⟹   XP_038934829
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27122,826,712 - 122,961,911 (+)NCBI
RefSeq Acc Id: XM_039078902   ⟹   XP_038934830
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27122,826,712 - 122,916,497 (+)NCBI
RefSeq Acc Id: XM_039078903   ⟹   XP_038934831
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27122,826,712 - 122,907,470 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001178718   ⟸   NM_001191789
- UniProtKB: F1LNJ1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242252   ⟸   XM_006242190
- Peptide Label: isoform X1
- UniProtKB: F1LNJ1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008763911   ⟸   XM_008765689
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000005438   ⟸   ENSRNOT00000005438
RefSeq Acc Id: XP_038934829   ⟸   XM_039078901
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038934830   ⟸   XM_039078902
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038934831   ⟸   XM_039078903
- Peptide Label: isoform X5
RefSeq Acc Id: ENSRNOP00000087057   ⟸   ENSRNOT00000104823
Protein Domains
Protein kinase   Roc

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LNJ1-F1-model_v2 AlphaFold F1LNJ1 1-2526 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13695599
Promoter ID:EPDNEW_R6123
Type:initiation region
Name:Lrrk2_1
Description:leucine-rich repeat kinase 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07132,857,642 - 132,857,702EPDNEW
RGD ID:13695610
Promoter ID:EPDNEW_R6124
Type:multiple initiation site
Name:AC108595_1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07132,984,204 - 132,984,264EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561168 AgrOrtholog
BioCyc Gene G2FUF-32379 BioCyc
Ensembl Genes ENSRNOG00000004048 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000005438 ENTREZGENE
  ENSRNOP00000005438.7 UniProtKB/TrEMBL
  ENSRNOP00000087057 ENTREZGENE
  ENSRNOP00000087057.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005438 ENTREZGENE
  ENSRNOT00000005438.8 UniProtKB/TrEMBL
  ENSRNOT00000104823 ENTREZGENE
  ENSRNOT00000104823.1 UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.10 UniProtKB/TrEMBL
  1.25.40.20 UniProtKB/TrEMBL
  2.130.10.10 UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/TrEMBL
  3.80.10.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7365592 IMAGE-MGC_LOAD
InterPro Ankyrin_rpt-contain_sf UniProtKB/TrEMBL
  ARM-like UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/TrEMBL
  COR UniProtKB/TrEMBL
  Kinase-like_dom UniProtKB/TrEMBL
  L_dom-like UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  Prot_kinase_cat_dom UniProtKB/TrEMBL
  Protein_kinase_ATP_BS UniProtKB/TrEMBL
  ROC_GTPase UniProtKB/TrEMBL
  Ser/Thr_kinase_AS UniProtKB/TrEMBL
  Small_GTP-bd_dom UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/TrEMBL
MGC_CLONE MGC:109585 IMAGE-MGC_LOAD
NCBI Gene 300160 ENTREZGENE
Pfam COR UniProtKB/TrEMBL
  LRR_8 UniProtKB/TrEMBL
  Pkinase UniProtKB/TrEMBL
PhenoGen Lrrk2 PhenoGen
PROSITE LRR UniProtKB/TrEMBL
  PROTEIN_KINASE_ATP UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/TrEMBL
  PROTEIN_KINASE_ST UniProtKB/TrEMBL
  ROC UniProtKB/TrEMBL
SMART LRR_TYP UniProtKB/TrEMBL
  S_TKc UniProtKB/TrEMBL
Superfamily-SCOP ARM-type_fold UniProtKB/TrEMBL
  Kinase_like UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
  WD40_like UniProtKB/TrEMBL
TIGRFAMs small_GTP UniProtKB/TrEMBL
UniProt A0A8I6GFN0_RAT UniProtKB/TrEMBL
  B4F7C3_RAT UniProtKB/TrEMBL
  F1LNJ1 ENTREZGENE, UniProtKB/TrEMBL
  Q5BJM3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Lrrk2  leucine-rich repeat kinase 2      Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 Lrrk2  leucine-rich repeat kinase 2      Symbol and Name status set to provisional 70820 PROVISIONAL