Lrrk1 leucine-rich repeat kinase 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Lrrk1provided by RGD
Official Full Name: leucine-rich repeat kinase 1provided by RGD
Primary source: RGD:1308000
See related: EnsemblRapid:ENSRNOG00000012730 AllianceGenome:RGD:1308000
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable identical protein binding activity and protein kinase activity. Predicted to be involved in positive regulation of canonical Wnt signaling pathway and signal transduction. Predicted to act upstream of or within several processes, including bone resorption; osteoclast development; and regulation of peptidyl-tyrosine phosphorylation. Predicted to be located in cytosol and mitochondrion. Predicted to be active in cytoplasm. Human ortholog(s) of this gene implicated in osteosclerotic metaphyseal dysplasia. Orthologous to human LRRK1 (leucine rich repeat kinase 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Spleen (RPKM 75.2), Lung (RPKM 63.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q22

Exon count:: 36

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (129254815..129390217, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (119844360..119972885, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (127166866..127301053, complement)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Lrrk1 is found in many areas of the P1 rat. Lrrk1 is present in adult rat brain, adrenal gland, liver, lung, spleen and kidney and also in embryonic brain, with declining gene activity after birth.
Title: 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.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables 3-phosphoinositide-dependent protein kinase activity	IEA Inferred from Electronic Annotation more info
enables AMP-activated protein kinase activity	IEA Inferred from Electronic Annotation more info
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables DNA-dependent protein kinase activity	IEA Inferred from Electronic Annotation more info
enables GTP binding	IEA Inferred from Electronic Annotation more info
enables Rho-dependent protein serine/threonine kinase activity	IEA Inferred from Electronic Annotation more info
enables eukaryotic translation initiation factor 2alpha kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AS1 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AS121 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AT120 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AXS139 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2BS14 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2BS36 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3S10 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3S28 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3S57 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T11 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T3 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T45 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T6 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H4S1 kinase activity	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein serine/threonine kinase activity	IEA Inferred from Electronic Annotation more info
enables ribosomal protein S6 kinase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within bone resorption	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
acts_upstream_of intracellular signal transduction	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of peptidyl-tyrosine phosphorylation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within osteoclast development	ISO Inferred from Sequence Orthology more info
acts_upstream_of peptidyl-tyrosine phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of intracellular signal transduction	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of peptidyl-tyrosine phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in signal transduction	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: leucine-rich repeat serine/threonine-protein kinase 1

NP_001178553.1

EC 2.7.11.1

XP_038968616.1

EC 2.7.11.1

XP_063118546.1

EC 2.7.11.1

XP_063118548.1

EC 2.7.11.1

XP_063118551.1

EC 2.7.11.1

XP_063118560.1

EC 2.7.11.1

XP_063118568.1

EC 2.7.11.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001191624.2 → NP_001178553.1 leucine-rich repeat serine/threonine-protein kinase 1

See identical proteins and their annotated locations for NP_001178553.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

D3ZRJ7

Related

ENSRNOP00000094655.2, ENSRNOT00000106564.2

Conserved Domains (11) summary

smart00220
Location:1247 → 1511

S_TKc; Serine/Threonine protein kinases, catalytic domain

COG1100
Location:635 → 781

Gem1; GTPase SAR1 family domain [General function prediction only]

COG4886
Location:279 → 513

LRR; Leucine-rich repeat (LRR) protein [Transcription]

cd00116
Location:273 → 464

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

cd00204
Location:91 → 214

ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...

cd14067
Location:1248 → 1523

STKc_LRRK1; Catalytic domain of the Serine/Threonine Kinase, Leucine-Rich Repeat Kinase 1

sd00033
Location:281 → 303

LRR_RI; leucine-rich repeat [structural motif]

pfam12796
Location:126 → 221

Ank_2; Ankyrin repeats (3 copies)

pfam16095
Location:844 → 1036

COR; C-terminal of Roc, COR, domain

sd00045
Location:156 → 186

ANK; ANK repeat [structural motif]

cl21455
Location:639 → 821

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086019.1 Reference GRCr8

Range

129254815..129390217 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063262481.1 → XP_063118551.1 leucine-rich repeat serine/threonine-protein kinase 1 isoform X2

UniProtKB/TrEMBL

A0A8I6B1B9, D3ZRJ7
XM_063262476.1 → XP_063118546.1 leucine-rich repeat serine/threonine-protein kinase 1 isoform X1

Related

ENSRNOP00000016959.7, ENSRNOT00000016959.8
XM_063262478.1 → XP_063118548.1 leucine-rich repeat serine/threonine-protein kinase 1 isoform X1

UniProtKB/TrEMBL

D3ZRJ7
XM_039112688.2 → XP_038968616.1 leucine-rich repeat serine/threonine-protein kinase 1 isoform X5

Conserved Domains (3) summary

cd14067
Location:543 → 818

STKc_LRRK1; Catalytic domain of the Serine/Threonine Kinase, Leucine-Rich Repeat Kinase 1

pfam16095
Location:139 → 331

COR; C-terminal of Roc, COR, domain

cl38936
Location:6 → 116

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
XM_063262490.1 → XP_063118560.1 leucine-rich repeat serine/threonine-protein kinase 1 isoform X3
XM_063262498.1 → XP_063118568.1 leucine-rich repeat serine/threonine-protein kinase 1 isoform X4