Ldlr low density lipoprotein receptor [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ldlrprovided by RGD
Official Full Name: low density lipoprotein receptorprovided by RGD
Primary source: RGD:2998
See related: EnsemblRapid:ENSRNOG00000009946 AllianceGenome:RGD:2998
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: LDLRA
Summary: Enables low-density lipoprotein particle receptor activity. Involved in several processes, including cholesterol homeostasis; positive regulation of triglyceride catabolic process; and response to glucagon. Located in caveola and recycling endosome membrane. Used to study atherosclerosis and xanthomatosis. Human ortholog(s) of this gene implicated in Alzheimer's disease; arteriosclerosis; familial hypercholesterolemia; hepatitis C; and migraine without aura. Orthologous to human LDLR (low density lipoprotein receptor). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Liver (RPKM 367.4), Adrenal (RPKM 281.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 8q13

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (28546191..28569075)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (20270020..20292981)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (22750425..22773305)

Chromosome 8 - NC_086026.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Deficiency of either Ldlr or Apoe genes induced hyperlipidemia, which promoted endothelial inflammation and led to typical atherosclerosis in rats on normal or Western diets.
Title: Hyperlipidemia induces typical atherosclerosis development in Ldlr and Apoe deficient rats.
This suggests that overexpression of HNF1alpha gene in liver of lipectomized rats can lead to overproduction of PCSK9. In conclusion, up-regulation of PCSK9, due to overexpression of HNF1alpha gene in liver of lipectomized rats and subsequently increase in circulating PCSK9 concentration lead to decrease in liver LDL-R level.
Title: Up-regulation of PCSK9 gene expression and diminished level of LDL-receptor in rat liver as a potential cause of post-lipectomy hypercholesterolemia.
up-regulation of intestinal gene expression of LDL-R and PCSK9 following voluntary wheel running
Title: Exercise training increased gene expression of LDL-R and PCSK9 in intestine: link to transintestinal cholesterol excretion.
LDLR is a relevant receptor for CNS drug delivery via receptor-mediated transcytosis and that the peptide vectors we developed have the potential to transport drugs
Title: Use of LDL receptor-targeting peptide vectors for in vitro and in vivo cargo transport across the blood-brain barrier.
Intrauterine growth restriction combined with a maternal high-fat diet increases hepatic cholesterol accumulation via increased LDL cholesterol uptake into the liver with resulting persistent increases in hepatic cholesterol accumulation.
Title: Intrauterine growth restriction combined with a maternal high-fat diet increases hepatic cholesterol and low-density lipoprotein receptor activity in rats.
Compared with the cholesterol-enriched restructured pork group, silicon-enriched restructured pork rats had lower VLDL compound concentrations and lower VLDL oxidation but greater Ldlr expression.
Title: Silicon-Enriched Restructured Pork Affects the Lipoprotein Profile, VLDL Oxidation, and LDL Receptor Gene Expression in Aged Rats Fed an Atherogenic Diet.
Gene expression of hepatic LDL-R, Lrp1, Pcsk9, SREBP-2 and HMGCoA-r were reduced (p<0.05) in ovariectomy compared to Sham rats.
Title: LDL receptor and Pcsk9 transcripts are decreased in liver of ovariectomized rats: effects of exercise training.
The LDL receptor could be located at once in clathrin-coated pits and caveolae.
Title: Distribution of the LDL receptor within clathrin-coated pits and caveolae in rat and human liver.
investigated 3-hydroxy 3-methylglutaryl coenzyme A reductase and LDLr in adult (3-month-old) and aged (12-month-old) male and female rats in four different brain regions
Title: Analysis of the protein network of cholesterol homeostasis in different brain regions: an age and sex dependent perspective.
LDLR mutant rats are a useful novel animal model of hypercholesterolemia and atherosclerosis.
Title: Hypercholesterolemia and atherosclerosis in low density lipoprotein receptor mutant rats.

Submit: New GeneRIF Correction See all GeneRIFs (25)

General gene information

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Markers

RH94592 (e-PCR)
- UniSTS:119840

RH94809 (e-PCR)
- UniSTS:120055

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables amyloid-beta binding	IEA Inferred from Electronic Annotation more info
enables amyloid-beta binding	ISO Inferred from Sequence Orthology more info
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables lipoprotein particle binding	IBA Inferred from Biological aspect of Ancestor more info
enables low-density lipoprotein particle binding	IEA Inferred from Electronic Annotation more info
enables low-density lipoprotein particle binding	ISO Inferred from Sequence Orthology more info
enables low-density lipoprotein particle receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables low-density lipoprotein particle receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables low-density lipoprotein particle receptor activity	IEA Inferred from Electronic Annotation more info
enables low-density lipoprotein particle receptor activity	ISO Inferred from Sequence Orthology more info
enables low-density lipoprotein particle receptor activity	TAS Traceable Author Statement more info	PubMed
enables molecular adaptor activity	ISO Inferred from Sequence Orthology more info
enables protease binding	IEA Inferred from Electronic Annotation more info
enables protease binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables very-low-density lipoprotein particle receptor activity	IEA Inferred from Electronic Annotation more info
enables very-low-density lipoprotein particle receptor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in amyloid-beta clearance	ISO Inferred from Sequence Orthology more info
involved_in amyloid-beta clearance by cellular catabolic process	IEA Inferred from Electronic Annotation more info
involved_in amyloid-beta clearance by cellular catabolic process	ISO Inferred from Sequence Orthology more info
involved_in artery morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in artery morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in cellular response to fatty acid	IEA Inferred from Electronic Annotation more info
involved_in cellular response to fatty acid	ISO Inferred from Sequence Orthology more info
involved_in cellular response to low-density lipoprotein particle stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to low-density lipoprotein particle stimulus	ISO Inferred from Sequence Orthology more info
involved_in cholesterol homeostasis	IBA Inferred from Biological aspect of Ancestor more info
involved_in cholesterol homeostasis	IEA Inferred from Electronic Annotation more info
involved_in cholesterol homeostasis	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within cholesterol homeostasis	ISO Inferred from Sequence Orthology more info
involved_in cholesterol homeostasis	ISO Inferred from Sequence Orthology more info
involved_in cholesterol import	IEA Inferred from Electronic Annotation more info
involved_in cholesterol import	ISO Inferred from Sequence Orthology more info
involved_in cholesterol metabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cholesterol metabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cholesterol transport	ISO Inferred from Sequence Orthology more info
involved_in cholesterol transport	ISO Inferred from Sequence Orthology more info
involved_in endocytosis	IEA Inferred from Electronic Annotation more info
involved_in endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within establishment of localization in cell	ISO Inferred from Sequence Orthology more info
involved_in high-density lipoprotein particle clearance	IEA Inferred from Electronic Annotation more info
involved_in high-density lipoprotein particle clearance	ISO Inferred from Sequence Orthology more info
involved_in intestinal cholesterol absorption	IEA Inferred from Electronic Annotation more info
involved_in intestinal cholesterol absorption	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lipid metabolic process	ISO Inferred from Sequence Orthology more info
involved_in lipid transport	IEA Inferred from Electronic Annotation more info
involved_in lipoprotein catabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within lipoprotein catabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lipoprotein metabolic process	ISO Inferred from Sequence Orthology more info
involved_in long-term memory	IEA Inferred from Electronic Annotation more info
involved_in long-term memory	ISO Inferred from Sequence Orthology more info
involved_in low-density lipoprotein particle clearance	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within low-density lipoprotein particle clearance	ISO Inferred from Sequence Orthology more info
involved_in low-density lipoprotein particle clearance	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of amyloid fibril formation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of amyloid fibril formation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of astrocyte activation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of astrocyte activation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of low-density lipoprotein particle clearance	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of low-density lipoprotein particle clearance	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of microglial cell activation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of microglial cell activation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protein metabolic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of receptor recycling	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of receptor recycling	ISO Inferred from Sequence Orthology more info
involved_in phagocytosis	IEA Inferred from Electronic Annotation more info
involved_in phagocytosis	ISO Inferred from Sequence Orthology more info
involved_in phospholipid transport	IEA Inferred from Electronic Annotation more info
involved_in phospholipid transport	ISO Inferred from Sequence Orthology more info
involved_in plasma lipoprotein particle clearance	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of inflammatory response	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of lysosomal protein catabolic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of lysosomal protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of triglyceride biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of triglyceride biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of triglyceride catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in receptor-mediated endocytosis	ISO Inferred from Sequence Orthology more info
involved_in receptor-mediated endocytosis involved in cholesterol transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in receptor-mediated endocytosis involved in cholesterol transport	IEA Inferred from Electronic Annotation more info
involved_in receptor-mediated endocytosis involved in cholesterol transport	ISO Inferred from Sequence Orthology more info
involved_in regulation of cholesterol metabolic process	IEA Inferred from Electronic Annotation more info
involved_in regulation of cholesterol metabolic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of phosphatidylcholine catabolic process	IEA Inferred from Electronic Annotation more info
involved_in regulation of phosphatidylcholine catabolic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein metabolic process	ISO Inferred from Sequence Orthology more info
involved_in response to caloric restriction	IEA Inferred from Electronic Annotation more info
involved_in response to caloric restriction	ISO Inferred from Sequence Orthology more info
involved_in response to estradiol	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to estrogen	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to ethanol	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to glucagon	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to hormone	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to hypoxia	IEP Inferred from Expression Pattern more info	PubMed
involved_in transcytosis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in Golgi apparatus	ISS Inferred from Sequence or Structural Similarity more info
part_of PCSK9-LDLR complex	IEA Inferred from Electronic Annotation more info
part_of PCSK9-LDLR complex	ISO Inferred from Sequence Orthology more info
located_in apical part of cell	IEA Inferred from Electronic Annotation more info
located_in apical part of cell	ISO Inferred from Sequence Orthology more info
located_in basolateral plasma membrane	IEA Inferred from Electronic Annotation more info
located_in basolateral plasma membrane	ISO Inferred from Sequence Orthology more info
located_in caveola	IDA Inferred from Direct Assay more info	PubMed
located_in cell surface	ISO Inferred from Sequence Orthology more info
located_in cell surface	ISS Inferred from Sequence or Structural Similarity more info
located_in clathrin-coated pit	IEA Inferred from Electronic Annotation more info
located_in clathrin-coated pit	ISO Inferred from Sequence Orthology more info
is_active_in early endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in early endosome	IEA Inferred from Electronic Annotation more info
located_in early endosome	ISO Inferred from Sequence Orthology more info
located_in early endosome	ISS Inferred from Sequence or Structural Similarity more info
located_in endosome	ISO Inferred from Sequence Orthology more info
located_in external side of plasma membrane	IEA Inferred from Electronic Annotation more info
located_in external side of plasma membrane	ISO Inferred from Sequence Orthology more info
located_in late endosome	IEA Inferred from Electronic Annotation more info
located_in late endosome	ISO Inferred from Sequence Orthology more info
located_in late endosome	ISS Inferred from Sequence or Structural Similarity more info
part_of low-density lipoprotein particle	IEA Inferred from Electronic Annotation more info
located_in lysosome	IEA Inferred from Electronic Annotation more info
located_in lysosome	ISO Inferred from Sequence Orthology more info
located_in lysosome	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
part_of receptor complex	IEA Inferred from Electronic Annotation more info
part_of receptor complex	ISO Inferred from Sequence Orthology more info
located_in recycling endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in somatodendritic compartment	IEA Inferred from Electronic Annotation more info
located_in somatodendritic compartment	ISO Inferred from Sequence Orthology more info
located_in sorting endosome	IEA Inferred from Electronic Annotation more info
located_in sorting endosome	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: low-density lipoprotein receptor

Names: LDL receptor

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_175762.3 → NP_786938.2 low-density lipoprotein receptor precursor

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000008

UniProtKB/TrEMBL

A6JNU1, G3V7A5

Related

ENSRNOP00000013496.3, ENSRNOT00000013496.5

Conserved Domains (6) summary

smart00179
Location:355 → 389

EGF_CA; Calcium-binding EGF-like domain

cd05819
Location:435 → 469

NHL; NHL repeat [structural motif]

cl18310
Location:435 → 628

NHL; NHL repeat unit of beta-propeller proteins

pfam00057
Location:196 → 232

Ldl_recept_a; Low-density lipoprotein receptor domain class A

pfam00058
Location:529 → 569

Ldl_recept_b; Low-density lipoprotein receptor repeat class B

pfam14670
Location:319 → 353

FXa_inhibition; Coagulation Factor Xa inhibitory site