Ldlr (low density lipoprotein receptor) - Rat Genome Database

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Gene: Ldlr (low density lipoprotein receptor) Rattus norvegicus
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Symbol: Ldlr
Name: low density lipoprotein receptor
RGD ID: 2998
Description: 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 aortic atherosclerosis; atherosclerosis; familial hyperlipidemia; fatty liver disease; 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); PARTICIPATES IN atherosclerosis pathway; bile acid transport pathway; endocytosis pathway; INTERACTS WITH (25R)-cholest-5-ene-3beta,26-diol; 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine; 1-naphthyl isothiocyanate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LDL receptor; LDLRA; low-density lipoprotein receptor
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Ldlrem4Mcwi   Ldlrem3Mcwi   Ldlrem1Mcwi   Ldlrem2Mcwi   Ldlrem1Sage   Ldlrem1   Ldlrem1Dlli  
Genetic Models: SD-Ldlrem1 SD-Ldlrem1Dlli SS-Ldlrem3Mcwi SS-Ldlrem4Mcwi SS-Ldlrem1Mcwi SS-Ldlrem2Mcwi SD-Ldlrem1Sage
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2820,270,020 - 20,292,981 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl820,270,041 - 20,294,580 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx824,305,445 - 24,328,327 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0822,600,993 - 22,623,875 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0820,499,706 - 20,522,587 (+)NCBIRnor_WKY
Rnor_6.0822,750,425 - 22,773,305 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl822,750,336 - 22,774,903 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0822,804,325 - 22,827,199 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4820,824,040 - 20,846,920 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1820,824,039 - 20,846,920 (+)NCBI
Celera821,660,761 - 21,683,616 (+)NCBICelera
RH 3.4 Map8178.16RGD
RH 3.4 Map8178.16RGD
Cytogenetic Map8q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(-)-trans-epsilon-viniferin  (ISO)
(25R)-cholest-5-ene-3beta,26-diol  (EXP,ISO)
(2R,4R)-1-[(2S)-5-(diaminomethylideneamino)-2-[(3-methyl-1,2,3,4-tetrahydroquinolin-8-yl)sulfonylamino]-1-oxopentyl]-4-methyl-2-piperidinecarboxylic acid  (ISO)
(S)-nicotine  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine  (EXP)
1-naphthyl isothiocyanate  (EXP)
11-dehydro-thromboxane B2  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-bromohexadecanoic acid  (ISO)
2-butoxyethanol  (ISO)
2-methylcholine  (ISO)
22-Hydroxycholesterol  (ISO)
25-hydroxycholesterol  (ISO)
26-hydroxycholesterol  (EXP,ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3,3',5-triiodo-L-thyronine  (EXP,ISO)
3-chloropropane-1,2-diol  (EXP)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxy-TEMPO  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acetamide  (EXP)
acetylsalicylic acid  (ISO)
acrolein  (ISO)
acrylamide  (ISO)
actinomycin D  (ISO)
aflatoxin B1  (ISO)
albuterol  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amiodarone  (EXP,ISO)
ammonium chloride  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
arachidonic acid  (ISO)
Archazolid B  (ISO)
argatroban  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atazanavir sulfate  (ISO)
atorvastatin calcium  (EXP,ISO)
atrazine  (ISO)
avobenzone  (ISO)
Azaspiracid  (ISO)
azoxystrobin  (ISO)
bathocuproine disulfonic acid  (ISO)
benzalkonium chloride  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
berberine  (EXP,ISO)
bicalutamide  (ISO)
bifenthrin  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
butan-1-ol  (ISO)
Butylbenzyl phthalate  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP)
caffeine  (EXP,ISO)
calcitriol  (ISO)
captan  (ISO)
carbamazepine  (ISO)
carbofuran  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
celastrol  (ISO)
chenodeoxycholic acid  (ISO)
chlordecone  (ISO)
chloroquine  (ISO)
chlorpromazine  (ISO)
cholesterol  (EXP,ISO)
cholic acid  (EXP)
choline  (ISO)
chromium(6+)  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clofibrate  (EXP)
clozapine  (ISO)
cobalt dichloride  (ISO)
colesevelam hydrochloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
cortisol  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
crocin-1  (EXP)
curcumin  (ISO)
cycloheximide  (ISO)
cyclosporin A  (ISO)
cyproconazole  (ISO)
D-glucose  (ISO)
DDE  (EXP)
deoxycholic acid  (ISO)
desmosterol  (ISO)
desogestrel  (ISO)
dexamethasone  (EXP,ISO)
Di-n-hexyl phthalate  (EXP)
diazinon  (EXP)
dibenzo[a,l]pyrene  (ISO)
dibutyl phthalate  (EXP,ISO)
dicrotophos  (ISO)
Dicyclohexyl phthalate  (EXP)
dieldrin  (ISO)
diethyl maleate  (EXP)
diisobutyl phthalate  (EXP)
diisononyl phthalate  (EXP)
dimethylarsinic acid  (ISO)
dinophysistoxin 1  (ISO)
dioxygen  (EXP)
dipentyl phthalate  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (EXP)
endosulfan  (EXP)
Enterolactone  (ISO)
epoxiconazole  (EXP,ISO)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
ezetimibe  (ISO)
fenthion  (ISO)
flufenamic acid  (ISO)
fluoranthene  (ISO)
flusilazole  (ISO)
flutamide  (EXP)
fluvastatin  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
gallic acid  (ISO)
Ganoderic acid A  (ISO)
gedunin  (ISO)
genistein  (ISO)
geraniol  (ISO)
Ginsenoside Rh4  (ISO)
glucose  (ISO)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
graphene oxide  (ISO)
GW 3965  (ISO)
haloperidol  (ISO)
hexaconazole  (ISO)
hexadecanoic acid  (ISO)
hydrazine  (ISO)
hydrogen peroxide  (ISO)
ibuprofen  (ISO)
indometacin  (ISO)
isobutanol  (ISO)
isoflavones  (ISO)
isotretinoin  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lead diacetate  (EXP,ISO)
lead(0)  (EXP)
lead(2+)  (EXP)
leflunomide  (ISO)
levonorgestrel  (ISO)
lipopolysaccharide  (EXP,ISO)
lithocholic acid  (ISO)
lovastatin  (EXP,ISO)
lycopene  (ISO)
menadione  (ISO)
metformin  (ISO)
methyl methanesulfonate  (ISO)
methylarsonic acid  (ISO)
methylmercury chloride  (ISO)
microcystin-LR  (ISO)
mifepristone  (ISO)
mitogen  (ISO)
monocrotophos  (EXP)
monosodium L-glutamate  (ISO)
N-desethylamiodarone  (ISO)
nefazodone  (ISO)
nickel atom  (ISO)
nickel dichloride  (ISO)
nicotine  (ISO)
obeticholic acid  (ISO)
okadaic acid  (ISO)
olanzapine  (ISO)
oleic acid  (ISO)
ozone  (EXP,ISO)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
permethrin  (EXP)
Phenelzine  (ISO)
phenobarbital  (ISO)
phenylephrine  (EXP)
phenylmercury acetate  (ISO)
phenylpropanolamine  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
phosgene  (ISO)
pioglitazone  (ISO)
pirinixic acid  (EXP,ISO)
piroxicam  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
pravastatin  (ISO)
proanthocyanidin  (EXP)
progesterone  (EXP,ISO)
pterostilbene  (ISO)
puerarin  (EXP)
puromycin  (ISO)
quercetin  (ISO)
quercetin 3-O-beta-D-glucofuranoside  (ISO)
quercetin 3-O-beta-D-glucopyranoside  (ISO)
raloxifene  (ISO)
rebaudioside A  (ISO)
resveratrol  (EXP,ISO)
rifampicin  (ISO)
risperidone  (ISO)
rotenone  (EXP)
rottlerin  (EXP)
SB 431542  (ISO)
selenium atom  (EXP)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (EXP,ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sotorasib  (ISO)
steviol  (ISO)
stevioside  (ISO)
streptozocin  (ISO)
sucrose  (EXP)
sulindac sulfide  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (ISO)
thapsigargin  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trametinib  (ISO)
triadimefon  (ISO)
trichloroethene  (EXP)
triphenyl phosphate  (ISO)
triphenylstannane  (EXP)
triptonide  (ISO)
tris(2-chloroethyl) phosphate  (ISO)
troglitazone  (ISO)
trovafloxacin  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
Yessotoxin  (ISO)
zearalenone  (EXP,ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
aging  (IEP)
amyloid-beta clearance  (ISO)
amyloid-beta clearance by cellular catabolic process  (ISO)
artery morphogenesis  (ISO)
cellular response to fatty acid  (ISO)
cellular response to low-density lipoprotein particle stimulus  (ISO)
cholesterol homeostasis  (IBA,IEP,ISO)
cholesterol import  (ISO)
cholesterol metabolic process  (ISO)
cholesterol transport  (ISO)
endocytosis  (IEA,IMP,ISO)
establishment of localization in cell  (ISO)
high-density lipoprotein particle clearance  (ISO)
intestinal cholesterol absorption  (ISO)
lipid metabolic process  (ISO)
lipoprotein catabolic process  (ISO)
lipoprotein metabolic process  (ISO)
long-term memory  (ISO)
low-density lipoprotein particle clearance  (ISO)
negative regulation of amyloid fibril formation  (ISO)
negative regulation of astrocyte activation  (ISO)
negative regulation of gene expression  (ISO)
negative regulation of low-density lipoprotein particle clearance  (ISO)
negative regulation of microglial cell activation  (ISO)
negative regulation of protein metabolic process  (ISO)
negative regulation of receptor recycling  (ISO)
phagocytosis  (ISO)
phospholipid transport  (ISO)
plasma lipoprotein particle clearance  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of inflammatory response  (ISO)
positive regulation of lysosomal protein catabolic process  (ISO)
positive regulation of triglyceride biosynthetic process  (ISO)
positive regulation of triglyceride catabolic process  (IMP)
receptor-mediated endocytosis  (IBA,ISO)
receptor-mediated endocytosis involved in cholesterol transport  (IBA,ISO)
regulation of cholesterol metabolic process  (ISO)
regulation of phosphatidylcholine catabolic process  (ISO)
regulation of protein metabolic process  (ISO)
response to caloric restriction  (ISO)
response to estradiol  (IEP)
response to estrogen  (IEP)
response to ethanol  (IEP)
response to glucagon  (IEP)
response to hormone  (IEP)
response to hypoxia  (IEP)
transcytosis  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Mutations in PCSK9 cause autosomal dominant hypercholesterolemia. Abifadel M, etal., Nat Genet. 2003 Jun;34(2):154-6.
2. Hypercholesterolemia and atherosclerosis in low density lipoprotein receptor mutant rats. Asahina M, etal., Biochem Biophys Res Commun. 2012 Feb 17;418(3):553-8. doi: 10.1016/j.bbrc.2012.01.067. Epub 2012 Jan 24.
3. The genetic association database. Becker KG, etal., Nat Genet. 2004 May;36(5):431-2.
4. The LDLR locus in Alzheimer's disease: a family-based study and meta-analysis of case-control data. Bertram L, etal., Neurobiol Aging. 2007 Jan;28(1):18.e1-4. Epub 2005 Dec 27.
5. Structure of the hamster low density lipoprotein receptor gene. Bishop RW J Lipid Res 1992 Apr;33(4):549-57.
6. Development of the ACTH and corticosterone response to acute hypoxia in the neonatal rat. Bruder ED, etal., Am J Physiol Regul Integr Comp Physiol. 2008 Oct;295(4):R1195-203. Epub 2008 Aug 13.
7. Functional interaction between APOE4 and LDL receptor isoforms in Alzheimer's disease. Cheng D, etal., J Med Genet. 2005 Feb;42(2):129-31.
8. Characterization of the estrogen-induced lipoprotein receptor of rat liver. Cooper AD, etal., J Lipid Res. 1987 Jan;28(1):59-68.
9. 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.
10. Low-density lipoprotein receptor structure and folding. Gent J and Braakman I, Cell Mol Life Sci. 2004 Oct;61(19-20):2461-70.
11. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
12. Genetic association of low density lipoprotein receptor and Alzheimer's disease. Gopalraj RK, etal., Neurobiol Aging. 2005 Jan;26(1):1-7.
13. Different expression of low density lipoprotein receptor and ApoE between young adult and old rat brains after ischemia. Hayashi T, etal., Neurol Res. 2006 Dec;28(8):822-5.
14. Association of low-density lipoprotein receptor polymorphisms and outcome of hepatitis C infection. Hennig BJ, etal., Genes Immun. 2002 Sep;3(6):359-67.
15. Lack of LDL receptor enhances amyloid deposition and decreases glial response in an Alzheimer's disease mouse model. Katsouri L and Georgopoulos S, PLoS One. 2011;6(7):e21880. Epub 2011 Jul 6.
16. Low-density lipoprotein receptor-mediated endocytosis of PEGylated nanoparticles in rat brain endothelial cells. Kim HR, etal., Cell Mol Life Sci. 2007 Feb;64(3):356-64.
17. Dietary isoflavones reduce plasma cholesterol and atherosclerosis in C57BL/6 mice but not LDL receptor-deficient mice. Kirk EA, etal., J Nutr. 1998 Jun;128(6):954-9.
18. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
19. Genetic study evaluating LDLR polymorphisms and Alzheimer's disease. Lamsa R, etal., Neurobiol Aging. 2008 Jun;29(6):848-55. Epub 2007 Jan 18.
20. Genetic polymorphisms of low density lipoprotein receptor can modify stroke presentation. Lee JD, etal., Neurol Res. 2010 Jun;32(5):535-40. Epub 2009 Jul 8.
21. Nucleotide sequence of the rat low density lipoprotein receptor cDNA. Lee LY, etal., Nucleic Acids Res 1989 Feb 11;17(3):1259-60.
22. Activation of the hepatic LDL receptor promoter by thyroid hormone. Lopez D, etal., Biochim Biophys Acta. 2007 Sep;1771(9):1216-25. Epub 2007 May 21.
23. The expression of native and oxidized LDL receptors in brain microvessels is specifically enhanced by astrocytes-derived soluble factor(s). Lucarelli M, etal., FEBS Lett 2002 Jul 3;522(1-3):19-23.
24. Harmful effects of increased LDLR expression in mice with human APOE*4 but not APOE*3. Malloy SI, etal., Arterioscler Thromb Vasc Biol. 2004 Jan;24(1):91-7. Epub 2003 Sep 11.
25. A common Lithuanian mutation causing familial hypercholesterolemia in Ashkenazi Jews. Meiner V, etal., Am J Hum Genet. 1991 Aug;49(2):443-9.
26. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
27. Investigation of an LDLR gene polymorphism (19p13.2) in susceptibility to migraine without aura. Mochi M, etal., J Neurol Sci. 2003 Sep 15;213(1-2):7-10.
28. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
29. Association of the low-density lipoprotein receptor with caveolae in hamster and rat liver. Ness GC, etal., Biochem Biophys Res Commun 2003 Mar 28;303(1):177-81.
30. Diabetes alters LDL receptor and PCSK9 expression in rat liver. Niesen M, etal., Arch Biochem Biophys. 2008 Feb 15;470(2):111-5. Epub 2007 Nov 22.
31. Genomic characterization of five deletions in the LDL receptor gene in Danish Familial Hypercholesterolemic subjects. Nissen PH, etal., BMC Med Genet. 2006 Jun 26;7:55.
32. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
33. Modified HMG-CoA reductase and LDLr regulation is deeply involved in age-related hypercholesterolemia. Pallottini V, etal., J Cell Biochem. 2006 Aug 1;98(5):1044-53.
34. Importance of proprotein convertase subtilisin/kexin type 9 in the hormonal and dietary regulation of rat liver low-density lipoprotein receptors. Persson L, etal., Endocrinology. 2009 Mar;150(3):1140-6. Epub 2008 Nov 13.
35. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
36. Influence of low-density lipoprotein (LDL) receptor on lipid composition, inflammation and parasitism during Toxoplasma gondii infection. Portugal LR, etal., Microbes Infect. 2008 Mar;10(3):276-84. Epub 2007 Dec 8.
37. GOA pipeline RGD automated data pipeline
38. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
39. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
40. Decreased transcription, expression and function of low-density lipoprotein receptor in leukocytes from patients with systemic lupus erythematosus. Rivas L, etal., Autoimmunity. 2009 May;42(4):266-8.
41. No association between low density lipoprotein receptor genetic variants and Alzheimer's disease risk. Rodriguez E, etal., Am J Med Genet B Neuropsychiatr Genet. 2006 Jul 5;141B(5):541-3.
42. Atherogenesis and metabolic dysregulation in LDL receptor-knockout rats. Sithu SD, etal., JCI Insight. 2017 May 4;2(9). pii: 86442. doi: 10.1172/jci.insight.86442.
43. The low-density lipoprotein receptor is regulated by estrogen and forms a functional complex with the estrogen-regulated protein ezrin in pituitary GH3 somatolactotropes. Smith PM, etal., Endocrinology. 2004 Jul;145(7):3075-83. Epub 2004 Mar 24.
44. Mechanisms of disease: genetic causes of familial hypercholesterolemia. Soutar AK and Naoumova RP, Nat Clin Pract Cardiovasc Med. 2007 Apr;4(4):214-25.
45. A tubular endosomal fraction from rat liver: biochemical evidence of receptor sorting by default. Verges M, etal., Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):10146-51.
46. Combined effects of apoE-CI-CII cluster and LDL-R gene polymorphisms on chromosome 19 and coronary artery disease risk. Wang C, etal., Int J Hyg Environ Health. 2006 May;209(3):265-73. Epub 2006 Feb 3.
47. A lipidomics study reveals hepatic lipid signatures associating with deficiency of the LDL receptor in a rat model. Wang HY, etal., Biol Open. 2016 Jul 15;5(7):979-86. doi: 10.1242/bio.019802.
48. Chronic alcohol consumption disrupted cholesterol homeostasis in rats: down-regulation of low-density lipoprotein receptor and enhancement of cholesterol biosynthesis pathway in the liver. Wang Z, etal., Alcohol Clin Exp Res. 2010 Mar 1;34(3):471-8. doi: 10.1111/j.1530-0277.2009.01111.x. Epub 2009 Dec 18.
49. Inflammatory stress exacerbates lipid-mediated renal injury in ApoE/CD36/SRA triple knockout mice. Xu ZE, etal., Am J Physiol Renal Physiol. 2011 Oct;301(4):F713-22. doi: 10.1152/ajprenal.00341.2010. Epub 2011 Jul 27.
50. Hyperlipidemia induces typical atherosclerosis development in Ldlr and Apoe deficient rats. Zhao Y, etal., Atherosclerosis. 2018 Apr;271:26-35. doi: 10.1016/j.atherosclerosis.2018.02.015. Epub 2018 Feb 12.
Additional References at PubMed
PMID:6091915   PMID:6299582   PMID:7848292   PMID:8626535   PMID:9788969   PMID:11092755   PMID:11120757   PMID:12072432   PMID:12746448   PMID:13130124   PMID:15140193   PMID:15166224  
PMID:15741654   PMID:15805190   PMID:16166565   PMID:16647292   PMID:17071966   PMID:17110914   PMID:17142622   PMID:17148552   PMID:17203467   PMID:17461796   PMID:17674160   PMID:17905649  
PMID:18175806   PMID:18341993   PMID:19946888   PMID:20005821   PMID:20458492   PMID:21763412   PMID:21792919   PMID:22081141   PMID:22383525   PMID:22848640   PMID:22927332   PMID:23280554  
PMID:23382219   PMID:23580231   PMID:24006456   PMID:24255059   PMID:24412220   PMID:24530906   PMID:24619822   PMID:25524771   PMID:26246324   PMID:26526611   PMID:26965651   PMID:27401460  
PMID:28108572   PMID:29938676   PMID:30483910  


Genomics

Comparative Map Data
Ldlr
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2820,270,020 - 20,292,981 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl820,270,041 - 20,294,580 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx824,305,445 - 24,328,327 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0822,600,993 - 22,623,875 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0820,499,706 - 20,522,587 (+)NCBIRnor_WKY
Rnor_6.0822,750,425 - 22,773,305 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl822,750,336 - 22,774,903 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0822,804,325 - 22,827,199 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4820,824,040 - 20,846,920 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1820,824,039 - 20,846,920 (+)NCBI
Celera821,660,761 - 21,683,616 (+)NCBICelera
RH 3.4 Map8178.16RGD
RH 3.4 Map8178.16RGD
Cytogenetic Map8q13NCBI
LDLR
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381911,089,463 - 11,133,820 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1911,089,462 - 11,133,820 (+)EnsemblGRCh38hg38GRCh38
GRCh371911,200,139 - 11,244,496 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361911,061,132 - 11,105,490 (+)NCBINCBI36Build 36hg18NCBI36
Build 341911,061,131 - 11,105,490NCBI
Celera1911,094,887 - 11,139,322 (+)NCBICelera
Cytogenetic Map19p13.2NCBI
HuRef1910,777,128 - 10,820,847 (+)NCBIHuRef
CHM1_11911,201,264 - 11,245,760 (+)NCBICHM1_1
T2T-CHM13v2.01911,216,460 - 11,260,830 (+)NCBIT2T-CHM13v2.0
Ldlr
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39921,634,872 - 21,661,215 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl921,634,779 - 21,661,215 (+)EnsemblGRCm39 Ensembl
GRCm38921,723,576 - 21,749,919 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl921,723,483 - 21,749,919 (+)EnsemblGRCm38mm10GRCm38
MGSCv37921,528,038 - 21,554,363 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36921,474,180 - 21,498,819 (+)NCBIMGSCv36mm8
Celera918,993,187 - 19,019,513 (+)NCBICelera
Cytogenetic Map9A3NCBI
cM Map97.87NCBI
Ldlr
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554952,114,434 - 2,138,056 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554952,114,702 - 2,135,584 (+)NCBIChiLan1.0ChiLan1.0
LDLR
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11911,357,311 - 11,402,736 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1911,357,311 - 11,396,791 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01910,640,225 - 10,683,728 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LDLR
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12050,115,175 - 50,152,443 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2050,048,736 - 50,152,355 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2049,988,705 - 50,026,032 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02050,636,154 - 50,673,474 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2050,636,157 - 50,673,423 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12049,846,492 - 49,883,796 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02050,273,144 - 50,310,479 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02050,515,859 - 50,553,174 (-)NCBIUU_Cfam_GSD_1.0
Ldlr
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118209,054,161 - 209,095,215 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366591,259,369 - 1,302,294 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049366591,259,405 - 1,300,545 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LDLR
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl269,828,332 - 69,864,827 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1269,828,348 - 69,864,823 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2270,193,426 - 70,206,818 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LDLR
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1610,062,204 - 10,091,780 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl610,062,790 - 10,091,377 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660749,815,946 - 9,867,321 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ldlr
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248282,999,169 - 3,021,987 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248282,999,122 - 3,021,893 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ldlr
151 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:220
Count of miRNA genes:154
Interacting mature miRNAs:170
Transcripts:ENSRNOT00000013496
Prediction methods:Microtar, Miranda, 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
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8767057852670578Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)8768895552688955Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8768895552688955Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)8873663553736635Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)8873663553736635Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)8971222053356647Rat
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81490675159906751Rat
61373Mcs4Mammary carcinoma susceptibility QTL 41.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)81629044461290444Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)81898416884531599Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat

Markers in Region
RH94592  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2820,292,786 - 20,292,978 (+)MAPPERmRatBN7.2
Rnor_6.0822,773,111 - 22,773,302NCBIRnor6.0
Rnor_5.0822,827,005 - 22,827,196UniSTSRnor5.0
RGSC_v3.4820,846,726 - 20,846,917UniSTSRGSC3.4
Celera821,683,422 - 21,683,613UniSTS
Cytogenetic Map8q13UniSTS
RH94809  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2820,269,978 - 20,270,230 (+)MAPPERmRatBN7.2
Rnor_6.0822,750,308 - 22,750,559NCBIRnor6.0
Rnor_5.0822,804,208 - 22,804,459UniSTSRnor5.0
RGSC_v3.4820,823,923 - 20,824,174UniSTSRGSC3.4
Celera821,660,644 - 21,660,895UniSTS
RH 3.4 Map8178.16UniSTS
Cytogenetic Map8q13UniSTS


Genetic Models

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 3 22 50 41 9 41 4 7 74 34 33 11 4
Low 21 7 10 4 4 1 8 4
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000013496   ⟹   ENSRNOP00000013496
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl820,270,041 - 20,294,580 (+)Ensembl
Rnor_6.0 Ensembl822,750,336 - 22,774,903 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000108195   ⟹   ENSRNOP00000080955
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl820,277,217 - 20,294,580 (+)Ensembl
RefSeq Acc Id: NM_175762   ⟹   NP_786938
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2820,270,096 - 20,292,981 (+)NCBI
Rnor_6.0822,750,425 - 22,773,305 (+)NCBI
Rnor_5.0822,804,325 - 22,827,199 (+)NCBI
RGSC_v3.4820,824,040 - 20,846,920 (+)RGD
Celera821,660,761 - 21,683,616 (+)RGD
Sequence:
RefSeq Acc Id: XM_039080999   ⟹   XP_038936927
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2820,270,020 - 20,291,828 (+)NCBI
Protein Sequences
Protein RefSeqs NP_786938 (Get FASTA)   NCBI Sequence Viewer  
  XP_038936927 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA32001 (Get FASTA)   NCBI Sequence Viewer  
  P35952 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_786938   ⟸   NM_175762
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000013496   ⟸   ENSRNOT00000013496
RefSeq Acc Id: XP_038936927   ⟸   XM_039080999
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000080955   ⟸   ENSRNOT00000108195
Protein Domains
EGF-like   LDL-receptor class A

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P35952-F1-model_v2 AlphaFold P35952 1-879 view protein structure

Transcriptome

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

Promoters
RGD ID:13695786
Promoter ID:EPDNEW_R6311
Type:initiation region
Name:Ldlr_1
Description:low density lipoprotein receptor
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_6.0822,750,416 - 22,750,476EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2998 AgrOrtholog
BioCyc Gene G2FUF-31411 BioCyc
Ensembl Genes ENSRNOG00000009946 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000013496 ENTREZGENE
  ENSRNOP00000013496.3 UniProtKB/TrEMBL
  ENSRNOP00000080955.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013496 ENTREZGENE
  ENSRNOT00000013496.4 UniProtKB/TrEMBL
  ENSRNOT00000108195.1 UniProtKB/TrEMBL
Gene3D-CATH 2.120.10.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  4.10.400.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro 6-blade_b-propeller_TolB-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-like_Ca-bd_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-type_Asp/Asn_hydroxyl_site UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_Ca-bd_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Growth_fac_rcpt_cys_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LDL_receptor-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LDLR_class-A_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LDLR_classB_rpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LDrepeatLR_classA_rpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:300438 UniProtKB/Swiss-Prot
NCBI Gene 300438 ENTREZGENE
Pfam EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ldl_recept_a UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ldl_recept_b UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB LDLR RGD
PhenoGen Ldlr PhenoGen
PRINTS LDLRECEPTOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE ASX_HYDROXYL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LDLRA_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LDLRA_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LDLRB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LDLa UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00135 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF57184 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF57424 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I5ZRX1_RAT UniProtKB/TrEMBL
  G3V7A5_RAT UniProtKB/TrEMBL
  LDLR_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Ldlr  Low density lipoprotein receptor      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization mainly located in caveolae in liver 1298981
gene_expression expressed in both brain microvessel endothelial cells and in astrocytes 633388
gene_regulation expression is upregulated in brain microvessel endothelial cells by co-cultivation with astrocytes 633388