Vdr (vitamin D receptor) - Rat Genome Database

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Gene: Vdr (vitamin D receptor) Rattus norvegicus
Analyze
Symbol: Vdr
Name: vitamin D receptor
RGD ID: 3959
Description: Exhibits calcitriol binding activity; nuclear receptor activity; and sequence-specific DNA binding activity. Is predicted to contribute to DNA-binding transcription factor activity and vitamin D response element binding activity. Involved in several processes, including cellular response to amyloid-beta; cellular response to vitamin D; and response to estradiol. Localizes to several cellular components, including T-tubule; chromatin; and nuclear lumen. Colocalizes with caveola. Biomarker of secondary hyperparathyroidism. Human ortholog(s) of this gene implicated in several diseases, including autoimmune disease (multiple); carcinoma (multiple); lipid storage disease (multiple); melanoma (multiple); and tuberculosis (multiple). Orthologous to human VDR (vitamin D receptor); PARTICIPATES IN altered p53 signaling pathway; tuberculosis pathway; INTERACTS WITH (+)-pilocarpine; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 1,25-dihydroxyvitamin D3 receptor; Nr1i1; nuclear receptor subfamily 1 group I member 1; vitamin D (1,25- dihydroxyvitamin D3) receptor; Vitamin D (1,25-dihydroxyvitamin D3) receptor; Vitamin D (125-dihydroxyvitamin D3) receptor; vitamin D3 receptor
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Vdrem1Thka   Vdrem2Thka  
Genetic Models: W-Vdrem1Thka W-Vdrem2Thka
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27128,987,981 - 129,037,677 (-)NCBI
Rnor_6.0 Ensembl7139,342,063 - 139,394,166 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07139,344,452 - 139,394,138 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07139,536,241 - 139,585,928 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47136,567,614 - 136,617,280 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17136,644,050 - 136,693,717 (-)NCBI
Celera7125,479,125 - 125,528,679 (-)NCBICelera
Cytogenetic Map7q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acquired immunodeficiency syndrome  (ISO)
Acute Hepatitis  (ISO)
Addison's disease  (ISO)
alopecia  (ISO)
amyotrophic lateral sclerosis  (ISO)
aortic valve stenosis  (ISO)
asthma  (ISO)
atherosclerosis  (ISO)
atopic dermatitis  (ISO)
autism spectrum disorder  (ISO)
autoimmune hepatitis  (ISO)
autosomal recessive limb-girdle muscular dystrophy type 2B  (ISO)
B-Cell Chronic Lymphocytic Leukemia  (ISO)
Barrett's esophagus  (ISO)
basal cell carcinoma  (ISO)
Behcet's disease  (ISO)
breast cancer  (ISO)
Breast Neoplasms  (ISO)
Bronchopulmonary Dysplasia  (ISO)
cholangitis  (ISO)
Chronic Hepatitis C  (ISO)
Chronic Periodontitis  (ISO)
coronary artery disease  (ISO)
Crohn's disease  (ISO)
diabetes mellitus  (ISO)
diabetic retinopathy  (ISO)
disease of cellular proliferation  (ISO)
Dwarfism  (ISO)
erythema nodosum  (ISO)
esophagus adenocarcinoma  (ISO)
Experimental Autoimmune Encephalomyelitis  (ISO)
Fabry disease  (ISO)
Familial Hypophosphatemic Rickets  (ISO)
fatty liver disease  (ISO)
Fetal Growth Retardation  (ISO)
genetic disease  (ISO)
Graves' disease  (ISO)
hepatitis B  (ISO)
hepatocellular carcinoma  (ISO)
human immunodeficiency virus infectious disease  (ISO)
Hypercalciuria  (IEP)
hypertension  (ISO)
Hypophosphatemic Rickets  (ISO)
Inflammation  (ISO)
Insulin Resistance  (ISO)
Intervertebral Disc Displacement  (ISO)
Knee Osteoarthritis  (ISO)
Lead Poisoning  (ISO)
leishmaniasis  (ISO)
lepromatous leprosy  (ISO)
liver cirrhosis  (ISO)
male breast cancer  (ISO)
Mammary Neoplasms, Experimental  (ISO)
melanoma  (ISO)
multiple sclerosis  (ISO)
Myocardial Reperfusion Injury  (ISO)
myopia  (ISO)
Neoplasm Metastasis  (ISO)
non-alcoholic fatty liver disease  (ISO)
obesity  (ISO)
osteoporosis  (ISO,ISS)
otosclerosis  (ISO)
Parathyroid Neoplasms  (ISO)
Parkinson's disease  (ISO)
peptic esophagitis  (ISO)
periodontitis  (ISO)
pneumonia  (ISO)
polycystic ovary syndrome  (ISO)
Postmenopausal Osteoporosis  (ISO)
primary biliary cholangitis  (ISO)
primary hyperparathyroidism  (ISO)
primary sclerosing cholangitis  (ISO)
prostate cancer  (ISO)
Prostatic Neoplasms  (ISO)
psoriasis  (ISO)
pulmonary tuberculosis  (ISO)
renal cell carcinoma  (ISO)
rheumatoid arthritis  (ISO)
rickets  (ISO)
secondary hyperparathyroidism  (IEP)
skin melanoma  (ISO)
Spinal Fractures  (ISO)
squamous cell carcinoma  (ISO)
Sunburn  (ISO)
Systemic Inflammatory Response Syndrome  (ISO)
temporal lobe epilepsy  (ISO)
transitional cell carcinoma  (ISO)
tuberculoid leprosy  (ISO)
tuberculosis  (ISO)
Turner syndrome  (ISO)
type 1 diabetes mellitus  (ISO)
type 2 diabetes mellitus  (ISO)
uremia  (ISO)
Urinary Calculi  (ISO)
Viral Bronchiolitis  (ISO)
Vitamin D Deficiency  (ISO)
vitamin D-dependent rickets  (ISO)
vitamin D-dependent rickets type 2A  (IMP,ISO)
vitiligo  (ISO)
Weight Gain  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(R)-noradrenaline  (ISO)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
24,25-Dihydroxyvitamin D  (ISO)
3,7-dihydropurine-6-thione  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (EXP,ISO)
3-methoxytyramine  (ISO)
3-oxo-5beta-cholanic acid  (ISO)
3-phenoxybenzoic acid  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
8-Br-cAMP  (ISO)
9-cis-retinoic acid  (ISO)
acetylsalicylic acid  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucose  (EXP)
alendronic acid  (ISO)
alfacalcidol  (ISO)
all-trans-retinoic acid  (ISO)
alpha-linolenic acid  (ISO)
alpha-naphthoflavone  (ISO)
ammonium chloride  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antirheumatic drug  (ISO)
arsenite(3-)  (ISO)
bafilomycin A1  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
bezafibrate  (ISO)
biphenyl-2-ol  (ISO)
bisdemethoxycurcumin  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
cadmium dichloride  (ISO)
calcidiol  (ISO)
calciol  (EXP,ISO)
calcipotriol  (ISO)
calcitriol  (EXP,ISO)
calcium atom  (EXP,ISO)
calcium(0)  (EXP,ISO)
captopril  (ISO)
carbon nanotube  (ISO)
carnosic acid  (ISO)
cefalotin  (ISO)
chenodeoxycholic acid  (EXP,ISO)
chloroacetaldehyde  (ISO)
cholanic acid  (ISO)
cholesterol  (ISO)
cholic acid  (ISO)
chromium(6+)  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
copper(II) sulfate  (ISO)
curcumin  (ISO)
cyclophosphamide  (EXP)
cyclosporin A  (ISO)
cytarabine  (ISO)
D-glucose  (EXP)
daunorubicin  (ISO)
desferrioxamine B  (ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
dimethylarsinic acid  (EXP)
dioxygen  (ISO)
disodium selenite  (ISO)
dopamine  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (ISO)
entinostat  (ISO)
estriol  (ISO)
etoposide  (ISO)
eugenol  (ISO)
Falecalcitriol  (ISO)
fenvalerate  (EXP)
flucythrinate  (ISO)
folic acid  (ISO)
fulvestrant  (ISO)
gamma-tocopherol  (ISO)
genistein  (ISO)
glucose  (EXP)
glycitein  (ISO)
Goe 6976  (ISO)
guggulsterone  (ISO)
GW 501516  (ISO)
hexachlorobenzene  (ISO)
homovanillic acid  (ISO)
idarubicin  (ISO)
iron atom  (ISO)
iron(0)  (ISO)
isopentenyl diphosphate  (ISO)
kaempferol  (ISO)
ketoconazole  (ISO)
lacidipine  (ISO)
lactacystin  (ISO)
lamivudine  (ISO)
lead diacetate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
levonorgestrel  (ISO)
lipopolysaccharide  (EXP,ISO)
lithocholic acid  (EXP,ISO)
LY294002  (ISO)
manidipine  (ISO)
Maxacalcitol  (ISO)
medroxyprogesterone acetate  (ISO)
mercaptopurine  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
methotrexate  (ISO)
methoxsalen  (ISO)
methyl beta-cyclodextrin  (ISO)
methylseleninic acid  (ISO)
N-nitrosodiethylamine  (ISO)
neomycin  (ISO)
nickel atom  (ISO)
nickel sulfate  (ISO)
O-methyleugenol  (ISO)
okadaic acid  (ISO)
paracetamol  (ISO)
paricalcitol  (ISO)
pentanal  (ISO)
phenobarbital  (EXP)
phenothrin  (ISO)
phorbol 13-acetate 12-myristate  (EXP,ISO)
phosphorus atom  (ISO)
phosphorus(.)  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
prednisone  (ISO)
promegestone  (ISO)
propanal  (ISO)
purine-6-thiol  (ISO)
pyridaben  (ISO)
quercetin  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
sodium atom  (ISO)
staurosporine  (ISO)
streptozocin  (EXP)
sunitinib  (ISO)
superoxide  (ISO)
suramin  (ISO)
tamoxifen  (EXP,ISO)
terbufos  (ISO)
tetrachloromethane  (EXP)
titanium dioxide  (ISO)
tocopherol  (ISO)
tributylstannane  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
uranium atom  (EXP)
valproic acid  (ISO)
vincristine  (ISO)
vitamin D  (EXP,ISO)
warfarin  (ISO)
zidovudine  (ISO)
zinc atom  (ISO)
zinc protoporphyrin  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
aging  (IEP)
animal organ morphogenesis  (ISO)
apoptotic signaling pathway  (IDA)
bile acid signaling pathway  (ISO)
calcium ion transport  (IEA,ISO)
cell differentiation  (IBA)
cell morphogenesis  (ISO)
cellular calcium ion homeostasis  (IEA,ISO)
cellular response to amyloid-beta  (IEP)
cellular response to vitamin D  (IEP)
decidualization  (ISO)
heart development  (IEP)
intestinal absorption  (IEA,ISO)
intracellular receptor signaling pathway  (IEA)
lactation  (IEA,ISO)
mammary gland branching involved in pregnancy  (IEA,ISO)
multicellular organism development  (IBA,ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of gene expression  (ISO)
negative regulation of keratinocyte proliferation  (ISO)
negative regulation of transcription by RNA polymerase II  (IBA,ISO)
negative regulation of transcription, DNA-templated  (ISO)
positive regulation of apoptotic process involved in mammary gland involution  (IEA,ISO)
positive regulation of gene expression  (ISO)
positive regulation of keratinocyte differentiation  (ISO)
positive regulation of transcription by RNA polymerase II  (IBA,ISO)
positive regulation of vitamin D 24-hydroxylase activity  (ISO)
regulation of calcidiol 1-monooxygenase activity  (IEA,ISO)
regulation of calcium ion transport  (IDA)
regulation of transcription by RNA polymerase II  (TAS)
regulation of transcription, DNA-templated  (IEA,ISO)
response to calcium ion  (IEP)
response to estradiol  (IEP)
skeletal system development  (IEA,ISO)
vitamin D receptor signaling pathway  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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Additional References at PubMed
PMID:9241280   PMID:9295274   PMID:10678179   PMID:10866662   PMID:11687634   PMID:11891224   PMID:12016314   PMID:12198242   PMID:12444213   PMID:12771291   PMID:15178742   PMID:15322135  
PMID:15456860   PMID:15589699   PMID:15589866   PMID:15601867   PMID:15601870   PMID:16130132   PMID:16521124   PMID:16549446   PMID:16720713   PMID:16835013   PMID:16927375   PMID:17054913  
PMID:17082781   PMID:17118558   PMID:17223341   PMID:17254542   PMID:17426122   PMID:17535892   PMID:17658451   PMID:17786964   PMID:17974622   PMID:18410228   PMID:18502116   PMID:18534255  
PMID:18556746   PMID:18591157   PMID:18710208   PMID:18813285   PMID:18936343   PMID:18997319   PMID:19091789   PMID:20236534   PMID:20236614   PMID:20304057   PMID:20369481   PMID:20512927  
PMID:20969950   PMID:21408608   PMID:22112050   PMID:22926646   PMID:23035695   PMID:23352937   PMID:23462137   PMID:23684983   PMID:23723390   PMID:24202304   PMID:24349534   PMID:24535566  
PMID:24607320   PMID:25425001   PMID:25503724   PMID:25823394   PMID:26342089   PMID:26347486   PMID:27009470   PMID:27351590   PMID:27589858   PMID:27818277   PMID:27989797   PMID:28303937  
PMID:28698609   PMID:28707894   PMID:28825325   PMID:28885847   PMID:29138801   PMID:29176823   PMID:29183808   PMID:29909574   PMID:30468500   PMID:30905826   PMID:32583376  


Genomics

Comparative Map Data
Vdr
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27128,987,981 - 129,037,677 (-)NCBI
Rnor_6.0 Ensembl7139,342,063 - 139,394,166 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07139,344,452 - 139,394,138 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07139,536,241 - 139,585,928 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47136,567,614 - 136,617,280 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17136,644,050 - 136,693,717 (-)NCBI
Celera7125,479,125 - 125,528,679 (-)NCBICelera
Cytogenetic Map7q36NCBI
VDR
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1247,841,537 - 47,943,048 (-)EnsemblGRCh38hg38GRCh38
GRCh381247,841,537 - 47,905,022 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371248,235,320 - 48,298,777 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361246,521,587 - 46,585,081 (-)NCBINCBI36hg18NCBI36
Build 341246,521,588 - 46,585,036NCBI
Celera1247,032,871 - 47,096,518 (-)NCBI
Cytogenetic Map12q13.11NCBI
HuRef1245,266,368 - 45,330,677 (-)NCBIHuRef
CHM1_11248,201,212 - 48,264,704 (-)NCBICHM1_1
Vdr
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391597,752,308 - 97,806,177 (-)NCBIGRCm39mm39
GRCm39 Ensembl1597,752,306 - 97,808,511 (-)Ensembl
GRCm381597,854,427 - 97,908,296 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1597,854,425 - 97,910,630 (-)EnsemblGRCm38mm10GRCm38
MGSCv371597,684,858 - 97,738,727 (-)NCBIGRCm37mm9NCBIm37
MGSCv361597,682,461 - 97,736,330 (-)NCBImm8
Celera1599,981,938 - 100,035,599 (-)NCBICelera
Cytogenetic Map15F1NCBI
Vdr
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555006,745,678 - 6,798,048 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555006,745,725 - 6,798,052 (-)NCBIChiLan1.0ChiLan1.0
VDR
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11241,661,688 - 41,766,192 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1241,702,742 - 41,766,192 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01240,828,413 - 40,891,700 (+)NCBIMhudiblu_PPA_v0panPan3
VDR
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1276,852,915 - 6,909,466 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl276,852,723 - 6,909,470 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2739,397,549 - 39,454,181 (-)NCBI
ROS_Cfam_1.0276,920,266 - 6,976,964 (+)NCBI
UMICH_Zoey_3.1276,857,514 - 6,914,062 (+)NCBI
UNSW_CanFamBas_1.0276,892,693 - 6,949,518 (+)NCBI
UU_Cfam_GSD_1.02739,686,018 - 39,742,660 (-)NCBI
Vdr
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494567,363,831 - 67,424,087 (+)NCBI
SpeTri2.0NW_0049365125,741,836 - 5,800,999 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VDR
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl578,205,810 - 78,267,321 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1578,205,807 - 78,266,505 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2581,279,217 - 81,338,475 (-)NCBISscrofa10.2Sscrofa10.2susScr3
VDR
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11144,062,198 - 44,126,295 (-)NCBI
ChlSab1.1 Ensembl1144,065,457 - 44,166,684 (-)Ensembl
Vdr
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248164,314,146 - 4,423,946 (+)NCBI


QTLs in Region (Rnor_6.0)
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)751251919145729302Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)771448715145729302Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)781645773140745067Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)796630946141630946Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7100028953145729302Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)7100160423140335001Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)7100192194145192194Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)7106564316145729302Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7111519266143965591Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7114825174145729302Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7115922628145729302Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7120746024145692398Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7121654760145729302Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7121986439143965591Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7122421276143965415Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7129412003145729302Rat


Genetic Models
This gene Vdr is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:115
Count of miRNA genes:85
Interacting mature miRNAs:99
Transcripts:ENSRNOT00000011601
Prediction methods: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.


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 27 2
Low 28 21 5 19 5 5 6 5 4 34 9 5
Below cutoff 15 36 36 36 3 5 39 4 7 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000082429   ⟹   ENSRNOP00000070446
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7139,342,063 - 139,394,166 (-)Ensembl
RefSeq Acc Id: NM_017058   ⟹   NP_058754
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27128,987,981 - 129,037,677 (-)NCBI
Rnor_6.07139,344,452 - 139,394,138 (-)NCBI
Rnor_5.07139,536,241 - 139,585,928 (-)NCBI
RGSC_v3.47136,567,614 - 136,617,280 (-)RGD
Celera7125,479,125 - 125,528,679 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_058754 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41089 (Get FASTA)   NCBI Sequence Viewer  
  EDL87095 (Get FASTA)   NCBI Sequence Viewer  
  P13053 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_058754   ⟸   NM_017058
- Sequence:
RefSeq Acc Id: ENSRNOP00000070446   ⟸   ENSRNOT00000082429
Protein Domains
NR LBD   Nuclear receptor

Transcriptome

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

Promoters
RGD ID:13695618
Promoter ID:EPDNEW_R6143
Type:initiation region
Name:Vdr_1
Description:vitamin D 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_6.07139,394,157 - 139,394,217EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3959 AgrOrtholog
Ensembl Genes ENSRNOG00000054420 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000070446 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000082429 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.565.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.50.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro DBD_VDR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NHR-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucl_hrmn_rcpt_lig-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nuclear_hrmn_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VitD_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_hrmn_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_NHR/GATA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24873 UniProtKB/Swiss-Prot
NCBI Gene 24873 ENTREZGENE
Pfam Hormone_recep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB VDR RGD
PhenoGen Vdr PhenoGen
PRINTS STRDHORMONER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  STROIDFINGER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VITAMINDR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE NR_LBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOLI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnF_C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48508 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V744_RAT UniProtKB/TrEMBL
  P13053 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-05-12 Vdr  vitamin D receptor  Vdr  vitamin D (1,25- dihydroxyvitamin D3) receptor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Vdr  vitamin D (1,25- dihydroxyvitamin D3) receptor  Vdr  vitamin D receptor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-12-14 Vdr  vitamin D receptor      Symbol and Name status set to approved 1299863 APPROVED
2002-06-10 Vdr  vitamin D receptor      Name updated 70585 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in osteoblasts 70308
gene_function binds vitamin D 70308
gene_function binds vitamin D 70543
gene_process mediates action of vitamin D as a transcription factor 70308
gene_process mediates action of vitamin D as a transcription factor 70543
gene_process functions in apoptosis in glioma cells 70308
gene_process functions in apoptosis in glioma cells 70543
gene_process expression is required, but not sufficient, for vitamin D mediated apoptosis in glioma cells 70308
gene_transcript has 10 exons