Vldlr (very low density lipoprotein receptor) - Rat Genome Database
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Gene: Vldlr (very low density lipoprotein receptor) Rattus norvegicus
Analyze
Symbol: Vldlr
Name: very low density lipoprotein receptor
RGD ID: 3963
Description: Predicted to have several functions, including reelin receptor activity; very-low-density lipoprotein particle binding activity; and very-low-density lipoprotein particle receptor activity. Involved in several processes, including cellular response to glucose starvation; cellular response to interleukin-1; and cellular response to lipopolysaccharide. Localizes to several cellular components, including apical part of cell; cell surface; and perinuclear region of cytoplasm. Biomarker of focal segmental glomerulosclerosis and nephrotic syndrome. Human ortholog(s) of this gene implicated in Alzheimer's disease; cerebellar ataxia, mental retardation and dysequlibrium syndrome; and dementia. Orthologous to human VLDLR (very low density lipoprotein receptor); PARTICIPATES IN altered Reelin signaling pathway; Reelin signaling pathway; INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: very low-density lipoprotein receptor; VLDL receptor; VLDL-R
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21224,813,539 - 224,850,400 (+)NCBI
Rnor_6.0 Ensembl1245,237,736 - 245,269,205 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01245,236,819 - 245,273,688 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01252,485,275 - 252,523,202 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41230,666,736 - 230,697,748 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11230,830,758 - 230,861,771 (+)NCBI
Celera1222,002,111 - 222,033,270 (+)NCBICelera
RH 3.4 Map11610.4RGD
Cytogenetic Map1q52NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-hydroxypropanoic acid  (ISO)
2-methoxyethanol  (EXP)
3,3',5,5'-tetrabromobisphenol A  (ISO)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
8-Br-cAMP  (ISO)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (EXP)
all-trans-retinoic acid  (EXP,ISO)
AM-251  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
ampicillin  (ISO)
androgen antagonist  (EXP)
antirheumatic drug  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bilirubin IXalpha  (ISO)
bisphenol A  (EXP,ISO)
Butylparaben  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
casticin  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
cisplatin  (EXP,ISO)
clofibrate  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cycloheximide  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
cypermethrin  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dibutyl phthalate  (EXP)
dichloroacetic acid  (ISO)
diclofenac  (ISO)
dioxygen  (ISO)
disodium selenite  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
enzacamene  (EXP)
ethanol  (ISO)
fenvalerate  (EXP)
fluoxetine  (EXP,ISO)
flutamide  (ISO)
folic acid  (ISO)
fonofos  (ISO)
formaldehyde  (ISO)
fructose  (ISO)
furan  (EXP)
gamma-hexachlorocyclohexane  (ISO)
geldanamycin  (EXP)
gemcitabine  (ISO)
genistein  (EXP,ISO)
geraniol  (ISO)
haloperidol  (EXP)
herbimycin  (EXP)
hexaconazole  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
indometacin  (EXP)
irinotecan  (EXP)
L-methionine  (ISO)
lead diacetate  (ISO)
methamphetamine  (ISO)
methapyrilene  (EXP)
methotrexate  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
mifepristone  (EXP)
mono(2-ethylhexyl) phthalate  (ISO)
nickel atom  (ISO)
nickel dichloride  (ISO)
nickel sulfate  (ISO)
ochratoxin A  (ISO)
olanzapine  (EXP)
oxaliplatin  (EXP)
paracetamol  (EXP,ISO)
parathion  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pioglitazone  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
prednisolone  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
radicicol  (EXP)
rimonabant  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
streptozocin  (ISO)
succimer  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
terbufos  (ISO)
Tesaglitazar  (EXP)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
Tributyltin oxide  (ISO)
trichloroethene  (EXP,ISO)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (EXP)
Tungsten carbide  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
vancomycin  (ISO)
vorinostat  (ISO)
zearalenone  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Boucher P, etal., J Biol Chem 2002 May 3;277(18):15507-13. Epub 2002 Feb 19.
2. Chen SJ, etal., Mol Ther. 2000 Sep;2(3):256-61.
3. Eck MV, etal., Atherosclerosis. 2005 Dec;183(2):230-7. Epub 2005 Jun 24.
4. Fatemi SH, etal., Biol Psychiatry. 2005 Apr 1;57(7):777-87.
5. Fatemi SH, etal., Schizophr Res. 2009 Jun;111(1-3):138-52. Epub 2009 Apr 9.
6. Garcia-Miranda P, etal., Exp Physiol. 2010 Apr;95(4):498-507. Epub 2009 Nov 27.
7. GOA data from the GO Consortium
8. Goudriaan JR, etal., Arterioscler Thromb Vasc Biol. 2001 Sep;21(9):1488-93.
9. Gudbrandsen OA, etal., Br J Nutr. 2008 Oct;100(4):776-85. Epub 2008 Mar 18.
10. Helbecque N, etal., Neurology 2001 May 8;56(9):1183-8.
11. Iwasaki T, etal., Endocrinology. 2005 Aug;146(8):3286-94. Epub 2005 May 5.
12. Jia L, etal., Cardiovasc Res. 2006 Feb 1;69(2):545-55. Epub 2005 Dec 22.
13. Jokinen EV, etal., J Biol Chem. 1994 Oct 21;269(42):26411-8.
14. Jossin Y, etal., Cereb Cortex 2003 Jun;13(6):627-33.
15. Kamataki A, etal., Biochem Biophys Res Commun 2002 May 10;293(3):1007-13.
16. Kobayashi K, etal., J Biol Chem. 1996 Mar 22;271(12):6852-60.
17. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
18. Liang K and Vaziri ND, Kidney Int. 1997 Jun;51(6):1761-5.
19. Liang K, etal., Kidney Int. 1998 Mar;53(3):626-30.
20. Loewen N, etal., Exp Eye Res. 2009 May;88(5):928-37. Epub 2009 Jan 8.
21. Luque JM, etal., Brain Res Dev Brain Res 2003 Feb 16;140(2):195-203.
22. Masuzaki H, etal., Circ Res. 1996 Jan;78(1):8-14.
23. MGD data from the GO Consortium
24. Nakamura Y, etal., Brain Res 1998 May 18;793(1-2):47-53.
25. NCBI rat LocusLink and RefSeq merged data July 26, 2002
26. Okuizumi K, etal., Nat Genet 1995 Oct;11(2):207-9.
27. OMIM Disease Annotation Pipeline
28. Pathak A, etal., Cereb Cortex. 2010 Apr 5.
29. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
30. RGD automated data pipeline
31. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
32. RGD automated import pipeline for gene-chemical interactions
33. Roberts CK, etal., Atherosclerosis. 2002 Mar;161(1):133-41.
34. Sato T, etal., Kidney Int. 2002 Jan;61(1):157-62.
35. Shakib K, etal., Proteomics. 2005 Jul;5(11):2819-38.
36. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
37. Yokoi N, etal., Brain Res Mol Brain Res 2003 Apr 10;112(1-2):1-7.
38. Zenimaru Y, etal., Biochem Biophys Res Commun. 2008 Apr 11;368(3):716-22. Epub 2008 Feb 8.
Additional References at PubMed
PMID:8083232   PMID:10571240   PMID:12526740   PMID:15082773   PMID:15950758   PMID:18778775   PMID:20711475   PMID:22429478   PMID:23382219   PMID:23990472   PMID:25644714   PMID:26751967  


Genomics

Comparative Map Data
Vldlr
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21224,813,539 - 224,850,400 (+)NCBI
Rnor_6.0 Ensembl1245,237,736 - 245,269,205 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01245,236,819 - 245,273,688 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01252,485,275 - 252,523,202 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41230,666,736 - 230,697,748 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11230,830,758 - 230,861,771 (+)NCBI
Celera1222,002,111 - 222,033,270 (+)NCBICelera
RH 3.4 Map11610.4RGD
Cytogenetic Map1q52NCBI
VLDLR
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl92,621,787 - 2,660,056 (+)EnsemblGRCh38hg38GRCh38
GRCh3892,621,786 - 2,660,056 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3792,621,787 - 2,660,056 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh3792,621,679 - 2,654,485 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3692,611,793 - 2,644,485 (+)NCBINCBI36hg18NCBI36
Build 3492,611,802 - 2,644,478NCBI
Celera92,540,058 - 2,572,749 (+)NCBI
Cytogenetic Map9p24.2NCBI
HuRef92,576,882 - 2,609,583 (+)NCBIHuRef
CHM1_192,622,117 - 2,656,450 (+)NCBICHM1_1
Vldlr
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391927,190,070 - 27,231,631 (+)NCBIGRCm39mm39
GRCm381927,216,480 - 27,254,231 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1927,216,484 - 27,254,231 (+)EnsemblGRCm38mm10GRCm38
MGSCv371927,291,510 - 27,328,721 (+)NCBIGRCm37mm9NCBIm37
MGSCv361927,284,529 - 27,316,717 (+)NCBImm8
Celera1928,001,119 - 28,038,314 (+)NCBICelera
Cytogenetic Map19C1NCBI
cM Map1921.77NCBI
Vldlr
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554347,013,092 - 7,050,103 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554347,013,092 - 7,050,103 (+)NCBIChiLan1.0ChiLan1.0
VLDLR
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.192,621,325 - 2,653,980 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl92,621,199 - 2,653,980 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v092,428,639 - 2,463,796 (+)NCBIMhudiblu_PPA_v0panPan3
VLDLR
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl191,241,509 - 91,272,495 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1191,242,010 - 91,277,030 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Vldlr
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365032,407,040 - 2,440,366 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VLDLR
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1219,173,504 - 219,210,343 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11219,178,501 - 219,210,332 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21245,001,226 - 245,032,858 (-)NCBISscrofa10.2Sscrofa10.2susScr3
VLDLR
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11276,900,551 - 76,933,601 (-)NCBI
ChlSab1.1 Ensembl1276,899,189 - 76,933,584 (-)Ensembl
Vldlr
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247367,280,478 - 7,316,897 (+)NCBI

Position Markers
WI-18746  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01245,268,658 - 245,268,806NCBIRnor6.0
Rnor_5.01252,518,172 - 252,518,320UniSTSRnor5.0
RGSC_v3.41230,697,669 - 230,697,817UniSTSRGSC3.4
Celera1222,032,723 - 222,032,871UniSTS
Cytogenetic Map1q51UniSTS
09.MMHAP31FLC3.seq  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01245,266,103 - 245,266,253NCBIRnor6.0
Rnor_5.01252,515,617 - 252,515,767UniSTSRnor5.0
RGSC_v3.41230,695,114 - 230,695,264UniSTSRGSC3.4
Celera1222,030,168 - 222,030,318UniSTS
Cytogenetic Map1q51UniSTS
RH94526  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01245,268,596 - 245,268,701NCBIRnor6.0
Rnor_5.01252,518,110 - 252,518,215UniSTSRnor5.0
RGSC_v3.41230,697,607 - 230,697,712UniSTSRGSC3.4
Celera1222,032,661 - 222,032,766UniSTS
RH 3.4 Map11610.4UniSTS
Cytogenetic Map1q51UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2292216Bw80Body weight QTL 803.230.0019body mass (VT:0001259)body weight (CMO:0000012)1233490105264802994Rat
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1236795785281795785Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1236265430281265430Rat
2302375Bw83Body weight QTL 834.870.0002body mass (VT:0001259)body weight (CMO:0000012)1215711860260711860Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1156446196274977688Rat
61455Niddm7Non-insulin dependent diabetes mellitus QTL 75.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1236763415258766873Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1161321152273792054Rat
724533Rf51Renal function QTL 515.30.0002kidney plasma flow trait (VT:0005524)renal plasma flow (CMO:0001914)1238830534278228767Rat
724538Kidm1Kidney mass QTL 13.2kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1233663100273792054Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1243272341282763074Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1244401175282365384Rat
734768Niddm59Non-insulin dependent diabetes mellitus QTL 59body mass (VT:0001259)body weight (CMO:0000012)1235850810280850810Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1244992467282365384Rat
1298084Thym4Thymus enlargement QTL 410.68thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1215828102260828102Rat
631658Cm7Cardiac mass QTL 75.320.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)1216324817261324817Rat
1331790Bp201Blood pressure QTL 2013.127arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1216213318245529710Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1167394665278228889Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1241482188281795785Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1191825895279986079Rat
1300168Bp170Blood pressure QTL 1702.76arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1227107736249206417Rat
1641926Teswt2Testicular weight QTL 22.82testis mass (VT:1000644)both testes wet weight (CMO:0000175)1215711860258765521Rat
1598821Rf55Renal function QTL 556.3renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1238824734279986079Rat
2300175Bmd40Bone mineral density QTL 4015.40.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)1221901238266901238Rat
2293655Bss36Bone structure and strength QTL 3610.660.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1221901238266901238Rat
2293674Bss39Bone structure and strength QTL 397.10.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)1221901238266901238Rat
2293694Bss38Bone structure and strength QTL 387.050.0001femur strength trait (VT:0010010)femur stiffness (CMO:0001674)1221901238266901238Rat
2293700Bmd27Bone mineral density QTL 276.60.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1244401175264636028Rat
2293701Bmd34Bone mineral density QTL 348.30.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)1244401175264636028Rat
631838Niddm36Non-insulin dependent diabetes mellitus QTL 360.01insulin secretion trait (VT:0003564)calculated pancreatic islet insulin release measurement (CMO:0001217)1205195290250195290Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1244401175282365384Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1217054291281795785Rat
634321Hc1Hypercalciuria QTL 12.91urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1193968438261264776Rat
634340Hcar5Hepatocarcinoma resistance QTL 58liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1236763415247065599Rat
1357335Bw39Body weight QTL 393.3body mass (VT:0001259)body weight (CMO:0000012)1215828102260828102Rat
1357399Bw45Body weight QTL 453.05body mass (VT:0001259)body mass index (BMI) (CMO:0000105)1225689973270689973Rat
1357404Bw42Body weight QTL 424.490.0001body mass (VT:0001259)body weight (CMO:0000012)1225689973270689973Rat
1600363Hc6Hypercalciuria QTL 62.7urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1195598053265002735Rat
1600374Mcs17Mammary carcinoma susceptibility QTL 173mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1215684498260684498Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1213476630278978026Rat
1600392Bw123Body weight QTL 1230.001body mass (VT:0001259)body weight (CMO:0000012)1244087148282763074Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1213476630278978026Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1213476630278978026Rat
1600397Edcs4Endometrial carcinoma susceptibility QTL 42.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)1226706329271706329Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1161321256273791893Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1196395041282763074Rat
1578778Pur4Proteinuria QTL 43.30.003total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1161321256273791893Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1161784169278228889Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1192639698278228889Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1161784169278228889Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1192639698278228889Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1161784169278228889Rat
1549910Bw54Body weight QTL 540.05body mass (VT:0001259)body weight (CMO:0000012)1236795785281795785Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1163796316282763074Rat
1358191Ept10Estrogen-induced pituitary tumorigenesis QTL 103.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)1210360774264802828Rat
2292220Bp306Blood pressure QTL 3063.470.00087arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1174905700264802994Rat
2312564Glom18Glomerulus QTL 182.40.003kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)1201358068252480016Rat
1358886Bp260Blood pressure QTL 2603.67arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1161784422246226103Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1230420627282645769Rat
1358898Bp255Blood pressure QTL 2553.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1208517798266948272Rat
1358916Kidm22Kidney mass QTL 223.32kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1230420627262031693Rat
1358292Cm37Cardiac mass QTL 376.20.00000081heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1216324817261324817Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1236265430281265430Rat
61376Bp42Blood pressure QTL 4223.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1215828102260828102Rat
61400Niddm1Non-insulin dependent diabetes mellitus QTL 111blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1238830408266793958Rat
61403Niddm4Non-insulin dependent diabetes mellitus QTL 4blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1225689973247836969Rat
8693618Alc25Alcohol consumption QTL 2530.28drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)1227509470249252048Rat
8693661Alc34Alcohol consumption QTL 342.20.611drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)1227509470249252048Rat
8655655Arrd2Age-related retinal degeneration QTL 27.79retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1202571665264802994Rat
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1122614824262664716Rat
8693637Alc29Alcohol consumption QTL 292.70.258drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)1227509470255131140Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1125875758262433692Rat
8552891Epfw5Epididymal fat weight QTL 54.4epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1210652654255652654Rat
7394701Uae46Urinary albumin excretion QTL 463.60.0056urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1221901238266901238Rat
7387289Uae45Urinary albumin excretion QTL 452.860.0021urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1244148899282763074Rat
8655855Arrd3Age-related retinal degeneration QTL 33.07lens clarity trait (VT:0001304)cataract incidence/prevalence measurement (CMO:0001585)1202571665264802994Rat
10053715Scort24Serum corticosterone level QTL 242.130.0088blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1242302911282763074Rat
10059587Bw173Body weight QTL 1733.230.025body mass (VT:0001259)body weight (CMO:0000012)1222492538267492538Rat
10059590Kidm44Kidney mass QTL 443.420.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1210990171255990171Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:106
Count of miRNA genes:66
Interacting mature miRNAs:85
Transcripts:ENSRNOT00000035814
Prediction methods:Miranda, 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 1 31 8 7 8 11 68 32 34 11 8
Low 2 12 43 35 12 35 6 3 7
Below cutoff 6 6 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000035814   ⟹   ENSRNOP00000036229
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1245,237,736 - 245,269,205 (+)Ensembl
RefSeq Acc Id: NM_013155   ⟹   NP_037287
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21224,814,456 - 224,845,920 (+)NCBI
Rnor_6.01245,237,736 - 245,269,205 (+)NCBI
Rnor_5.01252,485,275 - 252,523,202 (+)NCBI
RGSC_v3.41230,666,736 - 230,697,748 (+)RGD
Celera1222,002,111 - 222,033,270 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006231197   ⟹   XP_006231259
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21224,813,539 - 224,850,400 (+)NCBI
Rnor_6.01245,236,819 - 245,273,688 (+)NCBI
Rnor_5.01252,485,275 - 252,523,202 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006231198   ⟹   XP_006231260
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21224,814,022 - 224,850,400 (+)NCBI
Rnor_6.01245,237,281 - 245,273,688 (+)NCBI
Rnor_5.01252,485,275 - 252,523,202 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006231199   ⟹   XP_006231261
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21224,814,304 - 224,850,400 (+)NCBI
Rnor_6.01245,237,823 - 245,273,688 (+)NCBI
Rnor_5.01252,485,275 - 252,523,202 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588829   ⟹   XP_017444318
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21224,814,298 - 224,850,400 (+)NCBI
Rnor_6.01245,237,823 - 245,273,688 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588830   ⟹   XP_017444319
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21224,814,300 - 224,850,400 (+)NCBI
Rnor_6.01245,237,823 - 245,273,688 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039102103   ⟹   XP_038958031
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21224,813,940 - 224,850,400 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_037287   ⟸   NM_013155
- Peptide Label: precursor
- UniProtKB: F1LPV2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006231259   ⟸   XM_006231197
- Peptide Label: isoform X1
- UniProtKB: F1LPV2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006231260   ⟸   XM_006231198
- Peptide Label: isoform X1
- UniProtKB: F1LPV2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006231261   ⟸   XM_006231199
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017444318   ⟸   XM_017588829
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017444319   ⟸   XM_017588830
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000036229   ⟸   ENSRNOT00000035814
RefSeq Acc Id: XP_038958031   ⟸   XM_039102103
- Peptide Label: isoform X1
Protein Domains
EGF-like   LDL-receptor class A

Transcriptome

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

Promoters
RGD ID:13690836
Promoter ID:EPDNEW_R1361
Type:initiation region
Name:Vldlr_2
Description:very low density lipoprotein receptor
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R1362  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01245,237,719 - 245,237,779EPDNEW
RGD ID:13690838
Promoter ID:EPDNEW_R1362
Type:initiation region
Name:Vldlr_1
Description:very low density lipoprotein receptor
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R1361  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01245,237,862 - 245,237,922EPDNEW

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)
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/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WKY/Gcrc (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
WKY/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
WKY/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
WKY/NHsd (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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3963 AgrOrtholog
Ensembl Genes ENSRNOG00000027491 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000036229 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000035814 ENTREZGENE, 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
  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
  VLDLR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25696 UniProtKB/TrEMBL
NCBI Gene 25696 ENTREZGENE
PANTHER PTHR24270:SF16 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ldl_recept_a UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ldl_recept_b UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Vldlr 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
  SSF57424 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC230870
UniProt F1LPV2 ENTREZGENE, UniProtKB/TrEMBL
  P98166 ENTREZGENE, UniProtKB/Swiss-Prot


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