Lrp6 (LDL receptor related protein 6) - Rat Genome Database

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Gene: Lrp6 (LDL receptor related protein 6) Rattus norvegicus
Analyze
Symbol: Lrp6
Name: LDL receptor related protein 6
RGD ID: 1304749
Description: Predicted to enable several functions, including Wnt-protein binding activity; frizzled binding activity; and low-density lipoprotein particle receptor activity. Involved in several processes, including canonical Wnt signaling pathway; positive regulation of cytosolic calcium ion concentration; and response to peptide hormone. Located in neuronal cell body and synapse. Human ortholog(s) of this gene implicated in tooth agenesis. Orthologous to human LRP6 (LDL receptor related protein 6); PARTICIPATES IN Wnt signaling, canonical pathway; Wnt signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC312781; low density lipoprotein receptor-related protein 6; low-density lipoprotein receptor-related protein 6
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24167,266,581 - 167,400,155 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4167,270,353 - 167,400,497 (-)Ensembl
Rnor_6.04168,194,054 - 168,323,962 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4168,194,927 - 168,323,751 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04232,475,530 - 232,606,101 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44171,337,114 - 171,444,932 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14171,582,253 - 171,717,580 (-)NCBI
Celera4155,870,415 - 155,972,673 (-)NCBICelera
Cytogenetic Map4q43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1,4-phenylenediamine  (ISO)
17alpha-ethynylestradiol  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3,4-methylenedioxymethamphetamine  (EXP,ISO)
3-chloropropane-1,2-diol  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
acetamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
chloroprene  (EXP)
clofibric acid  (EXP)
curcumin  (EXP)
cyclosporin A  (ISO)
dibutyl phthalate  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
ethanol  (ISO)
ethosuximide  (EXP)
flutamide  (EXP)
formaldehyde  (ISO)
gingerol  (ISO)
glyphosate  (ISO)
hydrogen peroxide  (ISO)
hydroquinone O-beta-D-glucopyranoside  (ISO)
kojic acid  (ISO)
lithium chloride  (ISO)
menadione  (ISO)
mercury dichloride  (ISO)
methapyrilene  (EXP)
methotrexate  (ISO)
methylmercury chloride  (ISO)
N-nitrosodiethylamine  (EXP)
nefazodone  (EXP)
niclosamide  (EXP,ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
pluronic P-123  (EXP)
Poloxamer  (EXP)
SB 431542  (ISO)
simvastatin  (EXP)
tert-butyl hydroperoxide  (ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
troglitazone  (ISO)
trovafloxacin  (EXP)
urethane  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anterior/posterior pattern specification  (ISO)
axis elongation  (ISO)
axis elongation involved in somitogenesis  (IBA,ISO)
bone morphogenesis  (IBA,ISO)
bone remodeling  (IBA,ISO)
branching involved in mammary gland duct morphogenesis  (IBA,ISO)
canonical Wnt signaling pathway  (IMP,ISO)
canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development  (ISO)
canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation  (ISO)
cell migration involved in gastrulation  (ISO)
cell-cell adhesion  (IMP)
cellular response to cholesterol  (ISO)
cerebellum morphogenesis  (IBA,ISO)
cerebral cortex cell migration  (ISO)
cerebral cortex development  (IBA,ISO)
chemical synaptic transmission  (IBA,IMP)
convergent extension  (IBA,ISO)
dopaminergic neuron differentiation  (ISO)
dorsal/ventral axis specification  (ISO)
embryonic camera-type eye morphogenesis  (IBA,ISO)
embryonic digit morphogenesis  (ISO)
embryonic forelimb morphogenesis  (ISO)
embryonic hindlimb morphogenesis  (ISO)
embryonic limb morphogenesis  (IBA,ISO)
embryonic pattern specification  (IBA,ISO)
embryonic retina morphogenesis in camera-type eye  (IBA,ISO)
external genitalia morphogenesis  (IBA,ISO)
face morphogenesis  (IBA,ISO)
forebrain development  (ISO)
forebrain generation of neurons  (ISO)
forebrain radial glial cell differentiation  (ISO)
formation of radial glial scaffolds  (ISO)
gastrulation with mouth forming second  (ISO)
generation of neurons  (ISO)
heart looping  (ISO)
limb morphogenesis  (ISO)
mammary gland duct morphogenesis  (ISO)
mammary placode formation  (ISO)
midbrain development  (IBA,ISO)
midbrain-hindbrain boundary development  (IBA,ISO)
morphogenesis of an epithelium  (ISO)
negative regulation of epithelial cell proliferation  (ISO)
negative regulation of fat cell differentiation  (ISO)
negative regulation of non-canonical Wnt signaling pathway  (ISO)
negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis  (ISO)
negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis  (ISO)
negative regulation of planar cell polarity pathway involved in neural tube closure  (ISO)
negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis  (ISO)
negative regulation of planar cell polarity pathway involved in pericardium morphogenesis  (ISO)
negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis  (ISO)
negative regulation of protein kinase activity  (ISO)
negative regulation of protein phosphorylation  (ISO)
negative regulation of protein serine/threonine kinase activity  (ISO)
negative regulation of smooth muscle cell apoptotic process  (ISO)
neural crest cell differentiation  (IBA,ISO)
neural crest formation  (IBA,ISO)
neural tube closure  (IBA,ISO)
neural tube development  (ISO)
Norrin signaling pathway  (ISO)
odontogenesis of dentin-containing tooth  (IBA,ISO)
pericardium morphogenesis  (IBA,ISO)
positive regulation of apoptotic process  (ISO)
positive regulation of bone resorption  (ISO)
positive regulation of cell cycle  (ISO)
positive regulation of cytosolic calcium ion concentration  (IMP)
positive regulation of DNA-binding transcription factor activity  (IBA,ISO)
positive regulation of mesenchymal cell proliferation  (ISO)
positive regulation of neuron projection development  (ISO)
positive regulation of ossification  (ISO)
positive regulation of transcription by RNA polymerase II  (IBA,ISO)
positive regulation of transcription, DNA-templated  (ISO)
post-anal tail morphogenesis  (ISO)
primitive streak formation  (IBA,ISO)
protein localization to plasma membrane  (ISO)
receptor-mediated endocytosis involved in cholesterol transport  (IBA,ISO)
regulation of cell development  (ISO)
regulation of cell population proliferation  (ISO)
regulation of ossification  (IBA)
regulation of transcription, DNA-templated  (IMP)
response to folic acid  (ISO)
response to peptide hormone  (IEP)
retina morphogenesis in camera-type eye  (ISO)
roof of mouth development  (IBA,ISO)
skeletal system morphogenesis  (ISO)
somitogenesis  (ISO)
thalamus development  (IBA,ISO)
toxin transport  (IEA)
trachea cartilage morphogenesis  (IBA,ISO)
Wnt signaling pathway  (ISO)
Wnt signaling pathway involved in forebrain neuroblast division  (ISO)
Wnt signaling pathway involved in somitogenesis  (IBA,ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:591875   PMID:5893447   PMID:10545599   PMID:11029007   PMID:11029008   PMID:11357136   PMID:11448771   PMID:11742004   PMID:12121999   PMID:12857724   PMID:12897152   PMID:14715945  
PMID:14739301   PMID:15035989   PMID:15064719   PMID:15142971   PMID:15143170   PMID:15271658   PMID:15342729   PMID:15384171   PMID:15469977   PMID:15537447   PMID:15880584   PMID:15908424  
PMID:16126904   PMID:16263759   PMID:16365045   PMID:16543246   PMID:16564009   PMID:16805831   PMID:16890161   PMID:16920270   PMID:17050573   PMID:17239604   PMID:17569865   PMID:17888405  
PMID:18215320   PMID:18256198   PMID:18350154   PMID:18505367   PMID:18505732   PMID:18606138   PMID:18948618   PMID:18985738   PMID:19056682   PMID:19107203   PMID:19503830   PMID:19653321  
PMID:19700620   PMID:19705442   PMID:19795512   PMID:19795519   PMID:19910923   PMID:20059949   PMID:20093106   PMID:20093360   PMID:20093472   PMID:20137080   PMID:20351274   PMID:20359476  
PMID:21935433   PMID:21984209   PMID:22899650   PMID:23481549   PMID:23845000   PMID:25655048   PMID:26919115   PMID:27250245   PMID:29864925   PMID:30070011  


Genomics

Comparative Map Data
Lrp6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24167,266,581 - 167,400,155 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4167,270,353 - 167,400,497 (-)Ensembl
Rnor_6.04168,194,054 - 168,323,962 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4168,194,927 - 168,323,751 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04232,475,530 - 232,606,101 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44171,337,114 - 171,444,932 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14171,582,253 - 171,717,580 (-)NCBI
Celera4155,870,415 - 155,972,673 (-)NCBICelera
Cytogenetic Map4q43NCBI
LRP6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1212,116,025 - 12,267,044 (-)EnsemblGRCh38hg38GRCh38
GRCh381212,116,025 - 12,267,044 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371212,268,959 - 12,419,978 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361212,160,226 - 12,311,078 (-)NCBINCBI36hg18NCBI36
Build 341212,164,957 - 12,311,013NCBI
Celera1217,412,009 - 17,562,835 (-)NCBI
Cytogenetic Map12p13.2NCBI
HuRef1212,034,207 - 12,184,947 (-)NCBIHuRef
CHM1_11212,234,005 - 12,384,830 (-)NCBICHM1_1
Lrp6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396134,423,439 - 134,543,876 (-)NCBIGRCm39mm39
GRCm39 Ensembl6134,423,439 - 134,543,928 (-)Ensembl
GRCm386134,446,476 - 134,566,913 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6134,446,476 - 134,566,965 (-)EnsemblGRCm38mm10GRCm38
MGSCv376134,400,434 - 134,516,931 (-)NCBIGRCm37mm9NCBIm37
MGSCv366134,415,902 - 134,532,475 (-)NCBImm8
Celera6137,380,826 - 137,512,292 (-)NCBICelera
Cytogenetic Map6G1NCBI
cM Map665.37NCBI
Lrp6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554139,080,914 - 9,237,650 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554139,080,901 - 9,237,644 (-)NCBIChiLan1.0ChiLan1.0
LRP6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11212,508,108 - 12,658,074 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1212,508,108 - 12,657,973 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01212,121,411 - 12,288,590 (-)NCBIMhudiblu_PPA_v0panPan3
LRP6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12734,003,334 - 34,166,334 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2734,003,539 - 34,161,437 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2712,280,309 - 12,442,407 (-)NCBI
ROS_Cfam_1.02734,310,832 - 34,473,060 (+)NCBI
UMICH_Zoey_3.12734,203,210 - 34,365,409 (+)NCBI
UNSW_CanFamBas_1.02734,153,217 - 34,315,758 (+)NCBI
UU_Cfam_GSD_1.02712,010,982 - 12,174,011 (-)NCBI
Lrp6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494595,337,435 - 95,417,648 (+)NCBI
SpeTri2.0NW_0049365875,065,200 - 5,143,029 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LRP6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl560,149,028 - 60,314,689 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1560,149,041 - 60,318,719 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2563,564,404 - 63,674,461 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LRP6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11112,016,542 - 12,170,496 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1112,021,560 - 12,170,663 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606923,151,738 - 23,306,613 (+)NCBIVero_WHO_p1.0
Lrp6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475225,605,444 - 25,756,573 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D4Rat218  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24167,377,878 - 167,378,001 (+)MAPPERmRatBN7.2
Rnor_6.04168,301,506 - 168,301,628NCBIRnor6.0
Rnor_5.04232,583,645 - 232,583,767UniSTSRnor5.0
RGSC_v3.44171,449,064 - 171,449,187RGDRGSC3.4
RGSC_v3.44171,449,065 - 171,449,187UniSTSRGSC3.4
RGSC_v3.14171,693,875 - 171,694,377RGD
Celera4155,976,806 - 155,976,928UniSTS
FHH x ACI Map4107.8399RGD
FHH x ACI Map4107.8399UniSTS
Cytogenetic Map4q43UniSTS
RH133552  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24167,269,857 - 167,270,062 (+)MAPPERmRatBN7.2
Rnor_6.04168,194,929 - 168,195,133NCBIRnor6.0
Rnor_5.04232,477,068 - 232,477,272UniSTSRnor5.0
RGSC_v3.44171,337,116 - 171,337,320UniSTSRGSC3.4
Celera4155,870,417 - 155,870,621UniSTS
RH 3.4 Map41016.3UniSTS
Cytogenetic Map4q43UniSTS
RH142471  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24167,287,858 - 167,288,144 (+)MAPPERmRatBN7.2
Rnor_6.04168,212,930 - 168,213,215NCBIRnor6.0
Rnor_5.04232,495,069 - 232,495,354UniSTSRnor5.0
RGSC_v3.44171,355,117 - 171,355,402UniSTSRGSC3.4
Celera4155,888,418 - 155,888,703UniSTS
RH 3.4 Map41015.4UniSTS
Cytogenetic Map4q43UniSTS
AU047004  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24167,369,840 - 167,370,061 (+)MAPPERmRatBN7.2
Rnor_6.04168,293,468 - 168,293,688NCBIRnor6.0
Rnor_5.04232,575,607 - 232,575,827UniSTSRnor5.0
RGSC_v3.44171,441,027 - 171,441,247UniSTSRGSC3.4
Celera4155,968,768 - 155,968,988UniSTS
Cytogenetic Map4q43UniSTS
AU049275  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24167,371,389 - 167,371,549 (+)MAPPERmRatBN7.2
Rnor_6.04168,295,017 - 168,295,176NCBIRnor6.0
Rnor_5.04232,577,156 - 232,577,315UniSTSRnor5.0
RGSC_v3.44171,442,576 - 171,442,735UniSTSRGSC3.4
Celera4155,970,317 - 155,970,476UniSTS
Cytogenetic Map4q43UniSTS
Lrp6  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24167,373,370 - 167,373,721 (+)MAPPERmRatBN7.2
Rnor_6.04168,296,998 - 168,297,348NCBIRnor6.0
Rnor_5.04232,579,137 - 232,579,487UniSTSRnor5.0
RGSC_v3.44171,444,557 - 171,444,907UniSTSRGSC3.4
Celera4155,972,298 - 155,972,648UniSTS
Cytogenetic Map4q43UniSTS
Lrp6  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24167,308,574 - 167,310,036 (+)MAPPERmRatBN7.2
Rnor_6.04168,233,646 - 168,235,107NCBIRnor6.0
Rnor_5.04232,515,785 - 232,517,246UniSTSRnor5.0
RGSC_v3.44171,375,833 - 171,377,294UniSTSRGSC3.4
Celera4155,909,134 - 155,910,595UniSTS
Cytogenetic Map4q43UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4148090542168069246Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4124778595169778595Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:451
Count of miRNA genes:235
Interacting mature miRNAs:288
Transcripts:ENSRNOT00000066575
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.


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 2 38 43 27 19 27 8 8 74 35 36 11 8
Low 1 5 14 14 14 3 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000066575   ⟹   ENSRNOP00000063261
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4168,194,927 - 168,297,373 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082102   ⟹   ENSRNOP00000071445
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4167,270,353 - 167,400,497 (-)Ensembl
Rnor_6.0 Ensembl4168,195,479 - 168,323,751 (-)Ensembl
RefSeq Acc Id: NM_001107892   ⟹   NP_001101362
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24167,269,856 - 167,373,746 (-)NCBI
Rnor_6.04168,194,927 - 168,297,373 (-)NCBI
Rnor_5.04232,475,530 - 232,606,101 (-)NCBI
RGSC_v3.44171,337,114 - 171,444,932 (-)RGD
Celera4155,870,415 - 155,972,673 (-)RGD
Sequence:
RefSeq Acc Id: XM_017592658   ⟹   XP_017448147
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24167,266,581 - 167,400,155 (-)NCBI
Rnor_6.04168,194,054 - 168,323,962 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039107694   ⟹   XP_038963622
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24167,270,762 - 167,400,155 (-)NCBI
RefSeq Acc Id: XM_039107695   ⟹   XP_038963623
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24167,270,530 - 167,400,147 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001101362 (Get FASTA)   NCBI Sequence Viewer  
  XP_017448147 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963622 (Get FASTA)   NCBI Sequence Viewer  
  XP_038963623 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM01658 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001101362   ⟸   NM_001107892
- UniProtKB: D3ZUH9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017448147   ⟸   XM_017592658
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K0H3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071445   ⟸   ENSRNOT00000082102
RefSeq Acc Id: ENSRNOP00000063261   ⟸   ENSRNOT00000066575
RefSeq Acc Id: XP_038963623   ⟸   XM_039107695
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038963622   ⟸   XM_039107694
- Peptide Label: isoform X2
Protein Domains
EGF-like

Transcriptome

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

Promoters
RGD ID:13693449
Promoter ID:EPDNEW_R3973
Type:single initiation site
Name:Lrp6_1
Description:LDL receptor related protein 6
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R3974  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04168,297,283 - 168,297,343EPDNEW
RGD ID:13693461
Promoter ID:EPDNEW_R3974
Type:initiation region
Name:Lrp6_2
Description:LDL receptor related protein 6
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R3973  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04168,323,836 - 168,323,896EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 168297212 168297213 C T snv SR/JrHsd (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304749 AgrOrtholog
Ensembl Genes ENSRNOG00000006338 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000063261 UniProtKB/TrEMBL
  ENSRNOP00000071445 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066575 UniProtKB/TrEMBL
  ENSRNOT00000082102 UniProtKB/TrEMBL
Gene3D-CATH 2.120.10.30 UniProtKB/TrEMBL
  4.10.400.10 UniProtKB/TrEMBL
InterPro 6-blade_b-propeller_TolB-like UniProtKB/TrEMBL
  EG-like_dom UniProtKB/TrEMBL
  LDL_receptor-like_sf UniProtKB/TrEMBL
  LDLR_class-A_CS UniProtKB/TrEMBL
  LDLR_classB_rpt UniProtKB/TrEMBL
  LDrepeatLR_classA_rpt UniProtKB/TrEMBL
  Low_density_Lipo_rcpt-rel_p5/6 UniProtKB/TrEMBL
KEGG Report rno:312781 UniProtKB/TrEMBL
NCBI Gene 312781 ENTREZGENE
Pfam Ldl_recept_a UniProtKB/TrEMBL
  Ldl_recept_b UniProtKB/TrEMBL
PhenoGen Lrp6 PhenoGen
PIRSF LDL_recpt-rel_p5/6 UniProtKB/TrEMBL
PRINTS LDLRECEPTOR UniProtKB/TrEMBL
PROSITE LDLRA_1 UniProtKB/TrEMBL
  LDLRA_2 UniProtKB/TrEMBL
  LDLRB UniProtKB/TrEMBL
SMART EGF UniProtKB/TrEMBL
  LDLa UniProtKB/TrEMBL
  SM00135 UniProtKB/TrEMBL
Superfamily-SCOP LDL_rcpt_classA_cys-rich UniProtKB/TrEMBL
UniProt A0A0G2K0H3 ENTREZGENE, UniProtKB/TrEMBL
  D3ZUH9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-20 Lrp6  LDL receptor related protein 6  Lrp6  low density lipoprotein receptor-related protein 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Lrp6  low density lipoprotein receptor-related protein 6   Lrp6_predicted  low density lipoprotein receptor-related protein 6 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Lrp6_predicted  low density lipoprotein receptor-related protein 6 (predicted)      Symbol and Name status set to approved 70820 APPROVED