Lgr5 (leucine rich repeat containing G protein coupled receptor 5) - Rat Genome Database

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Gene: Lgr5 (leucine rich repeat containing G protein coupled receptor 5) Rattus norvegicus
Analyze
Symbol: Lgr5
Name: leucine rich repeat containing G protein coupled receptor 5
RGD ID: 1307733
Description: Predicted to enable G protein-coupled peptide receptor activity. Predicted to be involved in several processes, including activation of adenylate cyclase activity; adenylate cyclase-activating G protein-coupled receptor signaling pathway; and positive regulation of canonical Wnt signaling pathway. Predicted to act upstream of or within several processes, including epithelial cell proliferation involved in renal tubule morphogenesis; hair follicle development; and oocyte differentiation. Predicted to be located in nucleoplasm and trans-Golgi network membrane. Predicted to be integral component of plasma membrane. Orthologous to human LGR5 (leucine rich repeat containing G protein-coupled receptor 5); PARTICIPATES IN Wnt signaling, canonical pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 3,3',5,5'-tetrabromobisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: G protein-coupled receptor 49; Gpr49; leucine-rich repeat-containing G-protein coupled receptor 5; LOC299802
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
mRatBN7.2751,087,059 - 51,221,882 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl751,088,239 - 51,222,446 (-)Ensembl
Rnor_6.0758,447,097 - 58,587,787 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl758,448,277 - 58,587,787 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0758,458,486 - 58,596,253 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4754,737,745 - 54,876,664 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1754,758,873 - 54,897,394 (-)NCBI
Celera747,880,362 - 48,010,031 (-)NCBICelera
Cytogenetic Map7q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-butoxyethanol  (ISO)
3,3',5,5'-tetrabromobisphenol A  (EXP)
4,4'-sulfonyldiphenol  (ISO)
5-fluorouracil  (ISO)
6-bromoindirubin-3'-oxime  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromobenzene  (EXP)
buta-1,3-diene  (ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
CHIR 99021  (ISO)
choline  (ISO)
ciguatoxin CTX1B  (ISO)
clofibrate  (ISO)
cocaine  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
cyclosporin A  (ISO)
DAPT  (EXP)
deoxynivalenol  (ISO)
diarsenic trioxide  (ISO)
dioxygen  (ISO)
dodecanoic acid  (ISO)
dorsomorphin  (ISO)
entinostat  (ISO)
ethanol  (ISO)
flutamide  (EXP)
folic acid  (ISO)
fonofos  (ISO)
genistein  (ISO)
hydrogen peroxide  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
leflunomide  (ISO)
lithium chloride  (ISO)
menadione  (ISO)
methotrexate  (ISO)
methylmercury chloride  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
Monobutylphthalate  (ISO)
N-nitrosodiethylamine  (ISO)
nickel atom  (ISO)
okadaic acid  (ISO)
paracetamol  (ISO)
parathion  (ISO)
pentachlorophenol  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
senecionine  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
T-2 toxin  (ISO)
tamoxifen  (ISO)
terbufos  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
trichloroethene  (EXP,ISO)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Secreted and transmembrane wnt inhibitors and activators. Cruciat CM and Niehrs C, Cold Spring Harb Perspect Biol. 2013 Mar 1;5(3):a015081. doi: 10.1101/cshperspect.a015081.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:21693646   PMID:21727895   PMID:21795542   PMID:22815884   PMID:23374535   PMID:23439653   PMID:24680895   PMID:25158167   PMID:25535395   PMID:26582901   PMID:27339869   PMID:29018960  


Genomics

Comparative Map Data
Lgr5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2751,087,059 - 51,221,882 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl751,088,239 - 51,222,446 (-)Ensembl
Rnor_6.0758,447,097 - 58,587,787 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl758,448,277 - 58,587,787 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0758,458,486 - 58,596,253 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4754,737,745 - 54,876,664 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1754,758,873 - 54,897,394 (-)NCBI
Celera747,880,362 - 48,010,031 (-)NCBICelera
Cytogenetic Map7q22NCBI
LGR5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381271,439,129 - 71,586,310 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1271,439,798 - 71,586,310 (+)EnsemblGRCh38hg38GRCh38
GRCh371271,833,578 - 71,980,090 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361270,120,080 - 70,264,889 (+)NCBINCBI36hg18NCBI36
Celera1271,496,570 - 71,640,955 (+)NCBI
Cytogenetic Map12q21.1NCBI
HuRef1268,883,082 - 69,029,217 (+)NCBIHuRef
CHM1_11271,801,182 - 71,947,319 (+)NCBICHM1_1
T2T-CHM13v2.01271,417,543 - 71,563,815 (+)NCBI
Lgr5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910115,286,219 - 115,423,685 (-)NCBIGRCm39mm39
GRCm39 Ensembl10115,286,216 - 115,423,685 (-)Ensembl
GRCm3810115,450,314 - 115,587,780 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10115,450,311 - 115,587,780 (-)EnsemblGRCm38mm10GRCm38
MGSCv3710114,887,370 - 115,024,836 (-)NCBIGRCm37mm9NCBIm37
MGSCv3610114,855,736 - 114,991,603 (-)NCBImm8
Celera10117,380,191 - 117,518,061 (-)NCBICelera
Cytogenetic Map10D2NCBI
Lgr5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540511,507,083 - 11,574,569 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540511,507,083 - 11,574,504 (+)NCBIChiLan1.0ChiLan1.0
LGR5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11271,823,622 - 71,969,712 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1271,823,511 - 71,969,704 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01268,963,423 - 69,110,107 (+)NCBIMhudiblu_PPA_v0panPan3
LGR5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11013,009,028 - 13,136,685 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1013,007,843 - 13,136,998 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1012,948,043 - 13,075,055 (+)NCBI
ROS_Cfam_1.01013,142,096 - 13,269,246 (+)NCBI
ROS_Cfam_1.0 Ensembl1013,141,905 - 13,269,846 (+)Ensembl
UMICH_Zoey_3.11013,007,284 - 13,134,172 (+)NCBI
UNSW_CanFamBas_1.01013,254,327 - 13,381,408 (+)NCBI
UU_Cfam_GSD_1.01013,378,129 - 13,505,269 (+)NCBI
Lgr5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494545,064,817 - 45,197,890 (-)NCBI
SpeTri2.0NW_004936568530,314 - 662,524 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LGR5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl535,463,279 - 35,595,933 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1535,463,257 - 35,595,234 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2538,217,567 - 38,297,859 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LGR5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11167,054,004 - 67,202,574 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1167,141,531 - 67,202,547 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037178,451,865 - 178,599,246 (-)NCBIVero_WHO_p1.0
Lgr5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475026,186,733 - 26,358,043 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462475026,185,196 - 26,302,717 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH125648  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2751,210,448 - 51,210,722 (+)MAPPERmRatBN7.2
Rnor_6.0758,577,153 - 58,577,426NCBIRnor6.0
Rnor_5.0758,585,619 - 58,585,892UniSTSRnor5.0
RGSC_v3.4754,862,648 - 54,862,921UniSTSRGSC3.4
Celera747,998,852 - 47,999,125UniSTS
Cytogenetic Map7q22UniSTS
RH127654  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2751,209,874 - 51,210,093 (+)MAPPERmRatBN7.2
mRatBN7.2563,867,959 - 63,868,161 (+)MAPPERmRatBN7.2
Rnor_6.0564,784,687 - 64,784,888NCBIRnor6.0
Rnor_6.0758,576,579 - 58,576,797NCBIRnor6.0
Rnor_5.0758,585,045 - 58,585,263UniSTSRnor5.0
Rnor_5.0569,276,096 - 69,276,300UniSTSRnor5.0
RGSC_v3.4566,262,076 - 66,262,280UniSTSRGSC3.4
RGSC_v3.4754,862,074 - 54,862,292UniSTSRGSC3.4
Celera747,998,278 - 47,998,496UniSTS
Celera563,739,822 - 63,740,023UniSTS
RH 3.4 Map5563.39UniSTS
Cytogenetic Map7q22UniSTS
Cytogenetic Map5q22UniSTS
RH137145  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2751,210,570 - 51,210,778 (+)MAPPERmRatBN7.2
mRatBN7.2563,868,653 - 63,868,861 (+)MAPPERmRatBN7.2
Rnor_6.0564,785,381 - 64,785,588NCBIRnor6.0
Rnor_6.0758,577,275 - 58,577,482NCBIRnor6.0
Rnor_5.0758,585,741 - 58,585,948UniSTSRnor5.0
Rnor_5.0569,276,793 - 69,277,000UniSTSRnor5.0
RGSC_v3.4566,262,773 - 66,262,980UniSTSRGSC3.4
RGSC_v3.4754,862,770 - 54,862,977UniSTSRGSC3.4
Celera747,998,974 - 47,999,181UniSTS
Celera563,739,122 - 63,739,329UniSTS
Cytogenetic Map7q22UniSTS
Cytogenetic Map5q22UniSTS
AI598470  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2751,087,840 - 51,088,060 (+)MAPPERmRatBN7.2
Rnor_6.0758,447,879 - 58,448,098NCBIRnor6.0
Rnor_5.0758,459,268 - 58,459,487UniSTSRnor5.0
RGSC_v3.4754,737,347 - 54,737,566UniSTSRGSC3.4
Celera747,879,964 - 47,880,183UniSTS
RH 3.4 Map7477.41UniSTS
Cytogenetic Map7q22UniSTS
Lgr5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2751,089,682 - 51,090,995 (+)MAPPERmRatBN7.2
Rnor_6.0758,449,721 - 58,451,033NCBIRnor6.0
Rnor_5.0758,461,110 - 58,462,422UniSTSRnor5.0
RGSC_v3.4754,739,189 - 54,740,501UniSTSRGSC3.4
Celera747,881,806 - 47,883,118UniSTS
Cytogenetic Map7q22UniSTS
UniSTS:546842  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2751,088,784 - 51,089,718 (+)MAPPERmRatBN7.2
Rnor_6.0758,448,823 - 58,449,756NCBIRnor6.0
Rnor_5.0758,460,212 - 58,461,145UniSTSRnor5.0
Celera747,880,908 - 47,881,841UniSTS
Cytogenetic Map7q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)71965431752888450Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)72409960669099606Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72475184169751841Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72673740163902784Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)72940968353612950Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)72940968374409683Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72940968384928080Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73111283276112832Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)73429328279293282Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)73429328279293282Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)73796056982960569Rat
2303629Vencon3Ventilatory control QTL 37.25respiration trait (VT:0001943)respiration rate (CMO:0000289)74110969256793354Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
634326Hc3Hypercalciuria QTL 32.1urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)74278731487787314Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)74322875088228750Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)743747012108555253Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)743747099102228765Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)74486753389867533Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)74659007091590070Rat
10059605Kidm47Kidney mass QTL 472.910.05kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)74725178365728867Rat
2293696Bmd32Bone mineral density QTL 325.10.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)74765143992651439Rat
2293707Bss32Bone structure and strength QTL 327.640.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)74765143992651439Rat
2300178Bmd54Bone mineral density QTL 545.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)74765143992651439Rat
2293644Bmd29Bone mineral density QTL 295.40.0001femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)74765143992651439Rat
2293667Bss42Bone structure and strength QTL 427.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)74765143992651439Rat
2293678Bss24Bone structure and strength QTL 246.710.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)74765143992651439Rat
2293685Bmd21Bone mineral density QTL 214.20.0003femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)74765143992651439Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:69
Count of miRNA genes:49
Interacting mature miRNAs:60
Transcripts:ENSRNOT00000005814
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 2 2 2 10 13
Low 3 14 34 25 1 25 1 1 66 12 27 11 1
Below cutoff 20 19 13 9 13 6 6 8 13 1 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000005814   ⟹   ENSRNOP00000005814
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl751,088,239 - 51,222,446 (-)Ensembl
Rnor_6.0 Ensembl758,448,277 - 58,587,787 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104830   ⟹   ENSRNOP00000092645
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl751,088,239 - 51,222,446 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115154   ⟹   ENSRNOP00000095923
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl751,088,239 - 51,222,446 (-)Ensembl
RefSeq Acc Id: NM_001106784   ⟹   NP_001100254
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2751,088,239 - 51,221,882 (-)NCBI
Rnor_6.0758,448,277 - 58,587,787 (-)NCBI
Rnor_5.0758,458,486 - 58,596,253 (-)NCBI
RGSC_v3.4754,737,745 - 54,876,664 (-)RGD
Celera747,880,362 - 48,010,031 (-)RGD
Sequence:
RefSeq Acc Id: XM_039078716   ⟹   XP_038934644
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2751,087,059 - 51,157,705 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001100254 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934644 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D4AC13 (Get FASTA)   NCBI Sequence Viewer  
  EDM16685 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100254   ⟸   NM_001106784
- Peptide Label: precursor
- UniProtKB: D4AC13 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000005814   ⟸   ENSRNOT00000005814
RefSeq Acc Id: XP_038934644   ⟸   XM_039078716
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000095923   ⟸   ENSRNOT00000115154
RefSeq Acc Id: ENSRNOP00000092645   ⟸   ENSRNOT00000104830
Protein Domains
LRRNT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AC13-F1-model_v2 AlphaFold D4AC13 1-907 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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
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
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
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
BUF/N (2020)
Visual CSV TAB Printer
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
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
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
DA/OlaHsd (2019)
Visual CSV TAB Printer
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
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
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
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/Stm (2019)
Visual CSV TAB Printer
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
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
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
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
GK/FarMcwi (2019)
Visual CSV TAB Printer
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
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
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
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
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
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
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
LEW/Crl (2019)
Visual CSV TAB Printer
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
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
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
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
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
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
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
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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
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/NRrrcMcwi (2019)
Visual CSV TAB Printer
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
MR/N (2020)
Visual CSV TAB Printer
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
MWF/Hsd (2019)
Visual CSV TAB Printer
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
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
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
SR/JrHsd (2020)
Visual CSV TAB Printer
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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
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
WAG/RijCrl (2020)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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/NCrl (2019)
Visual CSV TAB Printer
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
WN/N (2020)
Visual CSV TAB Printer
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
Damaging Variants


Assembly: Rnor_5.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 58596226 58596227 G T snv SS/JrHsdMcwi (MCW), SS/JrHsdMcwi (KNAW), SS/Jr (KNAW), WN/N (KNAW)


Assembly: RGSC_v3.4
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 54876637 54876638 G T snv SS/JrHsdMcwi (MCW), SS/JrHsdMcwi (MDC), WN/N (KNAW), HCR/2Mco (UMich), HCR/1Mco (UMich), LCR/1Mco (UMich), SS/JrHsdMcwi (ICL)


Assembly: mRatBN7.2
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 51221855 51221856 G T snv WN/N (2020), SS/JrHsdMcwi (2019)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307733 AgrOrtholog
BioCyc Gene G2FUF-34059 BioCyc
Ensembl Genes ENSRNOG00000004221 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000005814 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000092645.1 UniProtKB/TrEMBL
  ENSRNOP00000095923.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005814 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000104830.1 UniProtKB/TrEMBL
  ENSRNOT00000115154.1 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/Swiss-Prot
InterPro GPCR_Rhodpsn UniProtKB/Swiss-Prot
  GPCR_Rhodpsn_7TM UniProtKB/Swiss-Prot
  Gphrmn_rcpt_fam UniProtKB/Swiss-Prot
  Leu-rich_rpt UniProtKB/Swiss-Prot
  Leu-rich_rpt_typical-subtyp UniProtKB/Swiss-Prot
  LRR_dom_sf UniProtKB/Swiss-Prot
  LRRNT UniProtKB/Swiss-Prot
KEGG Report rno:299802 UniProtKB/Swiss-Prot
NCBI Gene 299802 ENTREZGENE
Pfam 7tm_1 UniProtKB/Swiss-Prot
  LRR_1 UniProtKB/Swiss-Prot
  LRR_8 UniProtKB/Swiss-Prot
  LRRNT UniProtKB/Swiss-Prot
PhenoGen Lgr5 PhenoGen
PRINTS GLYCHORMONER UniProtKB/Swiss-Prot
  GPCRRHODOPSN UniProtKB/Swiss-Prot
PROSITE G_PROTEIN_RECEP_F1_2 UniProtKB/Swiss-Prot
  LRR UniProtKB/Swiss-Prot
SMART LRR_TYP UniProtKB/Swiss-Prot
  LRRNT UniProtKB/Swiss-Prot
UniProt A0A8I6ARJ9_RAT UniProtKB/TrEMBL
  A0A8I6GJW4_RAT UniProtKB/TrEMBL
  D4AC13 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-17 Lgr5  leucine rich repeat containing G protein coupled receptor 5  LOC687868  similar to Leucine-rich repeat-containing G-protein coupled receptor 5 precursor (G-protein coupled receptor 49) (Orphan G-protein coupled receptor FEX)  Data Merged 1643240 APPROVED
2006-11-20 LOC687868  similar to Leucine-rich repeat-containing G-protein coupled receptor 5 precursor (G-protein coupled receptor 49) (Orphan G-protein coupled receptor FEX)      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-03-30 Lgr5  leucine rich repeat containing G protein coupled receptor 5  Gpr49_predicted  G protein-coupled receptor 49 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-12 Gpr49_predicted  G protein-coupled receptor 49 (predicted)      Symbol and Name status set to approved 70820 APPROVED