Lhcgr (luteinizing hormone/choriogonadotropin receptor) - Rat Genome Database

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Gene: Lhcgr (luteinizing hormone/choriogonadotropin receptor) Rattus norvegicus
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Symbol: Lhcgr
Name: luteinizing hormone/choriogonadotropin receptor
RGD ID: 3007
Description: Enables several functions, including ATPase binding activity; identical protein binding activity; and peptide hormone binding activity. Involved in several processes, including G protein-coupled receptor signaling pathway; activation of adenylate cyclase activity; and arachidonic acid secretion. Located in several cellular components, including endoplasmic reticulum; endosome; and lysosome. Is integral component of plasma membrane and intrinsic component of external side of plasma membrane. Part of receptor complex. Human ortholog(s) of this gene implicated in Leydig cell hypoplasia; Leydig cell tumor; breast cancer; familial male-limited precocious puberty; and gonadal disease. Orthologous to human LHCGR (luteinizing hormone/choriogonadotropin receptor); PARTICIPATES IN G protein mediated signaling pathway via Galphas family; peptide and protein hormone signaling pathway; luteinizing hormone signaling pathway; INTERACTS WITH (E)-thiamethoxam; 1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane; 1,3-dinitrobenzene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LH receptor; LH/CG receptor; LH/CG-R; Lhr; LSH-R; LSHR; luteinizing hormone receptor; luteinizing hormone/chorionic gonadotropin receptor; lutropin-choriogonadotropic hormone receptor
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
mRatBN7.265,661,871 - 5,728,109 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl65,661,871 - 5,724,521 (+)Ensembl
Rnor_6.0612,493,182 - 12,554,482 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl612,493,943 - 12,554,439 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0622,455,216 - 22,516,430 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4612,613,622 - 12,651,587 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1612,613,621 - 12,651,587 (-)NCBI
Celera65,442,191 - 5,504,330 (+)NCBICelera
Cytogenetic Map6q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(E)-thiamethoxam  (EXP,ISO)
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (EXP)
1,2-dichloroethane  (ISO)
1,3-dinitrobenzene  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
17beta-estradiol 3-benzoate  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3',5'-cyclic AMP  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-tert-Octylphenol  (EXP)
8-Br-cAMP  (EXP,ISO)
acetamiprid  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
allethrin  (EXP)
alpha-naphthoflavone  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
Aroclor 1254  (EXP)
arsenite(3-)  (ISO)
atrazine  (EXP,ISO)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (EXP)
bucladesine  (EXP)
Butylbenzyl phthalate  (EXP)
cadmium atom  (EXP)
cadmium dichloride  (EXP,ISO)
chlorpyrifos  (ISO)
Chorionic gonadotropin  (EXP,ISO)
chromium(6+)  (EXP)
colforsin daropate hydrochloride  (ISO)
cyanamide  (ISO)
cyhalothrin  (EXP)
cypermethrin  (EXP)
DDE  (EXP)
deoxynivalenol  (ISO)
dexamethasone  (EXP)
dextran sulfate  (ISO)
Di-n-hexyl phthalate  (EXP)
dibutyl phthalate  (EXP,ISO)
dibutylstannane  (EXP)
Dicyclohexyl phthalate  (EXP)
diethyl phthalate  (EXP)
diethylstilbestrol  (EXP)
diheptyl phthalate  (EXP)
diisobutyl phthalate  (EXP)
diisononyl phthalate  (EXP)
dipentyl phthalate  (EXP)
disulfiram  (ISO)
fenvalerate  (EXP)
flurbiprofen  (EXP)
gamma-hexachlorocyclohexane  (EXP)
genistein  (EXP,ISO)
L-ascorbic acid  (EXP)
L-mimosine  (EXP,ISO)
leuprolide  (ISO)
LY294002  (EXP)
melittin  (ISO)
methoxychlor  (EXP)
mono(2-ethylhexyl) phthalate  (ISO)
monobenzyl phthalate  (ISO)
monoethyl phthalate  (ISO)
N-ethyl-N-nitrosourea  (EXP)
p-tert-Amylphenol  (EXP)
paraquat  (EXP)
perfluorododecanoic acid  (EXP)
perfluorooctanoic acid  (ISO)
picrotoxin  (EXP)
potassium dichromate  (EXP)
prostaglandin F2alpha  (EXP)
quercetin  (EXP)
resveratrol  (EXP)
sodium arsenite  (EXP,ISO)
sodium fluoride  (EXP)
sulfur dioxide  (ISO)
T-2 toxin  (ISO)
testosterone  (ISO)
testosterone enanthate  (EXP)
thiamethoxam  (EXP,ISO)
titanium dioxide  (ISO)
tofacitinib  (EXP)
triphenylstannane  (EXP)
tyrphostin AG 1478  (EXP)
uranium atom  (EXP)
vinclozolin  (EXP)
zearalenone  (ISO)
ziram  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of adenylate cyclase activity  (IBA,IDA,IEA,ISO)
adenylate cyclase-activating G protein-coupled receptor signaling pathway  (IBA,IEA,ISO)
adenylate cyclase-modulating G protein-coupled receptor signaling pathway  (IDA,IMP)
arachidonic acid secretion  (IDA)
cellular response to gonadotropin stimulus  (IEA,ISO)
cellular response to luteinizing hormone stimulus  (ISO,ISS)
central nervous system development  (IEP)
cognition  (ISO)
development of secondary male sexual characteristics  (IEA,ISO)
female gonad development  (ISO)
hormone-mediated signaling pathway  (IBA,IDA)
luteinizing hormone signaling pathway  (IBA,IDA,IEA,ISO)
male gonad development  (IBA,ISO)
ovarian follicle development  (IBA,IEA,ISO)
ovulation cycle process  (IBA,IEA,ISO)
phospholipase C-activating G protein-coupled receptor signaling pathway  (IBA,IDA,IEA,ISO)
positive regulation of calcium ion transport into cytosol  (IDA)
positive regulation of calcium-mediated signaling  (IDA)
positive regulation of hormone biosynthetic process  (IDA)
positive regulation of inositol trisphosphate biosynthetic process  (IEA,ISO)
positive regulation of release of sequestered calcium ion into cytosol  (IDA)
protein targeting to lysosome  (IMP)
regulation of steroid biosynthetic process  (IEP)
regulation of steroid hormone biosynthetic process  (IEA,ISO)
response to luteinizing hormone  (IDA)
response to xenobiotic stimulus  (IEP)
seminiferous tubule development  (IEA,ISO)
spermatogenesis  (IEA,ISO)
uterus development  (IEA,ISO)

Cellular Component

Molecular Function

References

References - curated
1. Aatsinki JT, etal., Mol Cell Endocrinol 1992 Mar;84(1-2):127-35.
2. Angelova K and Puett D, Endocrine 2002 Nov;19(2):147-54.
3. Angelova K, etal., J Biol Chem 2002 Aug 30;277(35):32202-13.
4. Apaja PM, etal., J Biol Chem. 2004 Jan 16;279(3):1899-906. Epub 2003 Oct 27.
5. Apaja PM, etal., Mol Biol Cell. 2006 May;17(5):2243-55. Epub 2006 Feb 22.
6. Bodek G, etal., Neoplasia. 2005 May;7(5):497-508.
7. Bukovsky A, etal., Reprod Biol Endocrinol. 2003 Jun 3;1:46.
8. Canto P, etal., Am J Med Genet. 2002 Mar 1;108(2):148-52.
9. Chu S, etal., Mol Hum Reprod. 2002 May;8(5):426-33.
10. Cooke BA, etal., Biochem Soc Trans. 1987 Feb;15(1):26-8.
11. Davis JS, etal., Biochem J. 1986 Sep 1;238(2):597-604.
12. Dirami G and Cooke BA, Toxicol Appl Pharmacol. 1998 Jun;150(2):393-401.
13. Dufau ML, etal., J Steroid Biochem. 1989 Oct;33(4B):715-20.
14. Evans BA, etal., J Med Genet. 1996 Feb;33(2):143-7.
15. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
16. GOA data from the GO Consortium
17. Horvat RD, etal., Mol Endocrinol. 2001 Apr;15(4):534-42.
18. Ji I and Ji TH, J Biol Chem. 1991 Aug 15;266(23):14953-7.
19. Kash JC and Menon KM, J Biol Chem. 1998 Apr 24;273(17):10658-64.
20. Kishi M and Ascoli M, Mol Endocrinol. 2000 Jun;14(6):926-36.
21. Kusuda S and Dufau ML, J Biol Chem. 1986 Dec 5;261(34):16161-8.
22. Lakkakorpi JT and Rajaniemi HJ, Mol Cell Endocrinol. 1994 Feb;99(1):39-47.
23. Lee C, etal., J Biol Chem 2002 May 3;277(18):15795-800.
24. Liu T, etal., J Neurochem. 2007 Mar;100(5):1329-39. Epub 2007 Jan 11.
25. McFarland KC, etal., Science. 1989 Aug 4;245(4917):494-9.
26. MGD data from the GO Consortium
27. Moraga PF, etal., J Endocrinol. 1997 Aug;154(2):201-9.
28. NCBI rat LocusLink and RefSeq merged data July 26, 2002
29. OMIM Disease Annotation Pipeline
30. Piersma D, etal., Breast Cancer Res. 2007;9(4):R51.
31. Piersma D, etal., Mol Cell Endocrinol. 2007 Sep 30;276(1-2):63-70. Epub 2007 Jul 17.
32. Pietila EM, etal., J Biol Chem. 2005 Jul 15;280(28):26622-9. Epub 2005 May 18.
33. Pipeline to import KEGG annotations from KEGG into RGD
34. Pipeline to import SMPDB annotations from SMPDB into RGD
35. Powell BL, etal., J Clin Endocrinol Metab. 2003 Apr;88(4):1653-7.
36. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
37. RGD automated import pipeline for gene-chemical interactions
38. Roche PC and Ryan RJ, J Biol Chem. 1989 Mar 15;264(8):4636-41.
39. Rodriguez MC and Segaloff DL, Endocrinology. 1990 Aug;127(2):674-81.
40. Sanchez-Yague J, etal., Endocrinology. 1993 Mar;132(3):1007-16.
41. Tsai-Morris CH, etal., J Biol Chem. 1990 Nov 15;265(32):19385-8.
42. Tuusa JT, etal., J Mol Biol. 2007 Aug 17;371(3):622-38. Epub 2007 Mar 15.
43. Yoshino M, etal., Biol Reprod 2002 Jun;66(6):1813-9.
44. Zaleska M, etal., Exp Biol Med (Maywood). 2004 Apr;229(4):335-44.
Additional References at PubMed
PMID:1976554   PMID:2019252   PMID:2040640   PMID:2281186   PMID:7776964   PMID:8026488   PMID:8305508   PMID:8571710   PMID:10493819   PMID:11145748   PMID:11847099   PMID:11940568  
PMID:11943741   PMID:12141913   PMID:12505611   PMID:15767047   PMID:15860556   PMID:15866423   PMID:15919743   PMID:15951841   PMID:16263716   PMID:16336998   PMID:17045394   PMID:17055149  
PMID:18313837   PMID:18467524   PMID:18494797   PMID:18653716   PMID:18848524   PMID:19293332   PMID:19716387   PMID:20610540   PMID:20619315   PMID:21389345   PMID:22367228   PMID:23175774  
PMID:23227193   PMID:23376535   PMID:23678542   PMID:23754802   PMID:24025743   PMID:24467743   PMID:25430649   PMID:25670721   PMID:26116232   PMID:26125464   PMID:26125466   PMID:27940300  
PMID:28605466   PMID:31041823   PMID:32422603  


Genomics

Comparative Map Data
Lhcgr
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.265,661,871 - 5,728,109 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl65,661,871 - 5,724,521 (+)Ensembl
Rnor_6.0612,493,182 - 12,554,482 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl612,493,943 - 12,554,439 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0622,455,216 - 22,516,430 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4612,613,622 - 12,651,587 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1612,613,621 - 12,651,587 (-)NCBI
Celera65,442,191 - 5,504,330 (+)NCBICelera
Cytogenetic Map6q12NCBI
LHCGR
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl248,686,774 - 48,755,730 (-)EnsemblGRCh38hg38GRCh38
GRCh38248,686,774 - 48,755,724 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37248,913,913 - 48,982,863 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36248,767,417 - 48,836,367 (-)NCBINCBI36hg18NCBI36
Build 34248,825,619 - 48,894,468NCBI
Celera248,754,221 - 48,823,183 (-)NCBI
Cytogenetic Map2p16.3NCBI
HuRef248,647,284 - 48,716,442 (-)NCBIHuRef
CHM1_1248,844,653 - 48,913,614 (-)NCBICHM1_1
Lhcgr
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391789,023,812 - 89,099,487 (-)NCBIGRCm39mm39
GRCm39 Ensembl1789,023,909 - 89,099,418 (-)Ensembl
GRCm381788,716,384 - 88,792,059 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1788,716,481 - 88,791,990 (-)EnsemblGRCm38mm10GRCm38
MGSCv371789,140,889 - 89,191,316 (-)NCBIGRCm37mm9NCBIm37
MGSCv361788,649,875 - 88,700,302 (-)NCBImm8
Celera1793,149,952 - 93,199,996 (-)NCBICelera
Cytogenetic Map17E4NCBI
cM Map1758.35NCBI
Lhcgr
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495544115,205,883 - 15,263,617 (-)NCBIChiLan1.0ChiLan1.0
LHCGR
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A49,728,994 - 49,798,780 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v02A48,808,822 - 48,879,021 (-)NCBIMhudiblu_PPA_v0panPan3
LHCGR
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11050,540,706 - 50,594,336 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1050,541,960 - 50,598,036 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1050,394,259 - 50,456,607 (-)NCBI
ROS_Cfam_1.01051,416,899 - 51,479,209 (-)NCBI
UMICH_Zoey_3.11051,119,798 - 51,182,164 (-)NCBI
UNSW_CanFamBas_1.01051,404,008 - 51,466,313 (-)NCBI
UU_Cfam_GSD_1.01051,595,139 - 51,657,483 (-)NCBI
Lhcgr
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629232,499,857 - 32,557,352 (+)NCBI
SpeTri2.0NW_0049365083,928,467 - 3,983,481 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LHCGR
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1391,964,415 - 92,023,821 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2397,929,099 - 97,949,675 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap3q22-q23NCBI
LHCGR
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11458,413,334 - 58,479,124 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604553,365,608 - 53,428,814 (-)NCBIVero_WHO_p1.0
Lhcgr
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473829,902,364 - 29,967,384 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH138460  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.265,724,913 - 5,725,162 (-)MAPPERmRatBN7.2
Rnor_6.0612,492,541 - 12,492,789NCBIRnor6.0
Rnor_5.0622,454,575 - 22,454,823UniSTSRnor5.0
RGSC_v3.4612,612,981 - 12,613,229UniSTSRGSC3.4
Celera65,504,723 - 5,504,971UniSTS
Cytogenetic Map6q12UniSTS
LHCGR  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.265,722,956 - 5,723,449 (-)MAPPERmRatBN7.2
Rnor_6.0612,494,254 - 12,494,746NCBIRnor6.0
Rnor_5.0622,456,288 - 22,456,780UniSTSRnor5.0
RGSC_v3.4612,614,694 - 12,615,186UniSTSRGSC3.4
Celera65,502,766 - 5,503,258UniSTS
Cytogenetic Map6q12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6127574569Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6127574569Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6127574569Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6127574569Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6127574569Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6134235784Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6137618905Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6139036266Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6141223769Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
2293706Bmd20Bone mineral density QTL 204.30.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6507449719988050Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449734434305Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1551
Count of miRNA genes:291
Interacting mature miRNAs:369
Transcripts:ENSRNOT00000022481, ENSRNOT00000045535, ENSRNOT00000048394, ENSRNOT00000064845, ENSRNOT00000073504, ENSRNOT00000074508
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

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 14
Low 1 3 1 1 22 19 2 1
Below cutoff 21 15 9 8 9 2 2 59 13 8 4 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022481   ⟹   ENSRNOP00000022481
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl65,661,871 - 5,724,521 (+)Ensembl
Rnor_6.0 Ensembl612,493,943 - 12,554,439 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096915   ⟹   ENSRNOP00000089069
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl65,661,871 - 5,722,952 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000098297   ⟹   ENSRNOP00000079785
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl65,661,871 - 5,724,521 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101191   ⟹   ENSRNOP00000092292
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl65,674,856 - 5,724,521 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000104322   ⟹   ENSRNOP00000081856
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl65,661,871 - 5,724,521 (+)Ensembl
RefSeq Acc Id: NM_012978   ⟹   NP_037110
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.265,661,871 - 5,724,521 (+)NCBI
Rnor_6.0612,493,182 - 12,554,482 (-)NCBI
Rnor_5.0622,455,216 - 22,516,430 (-)NCBI
RGSC_v3.4612,613,622 - 12,651,587 (-)RGD
Celera65,442,191 - 5,504,330 (+)RGD
Sequence:
RefSeq Acc Id: XM_039111807   ⟹   XP_038967735
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.265,671,998 - 5,728,109 (+)NCBI
RefSeq Acc Id: XM_039111808   ⟹   XP_038967736
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.265,687,605 - 5,728,109 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_037110   ⟸   NM_012978
- Peptide Label: precursor
- UniProtKB: P16235 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022481   ⟸   ENSRNOT00000022481
RefSeq Acc Id: XP_038967735   ⟸   XM_039111807
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038967736   ⟸   XM_039111808
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000092292   ⟸   ENSRNOT00000101191
RefSeq Acc Id: ENSRNOP00000081856   ⟸   ENSRNOT00000104322
RefSeq Acc Id: ENSRNOP00000089069   ⟸   ENSRNOT00000096915
RefSeq Acc Id: ENSRNOP00000079785   ⟸   ENSRNOT00000098297
Protein Domains
G_PROTEIN_RECEP_F1_2

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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
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)
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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
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BN/SsN (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
BUF/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
BXH2/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/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
COP/CrCrl (MCW & UW)
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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)
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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
F344/DuCrl (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
F344/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
F344/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
F344/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
F344/NRrrc (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
F344/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (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
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
FXLE16/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (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)
GK/FarMcwi (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
GK/Ox (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
HXB10/IpcvMcwi (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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (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: 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)
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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
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (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: 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)
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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: 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)
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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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (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: 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)
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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
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (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
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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)
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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
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)
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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
PVG/Seac (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: 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)
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)
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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)
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)
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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)
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
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 (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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3007 AgrOrtholog
Ensembl Genes ENSRNOG00000016712 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000022481 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022481 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro GPCR_Rhodpsn UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPCR_Rhodpsn_7TM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Gphrmn_rcpt_fam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LSH_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25477 UniProtKB/Swiss-Prot
NCBI Gene 25477 ENTREZGENE
Pfam 7tm_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Lhcgr PhenoGen
PRINTS GLYCHORMONER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPCRRHODOPSN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LSHRECEPTOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE G_PROTEIN_RECEP_F1_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  G_PROTEIN_RECEP_F1_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt F1LMG6_RAT UniProtKB/TrEMBL
  LSHR_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary P70646 UniProtKB/Swiss-Prot
  Q63807 UniProtKB/Swiss-Prot
  Q63808 UniProtKB/Swiss-Prot
  Q63809 UniProtKB/Swiss-Prot
  Q6LDI7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Lhcgr  Luteinizing hormone/choriogonadotropin receptor      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_regulation expression is regulated by the Early growth response gene-1 (Egr-1) 729311
gene_transcript has five alternative splicing forms which regulate the expression of the 90 kDa LH/CG receptor 727541