Cyp19a1 (cytochrome P450, family 19, subfamily a, polypeptide 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Cyp19a1 (cytochrome P450, family 19, subfamily a, polypeptide 1) Rattus norvegicus
Analyze
Symbol: Cyp19a1
Name: cytochrome P450, family 19, subfamily a, polypeptide 1
RGD ID: 2457
Description: Enables aromatase activity. Involved in several processes, including animal organ development; carboxylic acid metabolic process; and cellular hormone metabolic process. Located in several cellular components, including dendritic spine; neuronal cell body; and synaptic vesicle. Used to study endometriosis and polycystic ovary syndrome. Biomarker of hypertension; hypothyroidism; placental insufficiency; polycystic ovary syndrome; and protein-energy malnutrition. Human ortholog(s) of this gene implicated in several diseases, including aromatase excess syndrome; bladder neck obstruction; esophagus adenocarcinoma; ovarian disease (multiple); and prostate disease (multiple). Orthologous to human CYP19A1 (cytochrome P450 family 19 subfamily A member 1); PARTICIPATES IN aromatase inhibitor pathway; estradiol biosynthetic pathway; steroid hormone biosynthetic pathway; INTERACTS WITH (+)-catechin; (-)-epigallocatechin 3-gallate; (E)-thiamethoxam.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: aromatase; Cyp19; Cyp19a; CYPXIX; cytochrome P-450AROM; cytochrome P450 19 aromatase; cytochrome P450 19A1; cytochrome P450 19A1-like; cytochrome P450 family 19 subfamily a; cytochrome P450, 19, aromatase; cytochrome P450, subfamily 19; estrogen synthase; estrogen synthetase; LOC100359906; P-450AROM; p450arom
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: QTLs:   GLUCO126_H  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2854,553,165 - 54,580,758 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl854,553,165 - 54,580,758 (-)Ensembl
Rnor_6.0858,744,849 - 58,772,408 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl858,744,849 - 58,772,408 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0857,321,085 - 57,348,481 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.1857,671,013 - 57,691,109 (-)NCBI
Celera854,044,272 - 54,071,684 (-)NCBICelera
Cytogenetic Map8q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (EXP)
(-)-epigallocatechin 3-gallate  (EXP,ISO)
(E)-thiamethoxam  (EXP,ISO)
(S)-naringenin  (EXP,ISO)
(S)-nicotine  (EXP,ISO)
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (EXP,ISO)
1,1,1-Trichloro-2-(4-hydroxyphenyl)-2-(4-methoxyphenyl)ethane  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile  (ISO)
1-benzofuran  (ISO)
1-naphthylamine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3-Bis(3-hydroxybenzyl)butane-1,4-diol  (ISO)
2,4,6-tribromophenol  (ISO)
2,4,6-trichlorophenol  (ISO)
2,4-dibromophenol  (ISO)
2-bromophenol  (ISO)
2-Ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine  (ISO)
3',5'-cyclic AMP  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,3'-diindolylmethane  (ISO)
3,4-dichloroaniline  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-5-yl)benzonitrile  (ISO)
4-\{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino\}benzoic acid  (ISO)
4-Hydroxy-N-desmethyltamoxifen  (ISO)
4-nitrophenol  (EXP)
4-nonylphenol  (ISO)
4-tert-Octylphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
7-hydroxyflavanone  (ISO)
7-hydroxyflavone  (ISO)
8-Br-cAMP  (EXP,ISO)
9-cis-retinoic acid  (EXP,ISO)
acetaldehyde  (ISO)
afimoxifene  (ISO)
Aflatoxicol  (ISO)
aflatoxin B1  (ISO)
AH23848  (ISO)
albuterol  (ISO)
aldrin  (ISO)
all-trans-retinoic acid  (ISO)
allethrin  (EXP)
alpha-naphthoflavone  (ISO)
alternariol  (ISO)
aminoglutethimide  (ISO)
amitraz  (EXP)
amlodipine  (ISO)
ammonium chloride  (EXP)
amoxicillin  (ISO)
amphetamine  (ISO)
anastrozole  (ISO)
androgen antagonist  (EXP)
androst-4-ene-3,17-dione  (EXP,ISO)
androstane-3,17-diol  (EXP)
aniline  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP,ISO)
anthracene  (ISO)
apigenin  (ISO)
Aroclor 1254  (EXP,ISO)
arotinoid acid  (ISO)
arsenite(3-)  (ISO)
atorvastatin calcium  (EXP)
atrazine  (EXP,ISO)
benomyl  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzofurans  (ISO)
beta-naphthoflavone  (ISO)
bezafibrate  (ISO)
bicalutamide  (EXP)
bifenthrin  (EXP,ISO)
bifonazole  (ISO)
biochanin A  (ISO)
biphenyl-4-ol  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bitertanol  (EXP)
Butylbenzyl phthalate  (ISO)
Butylparaben  (EXP,ISO)
cadmium atom  (ISO)
caffeine  (EXP)
calcitriol  (ISO)
cannabidiol  (ISO)
carbendazim  (ISO)
carmustine  (ISO)
celecoxib  (ISO)
chlordecone  (ISO)
chlorogenic acid  (EXP)
chlorpyrifos  (ISO)
Chorionic gonadotropin  (EXP)
chromium(6+)  (EXP)
chrysin  (ISO)
citalopram  (ISO)
clotrimazole  (ISO)
cocaine  (EXP)
colforsin daropate hydrochloride  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cyanamide  (ISO)
cycloheximide  (EXP,ISO)
cyclosporin A  (ISO)
cyhalothrin  (EXP)
cyhexatin  (ISO)
cypermethrin  (EXP,ISO)
cyproconazole  (ISO)
cyproterone  (ISO)
D-aspartic acid  (EXP,ISO)
daidzein  (ISO)
DDE  (EXP,ISO)
DDT  (EXP,ISO)
decabromodiphenyl ether  (ISO)
dehydroepiandrosterone  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (EXP,ISO)
dibutylstannane  (ISO)
dichlorine  (EXP)
dicofol  (ISO)
dicrotophos  (ISO)
dienogest  (ISO)
diethyl phthalate  (EXP,ISO)
diethylstilbestrol  (EXP,ISO)
diisobutyl phthalate  (ISO)
diisononyl phthalate  (ISO)
dimethoate  (ISO)
dipentyl phthalate  (EXP)
disulfiram  (ISO)
doxorubicin  (EXP,ISO)
E-4031  (ISO)
endosulfan  (ISO)
enilconazole  (ISO)
enniatin  (ISO)
Enterolactone  (ISO)
enzacamene  (EXP)
epoxiconazole  (EXP,ISO)
equol  (ISO)
erlotinib hydrochloride  (ISO)
erythrosin B  (EXP)
estriol  (ISO)
estrone  (ISO)
ethanol  (EXP,ISO)
ethosuximide  (ISO)
exemestane  (ISO)
farnesol  (EXP)
fenarimol  (ISO)
fenbuconazole  (ISO)
fentin chloride  (ISO)
fentin hydroxide  (ISO)
fenvalerate  (EXP)
finasteride  (EXP,ISO)
fingolimod hydrochloride  (ISO)
flavanones  (ISO)
flavone  (ISO)
flavones  (ISO)
flavonoids  (EXP,ISO)
fluconazole  (ISO)
flufenoxuron  (ISO)
fluoxetine  (ISO)
flusilazole  (ISO)
flutamide  (EXP)
fluvoxamine  (ISO)
formestane  (EXP,ISO)
fulvestrant  (ISO)
gallic acid  (EXP)
gamma-hexachlorocyclohexane  (ISO)
Geniposidic acid  (EXP)
genistein  (EXP,ISO)
glyphosate  (EXP,ISO)
heptachlor  (ISO)
herbicide  (EXP,ISO)
hesperetin  (ISO)
hexaconazole  (ISO)
HT-2 toxin  (ISO)
ibuprofen  (ISO)
imidacloprid  (ISO)
indometacin  (EXP,ISO)
iodoacetic acid  (ISO)
iprodione  (ISO)
isoliquiritigenin  (ISO)
ketoconazole  (ISO)
L-ascorbic acid  (ISO)
lamotrigine  (ISO)
lead diacetate  (EXP)
leflunomide  (ISO)
letrozole  (EXP,ISO)
leuprolide  (ISO)
levetiracetam  (ISO)
linuron  (EXP)
lipopolysaccharide  (ISO)
LY294002  (EXP,ISO)
malathion  (EXP)
medroxyprogesterone acetate  (ISO)
melamine  (ISO)
melatonin  (EXP,ISO)
metformin  (EXP)
methadone  (ISO)
methomyl  (ISO)
methotrexate  (ISO)
methoxychlor  (EXP,ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
methyltestosterone  (ISO)
metolachlor  (ISO)
miconazole  (ISO)
microcystin-LR  (ISO)
mono(2-ethylhexyl) phthalate  (EXP,ISO)
monobenzyl phthalate  (ISO)
Monobutylphthalate  (ISO)
monoethyl phthalate  (ISO)
mycotoxin  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (EXP,ISO)
N-Nitrosopyrrolidine  (ISO)
nandrolone  (ISO)
naphthalene  (ISO)
nicotine  (EXP,ISO)
Niflumic acid  (ISO)
nimesulide  (EXP,ISO)
Nonylphenol  (ISO)
NS-398  (ISO)
obeticholic acid  (ISO)
ochratoxin A  (ISO)
oleuropein  (ISO)
Oxadiazon  (ISO)
oxcarbazepine  (ISO)
oxiconazole  (ISO)
oxybenzone  (EXP)
ozone  (EXP)
p-tert-Amylphenol  (ISO)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
parathion-methyl  (ISO)
paroxetine  (ISO)
pasireotide  (EXP)
pentachlorophenol  (ISO)
perflubron  (ISO)
perfluorononanoic acid  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
phenanthrene  (ISO)
phenobarbital  (ISO)
phenytoin  (ISO)
PhIP  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirimicarb  (ISO)
pirinixic acid  (EXP)
piroxicam  (ISO)
potassium dichromate  (EXP,ISO)
prochloraz  (EXP,ISO)
procymidone  (EXP)
profenofos  (EXP)
progesterone  (EXP,ISO)
propamocarb  (ISO)
propazine  (ISO)
propiconazole  (EXP,ISO)
propylparaben  (ISO)
prostaglandin E2  (EXP,ISO)
prostaglandin F2alpha  (EXP,ISO)
pyrene  (ISO)
quercetin  (EXP,ISO)
quinalphos  (ISO)
raloxifene  (ISO)
resveratrol  (EXP,ISO)
rolipram  (ISO)
rose bengal  (EXP)
rotenone  (ISO)
rottlerin  (ISO)
rutin  (EXP)
SB-239063  (EXP)
SC-58125  (ISO)
semicarbazide  (EXP)
serpentine asbestos  (ISO)
sertraline  (ISO)
silver atom  (EXP)
silver(0)  (EXP)
simazine  (ISO)
sodium arsenite  (EXP,ISO)
sodium fluoride  (ISO)
T-2 toxin  (ISO)
tamoxifen  (ISO)
tebuconazole  (ISO)
terbutylazine  (EXP)
testolactone  (ISO)
testosterone  (EXP,ISO)
testosterone enanthate  (EXP)
thiacloprid  (ISO)
thiamethoxam  (EXP,ISO)
tiagabine  (ISO)
titanium dioxide  (EXP,ISO)
toxaphene  (ISO)
triadimefon  (ISO)
tributylstannane  (EXP,ISO)
Tributyltin oxide  (ISO)
triclosan  (EXP)
triflusulfuron-methyl  (ISO)
triphenylstannane  (EXP,ISO)
tris(2-butoxyethyl) phosphate  (ISO)
tris(2-chloroethyl) phosphate  (ISO)
troglitazone  (EXP,ISO)
trovafloxacin  (ISO)
U-73122  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vecuronium bromide  (ISO)
vinclozolin  (EXP,ISO)
vitamin E  (EXP)
vorozole  (ISO)
zearalenone  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adrenal gland development  (IEP)
androgen catabolic process  (IEA,ISO)
androgen metabolic process  (IEA,IMP,ISO)
bile acid metabolic process  (IEP)
biphenyl metabolic process  (IEP)
bone development  (IEP)
C21-steroid hormone metabolic process  (IDA)
calcineurin-mediated signaling  (IMP)
cellular response to fibroblast growth factor stimulus  (IEP)
cellular response to follicle-stimulating hormone stimulus  (IEP)
cellular response to glucose stimulus  (IEP)
cellular response to gonadotropin stimulus  (IEP)
cellular response to hydrostatic pressure  (IEP)
dibenzo-p-dioxin metabolic process  (IEP)
estrogen biosynthetic process  (IDA)
female genitalia development  (IEA,ISO)
female gonad development  (IBA,IEA,ISO)
granulocyte differentiation  (IEP)
hippocampus development  (IEP)
hypothalamus development  (IEP)
luteinization  (IEP)
male gonad development  (IEP)
mammary gland development  (IEA,ISO)
melatonin metabolic process  (IEP)
negative regulation of bone resorption  (IMP)
negative regulation of chronic inflammatory response  (IEA,ISO)
negative regulation of macrophage chemotaxis  (IEA,ISO)
phthalate metabolic process  (IEP)
positive regulation of estradiol secretion  (IEA,ISO)
prostate gland growth  (IEA,ISO)
regulation of synapse structure or activity  (IMP)
response to cesium ion  (IEP)
response to estradiol  (IBA,IEP)
response to estrogen  (IEP)
response to herbicide  (IEP)
response to ionizing radiation  (IEP)
response to metal ion  (IEP)
response to morphine  (IEP)
response to organic cyclic compound  (IEP)
response to testosterone  (IEP)
response to xenobiotic stimulus  (IEP)
testosterone biosynthetic process  (IEA,ISO)
uterus development  (IEA,ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Aloisi AM, etal., Mol Pain. 2010 Oct 26;6:69.
2. Bois C, etal., J Mol Endocrinol. 2010 Sep;45(3):147-59. Epub 2010 Jun 16.
3. Bourguiba S, etal., Biol Reprod. 2003 Aug;69(2):592-601. Epub 2003 Apr 16.
4. Burul-Bozkurt N, etal., Naunyn Schmiedebergs Arch Pharmacol. 2010 Jul;382(1):33-41. Epub 2010 Apr 29.
5. Carreau S, etal., J Steroid Biochem Mol Biol 2001 Dec;79(1-5):203-8.
6. Carretero J, etal., Pituitary 2002 Jan;5(1):5-10.
7. Carswell HV, etal., J Steroid Biochem Mol Biol. 2005 Jun;96(1):89-91.
8. Catalano S, etal., J Biol Chem. 2010 Feb 19;285(8):5581-93. Epub 2009 Dec 21.
9. Ceccarelli I, etal., J Cell Physiol. 2009 Oct;221(1):1-4.
10. Chabrolle C, etal., Reprod Biol Endocrinol. 2008 Mar 19;6:11.
11. Colciago A, etal., Brain Res Dev Brain Res. 2005 Mar 31;155(2):107-16.
12. Colciago A, etal., Toxicol Appl Pharmacol. 2009 Aug 15;239(1):46-54. Epub 2009 May 21.
13. da Silva Faria T, etal., Nutrition. 2010 Oct;26(10):1000-7. Epub 2009 Dec 16.
14. Donadeu FX and Ascoli M, Endocrinology. 2005 Sep;146(9):3907-16. Epub 2005 May 26.
15. Ellem SJ, etal., Am J Pathol. 2009 Sep;175(3):1187-99. doi: 10.2353/ajpath.2009.081107. Epub 2009 Aug 21.
16. Escamilla-Hernandez R, etal., Endocrine. 2008 Feb;33(1):21-31. Epub 2008 Apr 10.
17. Escamilla-Hernandez R, etal., Mol Endocrinol. 2008 Aug;22(8):1842-52. Epub 2008 Jun 5.
18. Galmiche G, etal., Ann N Y Acad Sci. 2006 Jul;1070:286-92.
19. Galmiche G, etal., Endocrinology. 2006 Sep;147(9):4234-44. Epub 2006 Jun 8.
20. Gatson JW, etal., Endocrinology. 2010 Nov 3.
21. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
22. Gonzalez A, etal., Br J Cancer. 2007 Sep 17;97(6):755-60. Epub 2007 Aug 14.
23. Grignard E, etal., C R Biol. 2010 May;333(5):416-23. Epub 2010 Apr 24.
24. Grignard E, etal., Int J Toxicol. 2008 Jul-Aug;27(4):323-8.
25. Gulyaeva LF, etal., Adv Exp Med Biol. 2008;617:359-66.
26. Hapon MB, etal., Reprod Biol Endocrinol. 2010 Feb 11;8:14.
27. Hickey GJ, etal., Mol Endocrinol 1990 Jan;4(1):3-12.
28. Hobler C, etal., Toxicology. 2010 Oct 29;276(3):198-205. Epub 2010 Aug 12.
29. Hojo Y, etal., Proc Natl Acad Sci U S A. 2004 Jan 20;101(3):865-70. Epub 2003 Dec 23.
30. Hu MB, etal., Zhonghua Liu Xing Bing Xue Za Zhi. 2006 Apr;27(4):351-5.
31. Huang R and Poduslo SE, J Med Genet. 2006 Aug;43(8):e42.
32. Ito Y, etal., Proc Natl Acad Sci U S A. 1993 Dec 15;90(24):11673-7.
33. Jablonska O, etal., Int J Androl. 2010 Jan 4.
34. KEGG
35. Keskin HL, etal., Eur J Obstet Gynecol Reprod Biol. 2013 Apr;167(2):199-204. doi: 10.1016/j.ejogrb.2012.12.002. Epub 2013 Feb 8.
36. Kimoto T, etal., Endocrinology. 2010 Nov 3.
37. Kobayashi T, etal., J Reprod Dev. 2009 Dec;55(6):629-37. Epub 2009 Sep 7.
38. Lai WA, etal., J Mol Endocrinol. 2014 Oct;53(2):259-70. doi: 10.1530/JME-14-0048. Epub 2014 Jul 23.
39. Lee L, etal., Endocrinology. 2013 Jan;154(1):458-70. doi: 10.1210/en.2012-1610. Epub 2012 Nov 26.
40. Lin W, etal., Am J Pathol. 2011 Mar;178(3):1233-44. doi: 10.1016/j.ajpath.2010.11.056.
41. Lin W, etal., Sheng Li Xue Bao. 2013 Apr 25;65(2):171-7.
42. Liu Z, etal., Mol Endocrinol. 2009 May;23(5):649-61. Epub 2009 Feb 5.
43. MacKenzie SM, etal., J Endocrinol. 2008 Jan;196(1):123-30.
44. Maliqueo M, etal., Endocrinology. 2013 Jan;154(1):434-45. doi: 10.1210/en.2012-1693. Epub 2012 Nov 26.
45. Manigrasso MB, etal., Am J Physiol Renal Physiol. 2012 May 1;302(9):F1203-9. doi: 10.1152/ajprenal.00569.2011. Epub 2012 Feb 1.
46. McDonald CA, etal., Mol Endocrinol. 2006 Mar;20(3):608-18. Epub 2005 Nov 3.
47. MGD data from the GO Consortium
48. Miller WL Rev Endocr Metab Disord. 2009 Mar;10(1):3-17.
49. Miller WR, etal., Oncologist. 2008 Aug;13(8):829-37. Epub 2008 Aug 11.
50. Miyamoto H, etal., J Natl Cancer Inst. 2007 Apr 4;99(7):558-68.
51. Miyoshi T, etal., Mol Cell Endocrinol. 2010 Aug 30;325(1-2):84-92. Epub 2010 Apr 29.
52. Munetsuna E, etal., Endocrinology. 2009 Sep;150(9):4260-9. Epub 2009 Jun 4.
53. Nakamura E, etal., Endocrinology. 2010 Nov;151(11):5506-18. Epub 2010 Sep 1.
54. Napoli N, etal., Bone. 2013 Aug;55(2):309-14. doi: 10.1016/j.bone.2013.04.021. Epub 2013 May 1.
55. NCBI rat LocusLink and RefSeq merged data July 26, 2002
56. Nishizato Y, etal., Toxicol In Vitro. 2010 Mar;24(2):677-85. Epub 2009 Aug 7.
57. Noble LS, etal., J Clin Endocrinol Metab. 1996 Jan;81(1):174-9.
58. O'Grady SP, etal., Syst Biol Reprod Med. 2010 Aug;56(4):292-302.
59. OMIM Disease Annotation Pipeline
60. Payne AH and Hales DB, Endocr Rev. 2004 Dec;25(6):947-70.
61. Pietranera L, etal., Neuroscience. 2010 Nov 27.
62. Pinilla L, etal., Endocrinology. 2009 Jun;150(6):2889-97. Epub 2009 Feb 19.
63. Pipeline to import KEGG annotations from KEGG into RGD
64. RGD automated data pipeline
65. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
66. RGD automated import pipeline for gene-chemical interactions
67. Riancho JA, etal., J Clin Endocrinol Metab. 2007 Feb;92(2):660-5. Epub 2006 Nov 21.
68. Riancho JA, etal., Osteoarthritis Cartilage. 2010 Jul;18(7):927-33. doi: 10.1016/j.joca.2010.04.002. Epub 2010 Apr 22.
69. Rogler LE and Pintar JE, Mol Endocrinol. 1993 Mar;7(3):453-61.
70. Ryu JY, etal., J Toxicol Environ Health A. 2008;71(23):1542-9.
71. Santen RJ, etal., Ann Intern Med. 1982 Jan;96(1):94-101.
72. Schaeffer V, etal., Glia. 2010 Jan 15;58(2):169-80.
73. Shayu D and Rao AJ, Mol Cell Endocrinol. 2006 Apr 25;249(1-2):40-50. Epub 2006 Mar 29.
74. Slominski AT, etal., PLoS One. 2009;4(2):e4309. Epub 2009 Feb 3.
75. Soljancic A, etal., Am J Physiol Regul Integr Comp Physiol. 2013 Apr 3.
76. Srivastava DP, etal., J Neurosci. 2010 Oct 6;30(40):13454-60.
77. Streng T, etal., J Urol. 2002 Jul;168(1):298-302.
78. Takeda T, etal., J Pharmacol Exp Ther. 2009 Jun;329(3):1091-9. Epub 2009 Mar 10.
79. Tamura K, etal., Biol Reprod. 2007 May 23;.
80. Tinfo NS, etal., Reprod Toxicol. 2010 Nov 29.
81. Ugur PK, etal., Eur J Pharmacol. 2010 Nov 27.
82. van der Eerden BC, etal., J Endocrinol. 2004 Mar;180(3):457-67.
83. Vanderschueren D, etal., Calcif Tissue Int. 1996 Sep;59(3):179-83.
84. Wang H, etal., Mol Hum Reprod. 2011 Jun;17(6):386-91. doi: 10.1093/molehr/gar007. Epub 2011 Jan 31.
85. Wu IC, etal., Neoplasia. 2011 Apr;13(4):386-92. doi: 10.1593/neo.101722.
86. Xia X, etal., Zhong Nan Da Xue Xue Bao Yi Xue Ban. 2013 Jan;38(1):54-9. doi: 10.3969/j.issn.1672-7347.2013.01.010.
87. Xiong DH, etal., J Bone Miner Res. 2006 Nov;21(11):1678-95.
88. Xu C, etal., Toxicol Lett. 2010 Dec 15;199(3):323-32.
89. Xu XH, etal., Environ Toxicol Chem. 2010 Jan;29(1):176-81.
90. Zhou L, etal., Exp Neurol. 2007 Jan;203(1):72-81. Epub 2006 Sep 26.
Additional References at PubMed
PMID:2340950   PMID:7669221   PMID:8809197   PMID:9618522   PMID:9687153   PMID:11356695   PMID:14736734   PMID:15364411   PMID:15525594   PMID:16723702   PMID:16770574   PMID:17116232  
PMID:17227882   PMID:17693615   PMID:17804753   PMID:17909262   PMID:18097519   PMID:18287941   PMID:18296822   PMID:18313839   PMID:18401595   PMID:19129847   PMID:19583995   PMID:19698287  
PMID:19838799   PMID:20064538   PMID:20112740   PMID:20214950   PMID:20385561   PMID:20568448   PMID:21392135   PMID:21471296   PMID:21635821   PMID:21932034   PMID:23020785   PMID:23225240  
PMID:23405234   PMID:23606751   PMID:24287798   PMID:24518793   PMID:24556528   PMID:24679120   PMID:24718039   PMID:25036039   PMID:25447050   PMID:26054748   PMID:26482249   PMID:28822806  
PMID:28964927   PMID:29121167   PMID:29880879   PMID:29898754   PMID:30817060   PMID:34215832  


Genomics

Comparative Map Data
Cyp19a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2854,553,165 - 54,580,758 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl854,553,165 - 54,580,758 (-)Ensembl
Rnor_6.0858,744,849 - 58,772,408 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl858,744,849 - 58,772,408 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0857,321,085 - 57,348,481 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.1857,671,013 - 57,691,109 (-)NCBI
Celera854,044,272 - 54,071,684 (-)NCBICelera
Cytogenetic Map8q24NCBI
CYP19A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1551,208,057 - 51,338,601 (-)EnsemblGRCh38hg38GRCh38
GRCh381551,208,057 - 51,338,596 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371551,500,254 - 51,630,793 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361549,288,961 - 49,418,086 (-)NCBINCBI36hg18NCBI36
Celera1528,393,650 - 28,524,194 (-)NCBI
Cytogenetic Map15q21.2NCBI
HuRef1528,330,314 - 28,460,872 (-)NCBIHuRef
CHM1_11551,618,344 - 51,748,904 (-)NCBICHM1_1
Cyp19a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39954,073,221 - 54,175,448 (-)NCBIGRCm39mm39
GRCm39 Ensembl954,073,221 - 54,175,394 (-)Ensembl
GRCm38954,165,937 - 54,268,164 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl954,165,937 - 54,268,110 (-)EnsemblGRCm38mm10GRCm38
MGSCv37954,013,744 - 54,041,249 (-)NCBIGRCm37mm9NCBIm37
MGSCv36953,964,074 - 53,991,581 (-)NCBImm8
Celera951,408,025 - 51,435,376 (-)NCBICelera
Cytogenetic Map9A5.3NCBI
cM Map929.49NCBI
LOC102023780
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554093,266,233 - 3,313,142 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554093,198,622 - 3,313,072 (+)NCBIChiLan1.0ChiLan1.0
CYP19A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11548,486,688 - 48,616,347 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1548,486,688 - 48,521,554 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01530,152,924 - 30,282,854 (-)NCBIMhudiblu_PPA_v0panPan3
CYP19A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13016,954,020 - 17,056,728 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3016,957,215 - 16,988,353 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3016,883,348 - 16,914,898 (-)NCBI
ROS_Cfam_1.03017,098,681 - 17,221,672 (-)NCBI
UMICH_Zoey_3.13017,024,100 - 17,055,822 (-)NCBI
UNSW_CanFamBas_1.03017,141,587 - 17,173,348 (-)NCBI
UU_Cfam_GSD_1.03017,248,285 - 17,280,035 (-)NCBI
LOC101954950
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864095,258,165 - 95,328,751 (-)NCBI
SpeTri2.0NW_00493647113,107,603 - 13,136,910 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CYP19A2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1120,367,667 - 120,695,899 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11120,652,172 - 120,695,899 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21133,903,926 - 133,936,093 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CYP19A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12632,074,260 - 32,164,926 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2632,132,425 - 32,164,277 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666048109,028,218 - 109,061,355 (-)NCBIVero_WHO_p1.0
LOC101702005
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247319,053,644 - 9,100,212 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D8Arb12  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2854,580,298 - 54,580,749 (+)MAPPERmRatBN7.2
Rnor_6.0858,771,949 - 58,772,399NCBIRnor6.0
Rnor_5.0857,348,022 - 57,348,472UniSTSRnor5.0
Celera854,071,225 - 54,071,675UniSTS
SHRSP x BN Map839.17RGD
SHRSP x BN Map839.17UniSTS
FHH x ACI Map847.98RGD
Cytogenetic Map8q23-q24UniSTS
D8Wox16  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2854,580,498 - 54,580,715 (+)MAPPERmRatBN7.2
Rnor_6.0858,772,149 - 58,772,365NCBIRnor6.0
Rnor_5.0857,348,222 - 57,348,438UniSTSRnor5.0
Celera854,071,425 - 54,071,641UniSTS
Cytogenetic Map8q23-q24UniSTS
RH128871  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2854,555,121 - 54,555,308 (+)MAPPERmRatBN7.2
Rnor_6.0858,746,804 - 58,746,990NCBIRnor6.0
Rnor_5.0857,323,040 - 57,323,226UniSTSRnor5.0
RGSC_v3.4857,653,139 - 57,653,325UniSTSRGSC3.4
Celera854,046,227 - 54,046,413UniSTS
RH 3.4 Map8598.7UniSTS
Cytogenetic Map8q23-q24UniSTS
RH133046  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2854,553,027 - 54,553,228 (+)MAPPERmRatBN7.2
Rnor_6.0858,744,712 - 58,744,912NCBIRnor6.0
Rnor_5.0857,320,948 - 57,321,148UniSTSRnor5.0
RGSC_v3.4857,651,047 - 57,651,247UniSTSRGSC3.4
Celera854,044,135 - 54,044,335UniSTS
RH 3.4 Map8597.4UniSTS
Cytogenetic Map8q23-q24UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81490675159906751Rat
61373Mcs4Mammary carcinoma susceptibility QTL 41.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)81629044461290444Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)81898416884531599Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat
631842Inf1Infertility severity QTL 14.10.001seminal gland mass (VT:0010524)seminal vesicle wet weight (CMO:0001603)82266233067662330Rat
2303564Gluco43Glucose level QTL 433blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)82613018771130187Rat
2303572Insul13Insulin level QTL 132blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)82613018771130187Rat
631648Stl5Serum triglyceride level QTL 540.0003blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)82720571554998217Rat
1358892Kidm26Kidney mass QTL 263.69kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)82720571599103503Rat
1358896Bp262Blood pressure QTL 2622.89arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)82720571599103503Rat
1358907Cm40Cardiac mass QTL 401.89heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)82720571599103503Rat
1300146Rf17Renal function QTL 172.9renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)82824291273242912Rat
8662823Vetf5Vascular elastic tissue fragility QTL 51.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)82824291299525068Rat
724514Uae15Urinary albumin excretion QTL 152.9urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)82950266570386295Rat
1549908Neudeg1Neurodegradation QTL 15.50nervous system integrity trait (VT:0010566)logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)83018886794457446Rat
1331744Bp217Blood pressure QTL 2173.398arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815458482492Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
11556286Cm81Cardiac mass QTL 810.01heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)83084815461290444Rat
1359033Bp273Blood pressure QTL 273arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
2313046Bss78Bone structure and strength QTL 783.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)83084815482460899Rat
2313057Bss76Bone structure and strength QTL 7630.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)83084815482460899Rat
2313067Bss77Bone structure and strength QTL 773.10.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)83084815482460899Rat
2313088Bss75Bone structure and strength QTL 753.10.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)83084815482460899Rat
1578755Pur5Proteinuria QTL 53.30.0001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)830848154101699754Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)830848154101699754Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)830848154101699754Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)830848259105647037Rat
1298065Scl16Serum cholesterol level QTL 163.8blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)83085640475856404Rat
1582222Epfw2Epididymal fat weight QTL 23.20.0005epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)83173772976737729Rat
61358Bp39Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83555193880551938Rat
61464Niddm11Non-insulin dependent diabetes mellitus QTL 113.10.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83558203280582032Rat
1331838Niddm61Non-insulin dependent diabetes mellitus QTL 613.530.0004blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83646953599083736Rat
737824Hcar10Hepatocarcinoma resistance QTL 102.9liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)84071306682925667Rat
1358906Bp253Blood pressure QTL 25340.0004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)84071306693965294Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
1331769Rf39Renal function QTL 393.871urine output (VT:0003620)timed urine volume (CMO:0000260)84186687675097878Rat
1298079Activ2Activity QTL 29.50.000001voluntary movement trait (VT:0003491)rearing measurement (CMO:0001515)84186687686866876Rat
631216Stl9Serum triglyceride level QTL 94.710.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)84186701070386132Rat
70161Bp62Blood pressure QTL 622.90.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)84269268490165460Rat
12879882Am8Aortic mass QTL 80.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)84329616998968765Rat
12879878Bw183Body weight QTL 1830.001body mass (VT:0001259)body weight (CMO:0000012)84329616998968765Rat
12879879Cm99Cardiac mass QTL 990.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)84329616998968765Rat
12879880Cm100Cardiac mass QTL 1000.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)84329616998968765Rat
12879881Cm101Cardiac mass QTL 1010.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)84329616998968765Rat
12879883Kidm65Kidney mass QTL 650.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)84329616998968765Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)846531639119088624Rat
1331837Bw23Body weight QTL 234.190.00007body mass (VT:0001259)body weight (CMO:0000012)84653172299083736Rat
2303570Gluco48Glucose level QTL 482blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)84980583194805831Rat
2313086Bss60Bone structure and strength QTL 604.10.0001tibia length (VT:0004357)tibia length (CMO:0000450)85009524982460899Rat
4889938Bss89Bone structure and strength QTL 893.8tibia size trait (VT:0100001)tibia cortical bone volume (CMO:0001725)85009524982460899Rat
5684973Bss100Bone structure and strength QTL 1004.7tibia area (VT:1000281)tibia area measurement (CMO:0001382)85009524982460899Rat
1358912Bw51Body weight QTL 512.95body mass (VT:0001259)body weight (CMO:0000012)851351728107062046Rat
10402857Bp380Blood pressure QTL 3800.95arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
2301402Bp316Blood pressure QTL 3160.005arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
2293697Bmd39Bone mineral density QTL 39femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)85404374498968765Rat
1582243Bw66Body weight QTL 663.40.0048body mass (VT:0001259)body weight (CMO:0000012)85423764485365202Rat
1582254Kidm31Kidney mass QTL 313kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)85423764485365202Rat
631664Hcar3Hepatocarcinoma resistance QTL 32.90.0005liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)85423764499103503Rat
1300150Cm3Cardiac mass QTL 33.97heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)85423781455523877Rat
1300177Cm2Cardiac mass QTL 23.65heart mass (VT:0007028)heart weight (CMO:0000017)854259986100382532Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:168
Count of miRNA genes:125
Interacting mature miRNAs:139
Transcripts:ENSRNOT00000000212
Prediction methods:Microtar, Miranda, Rnahybrid
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 4
Low 20 4 17 4 1 1 38 7 16 9 1
Below cutoff 3 10 24 24 2 24 7 8 24 3 14 2 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000212   ⟹   ENSRNOP00000000212
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl854,553,165 - 54,580,378 (-)Ensembl
Rnor_6.0 Ensembl858,744,849 - 58,772,408 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099462   ⟹   ENSRNOP00000080443
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl854,553,934 - 54,580,758 (-)Ensembl
RefSeq Acc Id: NM_017085   ⟹   NP_058781
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2854,553,165 - 54,580,758 (-)NCBI
Rnor_6.0858,744,849 - 58,772,408 (-)NCBI
Rnor_5.0857,321,085 - 57,348,481 (-)NCBI
Celera854,044,272 - 54,071,684 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_058781 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein ABK88260 (Get FASTA)   NCBI Sequence Viewer  
  ABO65256 (Get FASTA)   NCBI Sequence Viewer  
  EDL95528 (Get FASTA)   NCBI Sequence Viewer  
  EDL95529 (Get FASTA)   NCBI Sequence Viewer  
  P22443 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_058781   ⟸   NM_017085
- Sequence:
RefSeq Acc Id: ENSRNOP00000000212   ⟸   ENSRNOT00000000212
RefSeq Acc Id: ENSRNOP00000080443   ⟸   ENSRNOT00000099462

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)
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (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
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