Rb1 (RB transcriptional corepressor 1) - Rat Genome Database

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Gene: Rb1 (RB transcriptional corepressor 1) Rattus norvegicus
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Symbol: Rb1
Name: RB transcriptional corepressor 1
RGD ID: 3540
Description: Predicted to enable several functions, including disordered domain specific binding activity; enzyme binding activity; and importin-alpha family protein binding activity. Involved in several processes, including negative regulation of apoptotic process; negative regulation of protein kinase activity; and spermatogenesis. Located in nucleus. Biomarker of acute kidney failure. Human ortholog(s) of this gene implicated in nervous system cancer (multiple); osteosarcoma; prostate cancer; small cell carcinoma; and urinary bladder cancer. Orthologous to human RB1 (RB transcriptional corepressor 1); PARTICIPATES IN ceramide signaling pathway; G1/S transition pathway; RNA polymerase III transcription pathway; INTERACTS WITH (Z)-3-butylidenephthalide; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: pp105; pRb; rb; retinoblastoma 1; Retinoblastoma 1 (including osteosarcoma); retinoblastoma-associated protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21548,371,295 - 48,502,473 (-)NCBI
Rnor_6.0 Ensembl1555,083,140 - 55,209,342 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01555,081,582 - 55,209,060 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01558,804,731 - 58,931,886 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41553,828,881 - 53,962,099 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11553,844,684 - 53,977,640 (-)NCBI
Celera1548,020,828 - 48,147,805 (-)NCBICelera
Cytogenetic Map15q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Acute Erythroleukemia  (ISO)
acute kidney failure  (IEP)
acute lymphoblastic leukemia  (ISO)
Adrenal Gland Neoplasms  (ISO)
adrenocortical carcinoma  (ISO)
Animal Mammary Neoplasms  (ISO)
Autosomal Recessive Woolly Hair  (ISO)
B-lymphoblastic leukemia/lymphoma  (ISO)
B-lymphoblastic leukemia/lymphoma with ETV6-RUNX1  (ISO)
basal cell carcinoma  (ISO)
bone osteosarcoma  (ISO)
brain ischemia  (ISO)
Breast Neoplasms  (ISO)
carcinoma  (ISO)
Cardiomegaly  (ISO)
cervix uteri carcinoma in situ  (ISO)
chromosome 13q14 deletion syndrome  (ISO)
disease of cellular proliferation  (ISO)
ductal carcinoma in situ  (ISO)
embryonal carcinoma  (ISO)
Endometrial Neoplasms  (ISO)
esophagus squamous cell carcinoma  (ISO)
Experimental Liver Neoplasms  (ISO)
Experimental Neoplasms  (ISO)
familial retinoblastoma  (ISO)
gastrointestinal stromal tumor  (ISO)
glioblastoma  (ISO)
glioblastoma proneural subtype  (ISO)
head and neck squamous cell carcinoma  (ISO)
hepatocellular carcinoma  (ISO)
Hereditary Neoplastic Syndromes  (ISO)
hereditary nonpolyposis colorectal cancer type 4  (ISO)
hypotrichosis 8  (ISO)
in situ carcinoma  (ISO)
Insulin Resistance  (ISO)
intellectual disability  (ISO)
intestinal pseudo-obstruction  (ISO)
lung non-small cell carcinoma  (ISO)
lung oat cell carcinoma  (ISO)
lung small cell carcinoma  (ISO)
Mammary Neoplasms, Experimental  (ISO)
medulloblastoma  (ISO)
Neoplasm Metastasis  (ISO)
obesity  (ISO)
oligodendroglioma  (ISO)
osteosarcoma  (ISO)
Ovarian Neoplasms  (ISO)
pancreatic cancer  (ISO)
Phyllodes Tumor  (ISO)
Pituitary Neoplasms  (IEP)
prostate cancer  (ISO)
Prostatic Neoplasms  (ISO)
renal cell carcinoma  (ISO)
retinoblastoma  (ISO)
seminoma  (ISO)
Sezary's disease  (ISO)
small cell carcinoma  (ISO)
Stevens-Johnson syndrome  (ISO)
trilateral retinoblastoma  (ISO)
urinary bladder cancer  (ISO)
Urinary Bladder Neoplasm  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(S)-colchicine  (ISO)
(S)-nicotine  (ISO)
(Z)-3-butylidenephthalide  (EXP,ISO)
1,2-dimethylhydrazine  (ISO)
1,3-thiazolidine-2,4-dione  (ISO)
15-deoxy-Delta(12,14)-prostaglandin J2  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-acetamidofluorene  (EXP)
2-butoxyethanol  (ISO)
2-cyclopenten-1-one  (ISO)
2-methylcholine  (ISO)
2-nitrofluorene  (EXP)
3-[3-(tert-butylsulfanyl)-1-(4-chlorobenzyl)-5-(propan-2-yl)-1H-indol-2-yl]-2,2-dimethylpropanoic acid  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (ISO)
3-aminobenzamide  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-nitropropanoic acid  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP,ISO)
4-\{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino\}benzoic acid  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-O-methylguanine  (ISO)
6-oxocampestanol  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
9-cis-retinoic acid  (ISO)
acetylsalicylic acid  (ISO)
aconitine  (ISO)
acrolein  (ISO)
acrylamide  (EXP)
Actein  (ISO)
acteoside  (ISO)
aflatoxin B1  (EXP,ISO)
aflatoxin M1  (ISO)
albuterol  (ISO)
all-trans-retinoic acid  (ISO)
alpha-hexachlorocyclohexane  (EXP)
alpha-naphthoflavone  (ISO)
alpha-pinene  (ISO)
alvocidib  (ISO)
amlodipine  (ISO)
ammonium chloride  (EXP)
amodiaquine  (ISO)
andrographolide  (ISO)
aniline  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arotinoid acid  (ISO)
arsenic trichloride  (ISO)
arsenous acid  (ISO)
Aspidin  (ISO)
atorvastatin calcium  (ISO)
auranofin  (ISO)
baicalein  (ISO)
benzene  (EXP,ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[e]pyrene  (ISO)
benzophenanthridine  (ISO)
beta-naphthoflavone  (EXP)
betulinic acid  (ISO)
bexarotene  (ISO)
bicalutamide  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
BMS-754807  (ISO)
bortezomib  (ISO)
brassinolide  (ISO)
bucladesine  (EXP,ISO)
buspirone  (EXP)
busulfan  (ISO)
butyric acid  (EXP,ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
calciol  (ISO)
calcitriol  (ISO)
calix[6]arene  (ISO)
calmidazolium  (ISO)
calyculin a  (ISO)
camptothecin  (ISO)
canertinib  (ISO)
capecitabine  (ISO)
captan  (ISO)
carbamazepine  (ISO)
cefaloridine  (EXP)
celecoxib  (ISO)
Chloramine  (ISO)
chlordecone  (ISO)
chlorohydrocarbon  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clofibric acid  (EXP)
colforsin daropate hydrochloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
cudraflavone B  (ISO)
cumene  (ISO)
curcumin  (ISO)
cycloheximide  (ISO)
dactolisib  (ISO)
daunorubicin  (ISO)
DDT  (ISO)
Deguelin  (ISO)
dehydroepiandrosterone  (EXP,ISO)
desferrioxamine B  (ISO)
dexamethasone  (EXP,ISO)
Diacetoxyscirpenol  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibutyl phthalate  (EXP)
diclofenac  (ISO)
dicoumarol  (ISO)
dieldrin  (EXP)
diethylstilbestrol  (EXP,ISO)
dioxygen  (ISO)
doxazosin  (EXP,ISO)
doxorubicin  (EXP,ISO)
ellagic acid  (EXP)
emodin  (ISO)
endosulfan  (ISO)
erlotinib hydrochloride  (ISO)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
ethyl trans-caffeate  (ISO)
etoposide  (ISO)
eugenol  (ISO)
everolimus  (ISO)
fenhexamid  (ISO)
ferulic acid  (EXP,ISO)
flavanone  (ISO)
flavonoids  (EXP)
flutamide  (EXP)
fluvastatin  (ISO)
folic acid  (ISO)
folpet  (ISO)
fucoidan  (ISO)
fulvestrant  (ISO)
furan  (EXP)
gadolinium trichloride  (ISO)
galangin  (ISO)
gamma-hexachlorocyclohexane  (EXP)
gamma-tocopherol  (ISO)
gefitinib  (ISO)
genistein  (ISO)
gentamycin  (EXP)
gingerol  (ISO)
glafenine  (EXP)
glutathione  (ISO)
GW 4064  (ISO)
heparin  (ISO)
heptachlor  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
hydroxyurea  (ISO)
ibuprofen  (EXP)
ICI 118551  (ISO)
indoles  (ISO)
indometacin  (EXP,ISO)
irinotecan  (ISO)
isocyanates  (ISO)
isoeugenol  (ISO)
ketamine  (EXP)
KN-93  (ISO)
L-cysteine  (ISO)
lead nitrate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
letrozole  (ISO)
levamisole  (ISO)
linsidomine  (ISO)
lipopolysaccharide  (ISO)
lithium chloride  (ISO)
lonafarnib  (ISO)
lopinavir  (ISO)
lovastatin  (EXP,ISO)
LY294002  (ISO)
lycopene  (ISO)
magnesium atom  (EXP)
maneb  (EXP)
masoprocol  (ISO)
Maxacalcitol  (ISO)
menadione  (ISO)
menaquinone  (ISO)
methapyrilene  (EXP,ISO)
methotrexate  (ISO)
methoxsalen  (ISO)
methoxyacetic acid  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (EXP)
methylseleninic acid  (ISO)
miconazole  (ISO)
mifepristone  (ISO)
mitomycin C  (ISO)
monosodium L-glutamate  (EXP)
motexafin gadolinium  (ISO)
myo-inositol hexakisphosphate  (ISO)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-(6-acetamidohexyl)acetamide  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-ethyl-N-nitrosourea  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
N-methyl-N-nitrosourea  (EXP)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
nefazodone  (EXP)
nelfinavir  (ISO)
nickel atom  (ISO)
nickel dichloride  (ISO)
nicotine  (ISO)
nimesulide  (EXP)
nitrogen dioxide  (ISO)
O-(chloroacetylcarbamoyl)fumagillol  (ISO)
O-methyleugenol  (EXP)
ochratoxin A  (ISO)
okadaic acid  (ISO)
oleic acid  (ISO)
olomoucine  (ISO)
orlistat  (ISO)
oxaliplatin  (ISO)
ozone  (ISO)
p-menthan-3-ol  (ISO)
paclitaxel  (ISO)
palbociclib  (ISO)
panaxydol  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
pentachlorophenol  (EXP)
pentobarbital  (EXP)
perfluorooctanoic acid  (ISO)
phenethyl caffeate  (EXP)
phenobarbital  (EXP)
phenylephrine  (EXP)
PhIP  (EXP,ISO)
phorbol 13-acetate 12-myristate  (ISO)
phosalone  (EXP)
pinosylvin  (ISO)
pioglitazone  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP)
piroxicam  (ISO)
prednisone  (ISO)
proanthocyanidin  (EXP)
procyanidin  (ISO)
progesterone  (ISO)
promethazine  (EXP)
pterostilbene  (EXP)
quercetin  (EXP,ISO)
radicicol  (ISO)
raloxifene  (ISO)
resveratrol  (EXP,ISO)
ritonavir  (ISO)
Ro 41-5253  (ISO)
romidepsin  (ISO)
rottlerin  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 203580  (ISO)
silibinin  (ISO)
simvastatin  (EXP,ISO)
sirolimus  (EXP,ISO)
sirtinol  (ISO)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP,ISO)
sodium dodecyl sulfate  (ISO)
sorafenib  (ISO)
sulforaphane  (ISO)
sulfur dioxide  (EXP)
sulindac  (ISO)
sulindac sulfide  (ISO)
sunitinib  (ISO)
T-2 toxin  (EXP)
tamoxifen  (EXP,ISO)
tanespimycin  (ISO)
Tanshinone I  (ISO)
tauroursodeoxycholic acid  (EXP)
tazarotene  (ISO)
temozolomide  (ISO)
Temsirolimus  (ISO)
terephthalic acid  (EXP)
teriflunomide  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP,ISO)
theophylline  (ISO)
thioacetamide  (EXP)
thiophenes  (ISO)
tocopherol  (ISO)
tolbutamide  (EXP)
toluene  (EXP)
toxaphene  (ISO)
trametinib  (ISO)
trans-isoeugenol  (ISO)
trans-pinosylvin  (ISO)
trichostatin A  (ISO)
tris(2-chloroethyl) phosphate  (ISO)
troglitazone  (ISO)
trovafloxacin  (EXP)
tunicamycin  (ISO)
tyrphostin AG 1478  (ISO)
urethane  (ISO)
ursodeoxycholic acid  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vincristine  (ISO)
vinyl carbamate  (ISO)
vorinostat  (ISO)
wortmannin  (EXP,ISO)
Y-27632  (ISO)
zebularine  (ISO)
zinc acetate  (ISO)
zinc atom  (ISO)
zinc sulfate  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
aortic valve morphogenesis  (IEA,ISO)
apoptotic process  (ISO)
cell differentiation  (IBA)
cell division  (IEA,ISO)
cell morphogenesis involved in neuron differentiation  (IBA,IEA,ISO)
cellular response to insulin stimulus  (ISO)
cellular response to xenobiotic stimulus  (IEA,ISO)
chondrocyte differentiation  (ISO)
chromatin organization  (IEA)
digestive tract development  (IEA,ISO)
enucleate erythrocyte differentiation  (IEA,ISO)
G1/S transition of mitotic cell cycle  (ISO)
glial cell apoptotic process  (IEA,ISO)
hepatocyte apoptotic process  (IEA,ISO)
maintenance of mitotic sister chromatid cohesion  (IEA,ISO)
myoblast differentiation  (IEA,ISO,ISS)
negative regulation of apoptotic signaling pathway  (IMP)
negative regulation of cell cycle  (IMP,ISO)
negative regulation of cell growth  (IEA,ISO,ISS)
negative regulation of cell population proliferation  (ISO)
negative regulation of cold-induced thermogenesis  (ISO,ISS)
negative regulation of epithelial cell proliferation  (IEA,ISO)
negative regulation of G1/S transition of mitotic cell cycle  (IBA,IEA,ISO)
negative regulation of gene expression  (IEA,ISO)
negative regulation of hepatocyte apoptotic process  (IMP)
negative regulation of inflammatory response  (IEA,ISO)
negative regulation of mitotic cell cycle  (ISO)
negative regulation of myofibroblast differentiation  (IEA,ISO)
negative regulation of protein kinase activity  (IEA,ISO,ISS)
negative regulation of protein serine/threonine kinase activity  (IMP)
negative regulation of smoothened signaling pathway  (IEA,ISO)
negative regulation of tau-protein kinase activity  (IMP)
negative regulation of transcription by RNA polymerase II  (IEA,ISO)
negative regulation of transcription involved in G1/S transition of mitotic cell cycle  (IEA,ISO)
negative regulation of transcription, DNA-templated  (ISO)
neuron apoptotic process  (IEA,ISO)
neuron differentiation  (ISO)
neuron maturation  (IEA,ISO)
neuron projection development  (IBA,IEA,ISO)
positive regulation of collagen fibril organization  (IEA,ISO)
positive regulation of extracellular matrix organization  (ISO)
positive regulation of macrophage differentiation  (IEA,ISO)
positive regulation of mitotic metaphase/anaphase transition  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (IEA,ISO)
positive regulation of transcription regulatory region DNA binding  (IEA,ISO)
protein localization to chromosome, centromeric region  (IEA,ISO)
Ras protein signal transduction  (IEA,ISO)
regulation of cell cycle  (ISO)
regulation of cell growth  (ISO)
regulation of cohesin loading  (IEA,ISO)
regulation of lipid kinase activity  (IEA,ISO,ISS)
regulation of mitotic cell cycle  (ISO)
sister chromatid biorientation  (IEA,ISO)
skeletal muscle cell differentiation  (IEA,ISO)
spermatogenesis  (IEP)
striated muscle cell differentiation  (IEA,ISO)
tissue homeostasis  (IEA,ISO)

Cellular Component

References

References - curated
1. Absalon S, etal., J Neurosci. 2013 Sep 11;33(37):14645-59. doi: 10.1523/JNEUROSCI.1327-13.2013.
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3. Bartkova J, etal., J Pathol. 2003 Jun;200(2):149-56.
4. Bettendorf O, etal., Genes Chromosomes Cancer. 2008 Jul;47(7):565-72.
5. Bieche I and Lidereau R, Mol Carcinog. 2000 Nov;29(3):151-8.
6. B├Ącklund LM, etal., Br J Cancer. 2005 Jul 11;93(1):124-30. doi: 10.1038/sj.bjc.6602661.
7. Choy KW, etal., Hum Mutat. 2002 Nov;20(5):408.
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14. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
15. Gill RM and Hamel PA, J Cell Biol. 2000 Mar 20;148(6):1187-201.
16. Gjidoda A and Henry RW, Biochim Biophys Acta. 2013 Mar-Apr;1829(3-4):385-92. doi: 10.1016/j.bbagrm.2012.09.011. Epub 2012 Oct 12.
17. GOA data from the GO Consortium
18. Goldhoff P, etal., J Neuropathol Exp Neurol. 2012 Jan;71(1):83-9. doi: 10.1097/NEN.0b013e31823fe8f1.
19. Haitel A, etal., Urology. 2001 Sep;58(3):477-81.
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21. Kommoss S, etal., Br J Cancer. 2007 Jan 29;96(2):306-13.
22. Kruse AJ, etal., Hum Pathol. 2008 Apr;39(4):573-8. Epub 2008 Jan 30.
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25. Marino S, etal., Genes Dev 2000 Apr 15;14(8):994-1004.
26. Mercader J, etal., Am J Physiol Endocrinol Metab. 2009 Jul;297(1):E184-93. doi: 10.1152/ajpendo.00163.2009. Epub 2009 May 5.
27. MGD data from the GO Consortium
28. Moreno-Navarrete JM, etal., Diabetes. 2013 Jun;62(6):1923-31. doi: 10.2337/db12-0977. Epub 2013 Jan 11.
29. Nakamura M, etal., Lab Invest. 2001 Jan;81(1):77-82.
30. NCBI rat LocusLink and RefSeq merged data July 26, 2002
31. Niu Y, etal., Zhonghua Zhong Liu Za Zhi. 2004 May;26(5):290-3.
32. OMIM Disease Annotation Pipeline
33. Ozaki T and Sakiyama S, DNA Cell Biol. 1996 Nov;15(11):975-9.
34. Pipeline to import KEGG annotations from KEGG into RGD
35. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
36. Qiu Z and Ghosh A, Neuron. 2008 Dec 10;60(5):775-87. doi: 10.1016/j.neuron.2008.09.040.
37. RGD automated data pipeline
38. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
39. RGD automated import pipeline for gene-chemical interactions
40. Semczuk A, etal., Arch Gynecol Obstet. 2004 Jan;269(2):104-10. Epub 2002 Nov 22.
41. Song H, etal., Cancer Res. 2006 Oct 15;66(20):10220-6.
42. Spandidos DA, etal., Anticancer Res. 1992 Jan-Feb;12(1):81-9.
43. Tan KA, etal., Biol Reprod. 2005 May;72(5):1151-60. Epub 2005 Jan 19.
44. Taylor M, etal., Hum Mutat. 2007 Mar;28(3):284-93.
45. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
46. Woitach JT, etal., Nat Genet 1998 Aug;19(4):371-4.
47. Yang QH, etal., J Infect. 2009 Jun;58(6):459-64. doi: 10.1016/j.jinf.2009.04.003. Epub 2009 Apr 17.
Additional References at PubMed
PMID:7665085   PMID:7797074   PMID:7958874   PMID:8245034   PMID:8288605   PMID:8336704   PMID:8441612   PMID:8612582   PMID:8889548   PMID:9054499   PMID:9178770   PMID:9448006  
PMID:9858607   PMID:10082561   PMID:10783144   PMID:10888886   PMID:10944455   PMID:11246230   PMID:11301474   PMID:11331592   PMID:11549719   PMID:12037672   PMID:12065415   PMID:12200151  
PMID:12221087   PMID:12695505   PMID:12757710   PMID:12853964   PMID:14693709   PMID:15069084   PMID:15084472   PMID:15169903   PMID:15459751   PMID:15509711   PMID:15541338   PMID:15542848  
PMID:15616565   PMID:15640164   PMID:15701640   PMID:15735701   PMID:15735762   PMID:15831459   PMID:15843406   PMID:15870077   PMID:15898111   PMID:16126730   PMID:16286473   PMID:16360038  
PMID:16407335   PMID:16513252   PMID:16616919   PMID:16896691   PMID:17257418   PMID:17540172   PMID:17989570   PMID:18348166   PMID:18351461   PMID:18364697   PMID:18583990   PMID:18656278  
PMID:18692063   PMID:18700867   PMID:19123049   PMID:19223331   PMID:19505811   PMID:20023236   PMID:20213763   PMID:20224733   PMID:20485545   PMID:20551165   PMID:20924203   PMID:21504794  
PMID:22147266   PMID:22885065   PMID:23371354   PMID:23487765   PMID:24068000   PMID:24726645   PMID:25100735   PMID:27056896   PMID:29304157  


Genomics

Comparative Map Data
Rb1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21548,371,295 - 48,502,473 (-)NCBI
Rnor_6.0 Ensembl1555,083,140 - 55,209,342 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01555,081,582 - 55,209,060 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01558,804,731 - 58,931,886 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41553,828,881 - 53,962,099 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11553,844,684 - 53,977,640 (-)NCBI
Celera1548,020,828 - 48,147,805 (-)NCBICelera
Cytogenetic Map15q11NCBI
RB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1348,303,744 - 48,599,436 (+)EnsemblGRCh38hg38GRCh38
GRCh381348,303,751 - 48,481,890 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371348,877,887 - 49,056,026 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361347,775,884 - 47,954,027 (+)NCBINCBI36hg18NCBI36
Build 341347,775,911 - 47,954,023NCBI
Celera1329,932,627 - 30,110,747 (+)NCBI
Cytogenetic Map13q14.2NCBI
HuRef1329,670,144 - 29,848,118 (+)NCBIHuRef
CHM1_11348,845,597 - 49,023,603 (+)NCBICHM1_1
Rb1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391473,430,298 - 73,563,446 (-)NCBIGRCm39mm39
GRCm39 Ensembl1473,421,113 - 73,563,262 (-)Ensembl
GRCm381473,192,858 - 73,325,951 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1473,183,673 - 73,325,822 (-)EnsemblGRCm38mm10GRCm38
MGSCv371473,595,309 - 73,725,598 (-)NCBIGRCm37mm9NCBIm37
MGSCv361471,929,656 - 72,059,895 (-)NCBImm8
Celera1470,715,843 - 70,870,859 (-)NCBICelera
Cytogenetic Map14D3NCBI
cM Map1438.73NCBI
Rb1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554311,960,661 - 2,124,576 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554311,960,765 - 2,124,576 (+)NCBIChiLan1.0ChiLan1.0
RB1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11348,155,608 - 48,326,396 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1348,155,795 - 48,324,575 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01329,453,872 - 29,624,665 (+)NCBIMhudiblu_PPA_v0panPan3
RB1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1223,061,621 - 3,204,625 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl223,063,239 - 3,257,726 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha223,090,617 - 3,235,458 (-)NCBI
ROS_Cfam_1.0223,143,918 - 3,320,581 (-)NCBI
UMICH_Zoey_3.1222,960,514 - 3,106,149 (-)NCBI
UNSW_CanFamBas_1.0223,023,421 - 3,169,707 (-)NCBI
UU_Cfam_GSD_1.0223,028,586 - 3,174,226 (-)NCBI
Rb1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945158,103,473 - 158,265,512 (+)NCBI
SpeTri2.0NW_0049365651,596,227 - 1,746,706 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RB1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1119,186,759 - 19,317,690 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11119,186,754 - 19,317,642 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21119,648,360 - 19,770,943 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RB1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1326,220,783 - 26,393,671 (+)NCBI
ChlSab1.1 Ensembl326,220,803 - 26,394,546 (+)Ensembl
Vero_WHO_p1.0NW_02366605717,512,606 - 17,688,151 (-)NCBI
Rb1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247486,358,588 - 6,533,217 (-)NCBI

Position Markers
RH94875  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21548,372,696 - 48,372,923 (+)MAPPER
Rnor_6.01555,082,984 - 55,083,210NCBIRnor6.0
Rnor_5.01558,806,133 - 58,806,359UniSTSRnor5.0
RGSC_v3.41553,830,283 - 53,830,509UniSTSRGSC3.4
Celera1548,022,230 - 48,022,456UniSTS
Cytogenetic Map15q12UniSTS
PMC104404P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
RGSC_v3.41553,962,001 - 53,962,504UniSTSRGSC3.4
Cytogenetic Map15q12UniSTS
M26391  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21548,372,900 - 48,372,983 (+)MAPPER
Rnor_6.01555,083,188 - 55,083,270NCBIRnor6.0
Rnor_5.01558,806,337 - 58,806,419UniSTSRnor5.0
RGSC_v3.41553,830,487 - 53,830,569UniSTSRGSC3.4
Celera1548,022,434 - 48,022,516UniSTS
Cytogenetic Map15q12UniSTS
BE098816  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21548,428,262 - 48,428,442 (+)MAPPER
Rnor_6.01555,138,656 - 55,138,835NCBIRnor6.0
Rnor_5.01558,861,789 - 58,861,968UniSTSRnor5.0
RGSC_v3.41553,887,416 - 53,887,595UniSTSRGSC3.4
Celera1548,077,756 - 48,077,935UniSTS
Cytogenetic Map15q12UniSTS
RH94505  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21548,372,062 - 48,372,257 (+)MAPPER
mRatBN7.21548,372,108 - 48,372,257 (+)MAPPER
Rnor_6.01555,082,396 - 55,082,544NCBIRnor6.0
Rnor_6.01555,082,350 - 55,082,544NCBIRnor6.0
Rnor_5.01558,805,545 - 58,805,693UniSTSRnor5.0
Rnor_5.01558,805,499 - 58,805,693UniSTSRnor5.0
RGSC_v3.41553,829,649 - 53,829,843UniSTSRGSC3.4
RGSC_v3.41553,829,695 - 53,829,843UniSTSRGSC3.4
Celera1548,021,642 - 48,021,790UniSTS
Celera1548,021,596 - 48,021,790UniSTS
Cytogenetic Map15q12UniSTS
RH138574  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21548,416,875 - 48,417,014 (+)MAPPER
Rnor_6.01555,127,281 - 55,127,419NCBIRnor6.0
Rnor_5.01558,850,398 - 58,850,536UniSTSRnor5.0
RGSC_v3.41553,875,791 - 53,875,929UniSTSRGSC3.4
Celera1548,066,406 - 48,066,544UniSTS
Cytogenetic Map15p11UniSTS
Cytogenetic Map15q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15162301382Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151071919155719191Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151549236072568189Rat
9590272Scort14Serum corticosterone level QTL 142.780.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)151698090761980907Rat
8694427Bw163Body weight QTL 1634.820.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)151698090761980907Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151724964162249641Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151809320881255430Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151851391388036354Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1526381041106550657Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1526381041106550657Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1526381041106550657Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152870974173709741Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)153321910189640841Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)153321910189640841Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)153321910189640841Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)153948079762596410Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153974955779033707Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153974955779033707Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)154106809486068094Rat
7411725Strs7Sensitivity to stroke QTL 73.8cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)154275724156027084Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1543097470106550657Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:677
Count of miRNA genes:300
Interacting mature miRNAs:381
Transcripts:ENSRNOT00000021752
Prediction methods:Microtar, Miranda
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 3 32 38 22 19 22 8 9 74 35 38 11 8
Low 11 19 19 19 2 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021752   ⟹   ENSRNOP00000021752
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1555,083,140 - 55,209,342 (-)Ensembl
RefSeq Acc Id: NM_017045   ⟹   NP_058741
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21548,371,295 - 48,502,302 (-)NCBI
Rnor_6.01555,081,582 - 55,209,060 (-)NCBI
Rnor_5.01558,804,731 - 58,931,886 (-)NCBI
RGSC_v3.41553,828,881 - 53,962,099 (-)RGD
Celera1548,020,828 - 48,147,805 (-)RGD
Sequence:
RefSeq Acc Id: XM_039092994   ⟹   XP_038948922
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21548,431,120 - 48,502,473 (-)NCBI
RefSeq Acc Id: XR_005493691
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21548,382,594 - 48,502,468 (-)NCBI
Protein Sequences
Protein RefSeqs NP_058741 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948922 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA42090 (Get FASTA)   NCBI Sequence Viewer  
  BAA04958 (Get FASTA)   NCBI Sequence Viewer  
  EDM02266 (Get FASTA)   NCBI Sequence Viewer  
  P33568 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_058741   ⟸   NM_017045
- Sequence:
RefSeq Acc Id: ENSRNOP00000021752   ⟸   ENSRNOT00000021752
RefSeq Acc Id: XP_038948922   ⟸   XM_039092994
- Peptide Label: isoform X1
Protein Domains
CYCLIN   DUF3452   RB_A   Rb_C

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 (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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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
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)
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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
MR/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
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (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 (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