Bad (BCL2-associated agonist of cell death) - Rat Genome Database

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Gene: Bad (BCL2-associated agonist of cell death) Rattus norvegicus
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Symbol: Bad
Name: BCL2-associated agonist of cell death
RGD ID: 620103
Description: Enables 14-3-3 protein binding activity; protein kinase B binding activity; and protein phosphatase 2B binding activity. Involved in several processes, including cellular response to chromate; positive regulation of cell death; and response to steroid hormone. Located in cytosol and mitochondrion. Used to study several diseases, including Parkinsonism; diabetic neuropathy; gastric ulcer; impotence; and middle cerebral artery infarction. Biomarker of several diseases, including acute kidney failure; artery disease (multiple); brain disease (multiple); obesity; and type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in endometrial cancer; lung non-small cell carcinoma; and pancreatic cancer. Orthologous to human BAD (BCL2 associated agonist of cell death); PARTICIPATES IN adenosine signaling pathway; ceramide signaling pathway; endometrial cancer pathway; INTERACTS WITH (R,R,R)-alpha-tocopherol; (S)-nicotine; 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Bad_v1; Bad_v2; bcl-2 associated death agonist; bcl-2-binding component 6; bcl-xL/Bcl-2-associated death promoter; bcl2 antagonist of cell death; Bcl2-antagonist of cell death; BCL2-associated agonist of cell death, variant 1; BCL2-associated agonist of cell death, variant 2; bcl2-associated death promoter; MGC72439
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21204,133,502 - 204,142,829 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1204,131,501 - 204,142,823 (+)Ensembl
Rnor_6.01222,198,516 - 222,207,459 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1222,198,534 - 222,207,453 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01229,189,271 - 229,198,306 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41209,617,373 - 209,626,292 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11209,775,802 - 209,784,722NCBI
Celera1201,667,864 - 201,676,765 (+)NCBICelera
Cytogenetic Map1q43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-epicatechin-3-O-gallate  (ISO)
(-)-Arctigenin  (ISO)
(R,R,R)-alpha-tocopherol  (EXP)
(S)-nicotine  (EXP,ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,3-Dinitropyrene  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-nitropyrene  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
1H-pyrazole  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-methoxy-17beta-estradiol  (ISO)
2-naphthylamine  (ISO)
3,3',5-triiodo-L-thyronine  (EXP,ISO)
3,3'-diindolylmethane  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-methylcholanthrene  (EXP)
3-nitropropanoic acid  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (ISO)
4-hydroxynon-2-enal  (ISO)
4-nonylphenol  (EXP)
5-azacytidine  (EXP)
5-fluorouracil  (EXP)
9,10-anthraquinone  (ISO)
acetochlor  (ISO)
acetylsalicylic acid  (ISO)
acrolein  (ISO)
AH23848  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
alloxan  (EXP)
alvocidib  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
anthocyanin  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
aprepitant  (ISO)
arachidonic acid  (ISO)
aristolochic acid  (ISO)
arjunolic acid  (EXP,ISO)
arsenite(3-)  (ISO)
arsenous acid  (EXP,ISO)
azadirachtin A  (ISO)
benzene  (EXP)
benzo[a]pyrene  (ISO)
Benzo[a]pyrene-7,8-diol  (ISO)
benzo[b]fluoranthene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
cadmium dichloride  (EXP,ISO)
cadmium sulfide  (ISO)
calciol  (ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
cannabidiol  (ISO)
capsaicin  (ISO)
carbon monoxide  (ISO)
carbon nanotube  (ISO)
carnosic acid  (ISO)
chlorpyrifos  (ISO)
chromium(6+)  (ISO)
ciglitazone  (EXP)
cisplatin  (ISO)
clonidine  (ISO)
clonidine (amino form)  (ISO)
clonidine (imino form)  (ISO)
cocaine  (ISO)
coenzyme Q10  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
cordycepin  (ISO)
coumarin  (ISO)
curcumin  (EXP,ISO)
cyclophosphamide  (EXP,ISO)
cyclosporin A  (EXP,ISO)
D-glucose  (ISO)
D-mannitol  (EXP)
dehydroepiandrosterone  (EXP)
delphinidin  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (EXP,ISO)
dibenzoylmethane  (ISO)
dibutyl phthalate  (EXP,ISO)
dicrotophos  (ISO)
diethanolamine  (EXP,ISO)
diethylstilbestrol  (ISO)
dimethylarsinic acid  (EXP,ISO)
dioscin  (ISO)
diosmin  (EXP)
dioxygen  (EXP,ISO)
doxorubicin  (EXP,ISO)
doxycycline  (ISO)
ellagic acid  (ISO)
endosulfan  (EXP)
entinostat  (EXP)
erlotinib hydrochloride  (ISO)
ethanol  (EXP)
ethyl methanesulfonate  (ISO)
eugenol  (ISO)
flufenamic acid  (ISO)
flufenoxuron  (ISO)
fluoxetine  (ISO)
flutamide  (EXP)
folic acid  (ISO)
folpet  (ISO)
fulvestrant  (EXP)
furosemide  (EXP)
Fusarenone X  (ISO)
gamma-aminobutyric acid  (EXP)
genistein  (EXP)
ginsenoside Rg1  (EXP)
glucose  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
graphite  (ISO)
hexadecanoic acid  (ISO)
hydralazine  (ISO)
hydrogen peroxide  (EXP,ISO)
hydroquinone  (ISO)
Idoxifene  (EXP)
indometacin  (ISO)
iron atom  (ISO)
iron(0)  (ISO)
isoflurane  (EXP)
juglone  (ISO)
ketoconazole  (EXP)
L-ascorbic acid  (EXP,ISO)
lead diacetate  (EXP)
Licochalcone A  (ISO)
lipopolysaccharide  (EXP)
LY294002  (EXP,ISO)
maneb  (ISO)
melamine  (ISO)
melatonin  (ISO)
mercury atom  (ISO)
mercury dichloride  (ISO)
mercury(0)  (ISO)
metformin  (ISO)
methoxychlor  (EXP)
methyl methanesulfonate  (ISO)
methylglyoxal  (ISO)
methylmercury chloride  (EXP,ISO)
microcystin-LR  (ISO)
mifepristone  (EXP,ISO)
mitomycin C  (ISO)
MK-2206  (ISO)
monodansylcadaverine  (ISO)
N-(4-aminobutyl)-5-chloronaphthalene-2-sulfonamide  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-acetylsphingosine  (ISO)
N-ethyl-N-nitrosourea  (ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-methyl-N-nitrosourea  (EXP)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
naringin  (EXP,ISO)
nickel dichloride  (EXP)
niclosamide  (ISO)
nicotine  (EXP,ISO)
norfloxacin  (ISO)
Obacunone  (ISO)
obeticholic acid  (ISO)
ochratoxin A  (EXP,ISO)
okadaic acid  (ISO)
omacetaxine mepesuccinate  (ISO)
oxaliplatin  (ISO)
oxybenzone  (EXP)
p-menthan-3-ol  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
PD 168393  (ISO)
pentachlorophenol  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
peroxynitrous acid  (ISO)
phenobarbital  (EXP)
phenylephrine  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
PK-11195  (EXP)
plumbagin  (EXP)
potassium dichromate  (EXP)
Pranoprofen  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
progesterone  (EXP)
propylparaben  (ISO)
pterostilbene  (ISO)
PX-866  (ISO)
quercetin  (EXP,ISO)
raloxifene  (ISO)
reactive oxygen species  (ISO)
resveratrol  (EXP,ISO)
rotenone  (EXP,ISO)
rottlerin  (ISO)
ruthenium atom  (ISO)
S-nitroso-N-acetyl-D-penicillamine  (ISO)
Salvianolic acid A  (EXP)
sildenafil citrate  (ISO)
simvastatin  (ISO)
sirolimus  (ISO)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP)
sodium fluoride  (ISO)
sorafenib  (ISO)
spironolactone  (EXP)
stilbenoid  (ISO)
streptozocin  (EXP)
sulforaphane  (ISO)
sulindac  (ISO)
sulindac sulfide  (ISO)
tacrolimus hydrate  (EXP,ISO)
tamoxifen  (ISO)
taurine  (EXP)
tauroursodeoxycholic acid  (EXP,ISO)
tert-butyl hydroperoxide  (EXP,ISO)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
tetrahydropalmatine  (ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
Thiotepa  (ISO)
thyroxine  (ISO)
tigecycline  (EXP)
Tiron  (ISO)
titanium dioxide  (ISO)
tomelukast  (EXP)
triamcinolone acetonide  (EXP)
tributylstannane  (ISO)
trichloroethene  (ISO)
trimethyltin  (ISO)
triptonide  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vanillic acid  (ISO)
vemurafenib  (ISO)
vorinostat  (ISO)
withaferin A  (ISO)
wortmannin  (EXP,ISO)
Y-27632  (ISO)
zoledronic acid  (ISO)
zolmitriptan  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of cysteine-type endopeptidase activity  (IBA,ISO)
activation of cysteine-type endopeptidase activity involved in apoptotic process  (ISO,ISS)
ADP metabolic process  (ISO,ISS)
apoptotic process  (ISO)
apoptotic signaling pathway  (ISO)
ATP metabolic process  (ISO,ISS)
cell population proliferation  (ISO)
cellular response to chromate  (IEP)
cellular response to hypoxia  (IBA,ISO)
cellular response to lipid  (ISO)
cellular response to mechanical stimulus  (ISO)
cellular response to nicotine  (ISO,ISS)
cerebral cortex development  (IEP)
cytokine-mediated signaling pathway  (ISO)
extrinsic apoptotic signaling pathway  (IBA,ISO)
extrinsic apoptotic signaling pathway in absence of ligand  (ISO)
extrinsic apoptotic signaling pathway via death domain receptors  (ISO)
glucose catabolic process  (ISO)
glucose homeostasis  (ISO,ISS)
intrinsic apoptotic signaling pathway  (IBA,ISO,ISS)
intrinsic apoptotic signaling pathway in response to DNA damage  (ISO)
pore complex assembly  (ISO,ISS)
positive regulation of apoptotic process  (ISO)
positive regulation of apoptotic process by virus  (ISO)
positive regulation of B cell differentiation  (ISO)
positive regulation of cysteine-type endopeptidase activity involved in apoptotic process  (ISO,ISS)
positive regulation of epithelial cell proliferation  (ISO,ISS)
positive regulation of glucokinase activity  (ISO,ISS)
positive regulation of granulosa cell apoptotic process  (IDA)
positive regulation of insulin secretion  (ISO,ISS)
positive regulation of insulin secretion involved in cellular response to glucose stimulus  (ISO)
positive regulation of intrinsic apoptotic signaling pathway in response to osmotic stress  (ISO)
positive regulation of mitochondrial membrane potential  (ISO,ISS)
positive regulation of neuron death  (IDA,IMP)
positive regulation of proteolysis  (ISO)
positive regulation of release of cytochrome c from mitochondria  (ISO)
positive regulation of T cell differentiation  (ISO)
positive regulation of type B pancreatic cell development  (ISO,ISS)
regulation of apoptotic process  (ISO)
regulation of cysteine-type endopeptidase activity involved in apoptotic process  (ISO)
regulation of mitochondrial membrane permeability  (IBA,ISO,ISS)
release of cytochrome c from mitochondria  (IBA,ISO)
response to amino acid  (IEP)
response to benzene  (IEP)
response to calcium ion  (IEP)
response to estradiol  (IEP)
response to ethanol  (IEP)
response to glucocorticoid  (IEP)
response to glucose  (IEP)
response to hormone  (IEP)
response to hydrogen peroxide  (IEP)
response to hypoxia  (IEP)
response to oleic acid  (IEP)
response to organic cyclic compound  (IEP)
response to organic substance  (IEP)
response to progesterone  (IEP)
response to testosterone  (IEP)
response to xenobiotic stimulus  (IEP)
spermatogenesis  (IEP)
suppression by virus of host apoptotic process  (ISO)
type B pancreatic cell proliferation  (ISO,ISS)

Cellular Component
cytoplasm  (IDA,ISO)
cytosol  (IBA,IDA,ISO)
mitochondrial outer membrane  (ISO,ISS)
mitochondrion  (IBA,IDA,ISO)

References

References - curated
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89. Yang CH, etal., Environ Toxicol. 2014 Nov 28. doi: 10.1002/tox.22078.
90. Yang YY, etal., Liver Transpl. 2012 Nov;18(11):1371-83. doi: 10.1002/lt.23520.
91. Yao XL, etal., J Neurotrauma. 2005 Jun;22(6):656-68.
92. Zhu Y, etal., Neurochem Int. 2005 Jan;46(2):127-35.
93. Zou DW, etal., Evid Based Complement Alternat Med. 2013;2013:989670. doi: 10.1155/2013/989670. Epub 2013 Oct 28.
Additional References at PubMed
PMID:7834748   PMID:9176392   PMID:9388232   PMID:10407019   PMID:11146504   PMID:11717309   PMID:11980919   PMID:12115603   PMID:12142566   PMID:12431371   PMID:12472766   PMID:12477932  
PMID:12531534   PMID:12761242   PMID:12838582   PMID:12931191   PMID:12944463   PMID:14967141   PMID:15231831   PMID:15451022   PMID:15469889   PMID:15896972   PMID:15978696   PMID:16087293  
PMID:16116448   PMID:16446153   PMID:16565486   PMID:16603546   PMID:16937528   PMID:17080661   PMID:17270021   PMID:17289999   PMID:17555943   PMID:17940884   PMID:18223655   PMID:18387192  
PMID:18402937   PMID:18614015   PMID:18640115   PMID:18676776   PMID:18779656   PMID:18832722   PMID:18852119   PMID:18936092   PMID:19171933   PMID:19593445   PMID:19667065   PMID:19885947  
PMID:19915011   PMID:20651836   PMID:20700721   PMID:20810912   PMID:20850791   PMID:21081150   PMID:21095239   PMID:21546903   PMID:21716255   PMID:21789211   PMID:21818658   PMID:22006182  
PMID:22099262   PMID:25072152   PMID:27690136   PMID:30911955   PMID:31784847  


Genomics

Comparative Map Data
Bad
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21204,133,502 - 204,142,829 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1204,131,501 - 204,142,823 (+)Ensembl
Rnor_6.01222,198,516 - 222,207,459 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1222,198,534 - 222,207,453 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01229,189,271 - 229,198,306 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41209,617,373 - 209,626,292 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11209,775,802 - 209,784,722NCBI
Celera1201,667,864 - 201,676,765 (+)NCBICelera
Cytogenetic Map1q43NCBI
BAD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1164,269,830 - 64,284,704 (-)EnsemblGRCh38hg38GRCh38
GRCh381164,269,828 - 64,284,704 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371164,037,300 - 64,052,176 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361163,793,878 - 63,808,740 (-)NCBINCBI36hg18NCBI36
Build 341163,793,877 - 63,808,740NCBI
Celera1161,364,184 - 61,379,075 (-)NCBI
Cytogenetic Map11q13.1NCBI
HuRef1160,365,093 - 60,379,900 (-)NCBIHuRef
CHM1_11163,920,295 - 63,935,173 (-)NCBICHM1_1
Bad
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39196,919,229 - 6,929,273 (+)NCBIGRCm39mm39
GRCm39 Ensembl196,919,229 - 6,929,267 (+)Ensembl
GRCm38196,941,861 - 6,951,905 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl196,941,861 - 6,951,899 (+)EnsemblGRCm38mm10GRCm38
MGSCv37197,016,345 - 7,026,383 (+)NCBIGRCm37mm9NCBIm37
MGSCv36197,008,899 - 7,018,937 (+)NCBImm8
Celera196,718,946 - 6,728,897 (+)NCBICelera
Cytogenetic Map19ANCBI
Bad
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542220,795,676 - 20,809,245 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542220,795,585 - 20,809,039 (+)NCBIChiLan1.0ChiLan1.0
BAD
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11162,971,808 - 62,986,304 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1162,971,808 - 62,986,257 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01159,626,981 - 59,641,824 (-)NCBIMhudiblu_PPA_v0panPan3
BAD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11852,781,335 - 52,791,789 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1852,781,921 - 52,791,405 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1851,388,992 - 51,398,261 (+)NCBI
ROS_Cfam_1.01853,826,736 - 53,836,956 (+)NCBI
ROS_Cfam_1.0 Ensembl1853,827,323 - 53,836,575 (+)Ensembl
UMICH_Zoey_3.11852,929,992 - 52,939,466 (+)NCBI
UNSW_CanFamBas_1.01852,505,744 - 52,514,998 (+)NCBI
UU_Cfam_GSD_1.01853,289,648 - 53,298,901 (+)NCBI
Bad
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049478,481,976 - 8,491,335 (+)NCBI
SpeTri2.0NW_0049365994,924,349 - 4,933,683 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BAD
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl27,830,920 - 7,842,863 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.127,831,192 - 7,842,864 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.226,897,866 - 6,909,685 (+)NCBISscrofa10.2Sscrofa10.2susScr3
BAD
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.119,949,717 - 9,964,433 (+)NCBIChlSab1.1chlSab2
ChlSab1.119,949,717 - 9,964,433 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl19,949,762 - 9,964,432 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666038107,289,663 - 107,305,295 (+)NCBIVero_WHO_p1.0
Bad
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476722,025,721 - 22,037,283 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH134341  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21204,142,556 - 204,142,747 (+)MAPPERmRatBN7.2
Rnor_6.01222,207,187 - 222,207,377NCBIRnor6.0
Rnor_5.01229,198,039 - 229,198,229UniSTSRnor5.0
RGSC_v3.41209,626,026 - 209,626,216UniSTSRGSC3.4
Celera1201,676,499 - 201,676,689UniSTS
RH 3.4 Map11509.7UniSTS
Cytogenetic Map1q43UniSTS
AW530352  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21204,132,630 - 204,132,782 (+)MAPPERmRatBN7.2
Rnor_6.01222,197,261 - 222,197,412NCBIRnor6.0
Rnor_5.01229,188,115 - 229,188,266UniSTSRnor5.0
RGSC_v3.41209,616,152 - 209,616,303UniSTSRGSC3.4
Celera1201,666,631 - 201,666,782UniSTS
RH 3.4 Map11521.1UniSTS
Cytogenetic Map1q43UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2292218Kidm35Kidney mass QTL 35kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1199368955224569684Rat
619613Bp77Blood pressure QTL 770.01arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1164747424209747424Rat
619613Bp77Blood pressure QTL 770.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1164747424209747424Rat
631214Bw61Body weight QTL613.40.0001intramuscular adipose amount (VT:0010044)intramuscular fat area (CMO:0001162)1173108781218108781Rat
2302375Bw83Body weight QTL 834.870.0002body mass (VT:0001259)body weight (CMO:0000012)1197697768242697768Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1144267353251128347Rat
70163Bw20Body weight QTL 205.1body mass (VT:0001259)body weight (CMO:0000012)1174133260219133260Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1150700142252085212Rat
724559Pancm1Pancreatic morphology QTL 17.1islet of Langerhans morphology trait (VT:0005215)pancreatic islet damage composite score (CMO:0001156)1181759564214537555Rat
724562Rends1Renal damage susceptibility QTL 10.05kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)1169537671214537671Rat
737828Hcas3Hepatocarcinoma susceptibility QTL 34.9liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)1144267353222987745Rat
1298084Thym4Thymus enlargement QTL 410.68thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1197814409242814409Rat
631658Cm7Cardiac mass QTL 75.320.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)1196248093241248093Rat
737977Bp160Blood pressure QTL 1600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1181133855226133855Rat
1331790Bp201Blood pressure QTL 2013.127arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1198211513225126682Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1156677124256448636Rat
1582206Kidm33Kidney mass QTL 336.9kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1188377360224054420Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)194642722214537671Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1176426412257976495Rat
1302787Stl25Serum triglyceride level QTL 252.70.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1180359209210702199Rat
1641926Teswt2Testicular weight QTL 22.82testis mass (VT:1000644)both testes wet weight (CMO:0000175)1197697768238755659Rat
1598853Memor3Memory QTL 34.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)1143506580212458660Rat
2300161Bmd43Bone mineral density QTL 438.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1171629477216629477Rat
2300174Bmd42Bone mineral density QTL 428.40.0001lumbar vertebra mineral mass (VT:0010511)bone mineral density (CMO:0001226)1171629477216629477Rat
2300175Bmd40Bone mineral density QTL 4015.40.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)1201554356246554356Rat
2300187Bmd41Bone mineral density QTL 418.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1171629477216629477Rat
2293654Bss30Bone structure and strength QTL 3032.650.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1171629477216629477Rat
2293655Bss36Bone structure and strength QTL 3610.660.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1201554356246554356Rat
2293673Bss27Bone structure and strength QTL 2718.630.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)1171629477216629477Rat
2293674Bss39Bone structure and strength QTL 397.10.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)1201554356246554356Rat
2293677Bss41Bone structure and strength QTL 419.380.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1171629477216629477Rat
2293689Bss47Bone structure and strength QTL 477.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)1171629477216629477Rat
2293693Bss22Bone structure and strength QTL 2233.520.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1171629477216629477Rat
2293694Bss38Bone structure and strength QTL 387.050.0001femur strength trait (VT:0010010)femur stiffness (CMO:0001674)1201554356246554356Rat
631838Niddm36Non-insulin dependent diabetes mellitus QTL 360.01insulin secretion trait (VT:0003564)calculated pancreatic islet insulin release measurement (CMO:0001217)1184550676229550676Rat
634312Bp143Blood pressure QTL 14330.0002arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1182623426219932796Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1199050459259647894Rat
634321Hc1Hypercalciuria QTL 12.91urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1178810256240830002Rat
634338Hcar4Hepatocarcinoma resistance QTL 44.6liver integrity trait (VT:0010547)liver tumorous lesion number to liver area ratio (CMO:0001210)1193422268214537671Rat
1357335Bw39Body weight QTL 393.3body mass (VT:0001259)body weight (CMO:0000012)1197814409242814409Rat
1600363Hc6Hypercalciuria QTL 62.7urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1203995416244113296Rat
1600374Mcs17Mammary carcinoma susceptibility QTL 173mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1197670404242670404Rat
1600380Niddm70Non-insulin dependent diabetes mellitus QTL 703.10.0008blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1176550523221550523Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1195804352257091168Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1150700247252085048Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1179567751260522016Rat
1578778Pur4Proteinuria QTL 43.30.003total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1150700247252085048Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)181591954219808434Rat
1300145Rf7Renal function QTL 72.96urine creatinine amount (VT:0010540)urine creatinine level (CMO:0000125)1185145134221264292Rat
1354606Bp246Blood pressure QTL 2463.6arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)1102813953218753816Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1177227632256448636Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1151162512256448636Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1177227632256448636Rat
1354653Despr9Despair related QTL 90.00019locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1167909849212909849Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1558658Bw59Body weight QTL 593.50.0003body mass (VT:0001259)body weight (CMO:0000012)1178784622223784622Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1153136852260522016Rat
1358191Ept10Estrogen-induced pituitary tumorigenesis QTL 103.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)1192825253243914732Rat
2292220Bp306Blood pressure QTL 3063.470.00087arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1164310393243914901Rat
2292222Bp307Blood pressure QTL 3073.060.0014arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1164310393213533942Rat
2293083Iddm25Insulin dependent diabetes mellitus QTL 254.18blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1181829673224569684Rat
2312420Pur17Proteinuria QTL 177.10.0001urine protein amount (VT:0005160)urine total protein excretion rate (CMO:0000756)1156677124218753816Rat
2312564Glom18Glomerulus QTL 182.40.003kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)1185356336231689108Rat
1358886Bp260Blood pressure QTL 2603.67arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1151162766225824951Rat
1358898Bp255Blood pressure QTL 2553.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1191019702246062233Rat
1549830Bss1Bone structure and strength QTL 14.8femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1172609619217609619Rat
1358292Cm37Cardiac mass QTL 376.20.00000081heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1196248093241248093Rat
1358294Bw37Body weight QTL 3750.000011body mass (VT:0001259)body weight (CMO:0000012)1171310381216310381Rat
61341Bp26Blood pressure QTL 26arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1169537671214537671Rat
61376Bp42Blood pressure QTL 4223.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1197814409242814409Rat
6903303Scl34Serum cholesterol QTL 342.50.0033blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)1180359209218108781Rat
8655655Arrd2Age-related retinal degeneration QTL 27.79retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1183970203243914901Rat
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1115540693238914717Rat
7771612Cm80Cardiac mass QTL 808.4heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)1149448574221264292Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1118608292241799120Rat
8552891Epfw5Epididymal fat weight QTL 54.4epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1193113876238113876Rat
7394701Uae46Urinary albumin excretion QTL 463.60.0056urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1201554356246554356Rat
8655855Arrd3Age-related retinal degeneration QTL 33.07lens clarity trait (VT:0001304)cataract incidence/prevalence measurement (CMO:0001585)1183970203243914901Rat
10059587Bw173Body weight QTL 1733.230.025body mass (VT:0001259)body weight (CMO:0000012)1202069611247069611Rat
10059590Kidm44Kidney mass QTL 443.420.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1191033875236033875Rat
10059600Bp378Blood pressure QTL 3783.080.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1176869060221869060Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:98
Count of miRNA genes:77
Interacting mature miRNAs:83
Transcripts:ENSRNOT00000028712, ENSRNOT00000067068
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 37 47 31 19 31 1 3 74 35 41 11 1
Low 6 10 10 10 7 8 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000028712   ⟹   ENSRNOP00000028712
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1204,131,501 - 204,142,823 (+)Ensembl
Rnor_6.0 Ensembl1222,198,534 - 222,207,453 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101503   ⟹   ENSRNOP00000096573
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1204,133,489 - 204,142,599 (+)Ensembl
RefSeq Acc Id: NM_022698   ⟹   NP_073189
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21204,133,904 - 204,142,823 (+)NCBI
Rnor_6.01222,198,534 - 222,207,453 (+)NCBI
Rnor_5.01229,189,271 - 229,198,306 (+)NCBI
RGSC_v3.41209,617,373 - 209,626,292 (+)RGD
Celera1201,667,864 - 201,676,765 (+)RGD
Sequence:
RefSeq Acc Id: XM_006230896   ⟹   XP_006230958
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21204,133,502 - 204,142,828 (+)NCBI
Rnor_6.01222,198,516 - 222,207,454 (+)NCBI
Rnor_5.01229,189,271 - 229,198,306 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006230897   ⟹   XP_006230959
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21204,134,068 - 204,142,829 (+)NCBI
Rnor_6.01222,198,708 - 222,207,459 (+)NCBI
Rnor_5.01229,189,271 - 229,198,306 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006230898   ⟹   XP_006230960
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21204,134,068 - 204,142,828 (+)NCBI
Rnor_6.01222,198,712 - 222,207,458 (+)NCBI
Rnor_5.01229,189,271 - 229,198,306 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039089714   ⟹   XP_038945642
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21204,133,502 - 204,142,824 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_073189   ⟸   NM_022698
- UniProtKB: O35147 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006230958   ⟸   XM_006230896
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006230960   ⟸   XM_006230898
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006230959   ⟸   XM_006230897
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000028712   ⟸   ENSRNOT00000028712
RefSeq Acc Id: XP_038945642   ⟸   XM_039089714
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000096573   ⟸   ENSRNOT00000101503

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 229190097 229190098 G T snv FHH/EurMcwi (MCW), ZF (KyushuU), SBN/Ygl (MCW), WN/N (KNAW), BUF/N (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), GK/Ox (KNAW), MNS/Gib (KNAW), SBN/Ygl (KNAW), SDLEF7/Barth (UDEL), Crl:SD (UDEL), BUF/MNa (KyushuU), HTX/Kyo (KyushuU), HWY/Slc (KyushuU), LEC/Tj (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), FHL/EurMcwi (MCW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 204134615 204134616 G T snv BUF/N (2020), FHH/EurMcwi (2019), WN/N (2020), PVG/Seac (2019), GK/FarMcwi (2019)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 222199245 222199246 G T snv CDR, WN/N (2020), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), Buf/N (MCW), WN/N (MCW), FHH/EurMcwi (RGD), FHL/EurMcwi (RGD), GK/Ox (RGD), MNS/Gib (RGD), SBN/Ygl (RGD), BUF/N (2020), FHH/EurMcwi (2019), GK/FarMcwi (2019), PVG/Seac (2019), CDS


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 209618084 209618085 G T snv FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MDC), BUF/N (KNAW), WN/N (KNAW), FHH/EurMcwi (ICL), LCR/2Mco (UMich), GK/Ox (ICL), MNS/Gib (ICL), SBN/Ygl (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), FHL/EurMcwi (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620103 AgrOrtholog
BIND 133989
  133990
Ensembl Genes ENSRNOG00000021147 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000028712 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000028712 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5598682 IMAGE-MGC_LOAD
InterPro BAD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:64639 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72439 IMAGE-MGC_LOAD
NCBI Gene 64639 ENTREZGENE
PANTHER PTHR28540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Bcl-2_BAD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Bad PhenoGen
UniProt BAD_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q6P7C5_RAT UniProtKB/TrEMBL
UniProt Secondary O70256 UniProtKB/Swiss-Prot
  Q9JHX1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-08-28 Bad  BCL2-associated agonist of cell death  Bad_v2  BCL2-associated agonist of cell death, variant 2  Data Merged 737654 PROVISIONAL
2018-08-28 Bad  BCL2-associated agonist of cell death  Bad_v1  BCL2-associated agonist of cell death, variant 1  Data Merged 737654 PROVISIONAL
2009-11-05 Bad  BCL2-associated agonist of cell death  Bad  Bcl2-antagonist of cell death  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-01 Bad  Bcl2-antagonist of cell death  Bad  bcl2-associated dea