Apoa1 (apolipoprotein A1) - Rat Genome Database

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Gene: Apoa1 (apolipoprotein A1) Rattus norvegicus
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Symbol: Apoa1
Name: apolipoprotein A1
RGD ID: 2130
Description: Enables amyloid-beta binding activity; cholesterol transfer activity; and lipase inhibitor activity. Involved in several processes, including lipid transport; peripheral nervous system axon regeneration; and response to estrogen. Located in cell surface; extracellular space; and nucleus. Part of discoidal high-density lipoprotein particle; intermediate-density lipoprotein particle; and low-density lipoprotein particle. Used to study arteriosclerosis and hyperthyroidism. Biomarker of several diseases, including fatty liver disease (multiple); hypertension; major depressive disorder; ocular hypertension; and sciatic neuropathy. Human ortholog(s) of this gene implicated in several diseases, including artery disease (multiple); familial visceral amyloidosis; hypolipoproteinemia (multiple); non-alcoholic steatohepatitis; and systemic lupus erythematosus. Orthologous to human APOA1 (apolipoprotein A1); PARTICIPATES IN altered lipoprotein metabolic pathway; forkhead class A signaling pathway; lipoprotein metabolic pathway; INTERACTS WITH (R,R,R)-alpha-tocopherol; 1-naphthyl isothiocyanate; 2,2,2-tetramine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: apo-AI; apoA-I; apolipoprotein A-1; apolipoprotein A-I; preproapolipoprotein A-I
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
mRatBN7.2846,527,251 - 46,529,035 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl846,527,144 - 46,529,035 (+)Ensembl
Rnor_6.0850,525,091 - 50,526,875 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl850,525,091 - 50,526,875 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0849,151,163 - 49,152,947 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera846,109,311 - 46,111,065 (+)NCBICelera
RH 3.4 Map8472.0RGD
Cytogenetic Map8q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Acute Lung Injury  (ISO)
Acute Tubulointerstitial Nephritis  (ISO)
adenocarcinoma  (ISO)
Alzheimer's disease  (ISO)
arteriosclerosis  (IDA,ISO)
atherosclerosis  (ISO)
Behcet's disease  (ISO)
Budd-Chiari syndrome  (ISO)
cardiomyopathy  (ISO)
cardiovascular system disease  (ISO)
cerebral amyloid angiopathy  (ISO)
Chemical and Drug Induced Liver Injury  (ISO)
cholangiocarcinoma  (ISO)
Chronic Hepatitis B  (ISO)
chronic kidney disease  (ISO)
congestive heart failure  (ISO)
coronary artery disease  (ISO)
Death  (ISO)
Diabetic Cardiomyopathies  (ISO)
Diabetic Nephropathies  (ISO)
Drug Eruptions  (ISO)
Dwarfism  (ISO)
Edema  (ISO)
end stage renal disease  (ISO)
Endotoxemia  (IDA,ISO)
Experimental Diabetes Mellitus  (IDA)
Experimental Liver Cirrhosis  (IDA)
Familial Amyloid Polyneuropathies  (ISO)
Familial Amyloidosis  (ISO)
familial isolated deficiency of vitamin E  (ISO)
familial visceral amyloidosis  (ISO)
fatty liver disease  (IEP)
hepatitis C  (ISO)
hepatoblastoma  (ISO)
hepatocellular carcinoma  (ISO)
human immunodeficiency virus infectious disease  (ISO)
Hypercholesterolemia  (ISO)
Hyperlipoproteinemia Type II  (ISO)
hypertension  (IEP,ISO)
hyperthyroidism  (IDA)
Hypertriglyceridemia  (ISO)
Hypoalphalipoproteinemias  (ISO)
hypolipoproteinemia  (ISO)
Hypoproteinemia  (IDA)
Hypoxia  (ISO)
idiopathic pulmonary fibrosis  (ISO)
Inflammation  (ISO)
intellectual disability  (ISO)
Kidney Reperfusion Injury  (ISO)
lipid metabolism disorder  (ISO)
liver cirrhosis  (ISO)
lung adenocarcinoma  (ISO)
Lung Neoplasms  (ISO)
major depressive disorder  (IEP)
malignant mesothelioma  (ISO)
membranous glomerulonephritis  (ISO)
Metabolic Syndrome  (ISO)
multiple sclerosis  (ISO)
myocardial infarction  (ISO)
nephrotic syndrome  (IEP)
non-alcoholic fatty liver disease  (ISO)
non-alcoholic steatohepatitis  (IEP,ISO)
obesity  (ISO)
ocular hypertension  (IEP)
pancreatic cancer  (ISO)
Parkinson's disease  (ISO)
Pediatric Obesity  (ISO)
polycystic kidney disease  (ISO)
primary hypoalphalipoproteinemia 1  (ISO)
primary hypoalphalipoproteinemia 2  (ISO)
pulmonary fibrosis  (ISO)
sciatic neuropathy  (IEP)
Sepsis  (IDA)
Stomach Neoplasms  (ISO)
Stroke  (ISO)
systemic lupus erythematosus  (ISO)
Tangier disease  (ISO)
transitional cell carcinoma  (IEP,ISO)
Transplant Rejection  (ISO)
type 1 diabetes mellitus  (ISO)
type 2 diabetes mellitus  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-taxifolin  (ISO)
(-)-ephedrine  (ISO)
(25R)-cholest-5-ene-3beta,26-diol  (ISO)
(R,R,R)-alpha-tocopherol  (EXP,ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
2,2,2-tetramine  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-di-tert-butyl-4-methylphenol  (ISO)
2,6-dinitrotoluene  (EXP)
2-amino-2-deoxy-D-glucopyranose  (ISO)
2-bromohexadecanoic acid  (EXP)
26-hydroxycholesterol  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP,ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,3',5-triiodo-L-thyronine  (EXP)
3-[3-(tert-butylsulfanyl)-1-(4-chlorobenzyl)-5-(propan-2-yl)-1H-indol-2-yl]-2,2-dimethylpropanoic acid  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acetylsalicylic acid  (EXP,ISO)
acrolein  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (ISO)
aldehydo-D-glucose  (EXP)
all-trans-retinoic acid  (EXP,ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
arachidonic acid  (ISO)
aristolochic acid  (ISO)
atazanavir sulfate  (ISO)
atenolol  (ISO)
benzalkonium chloride  (ISO)
benzo[a]pyrene  (ISO)
beta-D-glucosamine  (ISO)
bezafibrate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bucladesine  (ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
caesium atom  (EXP)
caffeine  (EXP,ISO)
captan  (ISO)
carbon nanotube  (ISO)
chenodeoxycholic acid  (ISO)
CHIR 99021  (ISO)
chlordecone  (ISO)
chlorpyrifos  (ISO)
cholesterol  (EXP,ISO)
choline  (EXP)
chromium atom  (ISO)
chromium trinitrate  (ISO)
chromium(6+)  (ISO)
ciprofibrate  (ISO)
cisplatin  (ISO)
clofibrate  (EXP,ISO)
Clofop  (EXP)
clonidine  (ISO)
clonidine (amino form)  (ISO)
clonidine (imino form)  (ISO)
cobalt dichloride  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
cypermethrin  (EXP)
cyproterone acetate  (ISO)
D-glucose  (EXP)
deoxycholic acid  (ISO)
dexamethasone  (EXP)
dichlorine  (ISO)
diethyl phthalate  (ISO)
dimethyl sulfoxide  (EXP,ISO)
disodium selenite  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
ethanol  (EXP)
ezetimibe  (ISO)
fenofibrate  (EXP,ISO)
fingolimod hydrochloride  (ISO)
flavonoids  (EXP)
folic acid  (EXP,ISO)
folpet  (ISO)
fonofos  (ISO)
fructose  (EXP,ISO)
fulvestrant  (ISO)
gemfibrozil  (ISO)
genistein  (EXP)
ginsenoside Rf  (ISO)
glucose  (EXP)
glutathione  (ISO)
glyburide  (ISO)
glycerol  (ISO)
glycidol  (EXP)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
glycolaldehyde  (ISO)
glyoxal  (ISO)
GW 4064  (ISO)
GW 501516  (ISO)
GW 7647  (ISO)
high-density lipoprotein cholesterol  (EXP,ISO)
homocysteine  (ISO)
hydrogen peroxide  (ISO)
hypochlorous acid  (ISO)
L-ascorbic acid  (EXP,ISO)
L-methionine  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
linalool  (ISO)
linoleic acid  (ISO)
lipopolysaccharide  (ISO)
lovastatin  (ISO)
mastoparan  (ISO)
menadione  (ISO)
mercury dibromide  (ISO)
methapyrilene  (ISO)
methylmercury chloride  (ISO)
microcystin-LR  (ISO)
morphine  (EXP)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosomorpholine  (EXP)
N-tosyl-L-phenylalanyl chloromethyl ketone  (ISO)
Nandrolone decanoate  (ISO)
nefazodone  (ISO)
nevirapine  (ISO)
nickel atom  (ISO)
nicotinic acid  (ISO)
nifedipine  (ISO)
nitrofen  (EXP)
nitroglycerin  (EXP)
O-methyleugenol  (ISO)
obeticholic acid  (ISO)
olanzapine  (ISO)
oleic acid  (ISO)
p-menthan-3-ol  (EXP)
palmitoleic acid  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
parathion  (ISO)
PCB138  (ISO)
pentetic acid  (ISO)
perfluorobutyric acid  (EXP)
perfluorohexanesulfonic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
phenobarbital  (EXP)
phenylmercury acetate  (ISO)
phenytoin  (ISO)
pirinixic acid  (EXP,ISO)
Polyoxyethylene dioleate  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
pravastatin  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP,ISO)
probucol  (ISO)
propanal  (ISO)
prostaglandin E2  (EXP)
prostaglandin J2  (ISO)
Ptaquiloside  (ISO)
pyrazinecarboxamide  (EXP)
pyrogallol  (ISO)
quercetin  (ISO)
quercetin 3-O-beta-D-glucofuranoside  (ISO)
quercetin 3-O-beta-D-glucopyranoside  (ISO)
resveratrol  (ISO)
rosuvastatin calcium  (ISO)
rotenone  (EXP)
salicylates  (ISO)
sarin  (EXP)
SB 203580  (ISO)
SB 431542  (ISO)
simvastatin  (EXP,ISO)
sodium arsenite  (ISO)
sodium chloride  (ISO)
sodium dichromate  (ISO)
sodium fluoride  (EXP,ISO)
stigmasterol  (ISO)
streptozocin  (EXP)
sulindac sulfide  (ISO)
sunitinib  (ISO)
tartrazine  (ISO)
taurocholic acid  (ISO)
tauroursodeoxycholic acid  (EXP)
terbufos  (ISO)
tetrachloromethane  (EXP)
tolcapone  (EXP)
Triptolide  (EXP)
triptonide  (ISO)
U-73122  (ISO)
ursodeoxycholic acid  (ISO)
valproic acid  (ISO)
vitamin E  (ISO)
warfarin  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adrenal gland development  (ISO)
animal organ regeneration  (IDA)
axon regeneration  (ISO)
blood vessel endothelial cell migration  (ISO)
cholesterol biosynthetic process  (IBA,ISO)
cholesterol efflux  (IBA,ISO)
cholesterol homeostasis  (IBA,ISO)
cholesterol import  (ISO)
cholesterol metabolic process  (ISO)
cholesterol transport  (IDA,ISO)
endothelial cell proliferation  (ISO)
ERK1 and ERK2 cascade  (ISO)
G protein-coupled receptor signaling pathway  (ISO)
glucocorticoid metabolic process  (ISO)
high-density lipoprotein particle assembly  (IBA,ISO)
high-density lipoprotein particle remodeling  (ISO)
integrin-mediated signaling pathway  (ISO)
intermembrane lipid transfer  (IEA)
lipid storage  (ISO)
lipoprotein biosynthetic process  (ISO)
lipoprotein metabolic process  (IBA)
negative chemotaxis  (ISO)
negative regulation of cell adhesion molecule production  (ISO)
negative regulation of cytokine production involved in immune response  (ISO)
negative regulation of heterotypic cell-cell adhesion  (ISO)
negative regulation of hydrolase activity  (ISO)
negative regulation of inflammatory response  (ISO)
negative regulation of interleukin-1 beta production  (ISO)
negative regulation of lipase activity  (IDA)
negative regulation of response to cytokine stimulus  (ISO)
negative regulation of tumor necrosis factor-mediated signaling pathway  (ISO)
negative regulation of very-low-density lipoprotein particle remodeling  (ISO)
peptidyl-methionine modification  (ISO)
peripheral nervous system axon regeneration  (IEP)
phosphatidylcholine biosynthetic process  (ISO)
phosphatidylcholine metabolic process  (IBA)
phospholipid efflux  (IBA,ISO)
phospholipid homeostasis  (ISO)
phospholipid metabolic process  (ISO)
phospholipid transport  (IDA)
positive regulation of cholesterol efflux  (ISO,ISS)
positive regulation of cholesterol esterification  (IBA,ISO)
positive regulation of fatty acid biosynthetic process  (IBA)
positive regulation of hydrolase activity  (ISO)
positive regulation of lipid biosynthetic process  (IBA)
positive regulation of lipoprotein lipase activity  (IBA)
positive regulation of phagocytosis  (ISO,ISS)
positive regulation of phospholipid efflux  (ISO,ISS)
positive regulation of Rho protein signal transduction  (ISO)
positive regulation of stress fiber assembly  (ISO)
positive regulation of substrate adhesion-dependent cell spreading  (ISO)
positive regulation of triglyceride catabolic process  (IBA)
protein localization  (ISO)
protein oxidation  (ISO)
protein stabilization  (ISO,ISS)
regulation of Cdc42 protein signal transduction  (ISO)
regulation of intestinal cholesterol absorption  (IBA,ISO)
regulation of protein phosphorylation  (ISO)
response to estrogen  (IEP)
response to nutrient  (IEP)
response to xenobiotic stimulus  (IEP)
reverse cholesterol transport  (IBA,ISO)
transforming growth factor beta receptor signaling pathway  (ISO)
triglyceride homeostasis  (IBA,ISO)
very-low-density lipoprotein particle remodeling  (IBA)
vitamin transport  (ISO)

References

References - curated
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89. Yamakawa-Kobayashi K, etal., Hum Mol Genet 1999 Feb;8(2):331-6.
90. Yoo KH, etal., Proteomics. 2009 Aug;9(15):3824-32. doi: 10.1002/pmic.200800753.
91. Zhang B, etal., Lipids Health Dis. 2010 Mar 29;9:34.
92. Zhang Z, etal., Am J Physiol Heart Circ Physiol. 2009 Aug;297(2):H866-73. doi: 10.1152/ajpheart.01232.2008. Epub 2009 Jun 26.
93. Zhou Y, etal., Am J Physiol Renal Physiol. 2008 Sep;295(3):F662-71. Epub 2008 Jul 9.
94. Zhu H, etal., Wei Sheng Yan Jiu. 2000 Mar 30;29(2):104-5.
95. Ziegler ME, etal., Transplantation. 2011 Aug 27;92(4):388-95. doi: 10.1097/TP.0b013e318225db6a.
Additional References at PubMed
PMID:190223   PMID:210174   PMID:1496008   PMID:1587806   PMID:1596514   PMID:3104518   PMID:4335615   PMID:6403543   PMID:6798036   PMID:7638166   PMID:7751823   PMID:7798939  
PMID:8049247   PMID:8647961   PMID:9186920   PMID:9275209   PMID:9300780   PMID:9325076   PMID:9327769   PMID:9415807   PMID:9507992   PMID:9651324   PMID:9684752   PMID:9795222  
PMID:10073953   PMID:10357841   PMID:10559507   PMID:10764676   PMID:11027668   PMID:11162594   PMID:11297421   PMID:11744719   PMID:12202492   PMID:12458630   PMID:12477932   PMID:12576517  
PMID:12651854   PMID:12810715   PMID:12859204   PMID:12869555   PMID:14595002   PMID:14703508   PMID:14718538   PMID:14747463   PMID:14967812   PMID:14993246   PMID:15140193   PMID:15269218  
PMID:15358760   PMID:15464323   PMID:15466405   PMID:15793583   PMID:15995171   PMID:16245952   PMID:16339487   PMID:16443932   PMID:16502470   PMID:16530456   PMID:16606364   PMID:16682745  
PMID:17071966   PMID:17154273   PMID:17655203   PMID:17676061   PMID:18457017   PMID:18719128   PMID:19056867   PMID:19199708   PMID:19433579   PMID:20133843   PMID:20495215   PMID:20551380  
PMID:20884842   PMID:21481393   PMID:21571275   PMID:22184756   PMID:22253414   PMID:22516433   PMID:22609356   PMID:22664934   PMID:23376485   PMID:23533145   PMID:23726972   PMID:24117066  
PMID:24155931   PMID:24316228   PMID:24702826   PMID:24769233   PMID:24814947   PMID:25305669   PMID:27068509   PMID:27472885   PMID:27477018   PMID:27559042   PMID:27881716   PMID:29581158  


Genomics

Comparative Map Data
Apoa1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2846,527,251 - 46,529,035 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl846,527,144 - 46,529,035 (+)Ensembl
Rnor_6.0850,525,091 - 50,526,875 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl850,525,091 - 50,526,875 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0849,151,163 - 49,152,947 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera846,109,311 - 46,111,065 (+)NCBICelera
RH 3.4 Map8472.0RGD
Cytogenetic Map8q22NCBI
APOA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl11116,835,751 - 116,837,622 (-)EnsemblGRCh38hg38GRCh38
GRCh3811116,835,751 - 116,837,950 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3711116,706,467 - 116,708,666 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3611116,211,679 - 116,213,548 (-)NCBINCBI36hg18NCBI36
Celera11113,864,272 - 113,866,141 (-)NCBI
Cytogenetic Map11q23.3NCBI
HuRef11112,638,728 - 112,640,597 (-)NCBIHuRef
CHM1_111116,591,221 - 116,593,090 (-)NCBICHM1_1
Apoa1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39946,139,928 - 46,141,767 (+)NCBIGRCm39mm39
GRCm39 Ensembl946,139,878 - 46,141,764 (+)Ensembl
GRCm38946,228,630 - 46,230,469 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl946,228,580 - 46,230,466 (+)EnsemblGRCm38mm10GRCm38
MGSCv37946,036,713 - 46,038,549 (+)NCBIGRCm37mm9NCBIm37
MGSCv36945,979,705 - 45,981,461 (+)NCBImm8
Celera943,517,584 - 43,519,420 (+)NCBICelera
Cytogenetic Map9A5.2NCBI
cM Map925.36NCBI
Apoa1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541218,170,331 - 18,172,298 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541218,170,331 - 18,172,298 (-)NCBIChiLan1.0ChiLan1.0
APOA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.111115,606,136 - 115,608,335 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11115,606,136 - 115,608,122 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v011111,673,539 - 111,675,428 (-)NCBIMhudiblu_PPA_v0panPan3
APOA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1516,740,071 - 16,742,081 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl516,740,130 - 16,741,943 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha516,792,234 - 16,794,244 (+)NCBI
ROS_Cfam_1.0516,686,357 - 16,688,357 (+)NCBI
UMICH_Zoey_3.1516,823,454 - 16,825,453 (+)NCBI
UNSW_CanFamBas_1.0516,726,037 - 16,728,039 (+)NCBI
UU_Cfam_GSD_1.0516,768,944 - 16,770,956 (+)NCBI
Apoa1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494799,189,637 - 99,191,475 (-)NCBI
SpeTri2.0NW_0049365422,111,055 - 2,112,626 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
APOA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl944,216,393 - 44,218,978 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1944,216,481 - 44,218,360 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2949,288,730 - 49,290,611 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap9p12-p11NCBI
APOA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11108,201,967 - 108,203,902 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1108,201,439 - 108,203,609 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604317,846,715 - 17,848,683 (+)NCBIVero_WHO_p1.0
Apoa1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462478412,249,283 - 12,251,215 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D8Arb27  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2846,527,999 - 46,528,287 (+)MAPPERmRatBN7.2
Rnor_6.0850,525,840 - 50,526,127NCBIRnor6.0
Rnor_5.0849,151,912 - 49,152,199UniSTSRnor5.0
Celera846,110,060 - 46,110,347UniSTS
SHRSP x BN Map836.96RGD
SHRSP x BN Map836.96UniSTS
Cytogenetic Map8q23-q24UniSTS
RH94461  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2846,528,994 - 46,529,180 (+)MAPPERmRatBN7.2
Rnor_6.0850,526,835 - 50,527,020NCBIRnor6.0
Rnor_5.0849,152,907 - 49,153,092UniSTSRnor5.0
Celera846,111,025 - 46,111,210UniSTS
RH 3.4 Map8472.0UniSTS
Cytogenetic Map8q23-q24UniSTS
Apoa1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2846,527,512 - 46,528,429 (+)MAPPERmRatBN7.2
Rnor_6.0850,525,353 - 50,526,269NCBIRnor6.0
Rnor_5.0849,151,425 - 49,152,341UniSTSRnor5.0
Cytogenetic Map8q23-q24UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8767057852670578Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)8768895552688955Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8768895552688955Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)8873663553736635Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)8873663553736635Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)8971222053356647Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81490675159906751Rat
61373Mcs4Mammary carcinoma susceptibility QTL 41.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)81629044461290444Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)81898416884531599Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat
631842Inf1Infertility severity QTL 14.10.001seminal gland mass (VT:0010524)seminal vesicle wet weight (CMO:0001603)82266233067662330Rat
2303564Gluco43Glucose level QTL 433blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)82613018771130187Rat
2303572Insul13Insulin level QTL 132blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)82613018771130187Rat
1359021Bp271Blood pressure QTL 2711.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)82664491246711092Rat
631648Stl5Serum triglyceride level QTL 540.0003blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)82720571554998217Rat
1358892Kidm26Kidney mass QTL 263.69kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)82720571599103503Rat
1358896Bp262Blood pressure QTL 2622.89arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)82720571599103503Rat
1358907Cm40Cardiac mass QTL 401.89heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)82720571599103503Rat
1331804Cm30Cardiac mass QTL 303.77443heart mass (VT:0007028)heart wet weight (CMO:0000069)82824291253961020Rat
1300146Rf17Renal function QTL 172.9renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)82824291273242912Rat
8662823Vetf5Vascular elastic tissue fragility QTL 51.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)82824291299525068Rat
2302278Gluco36Glucose level QTL 364.2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)82950266550095447Rat
724514Uae15Urinary albumin excretion QTL 152.9urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)82950266570386295Rat
1549908Neudeg1Neurodegradation QTL 15.50nervous system integrity trait (VT:0010566)logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)83018886794457446Rat
1331744Bp217Blood pressure QTL 2173.398arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815458482492Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
11556286Cm81Cardiac mass QTL 810.01heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)83084815461290444Rat
1359033Bp273Blood pressure QTL 273arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
2313046Bss78Bone structure and strength QTL 783.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)83084815482460899Rat
2313057Bss76Bone structure and strength QTL 7630.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)83084815482460899Rat
2313067Bss77Bone structure and strength QTL 773.10.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)83084815482460899Rat
2313088Bss75Bone structure and strength QTL 753.10.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)83084815482460899Rat
1578755Pur5Proteinuria QTL 53.30.0001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)830848154101699754Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)830848154101699754Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)830848154101699754Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)830848259105647037Rat
1298065Scl16Serum cholesterol level QTL 163.8blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)83085640475856404Rat
1582222Epfw2Epididymal fat weight QTL 23.20.0005epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)83173772976737729Rat
61358Bp39Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83555193880551938Rat
61464Niddm11Non-insulin dependent diabetes mellitus QTL 113.10.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83558203280582032Rat
1331838Niddm61Non-insulin dependent diabetes mellitus QTL 613.530.0004blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83646953599083736Rat
737824Hcar10Hepatocarcinoma resistance QTL 102.9liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)84071306682925667Rat
1358906Bp253Blood pressure QTL 25340.0004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)84071306693965294Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
1331769Rf39Renal function QTL 393.871urine output (VT:0003620)timed urine volume (CMO:0000260)84186687675097878Rat
1298079Activ2Activity QTL 29.50.000001voluntary movement trait (VT:0003491)rearing measurement (CMO:0001515)84186687686866876Rat
631216Stl9Serum triglyceride level QTL 94.710.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)84186701070386132Rat
5684993Bmd84Bone mineral density QTL 844.1tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)84269268450095447Rat
70161Bp62Blood pressure QTL 622.90.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)84269268490165460Rat
12879882Am8Aortic mass QTL 80.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)84329616998968765Rat
12879878Bw183Body weight QTL 1830.001body mass (VT:0001259)body weight (CMO:0000012)84329616998968765Rat
12879879Cm99Cardiac mass QTL 990.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)84329616998968765Rat
12879880Cm100Cardiac mass QTL 1000.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)84329616998968765Rat
12879881Cm101Cardiac mass QTL 1010.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)84329616998968765Rat
12879883Kidm65Kidney mass QTL 650.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)84329616998968765Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:53
Count of miRNA genes:51
Interacting mature miRNAs:51
Transcripts:ENSRNOT00000074357
Prediction methods:Microtar, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 45 45 39
Medium 2 4 2 2 2 2 1 12 2 2
Low 1 35 14 19 5 7 74 31 29 9 5
Below cutoff 8 1 2 3 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_012738 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AH002137 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC089820 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473975 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209434 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209676 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209742 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209776 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209818 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209830 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209842 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209900 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209928 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209958 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210024 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210048 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210126 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210161 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210244 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210354 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210367 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210371 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210443 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210470 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210544 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210644 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210653 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210722 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210732 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210743 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210863 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210880 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210914 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211297 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211535 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211571 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218075 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218078 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218079 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218230 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218325 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218519 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218525 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218659 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218663 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218837 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219021 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219052 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219074 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219278 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219479 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219515 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219577 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219728 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224655 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229884 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000198 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M00001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U79576 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U79577 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U79578 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X00558 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000074357   ⟹   ENSRNOP00000065206
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl846,527,144 - 46,529,035 (+)Ensembl
Rnor_6.0 Ensembl850,525,091 - 50,526,875 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092188   ⟹   ENSRNOP00000068933
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl846,527,306 - 46,529,035 (+)Ensembl
RefSeq Acc Id: NM_012738   ⟹   NP_036870
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2846,527,251 - 46,529,035 (+)NCBI
Rnor_6.0850,525,091 - 50,526,875 (+)NCBI
Rnor_5.0849,151,163 - 49,152,947 (+)NCBI
Celera846,109,311 - 46,111,065 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036870   ⟸   NM_012738
- Peptide Label: preproprotein
- UniProtKB: P04639 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000065206   ⟸   ENSRNOT00000074357
RefSeq Acc Id: ENSRNOP00000068933   ⟸   ENSRNOT00000092188

Transcriptome

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

Promoters
RGD ID:13695925
Promoter ID:EPDNEW_R6450
Type:multiple initiation site
Name:Apoa1_1
Description:apolipoprotein A1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0850,525,091 - 50,525,151EPDNEW

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)
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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)
ACI/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
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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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
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 49151643 49151644 A T snv LEC/Tj (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2130 AgrOrtholog
Ensembl Genes ENSRNOG00000045679 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000065206 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000074357 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7321674 IMAGE-MGC_LOAD
InterPro ApoA_E UniProtKB/Swiss-Prot
KEGG Report rno:25081 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108764 IMAGE-MGC_LOAD
NCBI Gene 25081 ENTREZGENE
Pfam Apolipoprotein UniProtKB/Swiss-Prot
PharmGKB APOA1 RGD
PhenoGen Apoa1 PhenoGen
TIGR TC230914
UniProt APOA1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O08877 UniProtKB/Swiss-Prot
  O09054 UniProtKB/Swiss-Prot
  Q5EBB2 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-11 Apoa1  apolipoprotein A1  Apoa1  apolipoprotein A-I  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Apoa1  apolipoprotein A-I    apolipoprotein A-1  Name updated 629478 APPROVED
2002-06-10 Apoa1  apolipoprotein A-1      Name updated 70585 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains sequence contains repeated sequence segments that may have originated by intragenic duplication of 11- or 22-amino acid amphipathic segments 1298547
gene_expression expressed in liver and intestine at adulthood and during the aging process 634656
gene_expression secreted by brain endothelial cells 1298673
gene_expression expressed in brain astrocytes 1298673
gene_function cofactor for lecithin cholesterolacyltransferase (LCAT)  
gene_homology parologous to apoaIV and apoE at sequences deriving from intergenic duplication-containing ancestral sequence 1298547
gene_physical_interaction binds lipids at intragenic duplication sequence structures 1298547
gene_process involved in formation of plasma cholesteryl esters  
gene_process promotes cholesterol efflux from tissues to liver for excretion  
gene_process activates lecithin:cholesterol acyltransferase action 1298547
gene_process may influence cholesterol efflux from peripheral cells to the liver 1298609
gene_process generates high density lipoproteins (HDL) via cellular interaction in the brain to facilitate intercellular cholesterol transport 1298673
gene_process facilitates a major source of cholesterol release by interacting with astrocytes to produce high density lipoprotein (HDL) 1298673
gene_process involvement in intercellular cholesterol trafficking is influenced by sphingomyelin 1298673
gene_process induces intercellular translocation of cholesterol, phospholipoprotein and caveolin-1 to cytosol in brain astrocytes 1298673
gene_process increases activity of sterol regulatory element-binding proteins (SREBP) 1 and 2 1298673
gene_process comprises the major protein component of high density lipoprotein (HDL) 1298673