Abca1 (ATP binding cassette subfamily A member 1) - Rat Genome Database

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Gene: Abca1 (ATP binding cassette subfamily A member 1) Rattus norvegicus
Analyze
Symbol: Abca1
Name: ATP binding cassette subfamily A member 1
RGD ID: 631344
Description: Enables ATPase-coupled transmembrane transporter activity and high-density lipoprotein particle binding activity. Involved in several processes, including cellular response to cholesterol; cellular response to drug; and lipid transport. Located in basolateral plasma membrane and cell surface. Biomarker of several diseases, including extrahepatic cholestasis; fatty liver disease; membranous glomerulonephritis; obesity; and premature menopause. Human ortholog(s) of this gene implicated in Alzheimer's disease; coronary artery disease; hypolipoproteinemia (multiple); obesity; and type 2 diabetes mellitus. Orthologous to human ABCA1 (ATP binding cassette subfamily A member 1); PARTICIPATES IN altered reverse cholesterol transport pathway; retinol metabolic pathway; reverse cholesterol transport pathway; INTERACTS WITH (25R)-cholest-5-ene-3beta,26-diol; (S)-nicotine; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: ATP-binding cassette sub-family A member 1; ATP-binding cassette, sub-family A (ABC1), member 1; ATP-binding cassette, subfamily A (ABC1), member 1; phospholipid-transporting ATPase ABCA1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2567,678,267 - 67,801,162 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl569,857,771 - 69,983,015 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0569,857,717 - 69,983,042 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0574,023,652 - 74,112,802 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4570,493,357 - 70,583,729 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1570,498,469 - 70,588,842 (-)NCBI
Celera566,575,764 - 66,665,022 (-)NCBICelera
Cytogenetic Map5q23-q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(24S)-24-hydroxycholesterol  (ISO)
(25R)-cholest-5-ene-3beta,26-diol  (EXP,ISO)
(R)-mevalonic acid  (ISO)
(S)-nicotine  (EXP,ISO)
1,1-dichloroethene  (ISO)
1,2,3-trilinolenoylglycerol  (ISO)
1,2,3-trilinoleoylglycerol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-di-tert-butyl-4-methylphenol  (ISO)
2,6-dinitrotoluene  (EXP)
22-Hydroxycholesterol  (EXP,ISO)
25-hydroxycholesterol  (EXP,ISO)
26-hydroxycholesterol  (EXP,ISO)
3',5'-cyclic AMP  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',5-triiodo-L-thyronine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-aminobenzamide  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-vinylcyclohexene dioxide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (ISO)
6-[1-(3,5,5,8,8-PENTAMETHYL-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)CYCLOPROPYL]PYRIDINE-3-CARBOXYLIC ACID  (ISO)
8-(4-chlorophenylthio)-cAMP  (ISO)
8-Br-cAMP  (EXP,ISO)
9-cis-retinoic acid  (EXP,ISO)
acetazolamide  (ISO)
acetylsalicylic acid  (ISO)
Adiponectin  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arachidonic acid  (ISO)
Aranidipine  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
aspartame  (ISO)
atorvastatin calcium  (ISO)
BAPTA  (ISO)
beauvericin  (ISO)
benzalkonium chloride  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
berberine  (ISO)
beta-hexachlorocyclohexane  (ISO)
bexarotene  (ISO)
bezafibrate  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bucladesine  (ISO)
buspirone  (EXP)
butan-1-ol  (EXP,ISO)
cadmium atom  (EXP)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
capsaicin  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chitosan  (EXP)
chloroprene  (ISO)
cholesterol  (EXP,ISO)
cholic acid  (EXP,ISO)
chromium atom  (ISO)
cilostazol  (ISO)
clobetasol  (ISO)
clofibrate  (EXP,ISO)
Colestilan  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (EXP,ISO)
daidzein  (ISO)
DDT  (ISO)
desmosterol  (ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (ISO)
difenoconazole  (EXP)
dioxygen  (ISO)
disodium selenite  (ISO)
disulfiram  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
efonidipine hydrochloride  (ISO)
endosulfan  (EXP)
enniatin  (ISO)
ethanol  (EXP,ISO)
ezetimibe  (ISO)
fenamidone  (ISO)
fenarimol  (EXP)
fenofibrate  (ISO)
fingolimod hydrochloride  (ISO)
flusilazole  (EXP)
fluvastatin  (ISO)
folic acid  (ISO)
fonofos  (ISO)
fructose  (EXP)
furan  (EXP)
gamma-hexachlorocyclohexane  (ISO)
gemfibrozil  (ISO)
genistein  (ISO)
glafenine  (EXP)
glutathione  (ISO)
glycerol 2-phosphate  (ISO)
glycitein  (ISO)
glycolaldehyde  (ISO)
glyoxal  (ISO)
graphene oxide  (ISO)
GW 3965  (EXP,ISO)
GW 4064  (ISO)
GW 501516  (ISO)
GW 6471  (EXP,ISO)
Heptachlor epoxide  (ISO)
hexadecanoic acid  (ISO)
high-density lipoprotein cholesterol  (ISO)
Insulin-like growth factor I  (ISO)
isoprenaline  (ISO)
isotretinoin  (EXP)
ketamine  (EXP)
ketoconazole  (EXP)
KT 5720  (ISO)
L-ascorbic acid  (ISO)
lansoprazole  (ISO)
lead diacetate  (EXP)
Licochalcone B  (ISO)
linoleic acid  (ISO)
lipopolysaccharide  (ISO)
lithocholic acid  (ISO)
lovastatin  (ISO)
malonaldehyde  (ISO)
mastoparan  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
methapyrilene  (EXP)
methotrexate  (ISO)
methylmercury chloride  (ISO)
mevastatin  (EXP,ISO)
miconazole  (ISO)
mifepristone  (EXP)
mitoxantrone  (ISO)
monocrotophos  (EXP)
monosodium L-glutamate  (ISO)
N-(2,2,2-TRIFLUOROETHYL)-N-\{4-[2,2,2-TRIFLUORO-1-HYDROXY-1-(TRIFLUOROMETHYL)ETHYL]PHENYL\}BENZENESULFONAMIDE  (EXP,ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
N-acetyl-L-cysteine  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-tosyl-L-phenylalanyl chloromethyl ketone  (ISO)
nickel dichloride  (ISO)
nicotine  (EXP,ISO)
nicotinic acid  (EXP,ISO)
nimesulide  (EXP)
NS-398  (ISO)
Nutlin-3  (ISO)
O-methyleugenol  (ISO)
obeticholic acid  (ISO)
oleic acid  (ISO)
omeprazole  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
palbociclib  (ISO)
palmitoleic acid  (ISO)
pantoprazole  (ISO)
paracetamol  (ISO)
paraoxon  (ISO)
paraquat  (ISO)
parathion  (ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phenytoin  (ISO)
picolinic acid  (ISO)
pioglitazone  (ISO)
pirinixic acid  (ISO)
pitavastatin  (EXP,ISO)
pitavastatin(1-)  (EXP,ISO)
pravastatin  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
propanal  (ISO)
propiconazole  (EXP)
prostaglandin J2  (ISO)
pyrazinecarboxamide  (EXP)
quercetin  (ISO)
resveratrol  (ISO)
rifampicin  (ISO)
Ro 31-8220  (ISO)
rosuvastatin calcium  (ISO)
rotenone  (EXP)
rutin  (EXP)
SB 203580  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (EXP,ISO)
sirolimus  (EXP,ISO)
sodium arsenite  (ISO)
Soman  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
tacrolimus hydrate  (EXP,ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
terbufos  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP,ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP)
tetracycline  (ISO)
tetramethylpyrazine  (ISO)
thalidomide  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
toluene  (EXP)
topotecan  (EXP)
triacsin C  (ISO)
tributylstannane  (ISO)
Tributyltin oxide  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
triolein  (ISO)
triphenyl phosphate  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vecuronium bromide  (ISO)
vincristine  (ISO)
vitexin  (ISO)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adenylate cyclase-activating G protein-coupled receptor signaling pathway  (ISO)
apolipoprotein A-I-mediated signaling pathway  (IEA)
cellular response to cholesterol  (IEP)
cellular response to cytokine stimulus  (IEP)
cellular response to high density lipoprotein particle stimulus  (ISO)
cellular response to lipopolysaccharide  (ISO)
cellular response to retinoic acid  (ISO)
cellular response to xenobiotic stimulus  (IEP)
cholesterol efflux  (ISO)
cholesterol homeostasis  (ISO)
cholesterol metabolic process  (ISO)
cholesterol transport  (IDA,IMP)
endosomal transport  (ISO)
export across plasma membrane  (ISO)
G protein-coupled receptor signaling pathway  (ISO)
high-density lipoprotein particle assembly  (ISO)
intermembrane lipid transfer  (IEA)
intracellular cholesterol transport  (ISO)
lipid transport  (IBA)
lipoprotein biosynthetic process  (IEP,IMP,ISO)
lipoprotein metabolic process  (ISO)
lysosome organization  (ISO)
peptide secretion  (ISO)
phagocytosis, engulfment  (ISO)
phospholipid efflux  (IBA,ISO)
phospholipid homeostasis  (ISO)
phospholipid translocation  (ISO)
phospholipid transport  (IDA,TAS)
platelet dense granule organization  (ISO)
positive regulation of cholesterol efflux  (ISO)
positive regulation of high-density lipoprotein particle assembly  (ISO)
protein lipidation  (ISO)
protein secretion  (ISO)
protein transmembrane transport  (ISO)
regulation of Cdc42 protein signal transduction  (ISO)
response to laminar fluid shear stress  (ISO)
response to nutrient  (IEP)
response to nutrient levels  (IEP)
response to xenobiotic stimulus  (IEP)
reverse cholesterol transport  (ISO)
signal release  (ISO)
sphingolipid translocation  (IEA)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Becker KG, etal., Nat Genet. 2004 May;36(5):431-2.
2. Bortnick AE, etal., Am J Physiol Lung Cell Mol Physiol 2003 Oct;285(4):L869-78. Epub 2003 Aug 08.
3. Brooks-Wilson A, etal., Nat Genet 1999 Aug;22(4):336-45.
4. Chao WT, etal., Biochem Biophys Res Commun. 2005 Jul 8;332(3):743-9.
5. Chen L, etal., Clin Lab. 2016 Sep 1;62(9):1643-1649. doi: 10.7754/Clin.Lab.2016.160105.
6. Clee SM, etal., J Clin Invest. 2000 Nov;106(10):1263-70.
7. Fukunaga K, etal., Am J Physiol Endocrinol Metab. 2018 Dec 1;315(6):E1232-E1241. doi: 10.1152/ajpendo.00134.2018. Epub 2018 Aug 21.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. Ghoneim RH, etal., Br J Nutr. 2015 Feb 14;113(3):507-16. doi: 10.1017/S0007114514003717. Epub 2015 Jan 23.
10. GOA data from the GO Consortium
11. Guan JZ, etal., Tohoku J Exp Med. 2003 Dec;201(4):251-9.
12. Guo L, etal., Eur J Pharmacol. 2006 Dec 3;551(1-3):80-6. Epub 2006 Sep 6.
13. Harrison EH Biochim Biophys Acta. 2012 Jan;1821(1):70-7. Epub 2011 Jun 12.
14. Hirayama T, etal., Hepatology. 2006 Sep;44(3):602-11.
15. Hoekstra M, etal., J Hepatol. 2005 Mar;42(3):400-7.
16. Jeon BH, etal., Metabolism. 2015 Nov;64(11):1444-53. doi: 10.1016/j.metabol.2015.07.014. Epub 2015 Jul 26.
17. Johnson AC, etal., Am J Pathol. 2003 Jan;162(1):283-91.
18. Katsube A, etal., Arterioscler Thromb Vasc Biol. 2016 Dec;36(12):2304-2314. doi: 10.1161/ATVBAHA.116.308472. Epub 2016 Oct 20.
19. Katzov H, etal., Hum Mutat 2004 Apr;23(4):358-67.
20. Kobayashi M, etal., Eur J Pharmacol. 2011 Jul 15;662(1-3):9-14. doi: 10.1016/j.ejphar.2011.04.043. Epub 2011 May 1.
21. Li Y, etal., Life Sci. 2014 Nov 18;118(1):27-33. doi: 10.1016/j.lfs.2014.10.003.
22. Liang H and Wang Y, Biochem Biophys Res Commun. 2018 Apr 6;498(3):473-480. doi: 10.1016/j.bbrc.2018.03.003. Epub 2018 Mar 2.
23. McNeish J, etal., Proc Natl Acad Sci U S A 2000 Apr 11;97(8):4245-50.
24. MGD data from the GO Consortium
25. Moon SH, etal., Cell. 2019 Jan 24;176(3):564-580.e19. doi: 10.1016/j.cell.2018.11.011. Epub 2018 Dec 20.
26. Morgado N, etal., Ann Nutr Metab. 2005 Nov-Dec;49(6):397-406. Epub 2005 Oct 14.
27. Ngo Sock ET, etal., Horm Metab Res. 2014 Jul;46(8):550-5. doi: 10.1055/s-0034-1370910. Epub 2014 Mar 11.
28. Ohashi R, etal., QJM. 2005 Dec;98(12):845-56. Epub 2005 Oct 28.
29. OMIM Disease Annotation Pipeline
30. RGD automated data pipeline
31. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
32. RGD automated import pipeline for gene-chemical interactions
33. Sahoo D, etal., J Lipid Res 2004 Jun;45(6):1122-31. Epub 2004 Mar 1.
34. Singaraja RR, etal., J Biol Chem 2001 Sep 7;276(36):33969-79. Epub 2001 Jun 21.
35. Tachibana M, etal., Exp Neurol. 2016 Mar;277:1-9. doi: 10.1016/j.expneurol.2015.12.003. Epub 2015 Dec 11.
36. Tai LM, etal., J Biol Chem. 2014 Oct 31;289(44):30538-55. doi: 10.1074/jbc.M114.600833. Epub 2014 Sep 12.
37. Takeyama Y, etal., Med Mol Morphol. 2017 Dec;50(4):227-237. doi: 10.1007/s00795-017-0166-7. Epub 2017 Jun 28.
38. Tamehiro N, etal., J Biol Chem. 2007 Jul 20;282(29):21090-9. Epub 2007 May 27.
39. Timmins JM, etal., J Clin Invest. 2005 May;115(5):1333-42. doi: 10.1172/JCI23915. Epub 2005 Apr 7.
40. Tovar AR, etal., J Lipid Res. 2005 Sep;46(9):1823-32. Epub 2005 Jul 1.
41. Villarreal-Molina MT, etal., Diabetes. 2007 Feb 7;.
42. Villarreal-Molina MT, etal., Diabetes. 2008 Feb;57(2):509-13. Epub 2007 Nov 14.
43. Wang Q, etal., Zhongguo Zhong Xi Yi Jie He Za Zhi. 2012 Sep;32(9):1245-8.
44. Wein S, etal., Biochem Pharmacol 2004 Mar 15;67(6):1195-202.
45. Wu Q, etal., Endocrinology 2003 Jun;144(6):2437-45.
Additional References at PubMed
PMID:9006906   PMID:10525055   PMID:10878804   PMID:11162594   PMID:11559713   PMID:11700048   PMID:11855831   PMID:12084722   PMID:12859204   PMID:12869555   PMID:14701824   PMID:14747463  
PMID:14754908   PMID:15163665   PMID:15210959   PMID:15269218   PMID:15358760   PMID:15469992   PMID:15520446   PMID:15520449   PMID:16204232   PMID:16443932   PMID:16702602   PMID:17148552  
PMID:17241464   PMID:17305370   PMID:17657311   PMID:17689492   PMID:17884990   PMID:19041881   PMID:19275878   PMID:19427182   PMID:19528336   PMID:19752193   PMID:19874424   PMID:19878707  
PMID:20137471   PMID:20215580   PMID:20584649   PMID:20643408   PMID:21402379   PMID:21605865   PMID:21957962   PMID:22179027   PMID:23220274   PMID:23931754   PMID:24097981   PMID:24117066  
PMID:24719980   PMID:24814386   PMID:25084135   PMID:25305669   PMID:25323823   PMID:26663205   PMID:26707062   PMID:26743528   PMID:28642575   PMID:28694219   PMID:28704619   PMID:29775222  
PMID:31608710   PMID:32505219  


Genomics

Comparative Map Data
Abca1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2567,678,267 - 67,801,162 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl569,857,771 - 69,983,015 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0569,857,717 - 69,983,042 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0574,023,652 - 74,112,802 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4570,493,357 - 70,583,729 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1570,498,469 - 70,588,842 (-)NCBI
Celera566,575,764 - 66,665,022 (-)NCBICelera
Cytogenetic Map5q23-q24NCBI
ABCA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9104,781,006 - 104,928,155 (-)EnsemblGRCh38hg38GRCh38
GRCh389104,781,006 - 104,928,155 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh379107,543,287 - 107,690,436 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369106,583,104 - 106,730,257 (-)NCBINCBI36hg18NCBI36
Build 349104,622,837 - 104,769,991NCBI
Celera978,048,593 - 78,195,737 (-)NCBI
Cytogenetic Map9q31.1NCBI
HuRef977,145,450 - 77,292,489 (-)NCBIHuRef
CHM1_19107,690,161 - 107,837,338 (-)NCBICHM1_1
Abca1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39453,030,789 - 53,159,988 (-)NCBIGRCm39mm39
GRCm39 Ensembl453,030,787 - 53,159,895 (-)Ensembl
GRCm38453,030,789 - 53,159,988 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl453,030,787 - 53,159,895 (-)EnsemblGRCm38mm10GRCm38
MGSCv37453,043,661 - 53,172,767 (-)NCBIGRCm37mm9NCBIm37
MGSCv36453,051,888 - 53,180,992 (-)NCBImm8
Celera453,009,587 - 53,133,003 (-)NCBICelera
Cytogenetic Map4B2NCBI
cM Map428.57NCBI
Abca1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541921,553,835 - 21,681,619 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541921,553,863 - 21,681,626 (+)NCBIChiLan1.0ChiLan1.0
ABCA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19104,076,516 - 104,224,188 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9104,076,516 - 104,224,188 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0975,948,831 - 76,096,136 (-)NCBIMhudiblu_PPA_v0panPan3
ABCA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11160,761,669 - 60,869,753 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1160,761,655 - 60,890,496 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1159,222,894 - 59,351,153 (-)NCBI
ROS_Cfam_1.01161,895,159 - 62,023,474 (-)NCBI
UMICH_Zoey_3.11160,416,579 - 60,544,839 (-)NCBI
UNSW_CanFamBas_1.01160,430,633 - 60,559,576 (-)NCBI
UU_Cfam_GSD_1.01161,125,735 - 61,254,053 (-)NCBI
Abca1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947175,953,909 - 176,088,687 (-)NCBI
SpeTri2.0NW_0049365597,177,887 - 7,312,660 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ABCA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1246,144,277 - 246,278,492 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11246,144,277 - 246,278,492 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21275,475,434 - 275,507,918 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ABCA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11234,587,123 - 34,734,936 (+)NCBI
ChlSab1.1 Ensembl1234,587,118 - 34,731,642 (+)Ensembl
Vero_WHO_p1.0NW_0236660357,887,897 - 8,035,290 (-)NCBI
Abca1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247586,449,583 - 6,590,244 (+)NCBI

Position Markers
D5Got6  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2567,768,132 - 67,768,317 (+)MAPPERmRatBN7.2
Rnor_6.0569,950,003 - 69,950,187NCBIRnor6.0
Rnor_5.0574,110,339 - 74,110,523UniSTSRnor5.0
RGSC_v3.4570,581,265 - 70,581,450RGDRGSC3.4
RGSC_v3.4570,581,266 - 70,581,450UniSTSRGSC3.4
RGSC_v3.1570,586,379 - 70,586,563RGD
Celera566,662,560 - 66,662,748UniSTS
RH 3.4 Map5459.5UniSTS
RH 3.4 Map5459.5RGD
RH 2.0 Map5382.7RGD
Cytogenetic Map5q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5189432042Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5193273395Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51136640934Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5152509878720537Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5166658771552720Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)59514842103580403Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512651967117554267Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51884791376608178Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)52907889974078899Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)52907889974078899Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)52964166174641661Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)52964166174641661Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531926122136640934Rat
1298067Scl15Serum cholesterol level QTL 154.80.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53440240979402409Rat
1302786Kidm8Kidney mass QTL 828.15kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)53440240979402409Rat
1598807Glom12Glomerulus QTL 122.7kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)53440240979402409Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)535225432108092802Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)535661945117554267Rat
1641922Alcrsp8Alcohol response QTL 8alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)53578875670742105Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535788756147487820Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540777918154732375Rat
1331773Scl26Serum cholesterol level QTL 263.065blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)54440427689432042Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)544404276134502294Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)547745646167946134Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54872203893587756Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)551418671147487820Rat
9589025Epfw7Epididymal fat weight QTL 720.660.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)55180442696804426Rat
7411561Bw134Body weight QTL 134240.001body mass (VT:0001259)body weight gain (CMO:0000420)55180442696804426Rat
2303615Vencon7Ventilatory control QTL 70.001respiration trait (VT:0001943)respiration rate (CMO:0000289)55330956898309568Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)555903593100903593Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)556902367101902367Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)556991667137729065Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)560072951133313852Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)561086525149030144Rat
2316954Rf57Renal function QTL 570kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)56108665393273130Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)561086653117554114Rat
61386Bp49Blood pressure QTL 4916.6cerebrum integrity trait (VT:0010549)brain infarction volume (CMO:0001013)561612600102331727Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)561612600168109659Rat
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)565696672129038896Rat
1598814Mcs13Mammary carcinoma susceptibility QTL 130.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)56839509671941113Rat
2290005Mcs24Mammary carcinoma susceptibility QTL 24mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)568838385113838385Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:35
Count of miRNA genes:29
Interacting mature miRNAs:35
Transcripts:ENSRNOT00000024564
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 2 57 41 19 41 3 3 58 22 36 11 3
Low 3 41 5 8 16 13 5 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024564   ⟹   ENSRNOP00000024564
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl569,857,771 - 69,983,015 (-)Ensembl
RefSeq Acc Id: NM_178095   ⟹   NP_835196
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2567,681,297 - 67,770,596 (-)NCBI
Rnor_6.0569,860,747 - 69,952,466 (-)NCBI
Rnor_5.0574,023,652 - 74,112,802 (-)NCBI
RGSC_v3.4570,493,357 - 70,583,729 (-)RGD
Celera566,575,764 - 66,665,022 (-)RGD
Sequence:
RefSeq Acc Id: XM_039109846   ⟹   XP_038965774
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2567,678,267 - 67,801,162 (-)NCBI
RefSeq Acc Id: XM_039109847   ⟹   XP_038965775
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2567,678,267 - 67,801,162 (-)NCBI
Protein Sequences
Protein RefSeqs NP_835196 (Get FASTA)   NCBI Sequence Viewer  
  XP_038965774 (Get FASTA)   NCBI Sequence Viewer  
  XP_038965775 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAO53557 (Get FASTA)   NCBI Sequence Viewer  
  BAF81890 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_835196   ⟸   NM_178095
- Sequence:
RefSeq Acc Id: ENSRNOP00000024564   ⟸   ENSRNOT00000024564
RefSeq Acc Id: XP_038965774   ⟸   XM_039109846
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038965775   ⟸   XM_039109847
- Peptide Label: isoform X2
Protein Domains
ABC transporter

Transcriptome

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

Promoters
RGD ID:13693741
Promoter ID:EPDNEW_R4266
Type:multiple initiation site
Name:Abca1_2
Description:ATP binding cassette subfamily A member 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R4267  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0569,966,836 - 69,966,896EPDNEW
RGD ID:13693742
Promoter ID:EPDNEW_R4267
Type:single initiation site
Name:Abca1_1
Description:ATP binding cassette subfamily A member 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R4266  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0569,982,955 - 69,983,015EPDNEW

Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:631344 AgrOrtholog
Ensembl Genes ENSRNOG00000018126 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000024564 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024564 UniProtKB/TrEMBL
InterPro ABC_A UniProtKB/TrEMBL
  ABC_transporter-like UniProtKB/TrEMBL
  ABC_transporter_CS UniProtKB/TrEMBL
  ABCA1 UniProtKB/TrEMBL
  ATPase_AAA+_core UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
KEGG Report rno:313210 UniProtKB/TrEMBL
NCBI Gene 313210 ENTREZGENE
PANTHER PTHR19229 UniProtKB/TrEMBL
  PTHR19229:SF34 UniProtKB/TrEMBL
Pfam ABC_tran UniProtKB/TrEMBL
PharmGKB ABCA1 RGD
PhenoGen Abca1 PhenoGen
PROSITE ABC_TRANSPORTER_1 UniProtKB/TrEMBL
  ABC_TRANSPORTER_2 UniProtKB/TrEMBL
SMART AAA UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A8J6V3_RAT UniProtKB/TrEMBL
  F1LNL3_RAT UniProtKB/TrEMBL
  Q80ZB2_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-25 Abca1  ATP binding cassette subfamily A member 1  Abca1  ATP-binding cassette, subfamily A (ABC1), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-11-16 Abca1  ATP-binding cassette, subfamily A (ABC1), member 1  Abca1  ATP-binding cassette, sub-family A (ABC1), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-11 Abca1  ATP-binding cassette, sub-family A (ABC1), member 1      Symbol and Name status set to approved 625702 APPROVED