Apob (apolipoprotein B) - Rat Genome Database

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Gene: Apob (apolipoprotein B) Rattus norvegicus
Analyze
Symbol: Apob
Name: apolipoprotein B
RGD ID: 2129
Description: Predicted to enable several functions, including cholesterol transfer activity; heparin binding activity; and lipase binding activity. Involved in several processes, including cellular response to tumor necrosis factor; response to estradiol; and triglyceride catabolic process. Located in several cellular components, including extracellular space; vesicle lumen; and vesicle membrane. Part of high-density lipoprotein particle; low-density lipoprotein particle; and very-low-density lipoprotein particle. Biomarker of fatty liver disease and nephrotic syndrome. Human ortholog(s) of this gene implicated in several diseases, including artery disease (multiple); biliary tract cancer (multiple); familial hyperlipidemia (multiple); hypobetalipoproteinemia (multiple); and sickle cell anemia. Orthologous to human APOB (apolipoprotein B); PARTICIPATES IN altered lipoprotein metabolic pathway; forkhead class A signaling pathway; lipoprotein metabolic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: Aa1064; Ac1-060; Apo B-100; ApoB-100; ApoB-48; apolipoprotein B (including Ag(x) antigen); apolipoprotein B PI; apolipoprotein B-100; apolipoprotein B-48
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
mRatBN7.2630,844,386 - 30,883,983 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl630,844,368 - 30,892,497 (+)Ensembl
Rnor_6.0633,176,826 - 33,216,381 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl633,176,778 - 33,224,997 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0642,956,372 - 42,995,922 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4631,508,060 - 31,548,083 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1631,546,139 - 31,550,758 (+)NCBI
Celera630,299,724 - 30,339,330 (+)NCBICelera
Cytogenetic Map6q14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
aortic valve stenosis  (ISO)
arteriosclerosis  (ISO)
Behcet's disease  (ISO)
beta thalassemia  (ISO)
bile duct cancer  (ISO)
biliary tract cancer  (ISO)
cardiovascular system disease  (ISO)
celiac disease  (ISO)
cerebral infarction  (ISO)
common bile duct neoplasm  (ISO)
coronary artery disease  (ISO)
Coronary Disease  (ISO)
Coumarin Sensitivity  (ISO)
Death  (ISO)
diabetes mellitus  (ISO)
Diabetic Nephropathies  (ISO)
diabetic retinopathy  (ISO)
dilated cardiomyopathy 1B  (ISO)
Drug-Related Side Effects and Adverse Reactions  (ISO)
Dyslipidemias  (ISO)
Endotoxemia  (IEP)
Experimental Diabetes Mellitus  (IEP)
familial combined hyperlipidemia  (ISO)
familial hypercholesterolemia  (ISO)
Familial Hypercholesterolemia due to Ligand-Defective Apolipoprotein B  (ISO)
familial hyperlipidemia  (ISO)
familial hypobetalipoproteinemia 1  (ISO)
familial hypobetalipoproteinemia 2  (ISS)
Familial Hypobetalipoproteinemia, Apolipoprotein B  (ISO)
familial isolated deficiency of vitamin E  (ISO)
fatty liver disease  (IEP,ISO)
gallbladder cancer  (ISO)
genetic disease  (ISO)
Hemorrhage  (ISO)
Hypercholesterolemia  (IEP,ISO)
Hypercholesterolemia, Autosomal Dominant, 3  (ISO)
Hyperlipoproteinemia Type II  (ISO)
hypertension  (ISO)
Hypertriglyceridemia  (IEP,ISO)
hypobetalipoproteinemia  (ISO)
Marfanoid Mental Retardation Syndrome, Autosomal  (ISO)
Metabolic Syndrome  (ISO)
myocardial infarction  (ISO)
Myocardial Ischemia  (ISO)
nephrotic syndrome  (IEP)
obesity  (ISO)
ovarian cancer  (ISO)
peripheral vascular disease  (ISO)
sickle cell anemia  (ISO)
spastic ataxia  (ISO)
Sudden Cardiac Death  (ISO)
type 1 diabetes mellitus  (ISO)
type 2 diabetes mellitus  (ISO)
warfarin resistance  (ISO)
warfarin sensitivity  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(+)-taxifolin  (ISO)
(-)-ephedrine  (ISO)
(R,R,R)-alpha-tocopherol  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-amino-2-deoxy-D-glucopyranose  (EXP,ISO)
2-hydroxypropanoic acid  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3-chloropropane-1,2-diol  (EXP)
4,4'-sulfonyldiphenol  (ISO)
5-fluorouracil  (ISO)
6-(4-chlorophenyl)imidazo[2,1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime  (ISO)
acetamide  (EXP)
acetic anhydride  (ISO)
acetylleucyl-leucyl-norleucinal  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (EXP,ISO)
aldehydo-D-glucose  (ISO)
allopurinol  (ISO)
aluminium atom  (ISO)
aluminium(0)  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
Aroclor 1254  (EXP)
atenolol  (ISO)
atorvastatin calcium  (EXP,ISO)
benazepril  (ISO)
bendroflumethiazide  (ISO)
benzene  (EXP)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
Benzo[k]fluoranthene  (ISO)
beta-D-glucosamine  (EXP,ISO)
bexarotene  (EXP)
bezafibrate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
buspirone  (EXP)
buta-1,3-diene  (ISO)
cadmium atom  (ISO)
caffeine  (EXP,ISO)
calcidiol  (EXP)
capsaicin  (EXP)
carbon nanotube  (ISO)
cefaloridine  (EXP)
cholesterol  (EXP)
choline  (ISO)
chromium(6+)  (ISO)
chrysin  (ISO)
cisplatin  (EXP)
clofibrate  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
cortisol  (ISO)
cyclophosphamide  (EXP)
cyclosporin A  (EXP,ISO)
cypermethrin  (EXP)
D-glucose  (ISO)
daunorubicin  (EXP)
dexamethasone  (EXP)
dextran sulfate  (ISO)
dicrotophos  (ISO)
diethyl phthalate  (ISO)
diethyl pyrocarbonate  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
elemental selenium  (EXP)
endosulfan  (EXP)
ethanol  (EXP,ISO)
ethanolamine  (EXP)
fenofibrate  (ISO)
ferulic acid  (ISO)
flavonoids  (ISO)
flutamide  (EXP)
fluvastatin  (ISO)
folic acid  (ISO)
fructose  (EXP,ISO)
gadolinium trichloride  (EXP)
gallic acid  (ISO)
gamma-hexachlorocyclohexane  (EXP)
gemfibrozil  (EXP,ISO)
genistein  (EXP)
gentamycin  (EXP)
glucose  (ISO)
graphite  (EXP)
GW 4064  (ISO)
GW 7647  (ISO)
hexadecanoic acid  (EXP)
hydrogen peroxide  (ISO)
indinavir  (ISO)
indometacin  (ISO)
irbesartan  (ISO)
ivermectin  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lactacystin  (ISO)
levonorgestrel  (ISO)
linsidomine  (EXP)
lovastatin  (ISO)
methapyrilene  (EXP)
methylmercury chloride  (ISO)
microcystin-LR  (ISO)
mifepristone  (ISO)
morphine  (ISO)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
Nandrolone decanoate  (ISO)
nickel atom  (ISO)
nicotinic acid  (ISO)
nitrofen  (EXP)
Nonylphenol  (EXP)
obeticholic acid  (ISO)
ochratoxin A  (EXP)
olanzapine  (ISO)
oleic acid  (EXP,ISO)
palmitoyl ethanolamide  (ISO)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
permethrin  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pioglitazone  (ISO)
pirinixic acid  (EXP,ISO)
potassium dichromate  (ISO)
Propiverine  (EXP)
quercetin  (EXP,ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
rifampicin  (ISO)
rimonabant  (ISO)
rosuvastatin calcium  (ISO)
SB 431542  (ISO)
selenium atom  (EXP)
simvastatin  (EXP,ISO)
sodium acetate trihydrate  (ISO)
sodium dichromate  (EXP)
sodium fluoride  (ISO)
sulindac  (ISO)
tamoxifen  (EXP)
tauroursodeoxycholic acid  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (EXP)
thapsigargin  (ISO)
thioacetamide  (ISO)
titanium dioxide  (ISO)
tolcapone  (ISO)
tremolite asbestos  (ISO)
trichloroethene  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
tunicamycin  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
valsartan  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
warfarin  (ISO)
wortmannin  (EXP)
zinc atom  (EXP,ISO)
zinc(0)  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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4. Andreotti G, etal., Int J Cancer. 2008 May 15;122(10):2322-9.
5. Aspichueta P, etal., J Endotoxin Res. 2006;12(3):181-92.
6. Avakian SD, etal., Clin Genet. 2001 Nov;60(5):381-4.
7. Avall-Lundqvist EH and Peterson CO, Acta Oncol. 1996;35(8):1007-10.
8. Baez S, etal., World J Gastroenterol. 2010 Jan 21;16(3):372-8.
9. Bartels ED, etal., Eur J Clin Invest. 2009 Mar;39(3):190-9.
10. Bartolome N, etal., Ann N Y Acad Sci. 2007 Jan;1096:55-69.
11. Becker KG, etal., Nat Genet. 2004 May;36(5):431-2.
12. Clarke MW, etal., Clin Chem. 2006 Jul;52(7):1339-45. Epub 2006 May 25.
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14. Corsetti JP, etal., J Clin Lipidol. 2016 Jul-Aug;10(4):842-850. doi: 10.1016/j.jacl.2016.03.003. Epub 2016 Mar 12.
15. Crooke RM, etal., J Lipid Res. 2005 May;46(5):872-84. doi: 10.1194/jlr.M400492-JLR200. Epub 2005 Feb 16.
16. Dhingra S and Bansal MP, Chem Biol Interact. 2006 May 15;161(1):49-56. Epub 2006 Apr 3.
17. Fredrikson GN, etal., Diabetologia. 2009 Jul;52(7):1426-33. Epub 2009 May 12.
18. Gaffney D, etal., Arterioscler Thromb Vasc Biol. 1995 Aug;15(8):1025-9.
19. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
20. GOA data from the GO Consortium
21. Griffin JL, etal., J Proteome Res. 2007 Jan;6(1):54-61.
22. Gusarova V, etal., J Biol Chem. 2007 Jul 6;282(27):19453-62. Epub 2007 May 11.
23. Hebbachi AM, etal., Biochem J. 1997 Aug 1;325 ( Pt 3):711-9.
24. Helio T, etal., J Intern Med. 1992 Jan;231(1):49-57.
25. Hirano T, etal., Metabolism. 1994 Feb;43(2):248-56.
26. Hirata RD, etal., Biochim Biophys Acta. 1999 Jan 29;1437(1):53-62.
27. Hobbs HH, etal., N Engl J Med. 1987 Sep 17;317(12):734-7.
28. Joles JA, etal., J Am Soc Nephrol. 1997 Dec;8(12):1870-6.
29. Konemori G, etal., Nippon Ronen Igakkai Zasshi. 1990 Jan;27(1):22-7.
30. Lally S, etal., Metabolism. 2007 Mar;56(3):430-8.
31. Leng SH, etal., Acta Pharmacol Sin. 2004 Apr;25(4):496-502.
32. Levy E, etal., J Biol Chem. 2002 May 10;277(19):16470-7. Epub 2002 Feb 5.
33. Li L, etal., J Lipid Res. 2006 Jan;47(1):67-77. Epub 2005 Oct 14.
34. Linden D, etal., J Biol Chem 2002 Jun 21;277(25):23044-53.
35. Maioli M, etal., Atherosclerosis. 1997 May;131(1):127-33.
36. Matsumoto A, etal., Biochem Biophys Res Commun 1987 Jan 15;142(1):92-9.
37. MGD data from the GO Consortium
38. Mulvihill EE, etal., Diabetes. 2009 Oct;58(10):2198-210. Epub 2009 Jul 10.
39. Nakajima K, etal., Atherosclerosis. 2006 Oct 10;.
40. NCBI rat LocusLink and RefSeq merged data July 26, 2002
41. Niemi J, etal., Ann Med. 2009 May 1:1-11.
42. Nishimaki-Mogami T, etal., J Lipid Res. 2002 Jul;43(7):1035-45.
43. OMIM Disease Annotation Pipeline
44. Pan JP, etal., J Formos Med Assoc. 1998 Apr;97(4):233-8.
45. Pan M, etal., Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5862-7. doi: 10.1073/pnas.0707460104. Epub 2008 Apr 7.
46. Pandey SN, etal., Liver Int. 2007 Sep;27(7):1008-15.
47. Patterson AP, etal., J Biol Chem 2003 Feb 28;278(9):7600-6.
48. Pei WD, etal., Int J Cardiol. 2007 Feb 14;115(3):293-6. Epub 2006 Jun 22.
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50. Perez S, etal., Biochim Biophys Acta. 2006 Feb;1761(2):160-71. Epub 2006 Mar 3.
51. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
52. Qiu W, etal., J Lipid Res. 2006 Aug;47(8):1749-61. Epub 2006 May 3.
53. RGD automated data pipeline
54. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
55. RGD automated import pipeline for gene-chemical interactions
56. Saad MF, etal., Diabetes Care. 2004 Jun;27(6):1324-9.
57. Scoffone HM, etal., Am J Cardiol. 2013 Nov 1;112(9):1499-504. doi: 10.1016/j.amjcard.2013.06.035. Epub 2013 Sep 13.
58. Shearer GC, etal., Kidney Int. 2001 Jan;59(1):179-89.
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60. Sparks JD, etal., Atherosclerosis. 1986 Sep;61(3):205-11.
61. Su JW, etal., Diabetes Care. 2009 Feb;32(2):e21.
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63. Tseng CH Clin Biochem. 2009 Jul;42(10-11):1019-24. Epub 2009 Mar 24.
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65. West NA, etal., Diabetes Care. 2009 Jan;32(1):175-80. Epub 2008 Oct 22.
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Additional References at PubMed
PMID:1917954   PMID:2563166   PMID:3235917   PMID:3417667   PMID:3860811   PMID:4363408   PMID:7126555   PMID:7593600   PMID:7878058   PMID:8245722   PMID:8460149   PMID:8855280  
PMID:8889548   PMID:8921909   PMID:9202070   PMID:9502790   PMID:9685400   PMID:9852051   PMID:10705993   PMID:10713055   PMID:10893242   PMID:11120757   PMID:11577082   PMID:12072432  
PMID:12477932   PMID:12917397   PMID:12960170   PMID:13130124   PMID:14570923   PMID:14970200   PMID:15124019   PMID:15308631   PMID:15520448   PMID:15790761   PMID:15797858   PMID:15863839  
PMID:16230502   PMID:16233946   PMID:16396637   PMID:16455790   PMID:16548883   PMID:16624317   PMID:17244792   PMID:17690102   PMID:18322245   PMID:19114110   PMID:20181985   PMID:20651008  
PMID:22257482   PMID:22326345   PMID:22363685   PMID:22546076   PMID:22580899   PMID:22897442   PMID:23533145   PMID:23911221   PMID:24334870   PMID:26184122   PMID:26616056   PMID:27068509  
PMID:27138255   PMID:27477018   PMID:27495870   PMID:28694219   PMID:31176989  


Genomics

Comparative Map Data
Apob
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2630,844,386 - 30,883,983 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl630,844,368 - 30,892,497 (+)Ensembl
Rnor_6.0633,176,826 - 33,216,381 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl633,176,778 - 33,224,997 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0642,956,372 - 42,995,922 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4631,508,060 - 31,548,083 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1631,546,139 - 31,550,758 (+)NCBI
Celera630,299,724 - 30,339,330 (+)NCBICelera
Cytogenetic Map6q14NCBI
APOB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl221,001,429 - 21,044,073 (-)EnsemblGRCh38hg38GRCh38
GRCh38221,001,429 - 21,044,073 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37221,224,301 - 21,266,945 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36221,077,806 - 21,120,450 (-)NCBINCBI36hg18NCBI36
Build 34221,135,952 - 21,178,597NCBI
Celera221,063,779 - 21,106,429 (-)NCBI
Cytogenetic Map2p24.1NCBI
HuRef220,956,976 - 20,999,627 (-)NCBIHuRef
CHM1_1221,153,564 - 21,196,210 (-)NCBICHM1_1
Apob
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39128,027,629 - 8,066,839 (+)NCBIGRCm39mm39
GRCm39 Ensembl128,027,648 - 8,066,835 (+)Ensembl
GRCm38127,977,629 - 8,016,839 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl127,977,648 - 8,016,835 (+)EnsemblGRCm38mm10GRCm38
MGSCv37127,984,483 - 8,023,645 (+)NCBIGRCm37mm9NCBIm37
MGSCv36128,003,656 - 8,042,849 (+)NCBImm8
Celera128,374,429 - 8,411,685 (+)NCBICelera
Cytogenetic Map12A1.1NCBI
cM Map123.53NCBI
Apob
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554693,436,450 - 3,478,424 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554693,437,422 - 3,478,408 (-)NCBIChiLan1.0ChiLan1.0
APOB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A21,100,349 - 21,142,545 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A21,100,356 - 21,145,129 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A20,986,464 - 21,029,004 (-)NCBIMhudiblu_PPA_v0panPan3
APOB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11715,877,937 - 15,916,032 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1715,878,244 - 15,915,135 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1715,842,555 - 15,879,853 (-)NCBI
ROS_Cfam_1.01716,030,075 - 16,067,405 (-)NCBI
ROS_Cfam_1.0 Ensembl1716,030,161 - 16,067,623 (-)Ensembl
UMICH_Zoey_3.11715,883,776 - 15,920,986 (-)NCBI
UNSW_CanFamBas_1.01715,891,112 - 15,928,422 (-)NCBI
UU_Cfam_GSD_1.01715,923,305 - 15,960,613 (-)NCBI
Apob
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629260,290,128 - 60,327,775 (-)NCBI
SpeTri2.0NW_00493649310,509,118 - 10,549,144 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
APOB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3117,250,096 - 117,316,200 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13117,250,096 - 117,316,200 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Pig Cytomap3q24-qterNCBI
APOB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11486,624,209 - 86,669,175 (+)NCBIChlSab1.1chlSab2
ChlSab1.11486,624,209 - 86,669,175 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1486,624,332 - 86,668,704 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604525,515,337 - 25,558,432 (-)NCBIVero_WHO_p1.0
Apob
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247383,579,747 - 3,622,508 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH130075  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2630,883,711 - 30,883,903 (+)MAPPERmRatBN7.2
Rnor_6.0633,216,110 - 33,216,301NCBIRnor6.0
Rnor_5.0642,995,651 - 42,995,842UniSTSRnor5.0
RGSC_v3.4631,547,812 - 31,548,003UniSTSRGSC3.4
Celera630,339,059 - 30,339,250UniSTS
RH 3.4 Map6123.98UniSTS
Cytogenetic Map6q14UniSTS
AI315052  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2630,882,756 - 30,882,962 (+)MAPPERmRatBN7.2
Rnor_6.0633,215,155 - 33,215,360NCBIRnor6.0
Rnor_5.0642,994,696 - 42,994,901UniSTSRnor5.0
RGSC_v3.4631,546,857 - 31,547,062UniSTSRGSC3.4
Celera630,338,104 - 30,338,309UniSTS
Cytogenetic Map6q14UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6134235784Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6137618905Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6139036266Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6141223769Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449734434305Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)61653614061536140Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)61653614071636405Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62033877762613667Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:168
Count of miRNA genes:121
Interacting mature miRNAs:131
Transcripts:ENSRNOT00000007371, ENSRNOT00000046811
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 12 12 12
Medium 1 31 29 29 2 2
Low 1 18 14 16 7 7 10 13 13 6 7
Below cutoff 1 6 1 1 1 28 18 19 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_019287 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AA997806 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC098761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB694353 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB771776 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB801343 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CV796295 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209668 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209795 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210622 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210787 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218405 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000164 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M11227 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M14952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M21842 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M23049 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M27440 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U53873 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X55969 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000007371   ⟹   ENSRNOP00000007371
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl630,844,386 - 30,883,980 (+)Ensembl
Rnor_6.0 Ensembl633,176,826 - 33,216,378 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000046811   ⟹   ENSRNOP00000039779
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl630,845,076 - 30,892,497 (+)Ensembl
Rnor_6.0 Ensembl633,176,778 - 33,224,997 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000105148   ⟹   ENSRNOP00000093102
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl630,844,368 - 30,883,980 (+)Ensembl
RefSeq Acc Id: NM_019287   ⟹   NP_062160
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2630,844,386 - 30,883,983 (+)NCBI
Rnor_6.0633,176,826 - 33,216,381 (+)NCBI
Rnor_5.0642,956,372 - 42,995,922 (+)NCBI
RGSC_v3.4631,508,060 - 31,548,083 (+)RGD
Celera630,299,724 - 30,339,330 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_062160   ⟸   NM_019287
- Peptide Label: precursor
- UniProtKB: Q7TMA5 (UniProtKB/Swiss-Prot),   F1M6Z1 (UniProtKB/TrEMBL),   Q4G047 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000039779   ⟸   ENSRNOT00000046811
RefSeq Acc Id: ENSRNOP00000007371   ⟸   ENSRNOT00000007371
RefSeq Acc Id: ENSRNOP00000093102   ⟸   ENSRNOT00000105148
Protein Domains
ApoB100_C   Vitellogenin

Transcriptome

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

Promoters
RGD ID:13694482
Promoter ID:EPDNEW_R5005
Type:multiple initiation site
Name:Apob_1
Description:apolipoprotein B
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_6.0633,176,813 - 33,176,873EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)