Apoc3 (apolipoprotein C3) - Rat Genome Database

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Gene: Apoc3 (apolipoprotein C3) Rattus norvegicus
Analyze
Symbol: Apoc3
Name: apolipoprotein C3
RGD ID: 2136
Description: Predicted to enable high-density lipoprotein particle receptor binding activity; lipase inhibitor activity; and phospholipid binding activity. Involved in several processes, including lipoprotein transport; negative regulation of oxidative phosphorylation; and positive regulation of triglyceride biosynthetic process. Located in extracellular space. Used to study hyperthyroidism; hypothyroidism; and type 1 diabetes mellitus. Biomarker of cholestasis. Human ortholog(s) of this gene implicated in several diseases, including apolipoprotein C-III deficiency; chronic kidney disease; coronary artery disease; familial hyperlipidemia (multiple); and glucose metabolism disease (multiple). Orthologous to human APOC3 (apolipoprotein C3); PARTICIPATES IN altered lipoprotein metabolic pathway; lipoprotein metabolic pathway; eicosanoid signaling pathway via peroxisome proliferator-activated receptor gamma; INTERACTS WITH (+)-schisandrin B; 1-nitropropane; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: apo-CIII; ApoC-III; apolipoprotein C-3; apolipoprotein C-III
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
mRatBN7.2846,531,478 - 46,533,658 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl846,531,478 - 46,533,583 (-)Ensembl
Rnor_6.0850,529,318 - 50,531,498 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl850,529,318 - 50,531,498 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0849,155,390 - 49,157,779 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.18159,618,812 - 159,618,833NCBI
Celera846,113,508 - 46,115,688 (-)NCBICelera
Cytogenetic Map8q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-ephedrine  (ISO)
1-methylphenanthrene  (ISO)
1-nitropropane  (EXP)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-diaminotoluene  (EXP)
2,6-diaminotoluene  (EXP)
2-acetamidofluorene  (EXP)
2-nitro-p-phenylenediamine  (EXP)
2-nitropropane  (EXP)
3,7-dihydropurine-6-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-acetylaminofluorene  (EXP)
4-hydroxyphenyl retinamide  (ISO)
4-nitro-1,2-phenylenediamine  (EXP)
5-fluorouracil  (ISO)
acetamide  (EXP)
aconitine  (EXP)
aflatoxin B1  (ISO)
allopurinol  (ISO)
azathioprine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
bexarotene  (EXP)
bezafibrate  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
buta-1,3-diene  (ISO)
butanal  (ISO)
caffeine  (ISO)
calcium dichloride  (ISO)
captan  (ISO)
carbon nanotube  (ISO)
chenodeoxycholic acid  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clofibrate  (EXP)
cobalt dichloride  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
daunorubicin  (EXP)
dexamethasone  (EXP,ISO)
diamminedichloroplatinum  (ISO)
dibenz[a,h]anthracene  (ISO)
dibenzo[a,l]pyrene  (ISO)
ethanol  (EXP)
fenofibrate  (EXP,ISO)
fluoranthene  (ISO)
folpet  (ISO)
furan  (EXP)
gemfibrozil  (EXP)
ginsenoside Rf  (ISO)
high-density lipoprotein cholesterol  (ISO)
hydrazine  (EXP)
hydrogen peroxide  (ISO)
indinavir  (ISO)
indometacin  (ISO)
L-methionine  (ISO)
linalool  (ISO)
menadione  (ISO)
mercaptopurine  (EXP)
methapyrilene  (EXP)
methylmercury chloride  (ISO)
microcystin-LR  (ISO)
N-nitrosodiethylamine  (ISO)
nickel atom  (ISO)
nitrofen  (EXP)
O-methyleugenol  (ISO)
obeticholic acid  (ISO)
olanzapine  (EXP)
oleic acid  (ISO)
oxybenzone  (EXP)
p-toluidine  (EXP)
paracetamol  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
phenobarbital  (EXP)
pioglitazone  (ISO)
pirinixic acid  (EXP,ISO)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
purine-6-thiol  (EXP)
quercetin  (ISO)
rifampicin  (ISO)
simvastatin  (EXP)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
sulindac  (ISO)
Tesaglitazar  (ISO)
testosterone  (EXP)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP)
tetracycline  (ISO)
tetramethylpyrazine  (ISO)
thapsigargin  (ISO)
titanium dioxide  (ISO)
transplatin  (ISO)
troglitazone  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cellular response to glucose stimulus  (IDA)
cholesterol efflux  (IEA,ISO)
cholesterol homeostasis  (IBA,IEA,ISO)
cholesterol metabolic process  (ISO)
chylomicron remnant clearance  (IEA,ISO)
G protein-coupled receptor signaling pathway  (IEA,ISO)
high-density lipoprotein particle remodeling  (IEA,ISO)
inflammatory response  (IEP)
lipid transport  (TAS)
lipoprotein metabolic process  (IEA)
lipoprotein transport  (IDA)
negative regulation of cholesterol import  (IEA,ISO)
negative regulation of fatty acid biosynthetic process  (IEA,ISO)
negative regulation of high-density lipoprotein particle clearance  (IBA,IEA,ISO)
negative regulation of lipid catabolic process  (ISO)
negative regulation of lipid metabolic process  (ISO)
negative regulation of lipoprotein lipase activity  (IBA,IEA,ISO)
negative regulation of low-density lipoprotein particle clearance  (IBA,IEA,ISO)
negative regulation of oxidative phosphorylation  (IDA)
negative regulation of receptor-mediated endocytosis  (IEA,ISO)
negative regulation of triglyceride catabolic process  (IBA,IEA,ISO)
negative regulation of very-low-density lipoprotein particle clearance  (IBA,IEA,ISO)
negative regulation of very-low-density lipoprotein particle remodeling  (IEA,ISO)
phospholipid efflux  (IEA,ISO)
positive regulation of triglyceride biosynthetic process  (IMP)
regulation of Cdc42 protein signal transduction  (IEA,ISO)
response to fatty acid  (IEP)
response to nutrient  (IEP)
response to peptide hormone  (IDA)
response to triglyceride  (IEP)
response to vitamin A  (IEP)
response to xenobiotic stimulus  (IEP)
triglyceride catabolic process  (IEA,ISO)
triglyceride homeostasis  (IBA,IEA,ISO)
triglyceride metabolic process  (ISO)
triglyceride mobilization  (ISO)

Cellular Component

Molecular Function

References

References - curated
1. al Muhtaseb N, etal., Pediatrics. 1992 May;89(5 Pt 1):936-41.
2. Andersson Y, etal., Arterioscler Thromb Vasc Biol. 1999 Jan;19(1):115-21.
3. Becker KG, etal., Nat Genet. 2004 May;36(5):431-2.
4. Blaufuss MC, etal., J Biol Chem. 1984 Feb 25;259(4):2452-6.
5. Caron S, etal., Arterioscler Thromb Vasc Biol. 2011 Mar;31(3):513-9. doi: 10.1161/ATVBAHA.110.220723. Epub 2010 Dec 23.
6. Ceccarelli V, etal., Mol Cell Biochem. 2011 Jan;347(1-2):29-39. doi: 10.1007/s11010-010-0609-0. Epub 2010 Oct 12.
7. Dallinga-Thie GM, etal., J Clin Invest. 1997 Mar 1;99(5):953-61.
8. Dallongeville J, etal., Int J Cardiol. 2006 Jan 13;106(2):152-6.
9. Dashti N and Ontko JA, Atherosclerosis. 1983 Dec;49(3):255-66.
10. Duivenvoorden I, etal., Diabetes. 2005 Mar;54(3):664-71.
11. Florez H, etal., Atherosclerosis. 2006 Sep;188(1):134-41. Epub 2005 Nov 18.
12. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
13. Gerritsen G, etal., J Lipid Res. 2005 Jul;46(7):1466-73. Epub 2005 May 1.
14. GOA data from the GO Consortium
15. Graham MJ, etal., Circ Res. 2013 May 24;112(11):1479-90. doi: 10.1161/CIRCRESAHA.111.300367. Epub 2013 Mar 29.
16. Haddad IA, etal., J Biol Chem 1986 Oct 5;261(28):13268-77.
17. Henderson HE, etal., Hum Genet. 1987 Jan;75(1):62-5.
18. Hokanson JE, etal., Diabetes. 2006 Mar;55(3):834-8.
19. Holmberg R, etal., Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10685-9. doi: 10.1073/pnas.1019553108. Epub 2011 Jun 13.
20. Hughes TA, etal., Metabolism. 1994 Mar;43(3):333-47.
21. Inoue T, etal., Invest Ophthalmol Vis Sci. 2013 Aug 9;54(8):5353-8. doi: 10.1167/iovs.13-12245.
22. Jong MC, etal., Arterioscler Thromb Vasc Biol. 1999 Mar;19(3):472-84.
23. Joven J, etal., Nephron. 1993;64(4):565-9.
24. Kamisako T and Ogawa H, J Gastroenterol Hepatol. 2007 Jan;22(1):125-31.
25. Kee F, etal., Atherosclerosis. 1999 Jul;145(1):187-95.
26. Kim J, etal., BMB Rep. 2010 Aug;43(8):535-40.
27. Klein RL, etal., J Diabetes Complications. 2005 Jan-Feb;19(1):18-25.
28. Konemori G, etal., Nippon Ronen Igakkai Zasshi. 1990 Jan;27(1):22-7.
29. Lee DM, etal., PLoS One. 2011;6(7):e22360. doi: 10.1371/journal.pone.0022360. Epub 2011 Jul 28.
30. Lin-Lee YC, etal., J Lipid Res. 1993 Feb;34(2):249-59.
31. Liu HK, etal., Yi Chuan Xue Bao. 2005 Jan;32(1):11-8.
32. MGD data from the GO Consortium
33. Miller M, etal., Arch Med Res. 2007 May;38(4):444-51. Epub 2007 Mar 26.
34. Morgan PE, etal., Free Radic Res. 2007 Dec;41(12):1301-12.
35. Nagasaki A, etal., Biochem Biophys Res Commun. 1994 Dec 30;205(3):1510-7.
36. NCBI rat LocusLink and RefSeq merged data July 26, 2002
37. Ng MC, etal., Clin Genet. 2006 Jul;70(1):20-8.
38. Nowakowska Fortuna E, etal., Kidney Blood Press Res. 2011;34(5):311-9. doi: 10.1159/000325648. Epub 2011 May 26.
39. OMIM Disease Annotation Pipeline
40. Ooi EM, etal., J Lipid Res. 2011 Apr;52(4):794-800. doi: 10.1194/jlr.M011163. Epub 2011 Feb 6.
41. Panin LE, etal., Bull Exp Biol Med. 2000 Aug;130(8):769-71.
42. Pipeline to import KEGG annotations from KEGG into RGD
43. RGD automated data pipeline
44. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
45. RGD automated import pipeline for gene-chemical interactions
46. Rodrigo E, etal., Transplant Proc. 2002 Feb;34(1):379.
47. Schoonjans K, etal., FEBS Lett. 1999 Jun 11;452(3):160-4.
48. Sedova L, etal., Int J Obes Relat Metab Disord. 2004 May;28(5):719-25.
49. Shen P and Howlett GJ, Inflammation. 1993 Apr;17(2):153-66.
50. Shimokata K, etal., Atherosclerosis. 2004 Jan;172(1):167-73.
51. Singh P, etal., Diab Vasc Dis Res. 2007 Jun;4(2):124-9.
52. Smith CE, etal., PLoS One. 2009;4(5):e5465. doi: 10.1371/journal.pone.0005465. Epub 2009 May 8.
53. Szpirer C, etal., Mamm Genome 1998 Sep;9(9):721-34
54. Tahvanainen E, etal., Arterioscler Thromb Vasc Biol. 1998 Nov;18(11):1810-7.
55. Takahashi H, etal., Acta Paediatr Jpn. 1996 Dec;38(6):634-9.
56. Tanaka S, etal., Hiroshima Daigaku Shigaku Zasshi 1975;8(2):168-75.
57. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
58. Tornero F, etal., Nefrologia. 2000 Jan-Feb;20(1):47-53.
59. Wang J, etal., Mol Biol Rep. 2012 May;39(5):5095-104. doi: 10.1007/s11033-011-1305-1. Epub 2011 Dec 8.
60. Windler E and Havel RJ, J Lipid Res. 1985 May;26(5):556-65.
61. Yamada Y, etal., Mol Genet Metab. 2004 Apr;81(4):282-90.
62. Zeng Q, etal., Hum Genet. 1995 Apr;95(4):371-5.
Additional References at PubMed
PMID:182536   PMID:1917954   PMID:3973011   PMID:4066713   PMID:8089130   PMID:8245722   PMID:8864964   PMID:9254056   PMID:11060345   PMID:11162594   PMID:11551841   PMID:11590213  
PMID:15576844   PMID:15778093   PMID:16443932   PMID:16935699   PMID:17142127   PMID:17154273   PMID:17336988   PMID:17438339   PMID:18635818   PMID:18767813   PMID:23376485   PMID:23533145  
PMID:24234421   PMID:24804986   PMID:27068509   PMID:27559042   PMID:28255847   PMID:28473603  


Genomics

Comparative Map Data
Apoc3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2846,531,478 - 46,533,658 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl846,531,478 - 46,533,583 (-)Ensembl
Rnor_6.0850,529,318 - 50,531,498 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl850,529,318 - 50,531,498 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0849,155,390 - 49,157,779 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.18159,618,812 - 159,618,833NCBI
Celera846,113,508 - 46,115,688 (-)NCBICelera
Cytogenetic Map8q22NCBI
APOC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl11116,829,706 - 116,833,072 (+)EnsemblGRCh38hg38GRCh38
GRCh3811116,829,907 - 116,833,072 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3711116,700,623 - 116,703,788 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3611116,205,834 - 116,208,997 (+)NCBINCBI36hg18NCBI36
Build 3411116,205,833 - 116,208,997NCBI
Celera11113,858,439 - 113,861,589 (+)NCBI
Cytogenetic Map11q23.3NCBI
HuRef11112,632,897 - 112,636,045 (+)NCBIHuRef
CHM1_111116,585,371 - 116,588,539 (+)NCBICHM1_1
Apoc3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39946,144,348 - 46,146,934 (-)NCBIGRCm39mm39
GRCm39 Ensembl946,144,231 - 46,146,934 (-)Ensembl
GRCm38946,233,050 - 46,235,636 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl946,232,933 - 46,235,636 (-)EnsemblGRCm38mm10GRCm38
MGSCv37946,041,134 - 46,043,380 (-)NCBIGRCm37mm9NCBIm37
MGSCv36945,984,046 - 45,986,292 (-)NCBImm8
Celera943,522,002 - 43,524,237 (-)NCBICelera
Cytogenetic Map9A5.2NCBI
cM Map925.36NCBI
Apoc3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541218,165,667 - 18,168,015 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541218,165,667 - 18,168,015 (+)NCBIChiLan1.0ChiLan1.0
APOC3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.111115,600,416 - 115,603,460 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11115,600,416 - 115,603,460 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v011111,667,816 - 111,670,861 (+)NCBIMhudiblu_PPA_v0panPan3
APOC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1516,744,423 - 16,746,992 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl516,744,423 - 16,746,992 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha516,796,585 - 16,799,154 (-)NCBI
ROS_Cfam_1.0516,690,907 - 16,693,492 (-)NCBI
UMICH_Zoey_3.1516,828,006 - 16,830,575 (-)NCBI
UNSW_CanFamBas_1.0516,730,571 - 16,733,151 (-)NCBI
UU_Cfam_GSD_1.0516,773,507 - 16,776,068 (-)NCBI
Apoc3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494799,184,897 - 99,187,178 (+)NCBI
SpeTri2.0NW_0049365422,106,927 - 2,108,412 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
APOC3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1944,211,171 - 44,213,538 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2949,283,407 - 49,285,786 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap9p13NCBI
APOC3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11108,196,283 - 108,199,274 (+)NCBI
ChlSab1.1 Ensembl1108,196,939 - 108,199,342 (+)Ensembl
Vero_WHO_p1.0NW_02366604317,851,374 - 17,853,839 (-)NCBI
Apoc3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462478412,244,565 - 12,246,790 (+)NCBI

Position Markers
D8Mit7  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2846,531,639 - 46,531,840 (+)MAPPERmRatBN7.2
Rnor_6.0850,529,480 - 50,529,680NCBIRnor6.0
Rnor_5.0849,155,552 - 49,155,752UniSTSRnor5.0
Celera846,113,670 - 46,113,870UniSTS
RH 3.4 Map8469.8RGD
RH 3.4 Map8469.8UniSTS
RH 2.0 Map8368.2RGD
Cytogenetic Map8q23-q24UniSTS
D8Wox4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2846,531,722 - 46,531,840 (+)MAPPERmRatBN7.2
Rnor_6.0850,529,563 - 50,529,680NCBIRnor6.0
Rnor_5.0849,155,635 - 49,155,752UniSTSRnor5.0
Celera846,113,753 - 46,113,870UniSTS
RH 3.4 Map8474.2RGD
RH 3.4 Map8474.2UniSTS
RH 2.0 Map8359.1RGD
Cytogenetic Map8q23-q24UniSTS
D8Rat85  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2846,531,718 - 46,531,839 (+)MAPPERmRatBN7.2
Rnor_6.0850,529,559 - 50,529,679NCBIRnor6.0
Rnor_5.0849,155,631 - 49,155,751UniSTSRnor5.0
Celera846,113,749 - 46,113,869UniSTS
RH 3.4 Map8474.3UniSTS
RH 3.4 Map8474.3RGD
RH 2.0 Map8357.5RGD
FHH x ACI Map839.2299RGD
Cytogenetic Map8q23-q24UniSTS
D8Arb7  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2846,531,733 - 46,531,902 (+)MAPPERmRatBN7.2
Rnor_6.0850,529,574 - 50,529,742NCBIRnor6.0
Rnor_5.0849,155,646 - 49,155,814UniSTSRnor5.0
Celera846,113,764 - 46,113,932UniSTS
SHRSP x BN Map836.96RGD
SHRSP x BN Map836.96UniSTS
FHH x ACI Map839.2199RGD
Cytogenetic Map8q23-q24UniSTS
RH134356  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2846,531,619 - 46,532,796 (+)MAPPERmRatBN7.2
Rnor_6.0850,529,460 - 50,530,636NCBIRnor6.0
Rnor_5.0849,155,532 - 49,156,708UniSTSRnor5.0
Celera846,113,650 - 46,114,826UniSTS
RH 3.4 Map8471.9UniSTS
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)systolic blood pressure (CMO:0000004)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)diastolic blood pressure (CMO:0000005)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)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
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088624Rat
1331837Bw23Body weight QTL 234.190.00007body mass (VT:0001259)body weight (CMO:0000012)84653172299083736Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:37
Count of miRNA genes:36
Interacting mature miRNAs:36
Transcripts:ENSRNOT00000074942
Prediction methods: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 27 27 21
Medium 20 18 18 2 2 13 2 2 2
Low 3 18 16 2 18 2 5 6 15 16 22 9 5
Below cutoff 22 1 1 2 29 6 15 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001271053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_012501 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AW917416 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473975 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209522 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209891 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210075 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210160 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210397 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210428 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210554 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210884 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211165 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211318 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211343 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211392 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211416 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211420 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211454 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218088 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218207 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218211 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218286 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219230 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000198 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000074942   ⟹   ENSRNOP00000067045
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl846,531,478 - 46,533,583 (-)Ensembl
Rnor_6.0 Ensembl850,529,318 - 50,531,498 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000090985   ⟹   ENSRNOP00000074692
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl850,529,318 - 50,531,423 (-)Ensembl
RefSeq Acc Id: NM_001271053   ⟹   NP_001257982
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2846,531,478 - 46,533,583 (-)NCBI
Rnor_6.0850,529,318 - 50,531,423 (-)NCBI
Rnor_5.0849,155,390 - 49,157,779 (-)NCBI
Celera846,113,508 - 46,115,613 (-)NCBI
Sequence:
RefSeq Acc Id: NM_012501   ⟹   NP_036633
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2846,531,478 - 46,533,658 (-)NCBI
Rnor_6.0850,529,318 - 50,531,498 (-)NCBI
Rnor_5.0849,155,390 - 49,157,779 (-)NCBI
Celera846,113,508 - 46,115,688 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001257982 (Get FASTA)   NCBI Sequence Viewer  
  NP_036633 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL95395 (Get FASTA)   NCBI Sequence Viewer  
  EDL95396 (Get FASTA)   NCBI Sequence Viewer  
  P06759 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_036633   ⟸   NM_012501
- Peptide Label: precursor
- UniProtKB: A0A0G2K8Q1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257982   ⟸   NM_001271053
- Peptide Label: precursor
- UniProtKB: A0A0G2K8Q1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074692   ⟸   ENSRNOT00000090985
RefSeq Acc Id: ENSRNOP00000067045   ⟸   ENSRNOT00000074942

Transcriptome

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

Promoters
RGD ID:13695927
Promoter ID:EPDNEW_R6452
Type:initiation region
Name:Apoc3_1
Description:apolipoprotein C3
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_6.0850,531,467 - 50,531,527EPDNEW

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)
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)
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
BXH2/CubMcwi (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
BXH3/CubMcwi (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
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)
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/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
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/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
FHH/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
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
FXLE16/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
FXLE18/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
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)
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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/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)
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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
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)
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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
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)
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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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/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
LL/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/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
LN/MavRrrcAek (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: 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)
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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
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (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)
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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
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2136 AgrOrtholog
Ensembl Genes ENSRNOG00000047503 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000067045 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074692 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000074942 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000090985 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.225.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Apo-CIII UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Apo_CIII_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24207 UniProtKB/TrEMBL
NCBI Gene 24207 ENTREZGENE
PANTHER PTHR14225 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Apo-CIII UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB APOC3 RGD
PhenoGen Apoc3 PhenoGen
TIGR TC218485
UniProt A0A0G2K8Q1 ENTREZGENE, UniProtKB/TrEMBL
  APOC3_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-04 Apoc3  apolipoprotein C3  Apoc3  apolipoprotein C-III  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Apoc3  apolipoprotein C-III    apolipoprotein C-3  Name updated 629478 APPROVED
2002-06-10 Apoc3  apolipoprotein C-3      Name updated 70585 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease increase in levels induces development of hypertriglyceridemia  
gene_expression expressed in liver and intestion in adulthood and during the aging process 634656
gene_expression expressed in liver and intestine in adulthood and during the aging process 634656
gene_function very low density lipoprotein (VLDL) protein that inhibits the enzymatic activity of lipoprotein lipase and hepatic lipase  
gene_process may delay catabolism of triglyceride-rich particles  
gene_process major component of lipid transport system 634656