Hmgcs2 (3-hydroxy-3-methylglutaryl-CoA synthase 2) - Rat Genome Database

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Gene: Hmgcs2 (3-hydroxy-3-methylglutaryl-CoA synthase 2) Rattus norvegicus
Analyze
Symbol: Hmgcs2
Name: 3-hydroxy-3-methylglutaryl-CoA synthase 2
RGD ID: 2804
Description: Enables hydroxymethylglutaryl-CoA synthase activity. Involved in several processes, including animal organ development; cellular response to lipid; and response to peptide hormone. Located in mitochondrial matrix. Biomarker of extrahepatic cholestasis. Orthologous to human HMGCS2 (3-hydroxy-3-methylglutaryl-CoA synthase 2); PARTICIPATES IN 3-hydroxy-3-methylglutaryl-CoA lyase deficiency pathway; 3-hydroxyisobutyric aciduria pathway; 3-methylcrotonyl CoA carboxylase 1 deficiency pathway; INTERACTS WITH (+)-schisandrin B; 1-benzylpiperazine; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 3-hydroxy-3-methylglutary-Coenzyme A synthase; 3-hydroxy-3-methylglutary-Coenzyme A synthase 2; 3-hydroxy-3-methylglutaryl coenzyme A synthase; 3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial); 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2; 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial); HMG-CoA synthase; Hmgcs1; hydroxymethylglutaryl-CoA synthase 2; hydroxymethylglutaryl-CoA synthase, mitochondrial; Mt3h3mg
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
mRatBN7.22185,875,609 - 185,903,505 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl2200,452,624 - 200,479,423 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02200,452,623 - 200,480,785 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02219,928,546 - 219,956,233 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42193,128,736 - 193,143,106 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12193,091,489 - 193,105,860 (+)NCBI
Celera2178,363,353 - 178,390,245 (+)NCBICelera
Cytogenetic Map2q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(+)-dexrazoxane  (ISO)
(+)-schisandrin B  (EXP)
1,2-dimethylhydrazine  (ISO)
1-benzylpiperazine  (EXP)
14-Deoxy-11,12-didehydroandrographolide  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)propanoic acid  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,3',5-triiodo-L-thyronine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-hydroxybutyric acid  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
ammonium chloride  (EXP)
Aroclor 1254  (ISO)
benzalkonium chloride  (ISO)
benzo[a]pyrene  (ISO)
Benzo[k]fluoranthene  (ISO)
bezafibrate  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP)
bromobenzene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
captan  (ISO)
carbon nanotube  (ISO)
carbonyl sulfide  (EXP)
cefaloridine  (EXP)
cetrorelix  (ISO)
chenodeoxycholic acid  (ISO)
chlorpyrifos  (ISO)
ciglitazone  (ISO)
ciguatoxin CTX1B  (ISO)
ciprofibrate  (ISO)
clofibrate  (EXP,ISO)
Clofop  (ISO)
cobalt dichloride  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
corticosterone  (EXP)
cyclosporin A  (ISO)
cytarabine  (ISO)
desogestrel  (ISO)
dexamethasone  (EXP)
dichlorine  (EXP)
dichloroacetic acid  (ISO)
diclofenac  (ISO)
dipentyl phthalate  (EXP)
diuron  (EXP)
dopamine  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP,ISO)
entinostat  (ISO)
ethanol  (EXP,ISO)
fenofibrate  (EXP,ISO)
fenoldopam  (EXP)
fipronil  (EXP,ISO)
flutamide  (EXP)
folic acid  (ISO)
folpet  (ISO)
fructose  (EXP)
fumonisin B1  (ISO)
furan  (EXP)
gadolinium trichloride  (EXP)
gemfibrozil  (EXP)
genistein  (EXP)
glafenine  (EXP)
glyphosate  (ISO)
GW 4064  (ISO)
GW 501516  (ISO)
GW 7647  (EXP,ISO)
Heptachlor epoxide  (ISO)
hydrazine  (ISO)
indometacin  (ISO)
iron atom  (EXP)
iron(0)  (EXP)
ketamine  (EXP)
lamivudine  (ISO)
lead diacetate  (ISO)
lithocholic acid  (ISO)
manganese atom  (EXP)
manganese(0)  (EXP)
manganese(II) chloride  (EXP)
menadione  (ISO)
methapyrilene  (EXP)
methimazole  (EXP)
methotrexate  (EXP)
morphine  (ISO)
N,N-diethyl-m-toluamide  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosomorpholine  (EXP)
N-Nitrosopyrrolidine  (ISO)
nevirapine  (EXP)
nickel atom  (ISO)
nickel dichloride  (EXP)
O-methyleugenol  (ISO)
oxybenzone  (EXP)
ozone  (EXP)
p-toluidine  (EXP)
paclitaxel  (EXP)
paracetamol  (EXP,ISO)
perfluorodecanoic acid  (ISO)
perfluorododecanoic acid  (ISO)
perfluoroheptanoic acid  (ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (EXP,ISO)
phenethyl caffeate  (EXP)
phenobarbital  (ISO)
PhIP  (EXP)
pirinixic acid  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (EXP)
propiconazole  (ISO)
prostaglandin F2alpha  (EXP)
pyrazinecarboxamide  (EXP)
pyrrolidine dithiocarbamate  (EXP)
quercetin  (EXP,ISO)
resveratrol  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP)
streptozocin  (EXP)
tacrolimus hydrate  (ISO)
tamoxifen  (ISO)
tebuconazole  (ISO)
Tesaglitazar  (EXP)
testosterone enanthate  (ISO)
Tetrachlorobisphenol A  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (ISO)
tetrathiomolybdate(2-)  (EXP)
thiacloprid  (ISO)
thioacetamide  (EXP)
thiophanate-methyl  (ISO)
titanium dioxide  (ISO)
tributylstannane  (EXP)
trichloroethene  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
troglitazone  (EXP,ISO)
urethane  (ISO)
ursodeoxycholic acid  (EXP)
valproic acid  (ISO)
vanadyl sulfate  (EXP)
zidovudine  (ISO)
zinc atom  (EXP)
zinc sulfate  (ISO)
zinc(0)  (EXP)
ziram  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
mitochondrial matrix  (IDA)
mitochondrion  (IBA,ISO,TAS)

Molecular Function

References

References - curated
1. Arias G, etal., Arch Biochem Biophys. 1997 Apr 15;340(2):287-98.
2. Arias G, etal., Mol Cell Biochem. 1998 Jan;178(1-2):325-33.
3. Asins G, etal., Biochem Pharmacol. 1994 Apr 20;47(8):1373-9.
4. Ayte J, etal., Biochem J. 1993 Nov 1;295 ( Pt 3):807-12.
5. Ayte J, etal., Proc Natl Acad Sci U S A 1990 May;87(10):3874-8.
6. Carlsson L, etal., Am J Physiol Endocrinol Metab. 2001 Oct;281(4):E772-81.
7. Cherbuy C, etal., Eur J Biochem. 2004 Jan;271(1):87-95.
8. Cullingford TE Prostaglandins Leukot Essent Fatty Acids. 2004 Mar;70(3):253-64.
9. Cullingford TE, etal., J Neurochem. 1998 Nov;71(5):1804-12.
10. de Boer VC, etal., Cell Mol Life Sci. 2006 Dec;63(23):2847-58.
11. Du ZY, etal., Lipids. 2010 May 28.
12. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
13. Gil-Gomez G, etal., Eur J Biochem 1993 Apr 15;213(2):773-9.
14. GOA data from the GO Consortium
15. Hegardt FG Biochimie. 1998 Oct;80(10):803-6.
16. Kiyosawa N, etal., Arch Toxicol. 2004 Aug;78(8):435-42. Epub 2004 Apr 24.
17. Konig B and Eder K, J Nutr Biochem. 2006 Jun;17(6):410-8. Epub 2005 Sep 23.
18. Kostiuk MA, etal., FASEB J. 2008 Mar;22(3):721-32. Epub 2007 Oct 30.
19. Lang C, etal., J Hepatol. 2002 Nov;37(5):564-71.
20. Lopez-Barahona M, etal., Eur J Endocrinol. 1996 Dec;135(6):709-15.
21. Madsen L, etal., Biochem Pharmacol. 1999 May 1;57(9):1011-9.
22. MGD data from the GO Consortium
23. Nadal A, etal., Biochem J. 2002 Aug 15;366(Pt 1):289-97.
24. NCBI rat LocusLink and RefSeq merged data July 26, 2002
25. Ness GC, etal., Arch Biochem Biophys. 1994 Jun;311(2):277-85.
26. Newsholme SJ, etal., Electrophoresis. 2000 Jun;21(11):2122-8.
27. OMIM Disease Annotation Pipeline
28. Pang Y, etal., Brain Res. 2001 Sep 28;914(1-2):15-22.
29. Patel TB and Clark JB, Biochem J. 1978 Dec 15;176(3):951-8.
30. Patel VB, etal., Free Radic Biol Med. 2007 Dec 1;43(11):1499-507. Epub 2007 Aug 16.
31. Pipeline to import KEGG annotations from KEGG into RGD
32. Pipeline to import SMPDB annotations from SMPDB into RGD
33. Quant PA, etal., Eur J Biochem. 1990 Jan 12;187(1):169-74.
34. RGD automated data pipeline
35. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
36. RGD automated import pipeline for gene-chemical interactions
37. Rodriguez JC, etal., J Biol Chem. 1994 Jul 22;269(29):18767-72.
38. Sato T, etal., Toxicology. 2006 Oct 29;227(3):248-61. Epub 2006 Aug 14.
39. Serra D, etal., Arch Biochem Biophys. 1993 Nov 15;307(1):40-5.
40. Serra D, etal., Eur J Biochem. 1996 Apr 1;237(1):16-24.
41. Steiner S, etal., Toxicol Lett. 2001 Mar 31;120(1-3):369-77.
42. Stocco C, etal., Endocrinology. 2001 Sep;142(9):4158-61.
43. Su SG, etal., Int J Biochem Cell Biol. 2017 Oct;91(Pt A):53-59. doi: 10.1016/j.biocel.2017.08.016. Epub 2017 Sep 1.
44. Thumelin S, etal., Biochem J. 1993 Jun 1;292 ( Pt 2):493-6.
45. Thumelin S, etal., J Lipid Res. 1999 Jun;40(6):1071-7.
46. Valera A, etal., J Clin Invest. 1993 Jul;92(1):4-11.
47. Yi W, etal., Nutrition. 2010 Feb 3.
Additional References at PubMed
PMID:12477932   PMID:12865426   PMID:14651853   PMID:15254779   PMID:18614015   PMID:20346956   PMID:23486364   PMID:23751782   PMID:24315375   PMID:25931508   PMID:26767982   PMID:27671501  


Genomics

Comparative Map Data
Hmgcs2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22185,875,609 - 185,903,505 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl2200,452,624 - 200,479,423 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02200,452,623 - 200,480,785 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02219,928,546 - 219,956,233 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42193,128,736 - 193,143,106 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12193,091,489 - 193,105,860 (+)NCBI
Celera2178,363,353 - 178,390,245 (+)NCBICelera
Cytogenetic Map2q34NCBI
HMGCS2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1119,748,002 - 119,768,905 (-)EnsemblGRCh38hg38GRCh38
GRCh381119,747,996 - 119,768,932 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371120,290,619 - 120,311,555 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361120,092,525 - 120,113,041 (-)NCBINCBI36hg18NCBI36
Build 341120,003,046 - 120,023,560NCBI
Celera1118,521,355 - 118,542,283 (-)NCBI
Cytogenetic Map1p12NCBI
HuRef1118,149,159 - 118,170,093 (-)NCBIHuRef
CHM1_11120,406,161 - 120,427,088 (-)NCBICHM1_1
Hmgcs2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39398,187,747 - 98,218,054 (+)NCBIGRCm39mm39
GRCm39 Ensembl398,187,751 - 98,218,054 (+)Ensembl
GRCm38398,280,431 - 98,310,738 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl398,280,435 - 98,310,738 (+)EnsemblGRCm38mm10GRCm38
MGSCv37398,084,354 - 98,114,661 (+)NCBIGRCm37mm9NCBIm37
MGSCv36398,365,840 - 98,396,137 (+)NCBImm8
Celera399,679,562 - 99,709,869 (+)NCBICelera
Cytogenetic Map3F2.2NCBI
cM Map342.74NCBI
Hmgcs2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543522,804,484 - 22,821,482 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543522,804,484 - 22,820,807 (-)NCBIChiLan1.0ChiLan1.0
HMGCS2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11117,776,165 - 117,796,679 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1117,775,770 - 117,796,679 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0182,778,489 - 82,798,987 (+)NCBIMhudiblu_PPA_v0panPan3
HMGCS2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11756,679,942 - 56,698,521 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1756,680,301 - 56,698,419 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1756,315,432 - 56,328,270 (-)NCBI
ROS_Cfam_1.01757,558,992 - 57,577,456 (-)NCBI
UMICH_Zoey_3.11756,594,625 - 56,613,171 (-)NCBI
UNSW_CanFamBas_1.01756,620,825 - 56,639,082 (-)NCBI
UU_Cfam_GSD_1.01757,237,948 - 57,256,436 (-)NCBI
Hmgcs2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505810,015,851 - 10,037,163 (+)NCBI
SpeTri2.0NW_0049366274,451,847 - 4,473,163 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC110260333
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4101,385,512 - 101,443,405 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14101,385,486 - 101,404,273 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
HMGCS2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12014,018,669 - 14,040,934 (+)NCBI
ChlSab1.1 Ensembl2014,019,692 - 14,041,016 (+)Ensembl
Vero_WHO_p1.0NW_02366603816,649,801 - 16,670,981 (+)NCBI
Hmgcs2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477215,432,612 - 15,464,343 (+)NCBI

Position Markers
D2Mgh10  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22185,876,309 - 185,876,470 (+)MAPPERmRatBN7.2
Rnor_6.02200,453,324 - 200,453,484NCBIRnor6.0
Rnor_5.02219,929,245 - 219,929,405UniSTSRnor5.0
Celera2178,364,029 - 178,364,187UniSTS
RH 3.4 Map21255.3UniSTS
RH 3.4 Map21255.3RGD
RH 2.0 Map2947.3RGD
SHRSP x BN Map272.7698RGD
Cytogenetic Map2q34UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598805Memor8Memory QTL 83exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)2157914311204022555Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2140566078217498545Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2147522550217498710Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246537589217498710Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243133606217498545Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243133606217498545Rat
61469Bp16Blood pressure QTL 165.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2184730446229730446Rat
70162Bp63Blood pressure QTL 635.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2184730446229730446Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2149114878225501939Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2181990297240020001Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256244671217498710Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2141583337217498710Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266828049217498710Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2147122993240020001Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2147122993240020001Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2183984665228984665Rat
1581502Esta3Estrogen-induced thymic atrophy QTL 3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2142053350204585731Rat
738013Alc15Alcohol consumption QTL 154.10.00022consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)2199380312244380312Rat
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2157914409217498545Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2116075644228737869Rat
1302793Bw16Body weight QTL 1650.0001body mass (VT:0001259)body weight (CMO:0000012)2169852800217498545Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2155965557254121739Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2155965557237742948Rat
1598833Bp295Blood pressure QTL 2953.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2161745602206745602Rat
1598838Bp290Blood pressure QTL 2901.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2181522444226522444Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2194378622239378622Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2116075644228737869Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2175403337239166203Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2118446646227707979Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2138901276217498710Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)275687495221880419Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2158159186217498710Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)283819608239166203Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266828236243550655Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)283819608243901375Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2158159186217498710Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2142053350228984665Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2118446793228582621Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2177680772243901375Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2118446646200453484Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2118446646200453484Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2200453324236318668Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2200453324236318668Rat
1359032Hrtrt18Heart rate QTL 18heart pumping trait (VT:2000009)heart rate (CMO:0000002)2169852670207612467Rat
2293084Iddm26Insulin dependent diabetes mellitus QTL 262.9blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2188838511228984665Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)278321410217498710Rat
61401Niddm2Non-insulin dependent diabetes mellitus QTL 24.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2159585731204585731Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2194998627239998627Rat
4889834Pur24Proteinuria QTL 245.80.014total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)2198704357217498710Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2197253963242253963Rat
7488929Bp366Blood pressure QTL 3660.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2199954569208081195Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2197253963242253963Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2197253963242253963Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2174160958219160958Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2177339806222339806Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2169852670243026643Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)283754907237610852Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2197253963242253963Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2149614466205573168Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2149614466205573168Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)216679272245624402Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:181
Count of miRNA genes:126
Interacting mature miRNAs:143
Transcripts:ENSRNOT00000026121
Prediction methods:Microtar, 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 27 21 21 1
Medium 2 12 24 20 12 20 37 24 33 11
Low 1 29 12 7 8 11 31 11 7 8
Below cutoff 2 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026121   ⟹   ENSRNOP00000026122
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2200,452,624 - 200,479,423 (+)Ensembl
RefSeq Acc Id: NM_173094   ⟹   NP_775117
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,875,634 - 185,902,134 (+)NCBI
Rnor_6.02200,452,648 - 200,479,415 (+)NCBI
Rnor_5.02219,928,546 - 219,956,233 (+)NCBI
RGSC_v3.42193,128,736 - 193,143,106 (+)RGD
Celera2178,363,353 - 178,390,245 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233002   ⟹   XP_006233064
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,875,609 - 185,903,505 (+)NCBI
Rnor_6.02200,452,623 - 200,480,785 (+)NCBI
Rnor_5.02219,928,546 - 219,956,233 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_775117   ⟸   NM_173094
- Peptide Label: precursor
- UniProtKB: Q68G44 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233064   ⟸   XM_006233002
- Peptide Label: isoform X1
- UniProtKB: Q68G44 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000026122   ⟸   ENSRNOT00000026121

Transcriptome

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

Promoters
RGD ID:13691601
Promoter ID:EPDNEW_R2126
Type:multiple initiation site
Name:Hmgcs2_1
Description:3-hydroxy-3-methylglutaryl-CoA synthase 2
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_6.02200,452,630 - 200,452,690EPDNEW

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)
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/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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2804 AgrOrtholog
Ensembl Genes ENSRNOG00000019120 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000026122 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000026121 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.47.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7112644 IMAGE-MGC_LOAD
  IMAGE:7132009 IMAGE-MGC_LOAD
InterPro HMG_CoA_synt_AS UniProtKB/Swiss-Prot
  HMG_CoA_synt_C_dom UniProtKB/Swiss-Prot
  HMG_CoA_synth_N UniProtKB/Swiss-Prot
  HMG_CoA_synthase_euk UniProtKB/Swiss-Prot
  Thiolase-like UniProtKB/Swiss-Prot
KEGG Report rno:24450 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93080 IMAGE-MGC_LOAD
  MGC:93081 IMAGE-MGC_LOAD
NCBI Gene 24450 ENTREZGENE
Pfam HMG_CoA_synt_C UniProtKB/Swiss-Prot
  HMG_CoA_synt_N UniProtKB/Swiss-Prot
PhenoGen Hmgcs2 PhenoGen
PROSITE HMG_COA_SYNTHASE UniProtKB/Swiss-Prot
Superfamily-SCOP SSF53901 UniProtKB/Swiss-Prot
TIGRFAMs HMG-CoA-S_euk UniProtKB/Swiss-Prot
UniProt HMCS2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q68G44 ENTREZGENE
UniProt Secondary F1M9Q5 UniProtKB/Swiss-Prot
  Q68G44 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-27 Hmgcs2  3-hydroxy-3-methylglutaryl-CoA synthase 2  Hmgcs2  3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-08-02 Hmgcs2  3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)  Hmgcs2  3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-24 Hmgcs2  3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)  Hmgcs2  3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-02-27 Hmgcs2  3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2      Typo in previous name 70292 APPROVED
2001-10-23 Hmgcs2  3-hydroxy-3-methylglutary-Coenzyme A synthase      Name withdrawn 68913 WITHDRAWN
2001-10-23 Hmgcs2  3-hydroxy-3-methylglutary-Coenzyme A synthase 2      Name updated to reflect Human and Mouse nomenclature 68913 APPROVED