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 cellular response to lipid; ketone body biosynthetic process; and response to peptide hormone. Located in mitochondrial matrix. Biomarker of extrahepatic cholestasis. Human ortholog(s) of this gene implicated in HMG-CoA synthase 2 deficiency. 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
Previously 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22185,875,609 - 185,903,505 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2185,875,616 - 185,902,130 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2193,524,494 - 193,551,482 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02191,333,168 - 191,359,836 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02186,157,074 - 186,184,065 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02200,452,623 - 200,480,785 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2200,452,624 - 200,479,423 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02219,928,546 - 219,956,233 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42193,128,736 - 193,143,106 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-butan-2-yl-4-[4-[4-[4-[[2-(2,4-dichlorophenyl)-2-(1,2,4-triazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy]phenyl]-1-piperazinyl]phenyl]-1,2,4-triazol-3-one  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,3',5-triiodo-L-thyronine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP,ISO)
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,ISO)
bromobenzene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
captan  (ISO)
carbon nanotube  (ISO)
carbonyl sulfide  (EXP)
carnosic acid  (ISO)
cefaloridine  (EXP)
cetrorelix  (ISO)
chenodeoxycholic acid  (ISO)
CHIR 99021  (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)
Cuprizon  (EXP)
cyclosporin A  (ISO)
cytarabine  (ISO)
desogestrel  (ISO)
dexamethasone  (EXP)
dichlorine  (EXP)
dichloroacetic acid  (ISO)
diclofenac  (ISO)
dimethylarsinic acid  (ISO)
dipentyl phthalate  (EXP)
diquat  (ISO)
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)
gentamycin  (EXP)
glafenine  (EXP)
glyphosate  (ISO)
GW 4064  (ISO)
GW 501516  (ISO)
GW 7647  (EXP,ISO)
Heptachlor epoxide  (ISO)
hydrazine  (ISO)
indometacin  (EXP,ISO)
iron atom  (EXP)
iron(0)  (EXP)
itraconazole  (ISO)
ketamine  (EXP)
ketoconazole  (ISO)
L-ascorbic acid  (ISO)
L-ascorbic acid 2-phosphate  (ISO)
lamivudine  (ISO)
lead diacetate  (ISO)
lithocholic acid  (ISO)
manganese atom  (EXP)
manganese(0)  (EXP)
manganese(II) chloride  (EXP)
menadione  (ISO)
methapyrilene  (EXP)
methidathion  (ISO)
methimazole  (EXP)
methotrexate  (EXP)
methylarsonic acid  (ISO)
morphine  (ISO)
Muraglitazar  (EXP)
N,N-diethyl-m-toluamide  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosomorpholine  (EXP)
N-Nitrosopyrrolidine  (ISO)
nevirapine  (EXP)
nickel atom  (ISO)
nickel dichloride  (EXP)
nitrofen  (EXP)
O-methyleugenol  (ISO)
oxybenzone  (EXP)
ozone  (EXP,ISO)
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 arsenate  (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  (EXP,ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
troglitazone  (EXP,ISO)
urethane  (ISO)
ursodeoxycholic acid  (EXP)
valproic acid  (ISO)
vanadyl sulfate  (EXP)
XAV939  (ISO)
zidovudine  (ISO)
zinc atom  (EXP)
zinc sulfate  (ISO)
zinc(0)  (EXP)
ziram  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. The effect of fasting/refeeding and insulin treatment on the expression of the regulatory genes of ketogenesis in intestine and liver of suckling rats. Arias G, etal., Arch Biochem Biophys. 1997 Apr 15;340(2):287-98.
2. The effect of dexamethasone treatment on the expression of the regulatory genes of ketogenesis in intestine and liver of suckling rats. Arias G, etal., Mol Cell Biochem. 1998 Jan;178(1-2):325-33.
3. The effect of etomoxir on the mRNA levels of enzymes involved in ketogenesis and cholesterogenesis in rat liver. Asins G, etal., Biochem Pharmacol. 1994 Apr 20;47(8):1373-9.
4. Methylation of the regulatory region of the mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase gene leads to its transcriptional inactivation. Ayte J, etal., Biochem J. 1993 Nov 1;295 ( Pt 3):807-12.
5. Rat mitochondrial and cytosolic 3-hydroxy-3-methylglutaryl-CoA synthases are encoded by two different genes. Ayte J, etal., Proc Natl Acad Sci U S A 1990 May;87(10):3874-8.
6. Effects of fatty acids and growth hormone on liver fatty acid binding protein and PPARalpha in rat liver. Carlsson L, etal., Am J Physiol Endocrinol Metab. 2001 Oct;281(4):E772-81.
7. Expression of mitochondrial HMGCoA synthase and glutaminase in the colonic mucosa is modulated by bacterial species. Cherbuy C, etal., Eur J Biochem. 2004 Jan;271(1):87-95.
8. The ketogenic diet; fatty acids, fatty acid-activated receptors and neurological disorders. Cullingford TE Prostaglandins Leukot Essent Fatty Acids. 2004 Mar;70(3):253-64.
9. Hormonal regulation of the mRNA encoding the ketogenic enzyme mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase in neonatal primary cultures of cortical astrocytes and meningeal fibroblasts. Cullingford TE, etal., J Neurochem. 1998 Nov;71(5):1804-12.
10. Chronic quercetin exposure affects fatty acid catabolism in rat lung. de Boer VC, etal., Cell Mol Life Sci. 2006 Dec;63(23):2847-58.
11. Dissimilar Properties of Vaccenic Versus Elaidic Acid in beta-Oxidation Activities and Gene Regulation in Rat Liver Cells. Du ZY, etal., Lipids. 2010 May 28.
12. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
13. The rat mitochondrial 3-hydroxy-3-methylglutaryl-coenzyme-A-synthase gene contains elements that mediate its multihormonal regulation and tissue specificity. Gil-Gomez G, etal., Eur J Biochem 1993 Apr 15;213(2):773-9.
14. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
15. Transcriptional regulation of mitochondrial HMG-CoA synthase in the control of ketogenesis. Hegardt FG Biochimie. 1998 Oct;80(10):803-6.
16. Molecular mechanism investigation of phenobarbital-induced serum cholesterol elevation in rat livers by microarray analysis. Kiyosawa N, etal., Arch Toxicol. 2004 Aug;78(8):435-42. Epub 2004 Apr 24.
17. Differential action of 13-HPODE on PPARalpha downstream genes in rat Fao and human HepG2 hepatoma cell lines. Konig B and Eder K, J Nutr Biochem. 2006 Jun;17(6):410-8. Epub 2005 Sep 23.
18. Identification of palmitoylated mitochondrial proteins using a bio-orthogonal azido-palmitate analogue. Kostiuk MA, etal., FASEB J. 2008 Mar;22(3):721-32. Epub 2007 Oct 30.
19. Impaired ketogenesis is a major mechanism for disturbed hepatic fatty acid metabolism in rats with long-term cholestasis and after relief of biliary obstruction. Lang C, etal., J Hepatol. 2002 Nov;37(5):564-71.
20. Post-transcriptional induction of beta 1-adrenergic receptor by retinoic acid, but not triiodothyronine, in C6 glioma cells expressing thyroid hormone receptors. Lopez-Barahona M, etal., Eur J Endocrinol. 1996 Dec;135(6):709-15.
21. Mitochondrial 3-hydroxy-3-methylglutaryl coenzyme A synthase and carnitine palmitoyltransferase II as potential control sites for ketogenesis during mitochondrion and peroxisome proliferation. Madsen L, etal., Biochem Pharmacol. 1999 May 1;57(9):1011-9.
22. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
23. Down-regulation of the mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase gene by insulin: the role of the forkhead transcription factor FKHRL1. Nadal A, etal., Biochem J. 2002 Aug 15;366(Pt 1):289-97.
24. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
25. Effect of squalene synthase inhibition on the expression of hepatic cholesterol biosynthetic enzymes, LDL receptor, and cholesterol 7 alpha hydroxylase. Ness GC, etal., Arch Biochem Biophys. 1994 Jun;311(2):277-85.
26. Two-dimensional electrophoresis of liver proteins: characterization of a drug-induced hepatomegaly in rats. Newsholme SJ, etal., Electrophoresis. 2000 Jun;21(11):2122-8.
27. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
28. Analysis of genes differentially expressed in astrocytes stimulated with lipopolysaccharide using cDNA arrays. Pang Y, etal., Brain Res. 2001 Sep 28;914(1-2):15-22.
29. Acetoacetate metabolism in rat brain. Development of acetoacetyl-coenzyme A deacylase and 3-hydroxy-3-methylglutaryl-coenzyme A synthase. Patel TB and Clark JB, Biochem J. 1978 Dec 15;176(3):951-8.
30. Effects of 4-hydroxynonenal on mitochondrial 3-hydroxy-3-methylglutaryl (HMG-CoA) synthase. Patel VB, etal., Free Radic Biol Med. 2007 Dec 1;43(11):1499-507. Epub 2007 Aug 16.
31. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
32. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
33. Glucagon activates mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase in vivo by decreasing the extent of succinylation of the enzyme. Quant PA, etal., Eur J Biochem. 1990 Jan 12;187(1):169-74.
34. GOA pipeline RGD automated data pipeline
35. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
36. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
37. Peroxisome proliferator-activated receptor mediates induction of the mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase gene by fatty acids. Rodriguez JC, etal., J Biol Chem. 1994 Jul 22;269(29):18767-72.
38. Restraint stress alters the duodenal expression of genes important for lipid metabolism in rat. Sato T, etal., Toxicology. 2006 Oct 29;227(3):248-61. Epub 2006 Aug 14.
39. Regulation of mitochondrial 3-hydroxy-3-methylglutaryl-coenzyme A synthase protein by starvation, fat feeding, and diabetes. Serra D, etal., Arch Biochem Biophys. 1993 Nov 15;307(1):40-5.
40. The expression of mitochondrial 3-hydroxy-3-methylglutaryl-coenzyme-A synthase in neonatal rat intestine and liver is under transcriptional control. Serra D, etal., Eur J Biochem. 1996 Apr 1;237(1):16-24.
41. Cholesterol biosynthesis regulation and protein changes in rat liver following treatment with fluvastatin. Steiner S, etal., Toxicol Lett. 2001 Mar 31;120(1-3):369-77.
42. Opposite effect of prolactin and prostaglandin F(2 alpha) on the expression of luteal genes as revealed by rat cDNA expression array. Stocco C, etal., Endocrinology. 2001 Sep;142(9):4158-61.
43. miR-107-mediated decrease of HMGCS2 indicates poor outcomes and promotes cell migration in hepatocellular carcinoma. 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. Developmental changes in mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase gene expression in rat liver, intestine and kidney. Thumelin S, etal., Biochem J. 1993 Jun 1;292 ( Pt 2):493-6.
45. Atypical expression of mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase in subcutaneous adipose tissue of male rats. Thumelin S, etal., J Lipid Res. 1999 Jun;40(6):1071-7.
46. Vanadate treatment restores the expression of genes for key enzymes in the glucose and ketone bodies metabolism in the liver of diabetic rats. Valera A, etal., J Clin Invest. 1993 Jul;92(1):4-11.
47. Mitochondrial HMG-CoA synthase partially contributes to antioxidant protection in the kidney of stroke-prone spontaneously hypertensive rats. 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 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2185,875,616 - 185,902,130 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2193,524,494 - 193,551,482 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02191,333,168 - 191,359,836 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02186,157,074 - 186,184,065 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02200,452,623 - 200,480,785 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2200,452,624 - 200,479,423 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02219,928,546 - 219,956,233 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42193,128,736 - 193,143,106 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh381119,747,996 - 119,768,932 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1119,748,002 - 119,768,905 (-)EnsemblGRCh38hg38GRCh38
GRCh371120,290,619 - 120,311,555 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361120,092,525 - 120,113,041 (-)NCBINCBI36Build 36hg18NCBI36
Build 341120,003,046 - 120,023,560NCBI
Celera1118,521,355 - 118,542,283 (-)NCBICelera
Cytogenetic Map1p12NCBI
HuRef1118,149,159 - 118,170,093 (-)NCBIHuRef
CHM1_11120,406,161 - 120,427,088 (-)NCBICHM1_1
T2T-CHM13v2.01119,761,239 - 119,782,165 (-)NCBIT2T-CHM13v2.0
Hmgcs2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39398,187,747 - 98,218,054 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl398,187,751 - 98,218,054 (+)EnsemblGRCm39 Ensembl
GRCm38398,280,431 - 98,310,738 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl398,280,435 - 98,310,738 (+)EnsemblGRCm38mm10GRCm38
MGSCv37398,084,354 - 98,114,661 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36398,365,840 - 98,396,137 (+)NCBIMGSCv36mm8
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
NHGRI_mPanPan11111,972,859 - 111,994,914 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0182,778,489 - 82,798,987 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11117,776,165 - 117,796,679 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1117,775,770 - 117,796,679 (+)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01757,558,992 - 57,577,456 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1757,554,455 - 57,577,399 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11756,594,625 - 56,613,171 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01756,620,825 - 56,639,082 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01757,237,948 - 57,256,436 (-)NCBIUU_Cfam_GSD_1.0
Hmgcs2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505810,015,851 - 10,037,163 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366274,451,823 - 4,473,223 (-)EnsemblSpeTri2.0
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 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2014,019,692 - 14,041,016 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603816,649,801 - 16,670,981 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hmgcs2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477215,432,198 - 15,467,797 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477215,432,612 - 15,464,343 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Hmgcs2
257 total Variants
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
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)281689826221035911Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2112456140212696837Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2112456140212696837Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2114837527185876470Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2114837527185876470Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2114837527211674221Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2114837675212549332Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2133914684202447032Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2135552573202446871Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2136445150202447032Rat
1581502Esta3Estrogen-induced thymic atrophy QTL 3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2136916935189599348Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2136916935213594495Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2141194931223265385Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2141194931223265385Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2141596551202447032Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2143157029210020885Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2143657411190602963Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2143657411190602963Rat
61401Niddm2Non-insulin dependent diabetes mellitus QTL 24.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2144599348189599348Rat
1598833Bp295Blood pressure QTL 2953.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2147798556192798556Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561221167075Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
1598805Memor8Memory QTL 83exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2150341585189039377Rat
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150341684202446871Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150540301202447032Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2150540301202447032Rat
1359032Hrtrt18Heart rate QTL 18heart pumping trait (VT:2000009)heart rate (CMO:0000002)2157142078192625452Rat
1358900Bw48Body weight QTL 484.88body mass (VT:0001259)body weight (CMO:0000012)2157142078211086598Rat
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)2157142078226277316Rat
1302793Bw16Body weight QTL 1650.0001body mass (VT:0001259)body weight (CMO:0000012)2157142209202446871Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2160564068205564068Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2161699179222436696Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2162765032207765032Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2164073756227146641Rat
1598838Bp290Blood pressure QTL 2901.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2166539266211539266Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2168358098223265385Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2168594495213594495Rat
61469Bp16Blood pressure QTL 165.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
70162Bp63Blood pressure QTL 635.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
2293084Iddm26Insulin dependent diabetes mellitus QTL 262.9blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2174930955213594495Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2179335906224335906Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2179946951224946951Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2182171407227171407Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2182171407227171407Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2182171407227171407Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2182171407227171407Rat
4889834Pur24Proteinuria QTL 245.80.014urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)2184114274202447032Rat
738013Alc15Alcohol consumption QTL 154.10.00022consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)2184165752229165752Rat
7488929Bp366Blood pressure QTL 3660.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2184974550193094998Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2185876309219753474Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2185876309219753474Rat

Markers in Region
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


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 21 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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2185,875,616 - 185,902,130 (+)Ensembl
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
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 Protein Sequences
RefSeq Acc Id: NP_775117   ⟸   NM_173094
- Peptide Label: precursor
- UniProtKB: P22791 (UniProtKB/Swiss-Prot),   F1M9Q5 (UniProtKB/Swiss-Prot),   Q68G44 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233064   ⟸   XM_006233002
- Peptide Label: isoform X1
- UniProtKB: P22791 (UniProtKB/Swiss-Prot),   F1M9Q5 (UniProtKB/Swiss-Prot),   Q68G44 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000026122   ⟸   ENSRNOT00000026121

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P22791-F1-model_v2 AlphaFold P22791 1-508 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2804 AgrOrtholog
BioCyc Gene G2FUF-51917 BioCyc
BioCyc Pathway PWY-922 [mevalonate pathway I (eukaryotes and bacteria)] BioCyc
  PWY66-367 [ketogenesis] BioCyc
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
PANTHER 3-HYDROXY-3-METHYLGLUTARYL COENZYME A SYNTHASE UniProtKB/Swiss-Prot
  HYDROXYMETHYLGLUTARYL-COA SYNTHASE, MITOCHONDRIAL UniProtKB/Swiss-Prot
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
UniProt F1M9Q5 ENTREZGENE
  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