Human Gene HMGCS1 (ENST00000325110.11_8) from GENCODE V47lift37
  Description: 3-hydroxy-3-methylglutaryl-CoA synthase 1, transcript variant 2 (from RefSeq NM_002130.8)
Gencode Transcript: ENST00000325110.11_8
Gencode Gene: ENSG00000112972.16_13
Transcript (Including UTRs)
   Position: hg19 chr5:43,287,572-43,313,514 Size: 25,943 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr5:43,291,233-43,299,067 Size: 7,835 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:43,287,572-43,313,514)mRNA (may differ from genome)Protein (520 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HMCS1_HUMAN
DESCRIPTION: RecName: Full=Hydroxymethylglutaryl-CoA synthase, cytoplasmic; Short=HMG-CoA synthase; EC=2.3.3.10; AltName: Full=3-hydroxy-3-methylglutaryl coenzyme A synthase;
FUNCTION: This enzyme condenses acetyl-CoA with acetoacetyl-CoA to form HMG-CoA, which is the substrate for HMG-CoA reductase.
CATALYTIC ACTIVITY: Acetyl-CoA + H(2)O + acetoacetyl-CoA = (S)-3- hydroxy-3-methylglutaryl-CoA + CoA.
PATHWAY: Metabolic intermediate biosynthesis; (R)-mevalonate biosynthesis; (R)-mevalonate from acetyl-CoA: step 2/3.
SUBCELLULAR LOCATION: Cytoplasm.
SIMILARITY: Belongs to the HMG-CoA synthase family.
SEQUENCE CAUTION: Sequence=AAH00297.2; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 78.67 RPKM in Esophagus - Mucosa
Total median expression: 964.51 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -35.50126-0.282 Picture PostScript Text
3' UTR -934.773661-0.255 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000590 - HMG_CoA_synt_AS
IPR013746 - HMG_CoA_synt_C
IPR013528 - HMG_CoA_synth_N
IPR010122 - HMG_CoA_synthase_euk
IPR016039 - Thiolase-like
IPR016038 - Thiolase-like_subgr

Pfam Domains:
PF01154 - Hydroxymethylglutaryl-coenzyme A synthase N terminal
PF08540 - Hydroxymethylglutaryl-coenzyme A synthase C terminal

SCOP Domains:
74788 - Cullin repeat-like
53901 - Thiolase-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2P8U - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q01581
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0004421 hydroxymethylglutaryl-CoA synthase activity
GO:0008144 drug binding
GO:0016740 transferase activity
GO:0016853 isomerase activity
GO:0042803 protein homodimerization activity
GO:0043177 organic acid binding

Biological Process:
GO:0001889 liver development
GO:0006629 lipid metabolic process
GO:0006694 steroid biosynthetic process
GO:0006695 cholesterol biosynthetic process
GO:0007420 brain development
GO:0008152 metabolic process
GO:0008202 steroid metabolic process
GO:0008203 cholesterol metabolic process
GO:0008299 isoprenoid biosynthetic process
GO:0008584 male gonad development
GO:0009645 response to low light intensity stimulus
GO:0009725 response to hormone
GO:0010033 response to organic substance
GO:0014070 response to organic cyclic compound
GO:0014074 response to purine-containing compound
GO:0016126 sterol biosynthetic process
GO:0019216 regulation of lipid metabolic process
GO:0033197 response to vitamin E
GO:0034698 response to gonadotropin
GO:0042493 response to drug
GO:0045540 regulation of cholesterol biosynthetic process
GO:0046690 response to tellurium ion
GO:0070723 response to cholesterol
GO:0071372 cellular response to follicle-stimulating hormone stimulus
GO:0071397 cellular response to cholesterol
GO:0071404 cellular response to low-density lipoprotein particle stimulus
GO:0071407 cellular response to organic cyclic compound

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AL050004 - Homo sapiens mRNA; cDNA DKFZp564P142 (from clone DKFZp564P142).
AK025736 - Homo sapiens cDNA: FLJ22083 fis, clone HEP14459, highly similar to HUM3H3M Homo sapiens 3-hydroxy-3-methylglutaryl coenzyme A synthase mRNA.
AK095492 - Homo sapiens cDNA FLJ38173 fis, clone FCBBF1000053, highly similar to HYDROXYMETHYLGLUTARYL-COA SYNTHASE, CYTOPLASMIC (EC 4.1.3.5).
BC082234 - Homo sapiens 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble), mRNA (cDNA clone IMAGE:3677631).
JD021929 - Sequence 2953 from Patent EP1572962.
JD032769 - Sequence 13793 from Patent EP1572962.
BC000297 - Homo sapiens 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble), mRNA (cDNA clone IMAGE:2819708), partial cds.
L25798 - Homo sapiens 3-hydroxy-3-methylglutaryl coenzyme A synthase mRNA, complete cds.
JD515460 - Sequence 496484 from Patent EP1572962.
DL491840 - Novel nucleic acids.
DL490413 - Novel nucleic acids.
JD266401 - Sequence 247425 from Patent EP1572962.
JD551719 - Sequence 532743 from Patent EP1572962.
AK315593 - Homo sapiens cDNA, FLJ96671, Homo sapiens 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble) (HMGCS1), mRNA.
BT007302 - Homo sapiens 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble) mRNA, complete cds.
AB529077 - Synthetic construct DNA, clone: pF1KB4086, Homo sapiens HMGCS1 gene for 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1, without stop codon, in Flexi system.
X66435 - H.sapiens mRNA for HMG-CoA-synthase.
BX537620 - Homo sapiens mRNA; cDNA DKFZp686E20188 (from clone DKFZp686E20188).
M15802 - Human hydroxymethylglutaryl-CoA (HMG CoA) synthase mRNA, 5' end.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
PWY-5910 - superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate)
PWY-922 - mevalonate pathway
PWY66-5 - superpathway of cholesterol biosynthesis

BioCarta from NCI Cancer Genome Anatomy Project
h_s1pPathway - SREBP control of lipid synthesis

Reactome (by CSHL, EBI, and GO)

Protein Q01581 (Reactome details) participates in the following event(s):

R-HSA-191323 HMGCS1 condenses Ac-CoA and ACA-CoA to form bHMG-CoA
R-HSA-1989781 PPARA activates gene expression
R-HSA-2426168 Activation of gene expression by SREBF (SREBP)
R-HSA-400206 Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
R-HSA-1655829 Regulation of cholesterol biosynthesis by SREBP (SREBF)
R-HSA-191273 Cholesterol biosynthesis
R-HSA-556833 Metabolism of lipids
R-HSA-8957322 Metabolism of steroids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B2RDL8, ENST00000325110.1, ENST00000325110.10, ENST00000325110.2, ENST00000325110.3, ENST00000325110.4, ENST00000325110.5, ENST00000325110.6, ENST00000325110.7, ENST00000325110.8, ENST00000325110.9, HMCS1_HUMAN, HMGCS, HMGCS1 , NM_002130, Q01581, uc317ruo.1, uc317ruo.2
UCSC ID: ENST00000325110.11_8
RefSeq Accession: NM_001098272.3
Protein: Q01581 (aka HMCS1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.