Human Gene CS (ENST00000548567.5) from GENCODE V44
  Description: citrate synthase (from HGNC CS)
RefSeq Summary (NM_004077): The protein encoded by this gene is a Krebs tricarboxylic acid cycle enzyme that catalyzes the synthesis of citrate from oxaloacetate and acetyl coenzyme A. The enzyme is found in nearly all cells capable of oxidative metablism. This protein is nuclear encoded and transported into the mitochondrial matrix, where the mature form is found. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000548567.5
Gencode Gene: ENSG00000062485.19
Transcript (Including UTRs)
   Position: hg38 chr12:56,271,701-56,300,391 Size: 28,691 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg38 chr12:56,273,084-56,285,918 Size: 12,835 Coding Exon Count: 9 

Page IndexSequence and LinksPrimersMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureOther SpeciesmRNA DescriptionsPathwaysOther Names
Data last updated at UCSC: 2023-08-18 09:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr12:56,271,701-56,300,391)mRNA (may differ from genome)Protein (400 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold

-  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

-  MalaCards Disease Associations
  MalaCards Gene Search: CS
Diseases sorted by gene-association score: critical illness polyneuropathy (18), cat-scratch disease (7), cerebral creatine deficiency syndrome 2 (6), bartonellosis (6), mitochondrial cardiomyopathy (6), cerebral creatine deficiency syndrome (5), carnitine palmitoyltransferase ii deficiency (5), diabetes mellitus, noninsulin-dependent (1)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 142.17 RPKM in Heart - Left Ventricle
Total median expression: 2609.06 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 -171.60471-0.364 Picture PostScript Text
3' UTR -372.801383-0.270 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.

-  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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Descriptions from all associated GenBank mRNAs
  BC004392 - Homo sapiens cDNA clone IMAGE:3635299, **** WARNING: chimeric clone ****.
BC000105 - Homo sapiens citrate synthase, mRNA (cDNA clone IMAGE:3509003), partial cds.
AK095856 - Homo sapiens cDNA FLJ38537 fis, clone HCHON2001233, highly similar to Citrate synthase, mitochondrial precursor (EC
BC072016 - Homo sapiens citrate synthase, mRNA (cDNA clone MGC:88727 IMAGE:6484456), complete cds.
BC010106 - Homo sapiens citrate synthase, mRNA (cDNA clone MGC:19593 IMAGE:3542491), complete cds.
BX640838 - Homo sapiens mRNA; cDNA DKFZp686D21216 (from clone DKFZp686D21216).
AK074956 - Homo sapiens cDNA FLJ90475 fis, clone NT2RP3002721, highly similar to Porcine citrate synthase mRNA.
JD181958 - Sequence 162982 from Patent EP1572962.
JD191002 - Sequence 172026 from Patent EP1572962.
JD230392 - Sequence 211416 from Patent EP1572962.
JD143191 - Sequence 124215 from Patent EP1572962.
JD171251 - Sequence 152275 from Patent EP1572962.
JD291328 - Sequence 272352 from Patent EP1572962.
JD419352 - Sequence 400376 from Patent EP1572962.
AK296249 - Homo sapiens cDNA FLJ56094 complete cds, highly similar to Citrate synthase, mitochondrial precursor (EC
JD475789 - Sequence 456813 from Patent EP1572962.
AK307625 - Homo sapiens cDNA, FLJ97573.
AF053631 - Homo sapiens citrate synthase mRNA, complete cds.
AF047042 - Homo sapiens citrate synthase mRNA, complete cds.
BT007414 - Homo sapiens citrate synthase mRNA, complete cds.
KJ901360 - Synthetic construct Homo sapiens clone ccsbBroadEn_10754 CS gene, encodes complete protein.
KJ890976 - Synthetic construct Homo sapiens clone ccsbBroadEn_00370 CS gene, encodes complete protein.
JD328533 - Sequence 309557 from Patent EP1572962.
DQ403132 - Homo sapiens citrate synthase (CS) mRNA, partial cds.
AK293263 - Homo sapiens cDNA FLJ55186 complete cds, highly similar to Citrate synthase, mitochondrial precursor (EC
AK098177 - Homo sapiens cDNA FLJ40858 fis, clone TRACH2016835.
CU674040 - Synthetic construct Homo sapiens gateway clone IMAGE:100017189 5' read CS mRNA.
CU679623 - Synthetic construct Homo sapiens gateway clone IMAGE:100017329 5' read CS mRNA.
DQ587522 - Homo sapiens piRNA piR-54634, complete sequence.
AF147410 - Homo sapiens full length insert cDNA clone YP58F11.
JD043890 - Sequence 24914 from Patent EP1572962.
JD196982 - Sequence 178006 from Patent EP1572962.
JD061513 - Sequence 42537 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00020 - Citrate cycle (TCA cycle)
hsa00630 - Glyoxylate and dicarboxylate metabolism
hsa01100 - Metabolic pathways

-  Other Names for This Gene
  Alternate Gene Symbols: A0A0C4DGI3, BX640838, ENST00000548567.1, ENST00000548567.2, ENST00000548567.3, ENST00000548567.4, uc001skr.1, uc001skr.2
UCSC ID: ENST00000548567.5
RefSeq Accession: NM_004077

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