Human Gene CS (ENST00000351328.8_8) from GENCODE V47lift37
  Description: citrate synthase (from RefSeq NM_004077.3)
Gencode Transcript: ENST00000351328.8_8
Gencode Gene: ENSG00000062485.19_17
Transcript (Including UTRs)
   Position: hg19 chr12:56,665,483-56,694,114 Size: 28,632 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr12:56,666,868-56,693,985 Size: 27,118 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:56,665,483-56,694,114)mRNA (may differ from genome)Protein (466 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CISY_HUMAN
DESCRIPTION: RecName: Full=Citrate synthase, mitochondrial; EC=2.3.3.1; Flags: Precursor;
CATALYTIC ACTIVITY: Acetyl-CoA + H(2)O + oxaloacetate = citrate + CoA.
PATHWAY: Carbohydrate metabolism; tricarboxylic acid cycle; isocitrate from oxaloacetate: step 1/2.
SUBUNIT: Homodimer (By similarity).
SUBCELLULAR LOCATION: Mitochondrion matrix.
MISCELLANEOUS: Citrate synthase is found in nearly all cells capable of oxidative metabolism.
SIMILARITY: Belongs to the citrate synthase family.
SEQUENCE CAUTION: Sequence=CAE45911.1; Type=Miscellaneous discrepancy; Note=Intron retention;
WEB RESOURCE: Name=Wikipedia; Note=Citrate synthase entry; URL="http://en.wikipedia.org/wiki/Citrate_synthase";

-  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

+  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: 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 -34.30129-0.266 Picture PostScript Text
3' UTR -373.001385-0.269 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
IPR016142 - Citrate_synth-like_lrg_a-sub
IPR002020 - Citrate_synthase-like
IPR016141 - Citrate_synthase-like_core
IPR019810 - Citrate_synthase_AS
IPR010109 - Citrate_synthase_euk

Pfam Domains:
PF00285 - Citrate synthase, C-terminal domain

SCOP Domains:
48256 - Citrate synthase

ModBase Predicted Comparative 3D Structure on O75390
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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 orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0004108 citrate (Si)-synthase activity
GO:0016740 transferase activity
GO:0046912 transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer

Biological Process:
GO:0005975 carbohydrate metabolic process
GO:0006099 tricarboxylic acid cycle
GO:0006101 citrate metabolic process

Cellular Component:
GO:0005634 nucleus
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0070062 extracellular exosome


-  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 2.3.3.1).
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 2.3.3.1).
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 2.3.3.1).
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
  BioCyc Knowledge Library
PWY66-398 - TCA cycle
PWY66-407 - superpathway of conversion of glucose to acetyl CoA and entry into the TCA cycle

Reactome (by CSHL, EBI, and GO)

Protein O75390 (Reactome details) participates in the following event(s):

R-HSA-1268022 TOMM40 complex translocates proteins from the cytosol to the mitochondrial intermembrane space
R-HSA-70975 Acetyl-CoA + H2O + Oxaloacetate => Citrate + CoA
R-HSA-1268020 Mitochondrial protein import
R-HSA-71403 Citric acid cycle (TCA cycle)
R-HSA-392499 Metabolism of proteins
R-HSA-71406 Pyruvate metabolism and Citric Acid (TCA) cycle
R-HSA-1428517 The citric acid (TCA) cycle and respiratory electron transport
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: CISY_HUMAN, ENST00000351328.1, ENST00000351328.2, ENST00000351328.3, ENST00000351328.4, ENST00000351328.5, ENST00000351328.6, ENST00000351328.7, NM_004077, O75390, Q71UT9, Q7KZH0, Q96FZ8, Q9BWN8, uc317ycd.1, uc317ycd.2
UCSC ID: ENST00000351328.8_8
RefSeq Accession: NM_004077.3
Protein: O75390 (aka CISY_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.