Human Gene ACLY (uc010wfy.2)
  Description: Homo sapiens ATP citrate lyase (ACLY), transcript variant 2, mRNA.
RefSeq Summary (NM_198830): ATP citrate lyase is the primary enzyme responsible for the synthesis of cytosolic acetyl-CoA in many tissues. The enzyme is a tetramer (relative molecular weight approximately 440,000) of apparently identical subunits. It catalyzes the formation of acetyl-CoA and oxaloacetate from citrate and CoA with a concomitant hydrolysis of ATP to ADP and phosphate. The product, acetyl-CoA, serves several important biosynthetic pathways, including lipogenesis and cholesterogenesis. In nervous tissue, ATP citrate-lyase may be involved in the biosynthesis of acetylcholine. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Dec 2014].
Transcript (Including UTRs)
   Position: hg19 chr17:40,023,179-40,075,272 Size: 52,094 Total Exon Count: 21 Strand: -
Coding Region
   Position: hg19 chr17:40,024,063-40,070,126 Size: 46,064 Coding Exon Count: 20 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:40,023,179-40,075,272)mRNA (may differ from genome)Protein (830 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMalacardsMGIOMIM
PubMedTreefamUniProtKBBioGrid CRISPR DB

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ACLY
CDC HuGE Published Literature: ACLY

-  MalaCards Disease Associations
  MalaCards Gene Search: ACLY
Diseases sorted by gene-association score: atrichia with papular lesions (6), acrocallosal syndrome (6)

-  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: 52.29 RPKM in Cells - Cultured fibroblasts
Total median expression: 1035.26 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -70.40163-0.432 Picture PostScript Text
3' UTR -229.84884-0.260 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
IPR017440 - Cit_synth/succinyl-CoA_lig_AS
IPR016142 - Citrate_synth-like_lrg_a-sub
IPR016143 - Citrate_synth-like_sm_a-sub
IPR002020 - Citrate_synthase-like
IPR016141 - Citrate_synthase-like_core
IPR003781 - CoA-bd
IPR005810 - CoA_lig_alpha
IPR005811 - CoA_ligase
IPR016040 - NAD(P)-bd_dom
IPR016102 - Succinyl-CoA_synth-like

Pfam Domains:
PF00285 - Citrate synthase, C-terminal domain
PF00549 - CoA-ligase
PF02629 - CoA binding domain
PF16114 - ATP citrate lyase citrate-binding

SCOP Domains:
48256 - Citrate synthase
51735 - NAD(P)-binding Rossmann-fold domains
52210 - Succinyl-CoA synthetase domains
56059 - Glutathione synthetase ATP-binding domain-like

ModBase Predicted Comparative 3D Structure on B4E3P0
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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 orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AB210035 - Homo sapiens mRNA for ACLY variant protein, partial cds, clone: hk02197.
BC006195 - Homo sapiens ATP citrate lyase, mRNA (cDNA clone MGC:1812 IMAGE:2959339), complete cds.
X64330 - H.sapiens mRNA for ATP-citrate lyase.
JD080335 - Sequence 61359 from Patent EP1572962.
JD262461 - Sequence 243485 from Patent EP1572962.
JD185932 - Sequence 166956 from Patent EP1572962.
JD304254 - Sequence 285278 from Patent EP1572962.
JD090878 - Sequence 71902 from Patent EP1572962.
JD511709 - Sequence 492733 from Patent EP1572962.
AK304802 - Homo sapiens cDNA FLJ55447 complete cds, highly similar to ATP-citrate synthase (EC 2.3.3.8).
JD409698 - Sequence 390722 from Patent EP1572962.
JD361347 - Sequence 342371 from Patent EP1572962.
AK095084 - Homo sapiens cDNA FLJ37765 fis, clone BRHIP2024742, highly similar to ATP-CITRATE.
JD217135 - Sequence 198159 from Patent EP1572962.
JD438177 - Sequence 419201 from Patent EP1572962.
U18197 - Human ATP:citrate lyase mRNA, complete cds.
AK295675 - Homo sapiens cDNA FLJ56442 complete cds, highly similar to ATP-citrate synthase (EC 2.3.3.8).
JD374728 - Sequence 355752 from Patent EP1572962.
JD280247 - Sequence 261271 from Patent EP1572962.
AK312315 - Homo sapiens cDNA, FLJ92623.
KJ890615 - Synthetic construct Homo sapiens clone ccsbBroadEn_00009 ACLY gene, encodes complete protein.
JF432308 - Synthetic construct Homo sapiens clone IMAGE:100073491 ATP citrate lyase (ACLY) gene, encodes complete protein.
AB384384 - Synthetic construct DNA, clone: pF1KSDB0058, Homo sapiens ACLY gene for ATP-citrate synthase, complete cds, without stop codon, in Flexi system.
JD186768 - Sequence 167792 from Patent EP1572962.
DL491764 - Novel nucleic acids.
DQ575356 - Homo sapiens piRNA piR-43468, complete sequence.
CU675293 - Synthetic construct Homo sapiens gateway clone IMAGE:100020482 5' read ACLY mRNA.
JD408483 - Sequence 389507 from Patent EP1572962.
JD273048 - Sequence 254072 from Patent EP1572962.
JD437050 - Sequence 418074 from Patent EP1572962.

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

BioCarta from NCI Cancer Genome Anatomy Project
h_malatexPathway - Shuttle for transfer of acetyl groups from mitochondria to the cytosol

-  Other Names for This Gene
  Alternate Gene Symbols: AK304802, B4E3P0, B4E3P0_HUMAN, NM_198830, NP_942127
UCSC ID: uc010wfy.2
RefSeq Accession: NM_198830
Protein: B4E3P0

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK304802.1
exon count: 21CDS single in 3' UTR: no RNA size: 2974
ORF size: 2493CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4721.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.