Human Gene CPT1A (ENST00000265641.10_7) from GENCODE V47lift37
  Description: carnitine palmitoyltransferase 1A, transcript variant 1 (from RefSeq NM_001876.4)
Gencode Transcript: ENST00000265641.10_7
Gencode Gene: ENSG00000110090.13_9
Transcript (Including UTRs)
   Position: hg19 chr11:68,522,351-68,609,384 Size: 87,034 Total Exon Count: 19 Strand: -
Coding Region
   Position: hg19 chr11:68,525,112-68,582,942 Size: 57,831 Coding Exon Count: 18 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:68,522,351-68,609,384)mRNA (may differ from genome)Protein (773 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CPT1A_HUMAN
DESCRIPTION: RecName: Full=Carnitine O-palmitoyltransferase 1, liver isoform; Short=CPT1-L; EC=2.3.1.21; AltName: Full=Carnitine O-palmitoyltransferase I, liver isoform; Short=CPT I; Short=CPTI-L; AltName: Full=Carnitine palmitoyltransferase 1A;
FUNCTION: Catalyzes the transfer of the acyl group of long-chain fatty acid-CoA conjugates onto carnitine, an essential step for the mitochondrial uptake of long-chain fatty acids and their subsequent beta-oxidation in the mitochondrion. Plays an important role in triglyceride metabolism.
CATALYTIC ACTIVITY: Palmitoyl-CoA + L-carnitine = CoA + L- palmitoylcarnitine.
ENZYME REGULATION: Inhibited by malonyl-CoA.
PATHWAY: Lipid metabolism; fatty acid beta-oxidation.
SUBUNIT: Homohexamer and homotrimer. Identified in a complex that contains at least CPT1A, ACSL1 and VDAC1. Also identified in complexes with ACSL1 and VDAC2 and VDAC3 (By similarity).
SUBCELLULAR LOCATION: Mitochondrion outer membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Strong expression in kidney and heart, and lower in liver and skeletal muscle.
INDUCTION: Up-regulated by fatty acids.
DOMAIN: A conformation change in the N-terminal region spanning the first 42 residues plays an important role in the regulation of enzyme activity by malonyl-CoA.
DISEASE: Defects in CPT1A are the cause of carnitine palmitoyltransferase 1A deficiency (CPT1AD) [MIM:255120]; also known as CPT-I deficiency or CPT1A deficiency. CPT1AD is a rare autosomal recessive metabolic disorder of long-chain fatty acid oxidation characterized by severe episodes of hypoketotic hypoglycemia usually occurring after fasting or illness. Onset is in infancy or early childhood.
SIMILARITY: Belongs to the carnitine/choline acetyltransferase family.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CPT1A";

-  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: CPT1A
Diseases sorted by gene-association score: cpt deficiency, hepatic, type ia* (1672), carnitine palmitoyltransferase ii deficiency (23), carnitine-acylcarnitine translocase deficiency (13), visceral steatosis (12), fatty acid oxidation disorders (8), obesity (1)
* = Manually curated disease association

-  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: 25.44 RPKM in Colon - Transverse
Total median expression: 579.94 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 -49.10155-0.317 Picture PostScript Text
3' UTR -1144.702761-0.415 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
IPR000542 - Carn_acyl_trans

Pfam Domains:
PF00755 - Choline/Carnitine o-acyltransferase
PF16484 - Carnitine O-palmitoyltransferase N-terminus

SCOP Domains:
52777 - CoA-dependent acyltransferases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2LE3 - NMR MuPIT


ModBase Predicted Comparative 3D Structure on P50416
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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 DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004095 carnitine O-palmitoyltransferase activity
GO:0016740 transferase activity
GO:0016746 transferase activity, transferring acyl groups
GO:0042802 identical protein binding
GO:1990698 palmitoleoyltransferase activity

Biological Process:
GO:0001676 long-chain fatty acid metabolic process
GO:0006006 glucose metabolic process
GO:0006629 lipid metabolic process
GO:0006631 fatty acid metabolic process
GO:0006635 fatty acid beta-oxidation
GO:0006641 triglyceride metabolic process
GO:0006853 carnitine shuttle
GO:0007623 circadian rhythm
GO:0009437 carnitine metabolic process
GO:0014070 response to organic cyclic compound
GO:0019216 regulation of lipid metabolic process
GO:0030855 epithelial cell differentiation
GO:0032000 positive regulation of fatty acid beta-oxidation
GO:0042493 response to drug
GO:0042755 eating behavior
GO:0046320 regulation of fatty acid oxidation
GO:0050796 regulation of insulin secretion
GO:0051260 protein homooligomerization
GO:0071398 cellular response to fatty acid

Cellular Component:
GO:0005739 mitochondrion
GO:0005741 mitochondrial outer membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031307 integral component of mitochondrial outer membrane
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  BC000185 - Homo sapiens carnitine palmitoyltransferase 1A (liver), mRNA (cDNA clone MGC:1772 IMAGE:3352642), complete cds.
KJ890965 - Synthetic construct Homo sapiens clone ccsbBroadEn_00359 CPT1A gene, encodes complete protein.
KR709763 - Synthetic construct Homo sapiens clone CCSBHm_00005747 CPT1A (CPT1A) mRNA, encodes complete protein.
KR709764 - Synthetic construct Homo sapiens clone CCSBHm_00005755 CPT1A (CPT1A) mRNA, encodes complete protein.
KR709765 - Synthetic construct Homo sapiens clone CCSBHm_00005757 CPT1A (CPT1A) mRNA, encodes complete protein.
KR709766 - Synthetic construct Homo sapiens clone CCSBHm_00005765 CPT1A (CPT1A) mRNA, encodes complete protein.
BT009791 - Homo sapiens carnitine palmitoyltransferase 1A (liver) mRNA, complete cds.
AK025307 - Homo sapiens cDNA: FLJ21654 fis, clone COL08589, highly similar to HUMCAPA Homo sapiens mitochondrial carnitine palmitoyltransferase I mRNA.
AK172798 - Homo sapiens cDNA FLJ23959 fis, clone HEP14351, highly similar to Carnitine O-palmitoyltransferase I, mitochondrial liver isoform (EC 2.3.1.21).
L39211 - Homo sapiens mitochondrial carnitine palmitoyltransferase I mRNA, complete cds.
AK314301 - Homo sapiens cDNA, FLJ95058, highly similar to Homo sapiens carnitine palmitoyltransferase 1A (liver) (CPT1A),nuclear gene encoding mitochondrial protein, mRNA.
AK309464 - Homo sapiens cDNA, FLJ99505.
JD023928 - Sequence 4952 from Patent EP1572962.
JD029355 - Sequence 10379 from Patent EP1572962.
JD035240 - Sequence 16264 from Patent EP1572962.
JD175934 - Sequence 156958 from Patent EP1572962.
JD138314 - Sequence 119338 from Patent EP1572962.
JD344704 - Sequence 325728 from Patent EP1572962.
JD148389 - Sequence 129413 from Patent EP1572962.
JD463904 - Sequence 444928 from Patent EP1572962.
JD478657 - Sequence 459681 from Patent EP1572962.
JD543377 - Sequence 524401 from Patent EP1572962.
JD140150 - Sequence 121174 from Patent EP1572962.
JD119040 - Sequence 100064 from Patent EP1572962.
AJ420378 - Homo sapiens partial mRNA for carnitine palmitoyltransferase I (CPT1A gene).
JD173638 - Sequence 154662 from Patent EP1572962.
JD331094 - Sequence 312118 from Patent EP1572962.
JD242761 - Sequence 223785 from Patent EP1572962.
DQ586637 - Homo sapiens piRNA piR-53749, complete sequence.
CU674080 - Synthetic construct Homo sapiens gateway clone IMAGE:100017803 5' read CPT1A mRNA.
X83113 - H.sapiens mRNA for carnitine palmitoyltransferase I.
JD271294 - Sequence 252318 from Patent EP1572962.
JD458522 - Sequence 439546 from Patent EP1572962.
JD458516 - Sequence 439540 from Patent EP1572962.
JD458521 - Sequence 439545 from Patent EP1572962.
JD458515 - Sequence 439539 from Patent EP1572962.
JD056230 - Sequence 37254 from Patent EP1572962.
JD271291 - Sequence 252315 from Patent EP1572962.
JD458510 - Sequence 439534 from Patent EP1572962.
JD406055 - Sequence 387079 from Patent EP1572962.
JD271292 - Sequence 252316 from Patent EP1572962.
JD458514 - Sequence 439538 from Patent EP1572962.
JD057274 - Sequence 38298 from Patent EP1572962.
JD406801 - Sequence 387825 from Patent EP1572962.
JD461601 - Sequence 442625 from Patent EP1572962.
JD458513 - Sequence 439537 from Patent EP1572962.
JD056228 - Sequence 37252 from Patent EP1572962.
JD458511 - Sequence 439535 from Patent EP1572962.
JD189481 - Sequence 170505 from Patent EP1572962.
JD516440 - Sequence 497464 from Patent EP1572962.
JD148921 - Sequence 129945 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
PWY-6111 - mitochondrial L-carnitine shuttle

BioCarta from NCI Cancer Genome Anatomy Project
h_leptinPathway - Reversal of Insulin Resistance by Leptin
h_cptPathway - Mitochondrial Carnitine Palmitoyltransferase (CPT) System

Reactome (by CSHL, EBI, and GO)

Protein P50416 (Reactome details) participates in the following event(s):

R-HSA-200406 CPT1A,B transfers PALM to CAR
R-HSA-1368082 RORA activates gene expression
R-HSA-1989781 PPARA activates gene expression
R-HSA-400253 Circadian Clock
R-HSA-400206 Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
R-HSA-200425 Import of palmitoyl-CoA into the mitochondrial matrix
R-HSA-5362517 Signaling by Retinoic Acid
R-HSA-556833 Metabolism of lipids
R-HSA-8978868 Fatty acid metabolism
R-HSA-9006931 Signaling by Nuclear Receptors
R-HSA-1430728 Metabolism
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: CPT1, CPT1A , CPT1A_HUMAN, ENST00000265641.1, ENST00000265641.2, ENST00000265641.3, ENST00000265641.4, ENST00000265641.5, ENST00000265641.6, ENST00000265641.7, ENST00000265641.8, ENST00000265641.9, NM_001876, P50416, Q8TCU0, Q9BWK0, uc317ida.1, uc317ida.2
UCSC ID: ENST00000265641.10_7
RefSeq Accession: NM_001876.4
Protein: P50416 (aka CPT1A_HUMAN or CPT1_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CPT1A:
cpt1a (Carnitine Palmitoyltransferase 1A Deficiency)

-  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.