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Aliases for CRAT Gene

Aliases for CRAT Gene

  • Carnitine O-Acetyltransferase 2 3 3 5
  • Carnitine Acetyltransferase 2 4
  • Carnitine Acetylase 3 4
  • CAT1 3 4
  • CAT 3 4
  • EC 4
  • NBIA8 3
  • CrAT 4

External Ids for CRAT Gene

Previous GeneCards Identifiers for CRAT Gene

  • GC09M122971
  • GC09M123503
  • GC09M125310
  • GC09M127233
  • GC09M128936
  • GC09M130896
  • GC09M131857
  • GC09M101464

Summaries for CRAT Gene

Entrez Gene Summary for CRAT Gene

  • This gene encodes carnitine O-acetyltransferase, a member of the carnitine acyltransferase family and a key metabolic pathway enzyme which plays an important role in energy homeostasis and fat metabolism. This enzyme catalyzes the reversible transfer of acyl groups from an acyl-CoA thioester to carnitine and regulates the ratio of acyl-CoA/CoA. It is found in both the mitochondria and the peroxisome. Alternative splicing results in transcript variants encoding different isoforms that may localize to different subcellular compartments. [provided by RefSeq, Oct 2016]

GeneCards Summary for CRAT Gene

CRAT (Carnitine O-Acetyltransferase) is a Protein Coding gene. Diseases associated with CRAT include Neurodegeneration With Brain Iron Accumulation 8 and Leukoregulin. Among its related pathways are Peroxisomal lipid metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include signaling receptor binding and carnitine O-acetyltransferase activity. An important paralog of this gene is CHAT.

UniProtKB/Swiss-Prot for CRAT Gene

  • Carnitine acetylase is specific for short chain fatty acids. Carnitine acetylase seems to affect the flux through the pyruvate dehydrogenase complex. It may be involved as well in the transport of acetyl-CoA into mitochondria.

Gene Wiki entry for CRAT Gene

Additional gene information for CRAT Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CRAT Gene

Genomics for CRAT Gene

GeneHancer (GH) Regulatory Elements for CRAT Gene

Promoters and enhancers for CRAT Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J129108 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 679.2 +0.7 661 4.3 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B CRAT PTPA UBE2V1P4 ENSG00000272593 SPOUT1 ENSG00000234055 LOC101929270 LOC100129352 LOC101929314
GH09J129136 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 29.5 -29.3 -29305 8.2 HDGF PKNOX1 FOXA2 SMAD1 ZFP64 ARID4B SIN3A FEZF1 YBX1 ZNF2 PTPA CRAT NUP188 GLE1 ENSG00000268707 URM1 TOR1B CIZ1 PKN3 CERCAM
GH09J129172 Promoter/Enhancer 2.2 FANTOM5 Ensembl ENCODE dbSUPER 22.4 -64.6 -64571 7.5 FEZF1 DMAP1 IRF4 YY1 ZNF213 ZNF143 SP3 NFYC PPARGC1A SSRP1 LOC105376289 ENSG00000268050 NUP188 CIZ1 ODF2 GLE1 CRAT SPOUT1 UBE2V1P4 ENSG00000272593
GH09J129131 Enhancer 1.1 ENCODE dbSUPER 40 -20.6 -20619 0.7 HDGF SMAD1 RB1 KLF17 SIN3A ZNF2 KLF5 IRF4 BRCA1 ZNF48 CRAT ENSG00000234055 URM1 NTMT1 C9orf50 NUP188 GC09P129130 PIR47941 PIR48172 GC09P129138
GH09J129166 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 20.2 -56.7 -56676 3.4 HDGF PKNOX1 CLOCK SIN3A ZBTB7B SLC30A9 FOS ATF7 SP3 SP5 CRAT NTMT1 C9orf106 PRRX2 ENSG00000268707 PIR38901 GC09P129149
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CRAT on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CRAT gene promoter:
  • YY1
  • NF-kappaB

Genomic Locations for CRAT Gene

Genomic Locations for CRAT Gene
16,396 bases
Minus strand
16,396 bases
Minus strand

Genomic View for CRAT Gene

Genes around CRAT on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CRAT Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CRAT Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CRAT Gene

Proteins for CRAT Gene

  • Protein details for CRAT Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Carnitine O-acetyltransferase
    Protein Accession:
    Secondary Accessions:
    • Q5T952
    • Q9BW16

    Protein attributes for CRAT Gene

    626 amino acids
    Molecular mass:
    70858 Da
    Quaternary structure:
    • Monomer.

    Three dimensional structures from OCA and Proteopedia for CRAT Gene

    Alternative splice isoforms for CRAT Gene


neXtProt entry for CRAT Gene

Post-translational modifications for CRAT Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CRAT Gene

Domains & Families for CRAT Gene

Gene Families for CRAT Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins
  • Transporters

Protein Domains for CRAT Gene

Suggested Antigen Peptide Sequences for CRAT Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the carnitine/choline acetyltransferase family.
  • Belongs to the carnitine/choline acetyltransferase family.
genes like me logo Genes that share domains with CRAT: view

Function for CRAT Gene

Molecular function for CRAT Gene

UniProtKB/Swiss-Prot Function:
Carnitine acetylase is specific for short chain fatty acids. Carnitine acetylase seems to affect the flux through the pyruvate dehydrogenase complex. It may be involved as well in the transport of acetyl-CoA into mitochondria.
UniProtKB/Swiss-Prot CatalyticActivity:
Acetyl-CoA + carnitine = CoA + O-acetylcarnitine.
GENATLAS Biochemistry:
carnitine acetyltransferase,localized in mitochondrial matrix,peroxisomes,and endoplasmic reticulum,specific for short chain fatty acyl-CoA (C2-C14)

Enzyme Numbers (IUBMB) for CRAT Gene

Phenotypes From GWAS Catalog for CRAT Gene

Gene Ontology (GO) - Molecular Function for CRAT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004092 carnitine O-acetyltransferase activity TAS --
GO:0005102 signaling receptor binding IPI 20178365
GO:0016740 transferase activity IEA --
GO:0016746 transferase activity, transferring acyl groups IEA --
genes like me logo Genes that share ontologies with CRAT: view
genes like me logo Genes that share phenotypes with CRAT: view

Animal Model Products

CRISPR Products

miRNA for CRAT Gene

miRTarBase miRNAs that target CRAT

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CRAT

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CRAT Gene

Localization for CRAT Gene

Subcellular locations from UniProtKB/Swiss-Prot for CRAT Gene

Endoplasmic reticulum. Peroxisome. Mitochondrion inner membrane; Peripheral membrane protein; Matrix side.
Isoform 1: Mitochondrion.
Isoform 2: Peroxisome.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CRAT gene
Compartment Confidence
mitochondrion 5
peroxisome 5
nucleus 3
endoplasmic reticulum 3
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear membrane (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CRAT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA,IDA 2351134
GO:0005743 mitochondrial inner membrane IEA --
GO:0005777 peroxisome IDA,IEA 2351134
GO:0005782 peroxisomal matrix TAS --
GO:0005783 endoplasmic reticulum IEA --
genes like me logo Genes that share ontologies with CRAT: view

Pathways & Interactions for CRAT Gene

genes like me logo Genes that share pathways with CRAT: view

Pathways by source for CRAT Gene

Gene Ontology (GO) - Biological Process for CRAT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006631 fatty acid metabolic process IEA --
GO:0019254 carnitine metabolic process, CoA-linked IDA 2351134
GO:0033540 fatty acid beta-oxidation using acyl-CoA oxidase TAS --
genes like me logo Genes that share ontologies with CRAT: view

No data available for SIGNOR curated interactions for CRAT Gene

Drugs & Compounds for CRAT Gene

(67) Drugs for CRAT Gene - From: DrugBank, DGIdb, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
L-Carnitine Approved, Investigational Pharma Target 0
Acetylcarnitine Approved, Investigational Pharma 44
(3-Carboxy-2-(R)-Hydroxy-Propyl)-Trimethyl-Ammonium Experimental Pharma Target 0
Propanoyl-CoA Experimental Pharma 0
Coenzyme A Investigational Nutra Target 0

(53) Additional Compounds for CRAT Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • AcCoA
  • Acetyl coenzyme A
  • S-Acetyl-CoA
  • S-Acetyl-coenzyme A
  • Ac-CoA
  • 3,7,11,15-Tetramethyl hexadecanoyl CoA
  • 3,7,11,15-Tetramethyl hexadecanoyl coenzyme A
  • Phytanoyl CoA
  • Phytanoyl coenzyme A
  • Phytanoyl-coenzyme A
  • 3-Carboxy-N,N,N-trimethyl-2-(1-oxopropoxy)-1-propanaminium inner salt
  • O-Propionylcarnitine
  • Propionyl carnitine
  • (+/-)-propionylcarnitine chloride
  • (3-Carboxy-2-hydroxypropyl)trimethyl-hydroxide ammonium inner salt
genes like me logo Genes that share compounds with CRAT: view

Transcripts for CRAT Gene

Unigene Clusters for CRAT Gene

Carnitine O-acetyltransferase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CRAT

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CRAT Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b · 8c · 8d ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17a ·
SP1: -
SP2: - - - - - -
SP3: - - -
SP5: -
SP6: - -
SP7: -
SP8: - - -

ExUns: 17b · 17c

Relevant External Links for CRAT Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CRAT Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CRAT Gene

mRNA differential expression in normal tissues according to GTEx for CRAT Gene

This gene is overexpressed in Muscle - Skeletal (x5.0).

Protein differential expression in normal tissues from HIPED for CRAT Gene

This gene is overexpressed in Heart (10.9), Tonsil (8.3), and Liver (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CRAT Gene

Protein tissue co-expression partners for CRAT Gene

NURSA nuclear receptor signaling pathways regulating expression of CRAT Gene:


SOURCE GeneReport for Unigene cluster for CRAT Gene:


mRNA Expression by UniProt/SwissProt for CRAT Gene:

Tissue specificity: Mostly in skeletal muscle, less in heart, liver and pancreas, only weakly detectable in brain, placenta, lung and kidney.

Evidence on tissue expression from TISSUES for CRAT Gene

  • Liver(4.6)
  • Muscle(3.4)
  • Nervous system(2.8)
  • Skin(2.7)
  • Heart(2.5)
genes like me logo Genes that share expression patterns with CRAT: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for CRAT Gene

Orthologs for CRAT Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for CRAT Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CRAT 34 33
  • 99.36 (n)
(Bos Taurus)
Mammalia MGC142781 34
  • 93 (a)
  • 89.51 (n)
(Canis familiaris)
Mammalia CRAT 34 33
  • 89.3 (n)
(Mus musculus)
Mammalia Crat 16 34 33
  • 86.42 (n)
(Rattus norvegicus)
Mammalia Crat 33
  • 86.26 (n)
(Monodelphis domestica)
Mammalia CRAT 34
  • 85 (a)
(Ornithorhynchus anatinus)
Mammalia CRAT 34
  • 82 (a)
(Gallus gallus)
Aves CRAT 34 33
  • 73.91 (n)
(Anolis carolinensis)
Reptilia CRAT 34
  • 79 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia crat.1 33
  • 73.17 (n)
(Danio rerio)
Actinopterygii crata 34 33
  • 71.19 (n)
CRAT (2 of 3) 34
  • 67 (a)
cratb 34
  • 54 (a)
hmzeh0248 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9411 33
fruit fly
(Drosophila melanogaster)
Insecta CG5122 34 35 33
  • 50.65 (n)
Cha 35
  • 35 (a)
CG1041 34 35
  • 34 (a)
CG5265 34 35
  • 33 (a)
(Caenorhabditis elegans)
Secernentea B0395.3 34 35 33
  • 47.85 (n)
cha-1 35
  • 31 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AAR124C 33
  • 47.34 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CAT2 36 34 33
  • 42.6 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0A02123g 33
  • 41.08 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU08002 33
  • 52.86 (n)
sea squirt
(Ciona savignyi)
Ascidiacea Cin.15540 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.15540 33
Species where no ortholog for CRAT was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CRAT Gene

Gene Tree for CRAT (if available)
Gene Tree for CRAT (if available)
Evolutionary constrained regions (ECRs) for CRAT: view image

Paralogs for CRAT Gene

Paralogs for CRAT Gene

(7) SIMAP similar genes for CRAT Gene using alignment to 6 proteins:

  • F2Z2C5_HUMAN
  • H0Y4Z7_HUMAN
  • H7C0E1_HUMAN
genes like me logo Genes that share paralogs with CRAT: view

Variants for CRAT Gene

Sequence variations from dbSNP and Humsavar for CRAT Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs1000015998 -- 129,110,231(-) T/ genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000387986 -- 129,106,052(-) GTGGTG/GTG intron_variant
rs1001043969 -- 129,095,865(-) G/A intron_variant
rs1001104761 -- 129,103,971(-) C/G intron_variant
rs1001349921 -- 129,106,976(-) G/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CRAT Gene

Variant ID Type Subtype PubMed ID
nsv509323 CNV insertion 20534489
nsv818725 CNV gain 17921354
nsv831729 CNV loss 17160897

Variation tolerance for CRAT Gene

Residual Variation Intolerance Score: 83.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.19; 61.86% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CRAT Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CRAT Gene

Disorders for CRAT Gene

MalaCards: The human disease database

(4) MalaCards diseases for CRAT Gene - From: HGMD, OMIM, ClinVar, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
neurodegeneration with brain iron accumulation 8
  • nbia8
carnitine palmitoyltransferase ii deficiency, infantile
  • carnitine palmitoyltransferase ii deficiency with hypoketotic hypoglycemia
- elite association - COSMIC cancer census association via MalaCards
Search CRAT in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CRAT

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CRAT: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CRAT Gene

Publications for CRAT Gene

  1. Structural and mutational characterization of L-carnitine binding to human carnitine acetyltransferase. (PMID: 15099582) Govindasamy L … Wu D (Journal of structural biology 2004) 3 4 22 25 58
  2. Structure of human carnitine acetyltransferase. Molecular basis for fatty acyl transfer. (PMID: 12562770) Wu D … McKenna R (The Journal of biological chemistry 2003) 3 4 22 25 58
  3. Molecular cloning of cDNAs encoding human carnitine acetyltransferase and mapping of the corresponding gene to chromosome 9q34.1. (PMID: 7829107) Corti O … DiDonato S (Genomics 1994) 2 3 4 22 58
  4. Divergent sequences in the 5' region of cDNA suggest alternative splicing as a mechanism for the generation of carnitine acetyltransferases with different subcellular localizations. (PMID: 7945262) Corti O … Finocchiaro G (The Biochemical journal 1994) 3 4 22 58
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58

Products for CRAT Gene

Sources for CRAT Gene

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