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The carnitine acetyltransferase gene (CRAT): A characterization of porcine transcripts with insights into the 5’-end variants of mammalian transcripts and their possible sub-cellular localization


Carnitine acetyltransferase (CRAT) is an important enzyme for energy homeostasis and fat metabolism. We characterized the predicted full length cDNA sequence of the porcine CRAT gene. Its structure is very similar to that in humans with respect to the size and organization of the 14 exons. We demonstrated the existence of a porcine alternative transcript resulting from a partial intron-retention at the 5’ end of exon 2. To perform a comparison of the 5’ end variants of the mammalian CRAT gene, we analyzed the Genbank data, and here we propose a new 5’ variant for dog, rat and mouse. In contrast to other mammals where this variant encodes a shorter protein (−21 aa in human, mouse and rat, and −14 aa in dog), the pig variant encodes for a longer protein (+18 aa). In all mammalian species, variant 1 has a high probability of a preferential mitochondrial sub-cellular localization. Nevertheless, it is not evident, in particular in porcine and dog species, that the second variant is associated with a different sub-cellular specificity.



carnitine acetyltransferase


human chromosome 9


expression sequence tag


variant n°1


amino acid


reverse transcription PCR


  1. Anderson, R.C. Carnitine palmitoyltransferase: a viable target for the treatment of NIDDM? Curr. Pharm. Des. 4 (1998) 1–16.

    PubMed  CAS  Google Scholar 

  2. Wagman, A.S. and Nuss, J.M. Current therapies and emerging targets for the treatment of diabetes. Curr. Pharm. Des. 7 (2001) 417–450.

    PubMed  Article  CAS  Google Scholar 

  3. Jogl, G., Hsiao, Y.S. and Tong, L. Structure and function of carnitine acyltransferases. Ann. NY Acad. Sci. 1033 (2004) 17–29.

    PubMed  Article  CAS  Google Scholar 

  4. Van der Leij, F.R., Huijkman, N.C., Boomsma, C., Kuipers, J.R. and Bartelds, B. Genomics of the human carnitine acyltransferase genes. Mol. Genet. Metab. 71 (2000) 139–153.

    PubMed  Article  Google Scholar 

  5. Zeibig, J., Karlic, H., Lohninger, A., Damsgaard, R. and Smekal, G. Do blood cells mimic gene expression profile alterations known to occur in muscular adaptation to endurance training? Eur. J. Appl. Physiol. 95 (2005) 96–104.

    PubMed  Article  CAS  Google Scholar 

  6. Markwell, M.A., McGroarty, E.J., Bieber, L.L. and Tolbert, N.E. The subcellular distribution of carnitine acyltransferases in mammalian liver and kidney. A new peroxisomal enzyme. J. Biol. Chem. 248 (1973) 3426–3432.

    PubMed  CAS  Google Scholar 

  7. Muller, C., Denis, M., Gentzbittel, L. and Faraut, T. The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species. Nucleic Acids Res. 32 (2004) W429–434.

    PubMed  Article  CAS  Google Scholar 

  8. Emanuelsson, O., Nielsen, H., Brunak, S. and von Heijne, G. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol. 300 (2000) 1005–1016.

    PubMed  Article  CAS  Google Scholar 

  9. Small, I., Peeters, N., Legeai, F. and Lurin, C. Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 4 (2004) 1581–1590.

    PubMed  Article  CAS  Google Scholar 

  10. Humphray, S.J., Scott, C.E., Clark, R., Marron, B., Bender, C., Camm, N., Davis, J., Jenks, A., Noon, A., Patel, M., Sehra, H., Yang, F., Rogatcheva, M.B., Milan, D., Chardon, P., Rohrer, G., Nonneman, D., de Jong, P., Meyers, S.N., Archibald, A., Beever, J.E., Schook, L.B. and Rogers, J. A high utility integrated map of the pig genome. Genome Biol. 8 (2007) R139.

    PubMed  Article  Google Scholar 

  11. Stamm, S., Ben-Ari, S., Rafalska, I., Tang, Y., Zhang, Z., Toiber, D., Thanaraj, T.A. and Soreq, H. Function of alternative splicing. Gene 344 (2005) 1–20.

    PubMed  Article  CAS  Google Scholar 

  12. Leipzig, J., Pevzner, P. and Heber, S. The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome. Nucleic Acids Res. 32 (2004) 3977–3983.

    PubMed  Article  CAS  Google Scholar 

  13. Zhang, L., Tao, L., Ye, L., He, L., Zhu, Y.Z., Zhu, Y.D. and Zhou, Y. Alternative splicing and expression profile analysis of expressed sequence tags in domestic pig. Genomics Proteomics Bioinformatics 5 (2007) 25–34.

    PubMed  Article  CAS  Google Scholar 

  14. Modrek, B. and Lee, C.J. Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nat. Genet. 34 (2003) 177–180.

    PubMed  Article  CAS  Google Scholar 

  15. Gorodkin, J., Cirera, S., Hedegaard, J., Gilchrist, M.J., Panitz, F., Jorgensen, C., Scheibye-Knudsen, K., Arvin, T., Lumholdt, S., Sawera, M., Green, T., Nielsen, B.J., Havgaard, J.H., Rosenkilde, C., Wang, J., Li, H., Li, R., Liu, B., Hu, S., Dong, W., Li, W., Yu, J., Staefeldt, H.H., Wernersson, R., Madsen, L.B., Thomsen, B., Hornshoj, H., Bujie, Z., Wang, X., Bolund, L., Brunak, S., Yang, H., Bendixen, C. and Fredholm, M. Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biol. 8 (2007) R45.

    PubMed  Article  Google Scholar 

  16. Corti, O., DiDonato, S. and Finocchiaro, G. Divergent sequences in the 5’ region of cDNA suggest alternative splicing as a mechanism for the generation of carnitine acetyltransferases with different subcellular localizations. Biochem. J. 303 (Pt 1) (1994) 37–41.

    PubMed  CAS  Google Scholar 

  17. Emanuelsson, O., Brunak, S., von Heijne, G. and Nielsen, H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc. 2 (2007) 953–971.

    PubMed  Article  CAS  Google Scholar 

  18. Yura, K., Shionyu, M., Hagino, K., Hijikata, A., Hirashima, Y., Nakahara, T., Eguchi, T., Shinoda, K., Yamaguchi, A., Takahashi, K., Itoh, T., Imanishi, T., Gojobori, T., and Go, M. Alternative splicing in human transcriptome: functional and structural influence on proteins. Gene 380 (2006) 63–71.

    PubMed  Article  CAS  Google Scholar 

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Correspondence to Annie Robic.

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Robic, A., Faraut, T., Liaubet, L. et al. The carnitine acetyltransferase gene (CRAT): A characterization of porcine transcripts with insights into the 5’-end variants of mammalian transcripts and their possible sub-cellular localization. Cell Mol Biol Lett 14, 90–99 (2009).

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Key words

  • Pig
  • CRAT
  • mRNA
  • Alternative splicing
  • Mammals
  • Fat metabolism
  • Leader peptide