Journal of Ocean University of China

, Volume 5, Issue 1, pp 12–20 | Cite as

Existence of microsatellites in expressed sequence tags of common carp (Cyprinus carpio L.) available in GenBank dbEST database

  • Hu Jingjie
  • Wang Xiaolong
  • Hu Xiaoli
  • Bao Zhenmin
Research Papers


Common carp expressed sequence tags (ESTs) were analyzed for the existence of microsatellites, or simple sequence repeats (SSRs). In the NCBI dbEST database, a total of 10612 sequences were registered before December 31, 2004. A complete search of 2–6 nucleotide microsatellites resulted in the identification of 513 SSR-containing ESTs, accounting for 4.8% of the total. Cluster analysis indicated that 73 sequences of SSR-containing ESTs fell into 27 groups and the remaining 440 ESTs were indenpendent. A total of 467 unique SSR-containing ESTs were identified. These EST-SSRs contained a variety of simple sequence types, and di- and tri-nucleotide repeats were the most abundant, accounting for 42.1% and 27.9% of the whole, respectively. Of the dinucleotide repeats, CA/TG was the most abundant, followed by GA/TC. BLASTx search showed that 38.1% of the SSR loci could be associated with genes or proteins of known or unknown function. BLASTx searches of SSR-containing ESTs also showed high frequencies (98/179) of hits on zebrafish sequences.

Key words

common carp microsatellites ESTs data mining 


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Copyright information

© Journal of Ocean University of China and Science Press 2006

Authors and Affiliations

  • Hu Jingjie
    • 1
  • Wang Xiaolong
    • 1
  • Hu Xiaoli
    • 1
  • Bao Zhenmin
    • 1
  1. 1.Laboratory of Marine Genetics and Breeding, Division of Life Science and BiotechnologyOcean University of ChinaQingdaoP. R. China

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