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

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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