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Isolation and characterization of simple repeat sequences from the yellow fin sea bream Acanthopagrus latus (Sparidae)

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Abstract

We isolated DNA fragments containing various repetitive elements from the genome of a sea bream Acanthopagrus latus. Sequence analysis indicated that two fragments have particularly interesting features. Fragment AL87 contained a tetranucleotide repeat and a quasipalindromic sequence. Sequence comparison suggested that AL87 may be a part of a gene encoding a serine/threonine protein kinase, and that the quasipalindrome is situated at the junction of an intron and an exon. Moreover, the quasipalindrome is conserved in several other fishes, even though it has the potential to form a stem-loop structure at the splicing site. Fragment AL79 contained a minisatellite sequence made up of six 30-bp units in tandem. DNase I sensitivity assays and statistical analyses showed the repeat region to be flexible when subjected to bending stress. In addition, atomic force microscopic imaging of AL79 showed the presence of highly curved (kinked) segments flanking the repeat region. The structural features of these repetitive elements may be key factors facilitating the amplification of the repeats.

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Abbreviations

AFM:

atomic force microscopy

bp:

base pairs

GnRH:

gonadotropin-releasing hormone gene

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Authors and Affiliations

  1. Department of Life Sciences, Osaka Prefecture University College of Integrated Arts and Sciences, 1-1 Gakuencho, 599-8531, Sakai, Osaka, Japan

    Gamal E. Elmesiry, Sayaka Okai, Shingo Hokabe & Mikio Kato

  2. Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, 160-8582, Shinjuku-ku, Tokyo, Japan

    Shinsei Minoshima & Nobuyoshi Shimizu

  3. National Food Research Institute, 2-1-12 Kannondai, 305-8642, Tsukuba, Japan

    Shigeru Sugiyama, Tomoyuki Yoshino & Toshio Ohtani

  4. National Institute of Oceanography and Fisheries, beside Qaietbay Citadel, Alexandria, Elanfoshy, Egypt

    Gamal E. Elmesiry

  5. Photon Medical Research Center, Hamamatsu University School of Medicine, 431-3192, Handayama, Hamamatsu, Japan

    Shinsei Minoshima

Authors
  1. Gamal E. Elmesiry
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  2. Sayaka Okai
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  3. Shingo Hokabe
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  4. Shinsei Minoshima
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  5. Shigeru Sugiyama
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  6. Tomoyuki Yoshino
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  7. Toshio Ohtani
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  8. Nobuyoshi Shimizu
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  9. Mikio Kato
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Correspondence to Mikio Kato.

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Elmesiry, G.E., Okai, S., Hokabe, S. et al. Isolation and characterization of simple repeat sequences from the yellow fin sea bream Acanthopagrus latus (Sparidae). Mol Biol Rep 32, 117–126 (2005). https://doi.org/10.1007/s11033-004-0566-3

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  • DOI: https://doi.org/10.1007/s11033-004-0566-3

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