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Nucleic Acids Research 2006 34(Database Issue):D552-D555; doi:10.1093/nar/gkj064
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Nucleic Acids Research, 2006, Vol. 34, Database issue D552-D555
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

DBTGR: a database of tunicate promoters and their regulatory elements

Nicolas Sierro1,*, Takehiro Kusakabe2, Keun-Joon Park1, Riu Yamashita1, Kengo Kinoshita1,3 and Kenta Nakai1

1Human Genome Center, The Institute of Medical Science, University of Tokyo 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan 2Department of Life Science, Graduate School of Life Science, University of Hyogo 3-2-1 Kouto, Kamigori, Ako-gun, Hyogo 678-1297, Japan 3Structure and Function of Biomolecules, SORST, JST 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan

*To whom correspondence should be addressed. Tel: +81 3 5449 5131; Fax: +81 3 5449 5133; Email: nsierro{at}hgc.jp

Received August 11, 2005. Revised October 8, 2005. Accepted October 8, 2005.

The high similarity of tunicates and vertebrates during their development coupled with the transparency of tunicate larvae, their well-studied cell lineages and the availability of simple and efficient transgenesis methods makes of this subphylum an ideal system for the investigation of vertebrate physiological and developmental processes. Recently, the sequencing of two different Ciona genomes has lead to the identification of numerous genes. In order to better understand the regulation of these genes, a database was created containing information on regulation of tunicate genes collected from literature. It includes for instance information regarding the minimal promoter length, the transcription factors involved and their binding sites, as well as the localization of the gene expression. Additionally, binding sites for characterized transcription factors were predicted based on published in vitro recognition sites. Comparison of the promoters of homologous genes in different species is also provided to allow identification of conserved cis elements. At the time of writing, information about 184 promoters, containing 73 identified binding sites and >2000 newly predicted binding sites is available. This database is accessible at http://dbtgr.hgc.jp.


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[Abstract] [Full Text] [PDF]


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