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DNA Research 2005 12(4):247-256; doi:10.1093/dnares/dsi011
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© The Author 2006. Kazusa DNA Research Institute
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@oxfordjournals.org

RARTF: Database and Tools for Complete Sets of Arabidopsis Transcription Factors

Kei Iida1,2,4,*, Motoaki Seki1,3, Tetsuya Sakurai1,2 6, Masakazu Satou1,2 6, Kenji Akiyama1,2 6, Tetsuro Toyoda2, Akihiko Konagaya2 and Kazuo Shinozaki1,3,5 6

1Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
2Genomic Knowledge Base Research Team, Bioinformatics Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
3Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute 3-1-1 Koyadai, Tsukuba 305-0074, Japan
4Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology 1266 Tamura-cho, Nagahama 526-0829, Japan
5CREST, Japan Science and Technology Corporation (JST) Japan

More than 5% of all genes in the Arabidopsis thaliana genome have been assumed to code for transcription factors. However, it has been difficult to accurately identify them. To construct proper sets of transcription factors, we used PSI-BLAST and InterProScan, and also checked several families manually. Especially to determine major Arabidopsis transcription factors (MYB, AP2/EREBP, bHLH, NAC, MADS, bZIP, WRKY), we compared the PSI-BLAST search results with those in recent reports. Finally, we identified 1968 proteins as transcription factors (7.4% of all Arabidopsis genes). We established a database named RARTF (RIKEN Arabidopsis Transcription Factor database, http://rarge.gsc.riken.jp/rartf/) based on the identified transcription factors. In RARTF, we provide information on the functional motif of transcription factors, full-length cDNAs, alternative pre-mRNA splicing events and Ac/Ds transposon-tagged mutants. We also provide expression profiles of 400 transcription factor genes in six experiments. We will report expression profiles of all transcription factor genes in various plant tissues under various stress and hormone conditions in the near future.

Key words: Arabidopsis thaliana; transcription factor; database; full-length cDNA; expression profile

*To whom correspondence should be addressed. Tel. +81-749-64-8100, Fax. +81-749-64-8126, E-mail: k_iida{at}nagahama-i-bio-ac.jp

6Present address: RIKEN Plant Science Center (PSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan

Communicated by Satoshi Tabata


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