RARTF: database and tools for complete sets of Arabidopsis transcription factors.
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.
Iida
Kei
K
Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Japan. k_iida@nagahama-i-bio-ac.jp
Seki
Motoaki
M
Sakurai
Tetsuya
T
Satou
Masakazu
M
Akiyama
Kenji
K
Toyoda
Tetsuro
T
Konagaya
Akihiko
A
Shinozaki
Kazuo
K
D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D018076:DNA, Complementary / Q000235:genetics / Q000378:metabolism; D030561:Databases, Nucleic Acid; D018745:Genome, Plant; D008969:Molecular Sequence Data; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
D029681:Arabidopsis Proteins; D018076:DNA, Complementary; D014157:Transcription Factors