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Related Concept Videos

The Eukaryotic Promoter Region02:40

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Plant Promoter Analysis: Identification and Characterization of Root Nodule Specific Promoter in the Common Bean
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ppdb: plant promoter database version 3.0.

Ayaka Hieno1, Hushna Ara Naznin, Mitsuro Hyakumachi

  • 1The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu City, Gifu 501-1193 Japan, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu City, Gifu 501-1193 Japan, Center for Sustainable Resource Science, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 Japan, Advanced Science Research Center, Kanazawa University, Takaramachi 13-1. Kanazawa City, Ishikawa 920-0934, Japan, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki City, Aichi 444-8585 Japan, Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki 444-8585, Japan, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D79104 Freiburg, Germany, Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Strasse 9, 35043 Marburg, Germany and Graduate School of Environmental Life Science, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522 Japan.

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|November 7, 2013
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Summary
This summary is machine-generated.

The updated Plant Promoter Database (PPDB 3.0) now includes more plant genomes and significantly expanded transcription start site data for Arabidopsis thaliana. This enhances promoter analysis and understanding of gene regulation in plants.

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Area of Science:

  • Plant molecular biology
  • Genomics
  • Bioinformatics

Background:

  • The Plant Promoter Database (PPDB) provides critical information on plant transcriptional regulatory elements.
  • Previous versions offered data on transcription start sites (TSSs) and core promoter structures.
  • Understanding promoter elements is essential for deciphering gene regulation.

Purpose of the Study:

  • To update and expand the Plant Promoter Database (PPDB) to version 3.0.
  • To enhance the scope of plant species and the depth of promoter information.
  • To improve the identification and annotation of transcriptional regulatory elements.

Main Methods:

  • Inclusion of new plant genomes (Arabidopsis thaliana, rice, Physcomitrella patens, poplar).
  • Addition of 34 million new TSS tag sequencing data for A. thaliana.
  • Integration of microarray data for predicting regulatory element groups (REGs).

Main Results:

  • PPDB version 3.0 offers expanded genomic coverage and significantly increased TSS data for A. thaliana.
  • The database now covers approximately 27,000 A. thaliana genes with finer promoter positioning.
  • New REG annotations provide insights into the putative physiological roles of regulatory elements.

Conclusions:

  • PPDB 3.0 represents a substantial advancement in plant promoter analysis resources.
  • The enhanced data facilitates more accurate promoter identification and functional prediction.
  • This updated database supports research in plant gene regulation and functional genomics.