Skip Navigation



Nucleic Acids Research Advance Access published online on October 18, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm785
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1418K) Freely available
Right arrow Screen PDF (556K) Freely available
Right arrowOA All Versions of this Article:
36/suppl_1/D977    most recent
gkm785v2
gkm785v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Yamamoto, Y. Y.
Right arrow Articles by Obokata, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Yamamoto, Y. Y.
Right arrow Articles by Obokata, J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

ppdb: a plant promoter database

Yoshiharu Y. Yamamoto and Junichi Obokata*

Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan

*To whom correspondence should be addressed. Tel/Fax: +81-52-789-3083; Email: obokata{at}gene.nagoya-u.ac.jp

Received August 14, 2007. Revised September 13, 2007. Accepted September 17, 2007.

ppdb (http://www.ppdb.gene.nagoya-u.ac.jp) is a plant promoter database that provides promoter annotation of Arabidopsis and rice. The database contains information on promoter structures, transcription start sites (TSSs) that have been identified from full-length cDNA clones and also a vast amount of TSS tag data. In ppdb, the promoter structures are determined by sets of promoter elements identified by a position-sensitive extraction method called local distribution of short sequences (LDSS). By using this database, the core promoter structure, the presence of regulatory elements and the distribution of TSS clusters can be identified. Although no differentiation of promoter architecture among plant species has been reported, there is some divergence of utilized sequences for promoter elements. Therefore, ppdb is based on species-specific sets of promoter elements, rather than on general motifs for multiple species. Each regulatory sequence is hyperlinked to literary information, a PLACE entry served by a plant cis-element database, and a list of promoters containing the regulatory sequence.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
B. Hedtke and B. Grimm
Silencing of a plant gene by transcriptional interference
Nucleic Acids Res., June 1, 2009; 37(11): 3739 - 3746.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
S. M. Brady and N. J. Provart
Web-Queryable Large-Scale Data Sets for Hypothesis Generation in Plant Biology
PLANT CELL, April 1, 2009; 21(4): 1034 - 1051.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
A. Yilmaz, M. Y. Nishiyama Jr., B. G. Fuentes, G. M. Souza, D. Janies, J. Gray, and E. Grotewold
GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses
Plant Physiology, January 1, 2009; 149(1): 171 - 180.
[Abstract] [Full Text] [PDF]

Home page
 Plant Cell PhysiolHome page
M. Mihara, T. Itoh, and T. Izawa
In Silico Identification of Short Nucleotide Sequences Associated with Gene Expression of Pollen Development in Rice
Plant Cell Physiol., October 1, 2008; 49(10): 1451 - 1464.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.