PLACE

A Database of Plant Cis-acting Regulatory DNA Elements

Important Note

Update of the data in the PLACE database was terminated in February 2007.

Dear Users, I am Curator of PLACE (http://www.dna.affrc.go.jp/PLACE/), a database of nucleotide sequence motifs found in PLAnt Cis-acting regulatory DNA Elements. This message is to inform you that the latest release (PLACE 30.0, 469 entries, Jan.8, 2007) will be the final one. That is, no update of the data is scheduled in the future, except for the possible correction of major error(s). The data collection for this database had been financially supported in part, from April 1996 to March 2001, by a grant from the Ministry of Agriculture, Forestry and Fisheries (MAFF) of Japan in the framework of the Research Project for New Recombinant DNA Techniques. The update of the database and the improvement of the analysis tools have been carried out by volunteers, without formal financial support specific for these purposes. I collect motifs and pertinent information by reading articles published in many journals for plant science, genetics, molecular biology, and biochemistry, etc. Although abstracts of the most of the papers are now available free of charge on line, I found reading the Results and Discussion sections essential to assess accurately the conclusion made by the authors and to extract important information for the database. After my departure from NIAS (previously known as NIAR) in March 2005, it became very difficult to have access to the most of these journals. I managed to borrow some plant-related journals from an acquaintance who personally subscribed them, but the subscription was terminated at the end of 2006. Therefore, to my regret, I decide to terminate the update of the database. We will try to maintain the PLACE web site as it is at NIAS for, at least, a couple of years or, if possible longer. The ftp site for downloading the data is available now, as before. Anyone interested in archiving these data are welcome to do so. I am very grateful to Dr. Y. Ugawa, a database specialist and the collaborator for PLACE from the beginning, former Head of MAFF DNA Bank/NIAR, and currently at Miyagi University of Education for his dedication and continuous encouragement, to Dr. Meena Sakharkar (Nanyang Technological University, Singapore) for kindly providing us with Web Signal Scan, and to a group of very talented Bioinformatics and Information Systems Specialists who have been dispatched to MAFF DNA Bank from Mitsubishi Space Software Co., LTD. Without their contribution, the construction, maintenance, updates and improvement of this database over a span of the past ten years was not possible. The database server has been, and is now maintained in MAFF DNA Bank at National Institute of Agrobiological Sciences (NIAS). I am very grateful to Dr. Y. Nagamura, current Head of MAFF DNA Bank, and his colleagues, for cooperation. If you have any question, please send e-mail to: kenhigo(at)jcom(dot)home(dot)ne(dot)jp Sincerely, Kenichi Higo, Ph.D. Curator of the PLACE database Ibaraki, Japan

What is PLACE?

PLACE is a database of motifs found in plant cis-acting regulatory DNA elements, all from previously published reports. It covers vascular plants only (But since April 2006, we changed the policy. See the release note for PLACE 26.0). In addition to the motifs originally reported, their variations in other genes or in other plant species reported later are also compiled. The PLACE database also contains a brief description of each motif and relevant literature with PubMed ID numbers. DDBJ/EMBL/GenBank nucleotide sequence databases accession numbers will be also included. See 'sample record'. List of entries can be found in 'place.dat'.

How to use

Information on cis-elements can be obtained by Keyword Search or SRS Keyword Search.

The query sequence can be searched for the presence of motifs identical with or similar to the previously reported cis-element motifs in the PLACE database by Signal Scan Search or by Homology Search (Sample of Signal Scan can be found in 'input.txt' and 'output.txt') .

You can submit batches of sequences to " Signal Scan Search, file upload" in FASTA format.

Reference to PLACE database:

Users are asked to cite the following article when publishing results, which have been obtained with the database described here.

Reference:
K. Higo, Y. Ugawa, M. Iwamoto and T. Korenaga (1999) Plant cis-acting regulatory DNA elements (PLACE) database:1999. Nucleic Acids Research Vol.27 No.1 pp. 297-300.

Copyright:

Copyright Kenichi Higo,1991-2006. All Rights Reserved.

Disclaimer:

We are responsible for accuracy of the database contents. If errors are brought to our attention, we will try to correct them. However, for contents and services available from this server, we do not warrant or assume any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed.

License for the PLACE database for commercial use:

For the time being, PLACE is free on the following conditions.

1. Please acknowledge the following facts in your application software (or WEB page or any pertinent publications) using PLACE that:
   1. PLACE has been constructed and maintained at NIAS (National Institute of Agrobiological Sciences).
   2. PLACE was made available by the courtesy of NIAS without charge.
2. Please cite our publication (Higo et al. Nucleic Acids Research 27:297-300 (1999)).
3. Also please inform your client that the PLACE is also available at our WEB site (URL http://www.dna.affrc.go.jp/PLACE/) free of charge.

If you accept these conditions, please send us a written notice via E-mail.

Academic use: Please note that PLACE is free for academic user.

Privacy Policies:

We collects user's information through standard Web logs for the purpose of site management. We store top and second level domain name for foreign domain, adding third domain name for Japanese domain.

We are not collecting keywords, sequences submitted for PLACE database query. Some results are kept one week for future browsing by the submitter. In this case, results are guarded from others view by generating random ID. For other results, all are purged when the process are done. We will not disclose keywords, sequences and results for others.

Contacting Information:

Database Contents:

Please send comments, corrections and requests for additional information to Dr. Higo by e-mail at:
or
Fax to +81-29-838-7408
Dr. Kenichi Higo
c/o Dr. Yoshiaki Nagamura
National Institute of Agrobiological Sciences
1-2 Kannondai 2-chome, Tsukuba, Ibaraki 305-8602
Japan

Web pages, server trouble, software inquiry:

Please send comments and requests for web pages, software and servers to Dr. Ugawa by e-mail at:
or
support staff at: (in urgent)

Other infomation:

Other information (History, Access logs...) can be found in
PLACE information page and Frequently Asked Questions page.

Plant Promoter and Regulatory Element Resources:

• AGRIS (http://arabidopsis.med.ohio-state.edu/)
  Currently contains two databases, AtcisDB (Arabidopsis thaliana cis-regulatory database) and AtTFDB (Arabidopsis thaliana transcriptionfactor database).
• AthaMap (http://www.athamap.de/)
  A genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana.
• AtProbe (http://exon.cshl.org/cgi-bin/atprobe/atprobe.pl)
  The Arabidopsis thaliana promoter binding element database, an aid to find binding elements and check data against the primary literature.
• DATF: Database of Arabidopsis Transcription Factors (http://datf.cbi.pku.edu.cn/)
  The Database of Arabidopsis Transcription Factors (DATF) contains known and predicted Arabidopsis transcription factors with sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and Nuclear Location Signals.
• DoOP: Databases of Orthologous Promoters (http://doop.abc.hu/)
  A database containing orthologous clusters of promoters from Homo sapiens, Arabidopsis thaliana and other organisms.
• GRASSIUS (http://grassius.org/)
  A public web resource composed by a collection of databases, computational and experimental resources that relate to the control of gene expression in the grasses, and their relationship with agronomic traits. GRASSIUS currently contains regulatory information on maize, rice, sorghum and sugarcane.
• PlantCare (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/)
  Database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences.
• PlantProm DB (http://linux1.softberry.com/berry.phtml?topic=plantprom&group=data&subgroup=plantprom)
  Database with annotated, non-redundant collection of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start sites (TSS) from various plant species.
• PlantTFDB: Plant Transcription Factor Database (http://plntfdb.bio.uni-potsdam.de/v2.0/)
  An integrative plant transcription factor database that provides a web interface to access large (close to complete) sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa(rice), Chlamydomonas reinhardtii and Ostreococcus tauri.
• PPDB (Plant Promoter DB) (http://ppdb.gene.nagoya-u.ac.jp/cgi-bin/index.cgi)
  Database that provides transcription start sites (TSS) and other structural information for Arabidopsis and rice promoters.
• Transfac (http://www.gene-regulation.com/pub/databases.html#transfac)
  Database on eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles. Commercial site.