Probes are tiled at an average resolution of 35 bp, as measured from the central position of adjacent 25-mer oligos, leaving a gap of approximately 10 bp between probes. Each promoter region covers approximately 7.5 kb upstream through 2.45 kb downstream of 5′ transcription start sites. For over 1,300 cancer-associated genes, coverage of promoter regions was expanded to include additional genomic content. This more extensive coverage spans from 10 kb upstream through 2.45 kb downstream of transcriptional start sites.
The array interrogates regions proximal to transcription start sites and contains probes for approximately 59 percent of CpG islands annotated by UCSC in NCBI human genome assembly (Build 34). The probes selected for the Human Promoter 1.0R Array are a subset of the probes used in the whole-genome ChIP array set, the GeneChip® Human Tiling 2.0R Array Set (P/N 900772).
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‘.
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‘) .
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.
Please acknowledge the following facts in your application software (or WEB page or any pertinent publications) using PLACE that:
PLACE has been constructed and maintained at NIAS (National Institute of Agrobiological Sciences).
PLACE was made available by the courtesy of NIAS without charge.
Please cite our publication (Higo et al. Nucleic Acids Research 27:297-300 (1999)).
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: Dr. Higo
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: Dr. Ugawa
or
support staff at: support (in urgent)
EPD
The Eukaryotic Promoter Database
Current Release 92
The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. [More details].
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