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.

An announcement on top page

Updates:

We try to update the database every three or four months. But we cannot promise it. Sometimes we cannot find any new cis-element motif to add after surveying papers published during two- to three-month period. In such case, we await one or two more months.

Release notes:

===PLACE 30.0, 469 entries, Jan.8, 2007=== Five new motifs were added. Information obtained from literature published in 2006 and before were added to the records previously registered to the PLACEdb. ===PLACE 29.0, 464 entries, Oct.9, 2006=== Six new motifs were added. Information obtained from literature published in 2006 and before were added to the records previously registered to the PLACEdb. ===PLACE 28.0, 458 entries, Aug.04, 2006=== Five new motifs were added. Information obtained from literature published in 2006 and before were added to the records previously registered to the PLACEdb. ===PLACE 27.0, 453 entries, May.31, 2006=== Two new motifs were added. Information obtained from literature published in 2006 and before were added to the records previously registered to the PLACEdb. ===PLACE 26.1, 451 entries, Apr.12, 2006=== Contamination of the record S000042 DE field to other records were fixed. This bug was found in releases 25.0, 25.0.1, 26.0. All these users are recommended to use 26.1. Sorry. ===PLACE 26.0, 451 entries, Apr.12, 2006=== Important notice!! Almost all the cis-element motifs so far compiled in PLACEdb were those found in vascular plants. We now start collecting motifs found in Chlamydomonas as well. The statement "It covers vascular plants only" found in "What is PLACE?" page need to be modified. Two new motifs found in Chlamydomonas reinhardtii were added. Information obtained from literature published in 2005 and before were added to the records previously registered to the PLACEdb. ===PLACE 25.0.1, 449 entries, Feb.11, 2006=== Part of DE lines apeared before SQ line. Deleted. ===PLACE 25.0, 449 entries, Feb.08, 2006=== One new motif was added. Information obtained from literature published in 2005 and before were added to the records previously registered to the PLACEdb. S000333 was removed because the motif sequence and ID were identical to those of S000313. Reference and other information in S000333 were moved to S000313. ===PLACE 24.0, 449 entries, Dec.04, 2005=== 10 new motifs were added. 9 of them were computationally identified and published in 2003. We did not include these because of our previous policy to exclude motifs without experimental evidence. We recently abandoned this policy, and thus added these motifs to the database (S000482-S000490). 3 references published on line in 2005 were added to the records previously registered to the PLACEdb. Other new information added. ===PLACE 23.1, 439 entries, Nov.11, 2005=== A user kindly informed us on error in the motif sequences of S000322 and S000323. S000322 (LS7ATPR1): The motif sequence previously shown was that of LS5. S000323 (LS5ATPR1): The motif sequence previously shown was that of LS7. The correction were made. We are very sorry for the error. ===PLACE 23.0, 439 entries, Nov.10, 2005=== Eight new motifs were added. Six references, four of them published in 2005, were added to the records previously registered to the PLACEdb. New information added. ===PLACE 22.0, 431 entries, Oct.27, 2005=== No addition of new motifs. Seven references, six of them published in 2005, were added to the records previously registered to the PLACEdb. New information added. ===PLACE 21.0, 431 entries, Aug.17, 2005=== Four new motifs were added. Several new references published in 2005, in addition to those published before, were added to the records previously registered to PLACEdb. ===PLACE 20.0, 427 entries, Apr.24, 2005=== Nine new motifs were added. Several new references published in 2005, in addition to those published before, were added to the records previously registered to PLACEdb. Previously we had collected only those motif sequence which had some experimental evidence, but from the PLACE rel. 20 on, we will include "consensus sequence" as well. These consensus sequences will be indicated in the RC as either "consensus sequence" or "in silico" or both to indicate the facts. ===PLACE 19.0, 418 entries, Mar.29, 2005=== Two new motifs were added. Several new references published in 2004, in addition to those published before, were added to the records previously registered to PLACEdb. ===PLACE 18.0, 416 entries, Nov.29, 2004=== Nine new motifs were added. Most of them were reported in 2004. Several new references published in 2004, in addition to those published before, were added to the records previously registered to PLACEdb. ===PLACE 17.0, 407 entries, Aug.19, 2004=== Four motifs were added. All were published in 2004. Several new references published in 2004 were added to the records previously registered to PLACEdb. ===PLACE 16.0, 403 entries, Apr.13, 2004=== One new motif was added. S000410 was deleted because the motif sequence and the reference were identical to those of S000431. Several new references published in 2004 were added to the records previously registered to PLACEdb. ===PLACE 15.0.1, 403 entries, Jan.30, 2004=== ^K control code contamination removed. ===PLACE 15.0, 403 entries, Jan.28, 2004=== 13 new motifs, the most of them published in 2003, were added. ===PLACE 14.0, 390 entries, Sep.30, 2003=== Ten new motifs, the most of them published in 2003, were added. ===PLACE 13.0, 380 entries, Jun.03, 2003=== Fifteen new motifs, all published in 2003, were added. ===PLACE 12.0, 365 entries, Dec.09, 2002=== Four new motifs and 14 references were added. ===PLACE 11.0, 361 entries, Sep.10, 2002=== Five new motifs and several references were added. ===PLACE 10.0, 356 entries, May.27, 2002=== Five new motifs and several references were added. ===PLACE 9.1, 351 entries, Apr.24, 2002=== Several motifs were deleted because these motifs were found in animal, not in plant. ===PLACE 9.0, 362 entries, Mar.12, 2002=== Seven new motifs and several references were added. ===PLACE 8.1, 355 entries, Nov.05, 2001=== Errors were corrected. Tissues where pertinent genes are expressed were added to the keyword (kw) fields of the many entries. ===PLACE 8.0, 355 entries, Sep.25, 2001=== PLACE 8.0 contains 355 entries. The latest entry is the accession number S000385. Many new literature and new findings were added to the previous entries. We were able to add S000385 ("evening element") because one ofthe users kindly informed us that this interesting element was missing. We welcome comments for improving this database. ===PLACE 7.1, 340 entries, Jul.13, 2001=== Ten literature and new findings were added to previous entries. ===PLACE 7.0, 340 entries, Mar.15, 2001=== PLACE 7.0 contains 340 records. The latest entry is accession number S000370. Many motifs reported in literatures published in year 2000 were included. Many new literature and new findings were added to previous entries. Errors, found and reported to us by users, were corrected. We appreciate their helpful comments. ===PLACE 6.01, 319 entries, Oct.02, 2000=== S000139 was deleted because the motif was identical to that of S000133. ID, DE, KW, OS for S000098 was corrected because the presence of this motif in the wheat peroxidase was not supported by experimental evidence. CArG and other new motifs were added. ===PLACE Release 5.1, 288 entries, Mar.07, 2000=== Errors corrected. ===PLACE Release 5.0, 288 entries, Feb.21, 2000=== Twenty-seven new motifs and pertinent references were added. Several references were added to the previously registerd motifs. ===PLACE Release 4.1, 251 entries, Nov.10, 1999=== One motif (S000214) was deleted. Two new motifs and relevant references were added. ===PLACE Release 4.0, 250 entries,Oct.19, 1999=== Forty-two new motifs and more than 60 references, including those published in 1999, were added. Some DE fields were updated. ===PLACE Release 3.1, 208 entries, Jun.18, 1998=== One PubMed ID added, PubMed ID modified. ===PLACE Release 3.0, 208 entries, May.25, 1998=== Many MYB-related factor binding sites were added. ===PLACE Release 2.3, 146 entries, Mar.25, 1998=== S000132 Reference modified. ===PLACE Release 2.2, 146 entries, Jan.16, 1998=== GenBank accession number added. ===PLACE Release 2.1, 146 entries, Oct.14, 1997=== PubMed IDs to (almost) all references. Scientific names of plant included. ===PLACE Release 2.0, 146 entries, Oct.09, 1997=== Release 2.0 contains 146 entries. "cold responsive element (CCGAC)" and others are added. PubMed IDs are missing in new records. ===PLACE Release 1.1.2, 102 entries, Sep.09, 1997=== No change in motif data. place.dat data alignment was changed from "DE+ID" to "unknown+ID". ===PLACE Release 1.1.1, 102 entries, Aug.25, 1997=== No change in motif data. Accession Number was changed to S+6 digits. ===PLACE Release 1.1, 102 entries, Aug.20, 1997=== Release 1.1 contains 103 motifs, because although new motifs were added some wereremoved because the original literature were not available by the time of release. Most of these and other empty fields were filled in Release 1.1. PubMed ID added. ===PLACE Release 1.0, 114 entries. Mar.31, 1997=== Release 1.0 is a test version. Some original literature in the reference are missing, and review article(s), some of them in Japanese, is cited.

Release notes (same documents) are also available on the FTP server:
http://ftp.dna.affrc.go.jp/pub/dna_place/relnotes.txt

Database Format, Fields and Symbols:

PLACE contains a brief description of each cis-element as document in EMBL-like format (See 'sample_seq.txt' for sample record). File formats and fields used in PLACE database are described in 'fields.txt' . The experimental evidence for each motif is given in the document in the field RC (Reference Criteria). The motifs compiled here are therefore not necessarily those of rigorously examined. User of this database should be aware of this fact, and should read original report(s) shown in the document(s) of each motif before using any of the results obtained for publication. The symbols used in addition to A, G, C, or T for these cis-acting element motifs are described in 'symbols.txt'.

Download Raw Data:

ASCII format (400KBytes)
http://ftp.dna.affrc.go.jp/pub/dna_place/place.seq
Signal_scan format (40KBytes)
http://ftp.dna.affrc.go.jp/pub/dna_place/place.dat
FASTA format (150KBytes)
http://ftp.dna.affrc.go.jp/pub/dna_place/place.fasta

To Save as a file, Select "Save as" menu in "File" menu in your browser.

All other raw data including older release can be downloadable by anonymous FTP from the FTP server:
http://ftp.dna.affrc.go.jp/pub/dna_place/
ftp://ftp.dna.affrc.go.jp/pub/dna_place/

Web-Page and Server Function Updates:

==2007== Jan.24 WAIS intaface has changed to use SFGate. ==2006== Feb.10 place.tab DE fields extended. Jan.09 Sight Design change by using CSS. FAQs added by ugawa. Jan.01 claris works file DE field multi column, extended. ==2005== Oct.31 SRS Keyword Search Menu added. May.27 Mail address of Dr. Higo was changed. May.23 A text output option is added to PLACE Signal Scan Search (File upload). This function was provided by support staff. ==2004== Jan.30 A work file "place.tab" in ftp directory renamed to ".place.tab" Jan.15 Download Log shows sum of FTP and HTTP. ==2003== Oct.30 "View and Download Raw Data" description added in index.html. Oct.27 FTP link to raw data redirect to HTTP link. Sep.30 Result link to NCBI Entrez/PubMed points new URL. ==2002== Nov.7 "Licence for the PLACE database for commercial use" added. Mar.27, Web Signal Scan Search(File upload) added. ==2001== Feb.21, Institute name, Fax and E-mail address of Higo was changed. ==2000== Feb.21, E-mail address of Ugawa was changed. ==1999== Feb.15, Reference information for new PLACE publication to NAR added. Ugawa. ==1998== Sep.7, Signal ScanWeb page updated (Citing infomation). Jul.8, PLACE WAIS Keyword search can search 'a-box' (hyphen includeing word). May.25, Release 3.0 change. Apr.21, PLACE Refernce NAR URL changed. OLD http://www.oup.co.uk/nar/Volume_26/Issue_01/html/gkb021_gml.html NEW http://www.oup.co.uk/nar/Volume_26/Issue_01/gkb021_gml.abs.html Mar.25, Signal Scan Sample output file changed. Feb.16, Results of queries have links to PLACE entries and PubMed server. Jan.19, Release 2.2 change. Reference information for PLACE publication to NAR added. Ugawa. ==1997== Nov.14, Reference information for PLACE (in press) added. Ugawa. Nov.07, FTP Server log page created. Ugawa. Nov.06, 'relnotes.txt' on ftp directory created. Ugawa. Oct.16, Release 2.1 change. Length limit note for submitting sequence in Web Signal Scan. Ugawa.Oct.09, Release 2.0 change. Ugawa. Sep.09, Release 1.1.2 change. Ugawa. Aug.20, Release 1.1 available. Log Pages added. Ugawa. Aug.13, Web Signal Scan Page added, Web Page Renewal. Ugawa. Mar.03, First version. Kenichi Higo. ==1997==

Server Access logs:

Web Page Access Logs (including Signal Scan)
Web Signal Scan Usage Logs (Signal Scan only)
FTP Server Logs (dna_place directory)

History of PLACE:

PLACE is based on an in-house database of plant DNA cis-elements compiled since 1991 by Dr. K.Higo (NIAS) for his own research. These cis-elements have been extracted from review articles as well as original literature. Since April 1996, the database construction has been supported through a grant given by the Ministry of Agriculture, Forestry and Fisheries (MAFF) of Japan in the framework of the Research Project for New Recombinant DNA Techniques. The database system was created by Dr. Y.Ugawa and Dr. K.Higo, became online in Mar.1997. Web Signal Scan was provided by Ms. Meena Sakharkar in Aug. 1997. The database server is maintained in MAFF DNA Bank at National Institute of Agrobiological Sciences in collaboration with Dr. Y. Nagamura and his colleagues.

Acknowledgements:

This work had been supported by the Ministry of Agriculture, Forestry and Fisheries (MAFF) of Japan in the framework of the Research Project for New Recombinant DNA Techniques in 1996.