PLACE

2016/08/22

Web Site: http://www.dna.affrc.go.jp/PLACE/
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/place/

The database of motifs found in plant cis-acting regulatory DNA elements based on previously published reports on vascular plants.

README Content

  1. Database Component
  2. Data Description
  3. License
  4. Update History
  5. Literature
  6. Contact address

1. Database Component

  1. README
  2. Main
  3. Reference
  4. Raw Data (ASCII format)
  5. Raw Data (Signal scan format)
  6. Raw Data (FASTA format)
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "PLACE" data.
File README_e.html(English)
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2.2 Main

Data name Main
Description of data contents Nucleotide sequence information. For each "Main" entry, there may be one or more "Reference" entries available.
File place_main.zip (48.9 KB)

Data items are the following:
Data itemDescription
Identifier Identifier
Accession number Accession number
Date (operation) author Date (operation) author
Description Description (regulation, gene, transacting factor, etc.)
Keywords Keywords
Species Species
Sequence Sequence of the cis-acting regulatory DNA element.

For the cis-acting elements the following symbols were used as codes representing A, G, C or T.

B: C, G or T
D: A, G or T
H: A, C or T
K: G or T
M: A or C
N: A, C, G or T
R: A or G
S: C or G
V: A, C or G
W: A or T
Y: C or T

(Mar. 31, 1997)
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2.3 Reference

Data name Reference
Description of data contents Literature information. For each "Main" entry, there may be one or more "Reference" entries available.
File place_reference.zip (52.5 KB)

Data items are the following:
Data itemDescription
Identifier Identifier
Authors Authors
Title Title
Literature data Literature data
Criteria Criteria (DNase I footprinting study / Chemical modifications / Gel retardation assay / homology / other)
PubMed PubMed ID
GenBank DDBJ/EMBL/GenBank accession number
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2.4 Raw Data (ASCII format)

Data name Raw Data (ASCII format)
Description of data contents The document in EMBL-like format that contains brief descriptions of individual cis-elements.
File place.seq.zip (110 KB)

Data items are the following:
Data itemDescription
ID Identifier
AC Accession number
DT Date (operation) author
DE Description (regulation, gene, transacting factor, etc.)
KW Keywords
OS Species
RA Authors
RT Title
RL Literature data
RC Criteria (DNase I footprinting study / Chemical modifications / Gel retardation assay / homology / other)
RD External Database (MEDLINE number or DDBJ/EMBL/GenBank accession number)
SQ Sequence of the cis-acting regulatory DNA element.

For the cis-acting elements the following symbols were used as codes representing A, G, C or T.

B: C, G or T
D: A, G or T
H: A, C or T
K: G or T
M: A or C
N: A, C, G or T
R: A or G
S: C or G
V: A, C or G
W: A or T
Y: C or T

(Mar. 31, 1997)
XX Data item delimiter
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2.5 Raw Data (Signal scan format)

Data name Raw Data (Signal scan format)
Description of data contents The document in Signal scan format that contains brief descriptions of individual cis-elements.
File place.dat.zip (7.4 KB)

Data items are the following:
Data itemDescription
Old data ID Identifier in old data (r01.1 or earlier : Identifier, r02.0 or later : "unknown")
ID Identifier (r01.1 or earlier : Name, r02.0 or later : Identifier)
Sequence Sequence of the cis-acting regulatory DNA element.

For the cis-acting elements the following symbols were used as codes representing A, G, C or T.

B: C, G or T
D: A, G or T
H: A, C or T
K: G or T
M: A or C
N: A, C, G or T
R: A or G
S: C or G
V: A, C or G
W: A or T
Y: C or T

(Mar. 31, 1997)
Sequence length Sequence length
Accession number Accession number
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2.6 Raw Data (FASTA format)

Data name Raw Data (FASTA format)
Description of data contents The document in FASTA format that contains brief descriptions of individual cis-elements.
File place.fasta.zip (36.3 KB)

Data items are the following:

For the cis-acting elements the following symbols were used as codes representing A, G, C or T.

B: C, G or T
D: A, G or T
H: A, C or T
K: G or T
M: A or C
N: A, C, G or T
R: A or G
S: C or G
V: A, C or G
W: A or T
Y: C or T

(Mar. 31, 1997)
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3. License

Last updated : 2016/08/22

You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.

Creative Commons License

The license for this database is specified in the Creative Commons Attribution-Share Alike 2.1 Japan.
If you use data from this database, please be sure attribute this database as follows: "PLACE © National Institute of Agrobiological Sciences licensed under CC Attribution-Share Alike 2.1 Japan".

The summary of the Creative Commons Attribution-Share Alike 2.1 Japan is found here.

With regard to this database, you are licensed to:

  1. freely access part or whole of this database, and acquire data;
  2. freely redistribute part or whole of the data from this database; and
  3. freely create and distribute database and other derivative works based on part or whole of the data from this database,

under the license, as long as you comply with the following conditions:

  1. You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any derivative work.
  2. You must distribute any derivative work based on part or whole of the data from this database under the license.
  3. You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.

2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
National Institute of Agrobiological Sciences
E-mail: bi[at]ml[dot]affrc[dot]go[dot]jp

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4. Update History

DateUpdate contents
2016/08/22 The contact address is changed.
2014/10/20 The URLs of the database maintenance site and the portal site are changed.
2014/07/17 PLACE English archive site is opened.
1997/03/31 PLACE (http://www.dna.affrc.go.jp/htdocs/PLACE/) is opened.
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5. Literature

Kenichi Higo*, Yoshihiro Ugawa and Masao Iwamoto
PLACE: A database on plant cis-acting regulatory DNA elements (A preliminary report)
5th International Society for Plant Molecular Biology, 1997, Abst. #891

Kenichi Higo*, Yoshihiro Ugawa, Masao Iwamoto and Hiromi Higo
PLACE: a database of plant cis-acting regulatory DNA elements
Nucleic Acids Research, 1998, Vol.26, No.1 :358-359
PMID: 9399873

Kenichi Higo*, Yoshihiro Ugawa, Masao Iwamoto and Tomoko Korenaga
Plant cis-acting regulatory DNA elements (PLACE) database: 1999
Nucleic Acids Research, 1999, Vol.27, No.1 :297-300
PMID: 9847208

6. Contact address

When you have any question about "PLACE", contact the following:

2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
National Institute of Agrobiological Sciences
E-mail: bi[at]ml[dot]affrc[dot]go[dot]jp

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