Mutant Panel

2023/06/27

Web Site: https://tos.nias.affrc.go.jp/

Database of rice (Nipponbare) Tos17 insertion mutant lines

README Content

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

1. Database Component

  1. README
  2. plant
  3. def_phenotype
  4. phenotype
  5. seq
  6. tos17_insertion
  7. flanking
  8. photograph
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2. Data Description

2.1 README

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

Data name plant
Description of data contents

Phenotype description of Tos17 insertion lines
File tos17_plant.csv.zip (1.4 MB)

Data items are the following:
Data itemDescription
plant Line name
sub Individual number
date observed date
image image file name
comment_j comment Japanese
comment_e comment English
phenotype keyword of phenotype
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2.3 def_phenotype

Data name def_phenotype
Description of data contents

Definition of phenotype.
File tos17_def_phenotype.csv.zip (1.4 KB)

Data items are the following:
Data itemDescription
id Phenotype ID
category_j Category in Japanese
category_e Category in English
description_j Phenotype name in Japanese
description_e Phenotype name in English
comment comment
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2.4 phenotype

Data name phenotype
Description of data contents

List of line name showing phenotype.
File tos17_phenotype.csv.zip (213 KB)

Data items are the following:
Data itemDescription
id Phenotype ID
name Strain Name
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2.5 seq

Data name seq
Description of data contents

Table of sequence name, line name and accession number.
File tos17_seq.csv.zip (550 KB)

Data items are the following:
Data itemDescription
Sequence Name Sequence name
Line Name Line name
Accession Accession number
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2.6 tos17_insertion

Data name tos17_insertion
Description of data contents

Insertion position of Tos17 relative to the rice genome reference sequence (Nipponbare, IRGSP-1.0) in each mutant line
File tos17_tos17_insertion.csv.zip (751 KB)

Data items are the following:
Data itemDescription
Chromosome Chromosome number
Position Position of Tos17 insertion
Direction Direction of Tos17
E-value E-value
Line name Line name
Sequence Name Name of Tos17 flanking sequence
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2.7 flanking

Data name flanking
Description of data contents

Fasta format file of Tos17 flanking sequence
File tos17_flanking.zip (11 MB)
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2.8 photograph

Data name photograph
Description of data contents

Photograph of mutant phenotype.
File tos17_photograph.zip (17 GB)
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3. License

Last updated : 2023/06/27

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 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "Mutant Panel © Akio Miyao licensed under CC Attribution-Share Alike 4.0 International".

The summary of the Creative Commons Attribution-Share Alike 4.0 International 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 adapted materials 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 adapted material.
  2. You must distribute any adapted material based on part or whole of the data from this database under CC Attribution-Share Alike 4.0 (or later), or CC Attribution-Share Alike Compatible License (the list is here).
  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.

E-mail:  miyaoat_markaffrc.go.jp

About Providing Links to This Database

You can freely provide links to all contents in this database. But, contents might be changed without notice.

 

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4. Update History

DateUpdate contents
2023/06/27 English archive site is opened. (Archive V1)
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5. Literature

Akio Miyao, Katsuyuki Tanaka, Kazumasa Murata, Hiromichi Sawaki, Shin Takeda, Kiyomi Abe, Yoriko Shinozuka, Katsura Onosato, Hirohiko Hirochika
Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome
Plant Cell/2003/15(8):1771-1780
PMID: 12897251

Akio Miyao, Yukimoto Iwasaki, Hidemi Kitano, Jun-Ichi Itoh, Masahiko Maekawa, Kazumasa Murata, Osamu Yatou, Yasuo Nagato, Hirohiko Hirochika
A large-scale collection of phenotypic data describing an insertional mutant population to facilitate functional analysis of rice genes
Plant Mol. Biol./2007/63(5):625-635
PMID: 17180734

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6. Contact address

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

miyaoat_markaffrc.go.jp
+81-29-838-6932
Akio Miyao

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