RMG

2016/08/22

Web Site: http://rmg.rice.dna.affrc.go.jp/
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/rmg/

The database of rice mitochondrial genome and its analysis results.

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 data
  3. Entire Sequence
  4. Genes (including RNA editing information)
  5. Plastid-like Seq in mt Genome
  6. Nuclear-like Seq in mt Genome
  7. tRNA
  8. Genomic Dynamism
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2. Data Description

2.1 README

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

Data name Main data
Description of data contents List of data items that are open to the public.
File rmg_main.zip (1 KB)
Data items are the following:
Data itemDescription
Title Title of the data
Sequence data file File name of the sequence data
Data file (CSV) File name of CSV formatted data
Data file (TogoDB) Name of the dataset on Simple search website (TogoDB)
Image file File name of the image

2.3 Entire Sequence

Data name Entire Sequence
Description of data contents The data for entire sequence of rice mitochondrial genome with a total length of 490,520bp. This sequence was registered in the International Nucleotide Sequence Database with accession numbers AB076665 and AB076666, and was later combined into a single accession number BA000029. It was also registered in the previous RAP-DB genome browser.
File rmg_seq.zip (142 KB)

2.4 Genes (including RNA editing information)

Data name Genes (including RNA editing information)
Description of data contents List of genes in the rice mitochondrial genome including information on ORF (open reading frames), transcription and RNA editing.
File rmg_gene.zip (3 KB)
Data items are the following:
Data itemDescription
Gene Gene.
Gene names ccmC, ccmFn, ccmFc and ccmB were proposed by Faivre-Nitschke et al. (2001).
Comment Comment
Transcription Transcription
nt: not tested
T: transcribed
N: not transcribed
Editing site Editing site
N: not transcribed
Previous reports on editing sites Previous reports on editing sites
Strand Strand
S: sense
A: antisense
exon1 start Start position of exon1
exon1 end End position of exon1
exon2 start Start position of exon2
exon2 end End position of exon2
exon3 start Start position of exon3
exon3 end End position of exon3
exon4 start Start position of exon4
exon4 end End position of exon4
exon5 start Start position of exon5
exon5 end End position of exon5

2.5 Plastid-like Seq in mt Genome

Data name Plastid-like Seq in mt Genome
Description of data contents List of characteristic features of DNA fragments that were migrated from the plastid genome to the mitochondrial genome. Information on sizes, positions, gene names, homologies and differences for individual fragments is available.
File rmg_plastid_like_seq.zip (2 KB)
Data items are the following:
Data itemDescription
Fragment no. Fragment number
Position in mtDNA Position in the mitochondrial DNA sequence
Fragment size(nt) Size of the fragment
Position in ptDNA Position in the plastid DNA sequence
(The position is based on Hiratsuka et al. (1989))
Genes Genes
Substitution Number of substitutions in the plastid DNA sequence
Deletion Number of nucleotide deletions in the plastid DNA sequence
(Number of deletion sites is shown in parentheses)
Insertion Number of nucleotide insertions in the plastid DNA sequence
(Number of insertion sites is shown in parentheses)
Homology(%) Percentage homology to the rice plastid DNA sequence

2.6 Nuclear-like Seq in mt Genome

Data name Nuclear-like Seq in mt Genome
Description of data contents List of sequence fragments in rice mitochondrial genome that showed similarity to nuclear retrotransposon and transposon sequences.
File rmg_nuclear_like_seq.zip (1 KB)
Data items are the following:
Data itemDescription
nuc. position Position of the sequence fragment in the rice mitochondrial genome
length Length of the sequence fragment
sense or antisense Sense or antisense strand
+: sense
-: antisense
organism Source of the most closely related transposon/retrotransposon sequence
kind of element Transposon or retrotransposon
R: retrotransposon
T: transposon
accession GenBank Accession number of the most closely related transposon/retrotransposon sequence
% Percentage homology to the most closely related transposon/retrotransposon sequence
definition Characteristics of the most closely related transposon/retrotransposon sequence

2.7 tRNA

Data name tRNA
Description of data contents Data contents are as follows:
Amino acid sequences of 23 tRNA from 17 species identified in the rice mitochondrial genome.
List of genes in rice, Arabidopsis and sugar beet mitochondrial genomes and their existence in mitochondrial genomes of other plants.
File rmg_trna.zip (1 KB)
Data items are the following:
Data itemDescription
Amino acids Amino acid binding to tRNA
tRNA tRNA gene indicated by the cognate amino acid in one-letter code
rice Rice
+: tRNA present
-: tRNA absent
y: pseudogene
a: mitochondrial tRNA
b: plastid-like tRNA
Miyata et al. (1998) was used as reference for rice trnP and trnR pseudogenes.
Arabidopsis Arabidopsis
+: tRNA present
-: tRNA absent
y: pseudogene
a: mitochondrial tRNA
b: plastid-like tRNA
Reference: Unseld et al. (1997)
sugarbeet Sugar beet
+: tRNA present
-: tRNA absent
y: pseudogene
a: mitochondrial tRNA
b: plastid-like tRNA
c: novel tRNA
Reference: Kubo et al. (2000b)

2.8 Genomic Dynamism

Data name Genomic Dynamism
Description of data contents List of sequences commonly found in mitochondria, plastid and nucleus of rice.The list represents mitochondrial and nuclear sequences with homology and mutations to the plastid sequences.From these results, the movement of plastid sequence fragments into the mitochondria and nucleus can be clarified.
File rmg_genomic_dynamism.zip (1 KB)
Data items are the following:
Data itemDescription
plastid sequence No. Plastid sequence number
Genes Genes on the plastid sequence
Length Length of the plastid sequence
Mutations of comparison with nuclear sequence Comparison with the most closely related nuclear sequence
sub: substitutions
del: deletions
ins: insertions
The total number of nucleotide alterations in the fragment is shown in parentheses
Homology Percentage homology to the most closely related nuclear sequence
Mutations of comparison with mt sequence Comparison with the most closely related mitochondrial sequence
sub: substitutions
del: deletions
ins: insertions
The total number of nucleotide alterations in the fragment is shown in parentheses
Homology Percentage homology to the most closely related mitochondrial sequence
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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: "Rice Mitochondrial Genome © 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

Date Update 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.
2013/12/17 The URL of the portal site is changed.
2013/08/07 RMG english archive site is opened.
2002/09/25 RMG (http://rmg.rice.dna.affrc.go.jp/) is opened.
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5. Literature

Notsu Y, Masood S, Nishikawa T, Kubo N, Akiduki G, Nakazono M, Hirai A, Kadowaki K.
The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants.
Mol Genet Genomics (2002) 268: 434–445
PMID: 12471441

6. Contact address

When you have any question about "RMG", 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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