RMG
2016/08/22Web 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
- README
- Main data
- Entire Sequence
- Genes (including RNA editing information)
- Plastid-like Seq in mt Genome
- Nuclear-like Seq in mt Genome
- tRNA
- Genomic Dynamism
2. Data Description
2.1 README
| Data name | README |
| Description of data contents | HTML file to describe "ClEST" data. |
| File | README_e.html(English) |
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 item | Description |
|---|---|
| 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 item | Description |
|---|---|
| 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 item | Description |
|---|---|
| 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 item | Description |
|---|---|
| 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 item | Description |
|---|---|
| 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 item | Description |
|---|---|
| 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 |
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.
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:
- freely access part or whole of this database, and acquire data;
- freely redistribute part or whole of the data from this database; and
- 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:
- 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.
- You must distribute any derivative work based on part or whole of the data from this database under the license.
- 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
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. |
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