Search for Database Metadata
| Database name ⇅ | DOI ⇅ | Database classification ⇅ | Organism ⇅ | Database description ⇅ | Features and manner of utilization of database ⇅ | Database maintenance site ⇅ | License ⇅ |
|---|---|---|---|---|---|---|---|
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RED
(Rice Expression Database) |
10.18908/lsdba.nbdc00315-000 |
Plant databases - Rice
Microarray, Gene Expression
|
Oryza sativa
(4530)
|
The Rice Expression Database (RED) is a database that aggregates the gene expression data that has been analyzed using 8987EST array in the Microarray Project that was underway as part of the Rice Genome Project. RED holds raw and normalized data from expression profiles obtained by the Rice Microarray Project and other research groups. |
If you are interested in a particular research subject, can find the appropriate "Research ID" from the red_subject_info table. You will then get the experimental data for the selected research.
|
CC BY-SA | |
|
ASTRA
(Alternative Splicing and Transcription Archives (ASTRA)) |
10.18908/lsdba.nbdc00371-000 |
Nucleotide Sequence Databases - Gene structure, introns and exons, splice sites
|
Oryza sativa
(4530)
Arabidopsis thaliana
(3702)
Homo sapiens
(9606)
Mus musculus
(10090)
Drosophila melanogaster
(7227)
Caenorhabditis elegans
(6239)
|
The database represents classified patterns of alternative splicing (AS) and alternative transcriptional initiation (ATI) in six eukaryotic genomes. |
This database enables to search and represent alternative splicing/transcriptional initiation genes and their patterns (ex: cassette) based on mapping results between full-length cDNA and genomic sequences. Furthermore the database output translated sequences of their isoforms. |
National Institute of Advanced Industrial Science and Technology, AIST. |
CC BY-SA |
|
RMOS
(Rice Microarray Opening Site) |
10.18908/lsdba.nbdc00194-000 |
Microarray Data and other Gene Expression Databases
Plant databases - Rice
|
Oryza sativa
(4530)
|
The Rice Microarray Opening Site is a database of comprehensive information for Rice Microarray Project (April 1999 - March 2003). Microarray is the powerful tool for understanding comprehensive gene expression at genome-wide level (for details, refer to the Technical Background Section). By using this system, it has become possible to isolate the genes quickly that confer resistances or are responsive to cold temperature, drought, unsuitable soil condition, insect pest and disease, etc. It has become possible by using this system to begin to quickly isolate the genes that confer such resistance. Also it has become possible to isolate which genes are expressed in particular tissues and organs. |
You can refer to the information of the general background for Microarray techniques and the research data related to the custom microarray we developed. |
National Institute of Agrobiological Sciences |
CC BY-SA |
|
RGP physicalmap
(Rice Genome Mapping and Sequencing Data from RGP, STAFF/NIAR, Japan) |
10.18908/lsdba.nbdc00318-06-000 |
Plant databases - Rice
Sequence
Physical map
|
Oryza sativa
(4530)
|
This site contains a physical map information of rice using yeast artificial chromosome (YAC) clones selected with the Rice Genome Research Program (RGP) DNA markers from 1994 through 1997 version. A rice YAC library of RGP was constructed from cultured cells of Oryza sativa L. cv. Nipponbare and contains 6934 clones with 350 kb average insert length. |
You can see the data files of yeast artificial chromosome (YAC) clones by figures and tables, which clones were selected with DNA markers in the Rice Genome Research Program (RGP) for each chromosome. In the tables, YAC clones selected with RGP DNA markers for each chromosome are shown along with the markers and the genetic distances. In the figures, the YAC physical maps of each divided region on the chromosomes are shown.
|
CC BY-SA | |
|
RGP caps
(RGP: 332 PCR-based genetic markers on rice chromosomes) |
10.18908/lsdba.nbdc00318-05-000 |
Plant databases - Rice
Sequence
PCR-based marker
|
Oryza sativa
(4530)
|
We have developed 332 PCR-based genetic markers including 161 sequence tagged site (STS) markers and 171 cleaved amplified polymorphic sequence (CAPS) markers.This site shows all information for these markers. |
The table (chr 1 to chr 12) summarizes all information for STS and CAPS markers, such as chromosomal location, primer sequences, size of amplified fragment (Nipponbare), restriction enzyme, etc. These markers have been developed to detect polymorphism between Nipponbare (japonica) and Kasalath (indica). Although detection of polymorphism of these markers will depend on the combination of varieties or lines, they may be used for the analysis of other combinations.
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CC BY-SA | |
| Database name | DOI | Database classification | Organism | Database description | Features and manner of utilization of database | Database maintenance site | License |