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Database name ⇅ DOI ⇅ Database classification ⇅ Organism ⇅ Database description ⇅ Features and manner of utilization of database ⇅ Database maintenance site ⇅ License ⇅
fRNAdb
(Functional RNA Database) 		10.18908/lsdba.nbdc00452-000
RNA sequence databases

fRNAdb is a novel database service that hosts a large collection of non-coding transcripts including annotated/non-annotated sequences from the H-inv database,
NONCODE and RNAdb. A set of computational analyses have been performed on the included sequences. These analyses include RNA secondary structure motif discovery, EST support evaluation, cis-regulatory element search, protein homology search, etc.

fRNAdb provides an efficient interface to help users filter out particular transcripts under their own criteria to sort out functional RNA candidates.

National Institute of Industrial Science and Technology (AIST), Tokyo Waterfront
*The original website was terminated.

 CC BY-SA
CREATE portal 10.18908/lsdba.nbdc00403-000
Proteomics Resources
Mus musculus (10090)

KDRI has cloned ~2000 mouse homologs of human KIAA genes and prepared ~2000 rabbit polyclonal antibodies against respective mouse KIAA (mKIAA) proteins. In the CREATE portal, you can see the results of experiments exploring the expression levels of mRNA and protein for 274 mKIAA genes in the InGaP database. You can also see the results of protein-protein interaction of 50 mKIAA proteins of which interaction interactions were identified by mass spectrometry analysis following immuno-precipitation with anti-mKIAA antibodies.

You can see the results of tissue-specific expression of mKIAA proteins. These data are useful to find out the sensitivity and specificity of the anti-mKIAA antibodies, because parts of anti-mKIAA antibodies prepared in the project can be obtained from the ProteinExpress. In the InCeP database, you can see protein-protein interaction data of mKIAA proteins, useful to predict their functions.

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 CC BY-SA
RPD
(Rice Proteome Database) 		10.18908/lsdba.nbdc00191-000
Proteomics Resources
Plant databases - Rice
Oryza sativa (4530)

Rice Proteome Database contains information on proteins identified from several organs and organelles on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) reference maps.

Proteins extracted from organs and subcellular compartments in rice on various growing stages were separated by 2D-PAGE. Based on 23 reference maps of 2D-PAGE, each of the proteins was purified and sequenced by gas-phase protein sequencer or mass spectrometry.
14724 identified proteins were mapped by 2D-PAGE. The information on 6011 proteins (e.g. Mw, pI, expression, the amino acid sequence and the result of homology searches) was cataloged and entered in the Rice Proteome Database.
The database is searchable by keyword, accession number, protein name, pI, Mw and amino acid sequence, or by selection of a spot on one of the 2D-PAGE maps. Cross-references are provided to tools for proteomics and to other databases.

National Institute of Agrobiological Sciences

 CC BY-SA
JSNP
(Japanese Single Nucleotide Polymorphisms) 		10.18908/lsdba.nbdc00114-000
Human Genes and Diseases - General polymorphism databases
Homo sapiens (9606)

A database of about 197,000 polymorphisms in Japanese population, with annotations such as genes, positions, amino acid substitutions

Allele frequencies in Japanese populatoin are also available.

Institute of Medical Science, University of Tokyo * Original website was terminated.

 CC BY-SA
RED II INAHO
(Rice Expression Database II INAHO) 		10.18908/lsdba.nbdc01557-000
Plant databases - Rice
Microarray, Gene Expression
Oryza sativa (4530)

The Rice Expression Database II INAHO (RED II INAHO) is a database that analyzed the gene expression of rice using a 60-mer oligonucleotide microarray to examine transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice.

You can get the experimental data from the redii_inaho_experiment table. Also, you can find the Accession number for a particular gene from the redii_inaho_probe table. Then, you will then get expression profiles under various experimental conditions against results of Array-BLAST.
 
References:
Yazaki J, Kishimoto N, Nagata Y, Ishikawa M, Fujii F, Hashimoto A, Shimbo K, Shimatani Z, Kojima K, Suzuki K, Yamamoto M, Honda S, Endo A, Yoshida Y, Sato Y, Takeuchi K, Toyoshima K, Miyamoto C, Wu J, Sasaki T, Sakata K, Yamamoto K, Iba K, Oda T, Otomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S.
Genomics approach to abscisic acid- and gibberellin-responsive genes in rice.
DNA Res. 2003 Dec 31;10(6):249-61.
PMID: 15029956
 
Yazaki J, Shimatani Z, Hashimoto A, Nagata Y, Fujii F, Kojima K, Suzuki K, Taya T, Tonouchi M, Nelson C, Nakagawa A, Otomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S.
Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis.
Physiol Genomics. 2004 Apr 13;17(2):87-100.
PMID: 14982972

National Institute of Agrobiological Sciences

 CC BY-SA
Database name DOI Database classification Organism Database description Features and manner of utilization of database Database maintenance site License