Database name

"Hana" means flower in Japanese. This database provides transcriptome information in a model flower plant (Oryza sativa) for annotated coding genes (RAP, TIGR) and sORF identified by Hanada et al (Genome research 2007).


Some of small coding genes play a significant role in various aspects of either plant development or stress response. However, it is believed that such the genes tend not to be identified because of the conservative nature of prediction algorithms. Using our recently published pipeline to infer small coding genes specifically, we identified many small coding genes with high coding potential in plant (Arabidopsis thaliana and Oryza sativa) genomes. Toward functional analysis of these small coding genes, we designed microarray to examine the expression profile of identified small coding genes and all annotated genes in various organs and various stress condition.

Designed microarray

Platform of this custom microarray is based on Agilent Technologies. Briefly, our custom microarray uses optimized 60-mer oligonucleotide probes and one-color labeling system. Most of probes were designed by e-array (Agilent). Out of designed probes, we chose a specific sequence which does not overlap with other gene sequences as a probe sequence. Since candidate probes of some genes cannot be designed by e-array, we designed probe sequences by ourselves. Please see the detailed method to make the probes in our paper. You can download all probe sequences from here.

Target genes

There are two genomes in Oryza sativa (RAP-DB and TIGR). Here, we identified sORF in the intergenic regions of RAP4 rice genome. Also, we identified sORFs in mRNA-line ncRNA genes. Since most of RAP genes are overlapped with TIGR genes, there are some TIGR specific genes. Therefore, TIGR specific genes are targeted in our microarray


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Table of target genes

  Annotated coding genes (RAP) Annotated coding genes (TIGR) Annotated ncRNA genes (RAP) Annotated ncRNA genes (TIGR)

sORF in intergenic regions

Number of genes