Abstract
The Rice Annotation Project Database (RAP-DB) is the annotation database for the genome sequence assembly of IRGSP. Since an updated japonica rice genome assembly, IRGSP build 5, was released in 2008, we have created new annotation data (IRGSP/RAP build 5). For better gene structure annotation that covers more rice genes, a system for cross-species FLcDNA mapping and protein mapping was developed. As a result, 34,902 loci with transcript evidence were identified. In addition, 9,975 loci with no transcript supports were predicted by ab initio gene prediction methods. We also provide rice gene family information based on MCL and BLAST searches. The gene family data contain sorghum and Arabidopsis proteins so that inter-specific gene family relationships are displayed. To further examine genome-wide conservation of genes, genomic sequences of indica rice and sorghum aligned to the IRGSP assembly are shown in GBrowse_syn. Here we present new functions and contents of the RAP-DB, which provides new data download system and manually curated functional annotation data as well as other useful genome information, such as organelle-derived regions and transposable elements.
