For the five organisms (H. sapiens, M. musculus, D. melanogaster, and A. thaliana, C. elegans) other than O. sativa, cDNA sequences were obtained from UniGene database. For the UniGene cDNAs, we chose those sequences that presumably code for mature protein coding sequences (CDSs) according to the annotation. For O. sativa, a full-length 32 k cDNA clone set and information of coding sequences were obtained from the Laboratory of Gene Expression, Department of Molecular Genetics, National Institute of Agrobiological Sciences (Kikuchi et al., 2003; ftp://cdna01.dna.affrc.go.jp/pub/data/CURRENT).
The genomic sequences of H. sapiens, M. musculus, D. melanogaster, and A. thaliana were obtained from NCBI (ftp://ftp.ncbi.nih.gov/genomes/). The genomic sequences of C. elegans and the draft contigs of O. sativa were obtained from Sanger Center (ftp://ftp.sanger.ac.uk/pub/) and TIGR Institute (ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/o_sativa/annotaion_dbs/pseudomolecules/version_3.0/), respectively.

As the first, mapping between full-length cDNAs and genome sequences by MEGABLAST. Following that, convertion to mapping data into bit arrays, detection of splicing patterns and distribution to the types. Genes were identificatified by cDNA annotations

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