The comprehensive analysis of alternatively spliced genes from rice full-length cDNA data

Abstract

We have collected and completely sequenced 28,469 full-length cDNA clones of Oryza sativa ssp. japonica cv. Nipponbare until December, 2002. These clones were functionally annotated and many types of protein informatics analysis were performed. In spite of discontinuity of BAC/PAC genome clones with 94 % coverage from japonica, our clones were mapped at the about 19000 TU (Transcriptional Units) by Blat program. Multiple clones were mapped at the same TU with variant patterns such as differences of initiation, termination and internal exon sites. To elucidate of the regulatory mechanism of expression alternatively spliced genes, clone sets with internal exon skip pattern were selected. Some candidates of genes comprised of the genes such as the membrane protein and enzymes (hydorolase, transferase etc.). We have verified that candidate genes are alternatively spliced in rice. Three-dimensional structure change of these proteins was also checked by SOSUI and SWISSPORT programs.