Large Scaled Detection Of Splice Junctions On MRNA In Plants And Construction Of Integrated Application Platform

Splicing of pre-mRNA after transcription plays an important role in gene expression. 3,199,967 SJs in 21 species plants which have been sequenced completely were deduced from the genome annotation files. With the rapid development of sequencing technology,the accuracy of the sequencing getting higher and higher, the cost of sequencing getting cheaper and cheaper,genome sequencing is widely used. Though, there is more plant species which have only EST sequences. EST-CDS alignment were utilised to determine SJs in plants which do not have genome sequences, 4,678,710 SJs were produced. Base distribution on the boundary of SJs were calculated to discard false positive. The law of base frequency on the boundary of SJs seems identical between these two species. Next to the 3' end of a SJ, the first base is mainly G in both Arabidopsis and oryza brachyantha, take the percentage of 0.492897 and 0.478398. the second base is mainly T and the ratio is 0.43761 and 0.43594 respectively. The rest of sequence is apt to consist of 4 kind of bases equally. On the other hand, to the 5' direction of a SJ, the first base is G dominantly on the left of SJs, the proportion is 0.726213 and 0.69928 in Arabidopsis and oryza brachyantha respectively. The base next is mainly A, the proportion is 0.618294 and 0.591047.Score system was applied screen potential false positive predictions. Arabidopsis and japonica were used on behalf of monocotyledons and dicotyledonous plan to validate the accuracy of predictions. E-PCR were performed to validate the prediction. It turns out that 77.4% of the predictions are accurate. A comprehensive platform was developed to store these SJ data and an online tool was made to detect SJs instantly. This study makes it possible to exploit the SJs in plant species which have only EST sequences available.