For example, mRNA Seq provided evidence of the existence of extended parts of previously annotated genes and of the differential regulation of their expression. AK240862, previously annotated as a non protein cod ing transcript, had additional predicted exons distal to the 5 end of the previous gene model, and it encoded an indole 3 glycerol phosphate lyase. Two neighboring genes were also similar to the indole 3 glycerol phosphate lyase gene, suggesting that all three genes were tandemly duplicated. Although all three genes were upregulated in response to salinity stress, their tis sue specificities and expression levels differed, suggesting that their functions diversified after gene duplication. mRNA Seq also provided evidence of expression of computationally predicted genes.

The existence Inhibitors,Modulators,Libraries of a number of genes computationally predicted in RAP DB has not been supported by ESTs or FL cDNAs. Here, 1,738 and 2,297 transcripts identified by mRNA Seq have been mapped on computationally predicted genes, the presence Inhibitors,Modulators,Libraries of which was not supported by experiments, suggesting the validity of the computationally predicted gene models in RAP DB. We will use these sequence based transcrip tome analyses to improve RAP DB. mRNA Seq provided details of the Cilengitide bridging sequences between exons, suggesting the presence of splicing junc tions, whereas array technology including whole gen ome tiling arrays provides no information on connecting exons. Because reads that bridge exon boundaries are not mapped directly to the genomic sequence, a mapping technique was required.

As a first step, the enumeration of all theoretical splicing junc tions within annotated transcripts allows the mapping of bridging reads by using statistical models. We found that 5. 0% to 5. 7% of reads formed pri mary bridges with previously annotated exons, this was not sufficient to discover sequences bridging unannotated transcripts. Programs Inhibitors,Modulators,Libraries such as TopHat and G Mo. R Se are designed to align reads to form potential splice junctions without relying on known splice sites. In this study, sequences flanking potential donor acceptor splice sites were joined Inhibitors,Modulators,Libraries to form canoni cal introns between neighboring islands by using TopHat. Even though we used TopHat for our prediction, some of the predicted transcripts remained to be separated unlike the case with the FL cDNA sequences because of the lack of sufficient bridging sequences between the exons, suggesting that more brid ging reads should be sequenced to connect predicted exons. Elongation of the length of each read may also enhance the chance to connect predicted exons. Sequence based transcriptome analysis for capturing salinity stress inducible genes in rice mRNA Seq comprehensively identified salinity stress inducible genes.