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To clarify whether these missing transcripts represented real changes of gene content between these cultivars, we examined the gene coverage by aligning the 93-11 genome (indica) to the Nipponbare reference genome.
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Some of the missing transcripts may represent genes responsible for executing layer-adding periclinal divisions and/or cell fate establishment.
As the package does not allow for missing data, only transcripts represented by all 6 replicates could be tested by this method.
Our simulation set-up generates both false positives (incorrect transcripts) and false negatives (missing transcripts).
Future Ensembl gene builds will hopefully identify the missing transcript.
Fig. 3 Examples of alternatively spliced transcripts represented by two oligos on the NSF45K array.
The signal intensities of 28,686 transcripts represented in the microarray were plotted against the RPKM values of corresponding transcripts (Supplementary Fig. S2).
Toxin transcripts represented 46% of the total ESTs.
Twenty-six of these 31 transcripts represented well-defined genes.
These transcripts represented a total of 12,966 unique genes.
All results therefore suggest that the Mito1 transcripts represent polyadenylated transcripts of the mitochondrial rpl2 gene.
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