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Genes containing one or more gaps or internal stop codons were excluded.
There were 17 genes containing one or two introns, six of which were tRNA genes.
** Genes containing one of two double-stranded RNA-binding domains were predicted to be Dicer-encoding genes.
An in silico analysis of the Arabidopsis nuclear genome has identified 3829 genes containing one or more ABREs [ 62].
An analogous analysis was performed with genes containing one or more UCRs within their introns [see Additional file 4].
Interestingly, each of these four transcriptional clusters was predominantly made up of genes containing one of a specific class of [-39,-26]-PLMs [-39,-26]-PLMs [-39,-26]-PLMs [-39,-26]-PLMs
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On average, 22.5% of upregulated genes contained one or more miRNA SCR, which was comparable to the frequency in the non-upregulated genes (Supplementary Table S3).
WRKY genes contain one or two highly conserved DNA binding domains interrupted by an intron.
Sixteen genes contain one or two introns, with six of the introns in tRNAs.
Most other SLEEPER genes contain one intron between the 5' UTR and their start-codons.
Most groups of SSSGP genes contain one intron (Additional file 1, Figures S1A, S1C, S1D).
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