For each alternatively spliced gene, the exon number was defined as the largest exon number of its all transcript isoforms.
All transcript levels refer to the one from the parental strain after 24 h (reference sample).
All transcript sequences were aligned to SwissProt using blastx (Camacho et al. 2009), and only the most similar target was kept with the e-value cutoff of 1 × 10−20.
Moreover, all transcript accumulations of sixteen genes tested for chloroplast development were abnormally influenced in tcd10 mutants, especially OsV4, OsRpoTp, V1, V2, RNRL, RNRS, 16SrRNA, rpl21 and OsDG2 were considerably down-regulated (Fig. 6c).
All variations were mapped to all transcript models, which led to multiple annotations for several loci.
Both methods rest on the biological assumption that all transcript level distributions are conserved in spite of any experimental perturbations.
The current method will generate a corrected gene model if one of the variant represents >50% of all transcript sequences at the site of the alternative splice.
All transcript levels were found for all lines to be >3 fold increased, compared to the wild type (data not shown).
Analyses of these data focused primarily measuring the relative abundance of transcripts of a gene, while treating most or all transcript isoforms as equivalent.
Due to these limitations, it is unlikely that the goal of completely characterizing the human transcriptome, including all transcript variants across all tissues, disease states, and developmental stages, will be accomplished by full-length cDNA sequencing alone.
This transcomplementation strategy provides a more strict control of specificity relative to controls that involve sense, scrambled or irrelevant sequences, because it takes into account all transcript sequences present in the bacterial cell and the effector sequences remain unchanged.
