Nonetheless, we find no evidence of intron gain via intron transposition, the only proposed transcript-mediated mechanism of intron gain.
We did not identify any intron gains that occurred via intron transposition in our dataset, the only proposed transcript-mediated mechanism of intron gain.
Other Bvg-activated transcripts in this group include the other TTSS regulators (BB1645, BB1646, and BB1642), three proposed two-component response regulatory proteins, and numerous proposed transcriptional regulators.
More recently, a transcription-based mechanism that would open chromatin for DNA methylation establishment at ICRs has been proposed, and transcripts derived from Kcnq1 promoters and possibly serving this function have been identified in mouse oocytes (22).
The GC content of 100 base windows centered on each genomic position are also shown and illustrate, within the proposed primary transcripts, an apparent correspondence between depth of coverage and GC content [ 31]. Figure 4A shows the transcriptional context of miR394b and the presence of a canonical intron supported by 14 Illumina reads (7 distinct sequences).
Based on the above data, we propose minimum transcript level 50 (MTL50) as a measure of stringent requirement, somewhat similar to the IC50 measure of enzyme inhibition.
They proposed that the transcript variants were generated as a result of intramolecular slippage.
Several methods have been proposed to estimate transcript expression levels (Katz et al., 2010; Li et al., 2010; Nicolae et al., 2010; Turro et al., 2011).
There has been a great deal of expectation that high-throughput sequencing technologies would allow a global and unbiased characterization of the transcriptome compared with microarrays and, consequently, several methods have been proposed for inferring transcript structures using sequence data.
To improve the performance of RNA-Seq quantification, an alignment-free method, Sailfish, has been recently proposed to quantify transcript abundances using all k-mers in the transcriptome, demonstrating the feasibility of designing an efficient alignment-free method for transcriptome quantification.
