A few EST clones suggest the alternative transcription of exon 6 that, however, leads to pseudo-transcripts.
For this analysis, the longest transcripts were selected and if alternative transcripts overlapped and extended the longest one, these extensions were annexed and this new pseudo-transcript was taken as the final model.
These pseudo-transcripts continue to be edited at low levels comparable to those of intact and putatively functional mitochondrial rps14 genes (Table 1).
Reiterative transcription, also known as transcript slippage or pseudo-templated transcription was documented as an intrinsic property of RNA polymerase from as early as 1964 [ 30].
By modifying our alignment protocol to systematically detect pseudo-templated nucleotides at transcript 5′ ends, we observed that up to 15% of S. agalactiae TSSs were associated with a reiterative transcription (Additional file 2).
In the absence of genuine biological replication, differential expression tests in DESeq were realised by defining the non-induced sorbitol samples "T70N SS" and "I56T SS" as pseudo-replicates, thus allowing transcript count variances to be estimated.
B. Initiation at the G residue led to reiterative transcription and incorporation of pseudo-templated G nucleotides at the transcript 5′ end (in green).
The proportion of transcripts with pseudo-templated nucleotides 5-1000%) and the number of added nucleotides (up to 10) were variable among TSSs.
To characterize reads corresponding to transcripts with pseudo-templated nucleotides on their 5′ ends, reads were first aligned by Bowtie with a seed of 25 nt and allowing no mismatches.
The transcript of BrPHP1, which is a pseudo-HP gene, was unaffected by drought treatment; BrPHP1 transcript was suppressed in high salinity conditions.
The splice graph is a directed acyclic graph whose vertices represent pseudo-exons and edges represent pairs of pseudo-exons immediately following one another in at least one transcript (which is witnessed by at least one spliced read).
