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As we are concerned with transcription initiation and elongation, we defined gene distances as the number of base pairs between the respective transcript boundaries (transcription start and end sites).
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Thereby, a flux is constrained to zero, if the respective transcript has not been observed.
In cases in which no UTR information was available, for the respective transcript 100 bp of the respective 3'-downstream and 5'-upstream genomic sequence were added.
However, there were no significant differences in the amount of the respective transcripts (Fig. 5e).
The respective transcripts were cloned from a mixed stage cDNA library from C. elegans.
In addition, these plasmids support the transcription of viral mRNA by polymerase II (Pol II), leading to the expression of viral protein(s) encoded by the respective transcripts.
MACE delivers a single next-generation sequence from the 3′-end of each individual cDNA molecule that precisely quantifies the respective transcripts.
Internal initiation is facilitated by specific RNA tertiary folds, called internal ribosomal entry sites (IRESs), in the 5′ untranslated region (UTR) of the respective transcripts.
For half of the differentially regulated proteins, the respective transcripts were also differentially regulated.
Cloned PCR products of each of the respective transcripts were used to generate external standard curves.
35.6% of the reference-mapped transcripts showed identity to known reference transcripts, and 29.4% of the transcripts were assigned to known transcript regions (including intronic regions), presumably displaying potentially novel isoforms for the respective transcripts.
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