For example, a reverse promoter in the COX1 gene generates antisense reads mapping to the first 336 nt of the transcript (Additional file 1: Figure S2).
Notably, there was no detectable effect of SSRP1-siRNA on synthesis of the first 40 nt of the pre-rRNA transcript.
In this case, the 5′-nt of the transcript displaces the σ3.2-loop, which is not modeled and presumably disordered.
When Ds1 provides both a donor and an acceptor, the exonized transcript combines the 1st to the i th exons, the first j nt of the i th intron, the Ds1 sequences until the junction site, the 8 nt upstream sequence, the i th intron starting from the (j + 1) nt to the end, and the sequences of the (i + 1 th to the (I + 1 th exons.
When Ds1 only provides a donor, the exonized transcript combines the 1st to the i th exons, the first j nt of the i th intron, the Ds1 sequences until the junction site, and the sequences of the (i + 1 th to the (I + 1 th exons.
In the case of the putative PolII transcripts, the high-scoring PSEA elements preferentially locate 50 nts upstream of the transcript start.
To examine the significance of the correlations between mappability and transcript length, expression levels, or evolutionary conservation (Figure 2C E), we separately each of the following genomic regions: the 200 intronic nt upstream of exons, the first 100 nt of exons, the terminal 100 nt of exons, and the 200 intronic nt downstream of exons.
Third, Cdx2 transcripts lacking this element show only transient localization, indicating that the 97 nt element provides anchorage/stability of the transcript in the apical region.
A second terminator structure can be found 370 nt upstream of the end of the transcript.
