Specifically, SsaChr6β2 as well as all putative β hemoglobin pseudogenes, including SsaChr6βψ1, SsaChr6βψ2, SsaChr6βψ3, were predicted as being transcribed from the negative strand, whereas all putative α hemoglobin pseudogenes (SsaChr6αψ1, SsaChr6αψ2) as well as SsaChr6α2 would be transcribed on the positive strand.
As shown in Table 3, the occurrence rates of terminal reads to general reads were 196 for the positive strand of IME-EF4, 344 for the negative strand of IME-EF4, 246 for the positive strand of IME-EFm1, and 341 for the negative strand of IME-EFm1.
Annotated genes in the ICP2 genome are shown as white boxes, with genes transcribed from the negative strand displaced downward.
As follows from the previous analysis, the typical features of core promoter elements are a) a narrow functional window and b) distribution on the positive strand is visibly different from those on the negative strand.
The M13 Reverse sequencing primer generated data from the negative strand.
We generated the reverse complement for those mRNAs transcribed from the negative strand.
As indicated above, it is interesting to note that all of the putatively functional α hemoglobin genes predicted to be transcribed from the positive strand and all β hemoglobin genes predicted to be transcribed from the negative strand are lacking a corresponding EST at this time.
This restriction was justified by observing only 3 ORFs on the negative strand from among 376 predictions from step one.
If the read is transcribed from positive strand, then its sequence is identical to the negative strand; therefore, its mapping orientation is denoted as negative, otherwise denoted as positive.
There was a bias in the generation of vsiRNAs from the plus strand of the genome in comparison to the negative strand.
As no infectious virus was recovered from cells transfected with MΔ5 and Mm1 transcripts, RT-PCR amplification of the negative strand RNA was performed to check if RNA replication occurred in the transfected cells.
