Similar to T7 and other Autographivirinae, all of the genes are transcribed in the forward direction [ 33, 38].
Although active RTEs need to be transcribed from their forward strand, the RTE sequences scattered around the highly transcribed genome could produce transcripts in both orientations.
The element predicted with the CLID 294 is located 3' to a protein-coding gene, too, and is transcribed from the forward strand in Synechocystis 6803.
Comparing the four rRNA operons within the A. orientalis genome, the first two, counted clockwise from dnaA, are both transcribed in the forward direction and their 16S rRNA sequences are slightly different (98 99% identity).
Annotation of left aligned data, as performed by many annotation tools, would thus give clinically discrepant annotation for the 339 (46 %) indels in genes transcribed from the forward DNA strand.
Annotation tools that do not incorporate the strand of the coding transcript would thus lead to calls discrepant with clinical annotation for 339 indels (those in genes transcribed from the forward DNA strand); 46 % of all indels in this individual.
As expected for other strongyloid nematodes [ 18], no atp8 subunit is present, and all genes are transcribed from the forward strand; all protein coding genes had open reading frames (ORFs).
What resulted he would later transcribe for forwarding to his publisher, but never revise, in principle he regarded revision as a form of lying.
miRNAs were subsequently amplified using 1 μl of the reverse transcribed sample, miRNA-specific forward and poly(T) adapter-specific reverse primers (additional file 6) under the same PCR-cycler conditions used in sqRT-PCR described above.
flag-tagged fam83f was amplified by PCR with inclusion of the sequence for the Flag-tag in the forward primer and reversely transcribed RNA as a template.
myc-tagged c1orf144 was amplified by PCR with inclusion of the sequence for the Myc-tag in the forward primer and reversely transcribed RNA as a template.
