The blue15 and yellow18 RHE often occur in tandem resulting in double hairpin and, in some cases, multiple hairpin structure.
The microRNA primary transcripts (pri-miRNAs) contain one or multiple hairpin secondary structures.
Indeed, since vertebrates do not show an abundance of RP-sites we suppose that they must have some other mechanism for efficiently splicing large introns, which might be intron folding via multiple sequential hairpin structures.
Some of these groups have consecutive numbers, indicating that they fall in genomic regions where multiple consecutive hairpin structures are present, all passing the selected parameter cutoffs, with very close start positions but spanning a region wider than three base pairs.
Although this analysis identified multiple possible miRNA precursor hairpin structures in the chromosome 14 transcript, none of these regions encoded known miRNAs in the miRBase database [59].
Multiple pri-miRNA designs were generated (pri-miRNA hairpin structures shown in Figure 6A), all based on the miR-122 pri-miRNA which is known to yield homogenous mature miRNA species following Drosha and Dicer processing [32].
The proposed RNA secondary structures, based on RNAfold and multiple alignment covariation analysis, highlight compensatory variations that maintain hairpin structures and, for sRk28, a potential pseudoknot structure.
Of course, multiple predictions generated by FindMiRNA for regions where more hairpin structures are putatively present fall in the same precursor similarity group, but should be considered alternative structures of the same putative miRNA and not multiple independent miRNAs.
RNA polymerase II transcribes miRNAs into long primary transcripts (pri-miRNAs) that are cut into miRNA precursors (pre-miRNAs) with typical hairpin structures, capped with a specially modified nucleotide at the 5' end and polyadenylated with multiple adenosines [ 6, 11].
These local hairpin structures are the featured substrates of Dicer-like 1 (DCL1).
