Secondary Structure
While the putative secondary structure consensus base pairing is confined to a short 5' stem-loop, much more extensive structures have been proposed for specific organisms such as in yeast. In addition to the 5' stem loop, all confirmed U6 snRNAs can form the proposed 3' intramolecular stem loop.
The U6 snRNA is known to form an extensive base-pair interactions with U4 snRNA. This interaction has been shown to be mutually exclusive to that of the 3' intramolecular stem loop.
Read more about this topic: U6 Spliceosomal RNA
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