Figure 4. Secondary structure prediction of Nfκb1 pre-mRNAs produced by AJ and B6 copy number variant.

The pknotsRG tool [77] was used to generate secondary structures for the 350 nucleotides segment spanning the 3-repeat structure of B6 (A) and the deletion variant characteristic of A/J (B). Unpaired bases are indicated in blue, yellow bases identifying nucleotides involved in pseudoknot structures. This analysis identifies a pseudoknot with elaborate intra-molecular complementarity which is disrupted in the A/J variant allele.