Figure 7.

The Ur element may hybridize with the 5′ss of the SL RNA. The UAYYUU of the Ur element on the trans-splicing pre-mRNA is predicted to hybridize with the 5′ss located on the SL RNA. This is analogous to the U1 role in cis-splicing, in which the U1 snRNA recognizes and base pairs with the pre-mRNA 5′ss, except in trans-splicing these roles would be inverted: The 5′ss is on the snRNP, while the proposed hybridizing sequence is on the pre-mRNA. This would position the 5′ss of the SL RNA ∼50 nt upstream of the 3′ss (trans-splice site), the same distance as the majority of C. elegans introns. Exons are indicated as boxes. Proposed Ur or known U1 base-pairing interactions are depicted as solid lines.