An intermediate stage in the process of eukaryotic RNA splicing is the formation of a lariat structure. It is anchored at an adenosine residue in intron between 10 and 50 nucleotides upstream of the 3' splice site. A short conserved sequence (the branch point sequence) functions as the recognition signal for the site of lariat formation. During the splicing process, this conserved sequence towards the end of the intron forms a lariat structure with the beginning of the intron. The final step of the splicing process occurs when the two exons are joined and the intron is released as a lariat RNA.
Several investigators found the branch point sequences in different organisms including yeast, human, fruit fly, rat, and plants. Senapathy found that, in all of these sequences, the codon ending at the branch point adenosine is consistently a stop codon. What is interesting is that two of the three stop codons (TAA and TGA) occur almost all of the time at this position.
These findings led Senapathy to propose that the branch point signal originated from stop codons. The finding that two different stop codons (TAA and TGA) occur within the lariat signal with the branching point as the third base of the stop codons corroborates this proposal. As the branching point of the lariat occurs at the last adenine of the stop codon, it is possible that the spliceosome machinery that originated for the elimination of the stop codons from the primary RNA sequence created an auxiliary stop-codon sequence signal as the lariat sequence to aid its splicing function.
The small nuclear U2 RNA found in splicing complexes is thought to aid splicing by interacting with the lariat sequence. Complementary sequences for both the lariat sequence and the acceptor signal are present in a segment of only 15 nucleotides in U2 RNA. Further, the U1 RNA has been proposed to function as a guide in splicing to identify the precise donor splice junction by complementary base-pairing. The conserved regions of the U1 RNA thus include sequences complementary to the stop codons. These observations enabled Senapathy to predict that stop codons had operated in the origin of not only the splice-junction signals and the lariat signal, but also some small nuclear RNAs.