The goal of the study was to globally identify the SL trans-spliced mRNAs of Ciona intestinalis tailbud embryos, and to map trans-splice acceptor sites onto the genome. 5'-segments of SL trans-spliced mRNAs were amplified by SL-PCR following random-primed reverse transcription. SL-PCR products were sequenced using 454 technology on the Roche 454 GS 20 intrument.