Pea cytochrome oxidase subunit II gene has no intron and generates two mRNA transcripts with different 5′-termini

We have isolated and sequenced the cytochrome oxidase subunit II (COII) gene from pea mitochondria. The coding sequence (777 bp) shows over 90% homology to the COII genes from three monocotyledonous plants (rice, maize and wheat) and one dicotyledonous plant (Oenothera berteriana) Several codons are deleted, however, in the pea COII gene. Of interest is the deletion in pea of the last three codons, including the stop codon, found at the 3′ end of the other four COII genes. Instead, a new stop codon has been created due to a single-base substitution at the 13th bp downstream from the position of the original stop codon. This pea gene does not contain an intron which is found in all three monocots. Two distinct 5′ termini of the pea COII transcripts have been identified by S1 nuclease mapping, one at 285 bp (site I) and the other at 302 bp (site II) upstream from the ATG codon. They are located at two identical sites within nearly perfect direct repeats. Transcripts with the 5′ end corresponding to site I occur five time more frequently than those with the 5′ end corresponding to site II. Both transcripts have the same 3′ terminus which has been mapped to be at 193 to 195 bp downstream from the stop codon.