Universal rule for coding sequence construction: TA/CG deficiency-TG/CT excess.

Abstract

Each coding sequence is a finite resource as to the number and composition of four bases. Accordingly, the excessive recurrence of one base oligomer entails the noticeable underrepresentation by the other, so that if the former is the same in most, if not all, of the coding sequences, the latter too must necessarily be the same in all. Indeed, a previous series of studies on 20-odd divergent coding sequences established CTG as one of the most frequently recurring base trimers (if not the most frequent), and this excess was compensated by the underrepresentation by CG and TA dimer-containing base trimers. In this study, I have analyzed three additional coding sequences and reanalyzed one previously studied coding sequence. These four, derived from man, a plant, and a fish, were of variously lopsided base compositions that were not at all conducive to high recurrences of either CT dimer or CT and TG. Yet, the excess of CT and TG dimers accompanied by complementary deficiency of CG and TA dimers emerged as the common rule. Thus, I propose the above as the universal rule of coding sequence construction. The underrepresentation by CG and TA dimers within coding sequences explains why regulatory signals in intergenic spacers are of two kinds: one, TA dimer rich; and the other, CG dimer rich.