APPENDIX A The SV40 Nucleotide Sequence

Abstract

The SV system is based on the SV40 DNA sequence reported by Fiers et al. (1978), with further corrections as modifed by Fiers (van Heuverswyn and Fiers 1979). The sequence therefore contains 5243 nucleotides.

In agreement with Fiers et al. (1978), the 27-base palindrome at the BglI recognition site is taken as the reference origin of the SV system. The centermost nucleotide in the palindrome is defined as nucleotide 0/5243. The entire genome is numbered in a clockwise sense from the reference origin, from nucleotide 1 to nucleotide 5243 (5′ – 3′). This clockwise sense is the same sense as the EcoRI map unit direction, as the Weissman sequence (Reddy et al. 1978b), and as the late RNA sense only of the Fiers sequence. Fiers’ suggestion of providing a separate additional numbering system in the sense of the early RNA is not adopted here.

The nucleotide sequence of the strand in the sense of the late and early RNAs is presented in Sections 1 and 2, respectively. Additional data about nucleotide and dinucleotide frequencies accompany each sequence

3. Conversion between the SV Numbering System and Coordinates Used by Others
We introduce the following abbreviations:

SV = SV numbering

FE = Fiers “early sense” numbers (Fiers et al. 1978)

FL = Fiers “late sense” numbers (Fiers et al. 1978)

mu = EcoRI map units

W = Weissman numbers (Reddy et al. 1978)

Due to numerous differences between the original Fiers and Weissman sequences and the one used here, conversion between the three...