APPENDIX D Sequences of Retroviral LTRs

Abstract

The sequences of retroviral LTRs are given for the coding strands of proviruses and are presented as though each LTR were present in circular DNA bearing one copy of the LTR (see Chapter 5, Fig. 5.4). Structural features are indicated as described below. There is considerable variation in the length and sequence of the LTRs from different isolates of the same retrovirus, with most of the differences occurring in the U₃ region; hence deviation from the sequences presented here should be anticipated in new isolates.

For several of the LTRs presented, alternative sequences were available; the sequences employed were chosen arbitrarily. The nature of sequence variation in the LTRs can be better appreciated by consulting the alternative references listed for each LTR sequence.

The numbering of nucleotides in the format used here is arbitrary and does not begin with the first residue of the LTR in most cases. Definition of most of the symbols can be found in Chapter 4 and Appendix A. Sequences shown here generally include the polypurine tract (PPT) adjacent to the 5′ boundary of the LTR and the tRNA primer binding site (PBS) at the 3′ boundary. (The 5′ and 3′ boundaries are indicated by vertical arrows.) The PPT is an A-G-rich sequence of up to 20 nucleotides; the PBS is an 18-nucleotide sequence that is perfectly complementary to the 18 nucleotides at the 3′ terminus of the appropriate tRNA primer (see Appendix C). These sites are important in the initiation of synthesis of plus and...