APPENDIX A Nomenclature

Abstract

Communication among retrovirologists has been greatly simplified over the past decade by the general acceptance of conventional names for structural and genetic features of viral genomes, for viral mutants, and for virus-coded proteins. As a convenient summary to assist reading of the text and use of the ensuing Appendixes, we provide here the major definitions and rules that now govern the appellation of retroviral genes, noncoding regions of genomes, mutants, and proteins; in some cases, references are provided for more detailed explanations of these terms and symbols.

1. Structural and Genetic Features of Retroviral Genomes
A full account of the properties of retroviral genomes is provided in Chapter 4. Here, we simply reiterate the definitions of regions of the genome important for interpretation of the maps and sequences presented in Appendixes B through F.

a. The Regions of Replication-competent Retroviral RNA
Cap site: The penultimate nucleotide at the 5′ end of the viral RNA subunit, presumably the initiating nucleotide in an RNA transcript of proviral DNA; linked to a methylated “cap” ribonucleotide by a 5′-5′ linkage.

R: A short sequence (13–60 nucleotides) repeated at both ends of the RNA subunit, exclusive of the cap nucleotide at the 5′ terminus and the poly(A) tract at the 3′ terminus; also present twice in viral DNA as part of the LTR.

U₅: A sequence of about 80–120 nucleotides, positioned between R and PB(−), present once in viral RNA and twice in the viral DNA product of reverse transcription; it forms part...