The positions of the nine HIV genes are shown in green. The red double line indicates a DNA copy of the viral genome which has become integrated into the host DNA (gray). Note that the coding regions of many genes overlap, and those of tat and rev are split by introns. The blue line at the bottom of the figure represents the pre-mRNA transcript of the viral DNA showing the locations of all the possible splice sites (arrows). There are many alternative ways of splicing the viral transcript; for example the env mRNAs retain the intron that has been spliced out of the tat and rev mRNAs. The Rev response element (RRE) is indicated by a blue ball and stick. It is a 234-nucleotide long stretch of RNA that folds into a defined structure; Rev recognizes a particular hairpin (see Figure 6-94) within this larger structure.

The gag gene codes for a protein that is cleaved into several smaller proteins that form the viral capsid. The pol gene codes for a protein that is cleaved to produce reverse transcriptase (which transcribes RNA into DNA) as well as the integrase involved in integrating the viral genome (as double-stranded DNA) into the host genome. Pol is produced by ribosomal frameshifting of translation that begins at gag (see Figure 6-78). The env gene codes for the envelope proteins (see Figure 5-73). Tat, Rev, Vif, Vpr, Vpu, and Nef are small proteins with a variety of functions. For example, Rev regulates nuclear export (see Figure 7-97) and Tat regulates the elongation of transcription across the integrated viral genome (see p. 436).