The viral RNAs generated by transcription can have several fates.  The unspliced RNA can be translated to yield the Gag protein, which is a polyprotein comprised of the viral structural proteins matrix ( MA), capsid (CA), and nucleocapsid (NC). The name Gag derives from the early history of retrovirology, and stands for "group-specific antigen", derived from the fact that antibody responses tended to be elicited by the retroviral CA protein, which provided tools for sorting retroviruses into groups. About one time in twenty, the stop codon at the end of gag is bypassed, and the pol reading frame is translated, yielding the protease (PR), reverse transcriptase (RT), and integrase (IN) enzymes. Singly spliced messages produce the Env protein (gp120 and gp41). The gag, pol, and env genes are found in all retroviruses, but HIV encodes a variety of further proteins. In fact, RNA splicing of the HIV genomic transcript yields more than >113 splice variants.  Several of these proteins (Vif, Vpr, Vpx, Nef, and Vpu), produced from singly spliced or multiply spliced messages, are known or suspected to interfere with host anti-viral responses. Multiply spliced messages also produce the transcriptional elongation factor Tat and the RNA export factor Rev.
- Karn J, Stolzfus CM. 2012. HIV: Transcriptional and Posttranscriptional Regulation of HIV-1 Gene Expression. in HIV From Biology to Prevention and Treatment, pp. 77 Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
- KE Ocwieja1, S Sherrill-Mix, R Mukherjee, R Custers-Allen, P David, M Brown, S Wang, DR Link, J Olson, K Travers, E Schadt, and FD Bushman. 2012. Dynamic regulation of HIV-1 mRNA populations analyzed by single molecule enrichment and long read sequencing. 2012 Aug 25. Data for this study can be found using this reference.