Group-specific antigen

Numbering system By convention, the HIV genome is numbered according to HIV-1 group M subtype B reference strain HXB2. Transcription and mRNA processing After a virus enters a target cell, the viral genome is integrated into the host cell chromatin. RNA polymerase II then transcribes the 9181 nucleotide full-length viral RNA. HIV Gag protein is encoded by the HIV gag gene, HXB2 nucleotides 790-2292. HIV MA also makes contacts with the HIV trans-membrane glycoprotein gp41 in the assembled virus and, indeed, may have a critical role in recruiting Env glycoproteins to viral budding sites. Once Gag is translated on ribosomes, Gag polyproteins are myristoylated at their N-terminal glycine residues by N-myristoyltransferase 1. This is a critical modification for plasma membrane targeting. In the membrane-unbound form, the MA myristoyl fatty acid tail is sequestered in a hydrophobic pocket in the core of the MA protein. SP1 Spacer peptide 1 (SP1, previously 'p2') is a 14-amino acid polypeptide intervening between CA and NC. Cleavage of the CA-SP1 junction is the final step in viral maturation, which allows CA to condense into the viral capsid. SP1 is unstructured in solution but, in the presence of less polar solvents or at high polypeptide concentrations, it adopts an α-helical structure. In scientific research, western blots for CA (24 kDa) can indicate a maturation defect by the high relative presence of a 25 kDa band (uncleaved CA-SP1). SP1 plays a critical role in HIV particle assembly, It recruits cellular proteins TSG101 (a component of ESCRT-I) and ALIX to initiate virus particle budding from the plasma membrane. p6 has no known function in the mature virus. ==In endogenous retroviruses==

Both Human endogenous retrovirus K and Human Endogenous Retrovirus-W copies carry gag genes, usually damaged, that are expressed widely. There is a long history of speculating their involvement in multiple sclerosis and other neurological disorders. ==In other viruses==

The gag gene of Spumaretrovirinae (e.g. ) and Metaviridae (e.g. ) only have a recognizable nucleocapsid part. It also lacks a myristoylation sequence. The Spumaretroviral (SV) gag is related to orthoretrovieral gag, as structural work has shown that part of the N-terminal domain shares functional and structural homology with the typical capsid protein. The SV gag is not processed like the orthoretrovieral gag; only a tiny 3kDa cut at the C-terminal is required, and other cleavage sites are generally inefficient. The Metaviral (MV, Ty3/gypsy) gag, too, is known to have a structurally homologous capsid protein. Each capsid is assembled from 540 proteins. Unlike orthoretroviral CA proteins, it does not require dramatic maturation. The animal Activity-regulated cytoskeleton-associated protein (ARC) gene is repurposed from the metaviral gag. This gene is responsible for transporting mRNA among neural cells, a key part of neuroplasticity. It has independently arose in Tetrapoda and Drosophila. Caulimoviridae members rarely get a gag assignment to its capsid-containing ORF, but the CP-PRO-POL layout does show analogy with the canonical gag-pol setup. Whether the parts stick together into a polyprotein depends on the genus. == See also ==