Synonymous site conservation in the HIV-1 genome

Table 2 Summary of stretches with significantly low Ks, ranked according to StretchFinder

Rank	ORF	Pos. in ORF	Overlap	Regulatory element	Remark
1	pol	898-937		+	Contains the cPPT, the CTS and the DNA flap regions. The first two regions are involved in regulation of reverse transcription of the genome, and the third in translocation of the genome to the nucleus.
2	vif	173-186	+		Overlaps Vpr 1–14. In this region of Vpr there is a conserved homo-ologimerization domain.
3	tat	65-98	+		Overlaps Rev 18–52 (as well as Env 719–744), which includes the conserved homo-multimerization region and RNA-binding domain.
4	pol	986-1003	+		Overlaps Vif 1-18
5	nef	88-99		+	Contains the PPT (a primer for reverse transcription)
6	tat	41-52	+		Sites 47–52 overlap Rev 1–6.
6	tat	41-52	+		Unexplained low Ks in sites 41-46
7	env	728-744	+		Equivalent to region (3) (overlap of functional elements in Rev)
8	pol	7-31	+		Overlaps Gag 442–448 and Gag 454-463
9	gag	488-496	+		Overlaps Protease 1-9
10	vif	1-21	+		Equivalent to region (4) (overlaps Pol 986–1003)
11	rev	2-9	+		Overlaps Tat 49–56: conserved nuclear localization signal and RNA binding domain
12	env	535-541		+	RRE
13	env	2-5	+		Overlaps Vpu 56-60
14	pol	82-107			Unexplained low Ks
15	gag	2-5		+	Four RNA loops (SL1-4) of the HIV-1 packaging signal. Gag 2–5 overlaps the fourth loop SL4.
16	env	570-608		+	RRE
17	vpu	74-80	+		Overlaps Env.
18	rev	58-75	+		Overlaps Env 240-257
19	pol	939-954		+	Pol 939–947 forms the CTS end.
19	pol	939-954		+	Unexplained low Ks at sites 948-954
20	env	495-531		+	RRE
21	vif	114-143			Unexplained low Ks

Regions which could not be fully accounted for (whether as part of a regulatory domain or as part of an overlapped region) are marked in bold.

ISSN: 2730-7182