Imperfect DNA mirror repeats in the gag gene of HIV-1 (HXB2) identify key functional domains and coincide with protein structural elements in each of the mature proteins

Table 6 Both mIMRs and rdIMRs coincide with PSEs in each mature protein and the polyprotein

DNA segment	MIMRs			mIMRs terminated by reverse dinucleotides			rdIMRs
	N*	max	FET	N*	max	FET	N*	length	max	FET
			p-value			p-value				p-value
MA-CA-p2-NC	4337	-7	0.0513	2141	-7	0.0190	2529	all	4	0.0163
MA-CA-p2-NC							1267	≥ 16 nt	5	0.0526
MA-CA-p2	3907	-8	0.0084	2045	-7	0.0085	2196	all		none
MA-CA-p2							1302	≥ 15 nt	-5	0.0356
MA – K&S	1463	-8	0.0088	746	-8	0.0034				none
MA – promotif										none
MA – promotif							502	≥ 15 nt	3	0.0154
CA	2364	7	0.0103	1312	6	0.0409	1354	all	4	0.0757
CA							637	≥ 16 nt	-2	0.0019
NC	421	-2	0.0004	144	-1	0.0110	334	all	1	0.0019
NC							149	≥ 16 nt	7	0.0422
NC							114	≥ 19 nt	7	0.0027

The coincidence of IMRs and PSEs was tested for each of the sequentially cleaved segments, and found to be valid for all of them. For most segments, the correlation is improved when short IMRs below the essential value are removed, indicating that the coincidence is related to sequence segments longer than 15 nt.

ISSN: 1743-422X