Skip to main content

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

From: 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

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
  1. 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.