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Table 8 mIMRs and rdIMRs that are ≥66% symmetric

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

  mIMR DNA mIMR AA Protein function rdIMR AA
len begin end begin end   begin end
37 1158 1194 386 398 1st cys-his box   
37 1314 1350 438 450 p1-p6 cleavage site F449..L450 440 445
36 1087 1122 362 374 p2 helix, most of p2 A364..M377 364 373
36 1349 1384 450 461 L domain P455..P459 448 456
30 74 103 25 34 residues essential to binding to cell membrane 25 36
28 1302 1329 434 443 most of p1 F433..F448 436 442
27 17 43 6 14 myristoylation 8 13
26 562 587 187 196 bridges CA H3 and CA H4 helices 189 195
25 322 346 107 115 part of MA H5 helix T97..A120 107 113
25 478 502 159 167 bridges CA H1 and CA H2 helices   
25 734 758 245 253 bridges CA H6 helix and downstream B-sheet   
25 930 954 310 318 CA H9 helix, endocytosis signal T311..Q324 310 318
25 1022 1046 341 349 CA H11 helix L343..C350 343 351
25 1404 1428 468 476 T471A mutation leads to incomplete separation from host cell membrane   
24 356 379 119 126 labile structure at end of MA 123 128
24 838 861 279 287 required for dimer interface 278 284
24 1146 1169 382 390 g helix, near start p7   
23 772 794 257 265 CA H7, potential NEC cleavage site 256 268
23 1189 1211 396 404 1st cys-his box   
22 1253 1274 418 425 2cd cys-his box 416 427
21 1 21 0 7 minimum signal required for myristoylation 0 7
21 268 288 89 96 loop with highly variable charge btwn MA H4-H5 90 100
21 361 381 120 127 near end of MA 123 128
21 1238 1258 413 419 2cd cys-his box C412..H421 406 421
21 1274 1294 425 431 ends at p7-p1 cleavage site N432..F433 426 433
20 990 1009 330 336 CA H10 helix, endocytosis signal P328..L337 426 433
19 63 81 21 27 basic residues essential to binding P23..H33 23 33
19 159 177 53 59 MA H3 helix, mutations affect virus assembly 51 57
19 192 210 64 70 MA H3 helix, mutations affect virus assembly 62 71
19 305 323 102 108 part of MA H5 helix, potential PDZ domain binding   
19 956 974 319 325 CA H9 helix, endocytosis signal Q311..Q324 316 323
19 1060 1078 353 359 G-rich segment at end CA   
19 1427 1445 476 482 end of Gag-PolTF 476 481
18 468 485 156 162 CA H1 helix   
18 541 558 180 186 CA H3 helix, D184 essential to mature capsid   
18 886 903 295 301 MHR 299 306
18 919 936 306 312 deletion causes major defect in particle formation 304 310
18 956 973 319 324 CA H9 helix, endocytosis signal T311..Q324 316 323
18 1389 1406 463 469 ubiquitin-gag conjugates found L449..Q500 460 470
18 1461 1478 487 493 vpr packaging L489..F493 487 493
  1. Increased stringency for symmetry results in substantial overlap of mIMRs and rdIMRs. Many of the mIMRs listed in this table are relatively short and therefore do not appear in Tables 3, 4 or 5.
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Virology Journal

ISSN: 1743-422X