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Table 5 rdIMRs in gag ranked by length

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

Beg   end rd-IMRs nt prot AA structure or function
1215 ca .. ac 1261 $1-gag 47 NC R406..H421 primer annealing; Cys-His box
767 tc .. ct 803 $2-gag 37 CA I256..L268 N-terminal CA-H7 helix
73 gg .. gg 108 $3-gag 36 MA G025..W036 nuclear localization signal 1(NLS1)
1245 at .. ta 1279 $4-gag 35 NC C416..T427 Zn finger motifs. 2cd cys-his box
267 tc .. ct 300 $5-gag 34 MA Q090..A100 I92..V95 affect struct orientation of MA-H5
168 ct .. tc 200 $6-gag 33 MA C057..S067 MA H3 helix, C57S prevents particle fmtn
68 ca .. ac 97 $7-gag 30 MA P023..H033 basic residues target, bind Gag to PM
1379 aa .. aa 1408 $8-gag 30 p6 E460..T470 possible association with ubiquitin
184 gg .. gg 212 $9-gag 29 MA G062..G071 C-terminal MA-H3 helix
198 at .. ta 226 $10-gag 29 MA P066..R076 essential to structural transformation
246 ag .. ga 274 $11-gag 29 MA A083..I092 mutations retarget assembly
232 tt .. tt 259 $12-gag 28 MA L078..C087 MA-H4 central to 3D structure
1091 ct .. tc 1118 $13-gag 28 - A364..S373 cleavage site, most of p2
618 tg .. gt 644 $14-gag 27 CA E207..V215 C-terminal CA-H4 helix, CypA interaction
1074 ta .. at 1100 $15-gag 27 - K359..M367 cleavage CA-p2
490 tt .. tt 515 $16-gag 26 CA F164..F172 folds against MHR
1108 ag .. ga 1131 $17-gag 24 - V370..M378 cleavage site p2-p7, phosphorylation
385 ag .. ga 409 $18-gag 25 - S129..N137 spans cleavage site MA-CA
894 cc .. cc 918 $19-gag 25 CA R299..A306 end MHR
964 tt .. tt 988 $20-gag 25 CA L322..C330 interacts with LysRS
1027 ct .. tc 1051 $21-gag 25 CA L343..Q351 interacts with LysRS
650 ca .. ac 673 $22-gag 24 CA P217..P225 CypA interaction; surface of virion core
1043 ca .. ac 1066 $23-gag 24 CA T348..P356 interacts with LysRS
590 cc .. cc 612 $24-gag 23 CA A197..T204 N-terminal CA-H4 helix
931 ca .. ac 953 $25-gag 23 CA Q311..T318 N-terminal CA-H9 helix, LysRS interaction
1275 tt .. tt 1297 $26-gag 23 NC C426..F433 cleavage site p7-p1
12 ag .. ga 33 $27-gag 22 MA A005..G011 links myristoylation and calmodulin-binding
712 gg .. gg 733 $28-gag 22 CA G238..E245 links CA-H5 and -H6 helices
1109 ta .. at 1130 $1-p2 22   V370..M377 cleavage site p2-p7, phosphorylation
1 at .. ta 21 $1-MA 21   M001..V007 minimum signal required for myristoylation
135 ag .. ga 155 $2-MA 21   V046..S052 tether btwn MA at viral membrane and CA
150 gt .. tg 170 $3-MA 21   L051..C057 L50A-L51A prevents particle formation
109 gc .. cg 128 $4-MA 20   A037..R043 binds HIV to plasma membrane, calmodulin
327 ca .. ac 346 $5-MA 20   K110..Q116 nuclear localization signal 2
45 at .. ta 63 $6-MA 19   W016..L021 mutations retarget particle fmtn to Golgi
166 gg .. gg 184 $7-MA 19   G056..G062 G56E, C57D, C57S, I60E elim replication
95 aa .. aa 112 $8-MA 18   K032..S038 binds HIV to plasma membrane, calmodulin
139 aa .. aa 156 $9-MA 18   N047..E052 ?
320 ag .. ga 337 $10-MA 18   E107..K113 nuclear localization signal 2
22 tt .. tt 38 $11-MA 17   L008..L013 ?
367 gg .. gg 382 $12-MA 16   G123..V128 start labile structure near cleavage site
565 aa .. aa 585 $1-CA 21   N189..Q195 connects CA-H3 and CA-H4 helices
647 at .. ta 667 $2-CA 21   H216..I223 CypA interaction; surface of virion core
676 gg .. gg 696 $3-CA 21   G226..R232 CypA interaction; surface of virion core
947 gg .. gg 967 $4-CA 21   W316..V323 CA H9 helix, endocytosis signal
1039 at .. ta 1059 $5-CA 21   M347..V353 interacts with LysRS
832 ag ga 851 $6-CA 20   S278..D284 necessary for formation of dimer interface
910 ct .. tc 929 $7-CA 20   L304..S310 spans CA-H8-H9 helices
927 tt .. tt 946 $8-CA 20   S310..W316 N-terminal, LysRS interaction site
1306 aa .. aa 1325 $1-p1 20   K436..K442 start is slip site, p1 protein
1319 cc .. cc 1334 $2-p1 16   S440..P445 middle, p1 protein
  1. The rank of each rdIMR within the entire gag gene was determined first, then rank within each mature protein. Multiple rdIMRs of the same length were ordered by sequence position.