CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1083
Accession number AX316202
Name HXB2_patent
SubtypeB
CountryUnited Kingdom
Submitted to NCBI 2001
PatientLAI
CommentsPatent

AX316202 isolate has foldings of [DIS region] [PBS region] [Core poly(A) site] [123nt 3' terminus] [USE domain, TAR, polyA] [USE region] [227nt 3' terminus] [Complete poly(A) region] [USE, TAR, polyA] .

The region encompassing 123 nt 3' terminus

The primary sequence:

cactgcttaa gcctcaataa agcttgcctt gagtgcttca agtagtgtgt gcccgtctgt tgtgtgactc tggtaactag agatccctca gaccctttta gtcagtgtgg aaaatctcta gca

Isolates with identical sequences of region:

A04321(#1102) A07867(#1105) AB221005(#685) AB221125(#732) AB221126(#733) AB253432(#914) AB287371(#937) AB485649(#2729) AF003888(#1197) AF004394(#22) AF033819(#1391) AF042101(#123) AF196708(#1279) AF196710(#1281) AF196712(#1283) AX419821(#1535) AX772015(#1086) AY118159(#1420) AY452657(#1337) AY452660(#1340) AY452661(#1341) AY610991(#2052) AY851673(#2094) AY851674(#2095) AY851681(#2102) AY851682(#2103) AY970949(#1154) BD410064(#1089) CS793683(#3475) CS793684(#1093) D86068(#1094) D86069(#1095) DL260745(#1670) DM461230(#3476) DM461231(#3477) DQ295192(#569) EF363124(#966) EF370257(#1729) EF370362(#1794) EU047603(#1623) EU047606(#1600) EU047619(#1821) EU047656(#1859) EU541617(#1046) FB341548(#1902) FB707281(#1903) FW371672(#3839) HH978650(#3848) HI553377(#3879) K02013(#19) K02083(#70) K03455(#1182) L28869(#2437) L28870(#2438) L28871(#2439) L28872(#2440) L28873(#2441) L28874(#2442) L28877(#2445) L28880(#2448) L28906(#2474) M26727(#12) M38429(#15) NC_001802(#0) U12055(#11) U24466(#2380) U24468(#2488) U24469(#2489) U24470(#2490) U24471(#2491) U24472(#2492) U24473(#2493) U24474(#2494) U24478(#2495) U24479(#2496) U24480(#2497) U34603(#33) U69584(#254) U69585(#255) U69590(#260) U69591(#261) U69593(#263) U73099(#2524) U80508(#2527) U80514(#2533) U80519(#2538) U80520(#2539) U80521(#2540) U80525(#2544) U80526(#2545) U80527(#2546) U80530(#2549) U80533(#2552) U80539(#2558) U81454(#2559) U81470(#2575) U81477(#2582) U89856(#2589) U89857(#2590) U89859(#2592) U89860(#2593) U89861(#2594) U89863(#2596) U89864(#2597) U89865(#2598) U89866(#2599) X01762(#64)

The optimal secondary structure:


The suboptimal structures within ΔΔG ≤ 4 kcal/mole of the minimum free energy