CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1074
Accession number AF290031
Name C.96BW06.F20LTR
SubtypeC
CountryBotswana
Sampling year 1996
Patient96BW06

AF290031 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 gagtgctcta agtagtgtgt gcccatctgt tatatggact ctggtaacta gagatccctc agaccctttt ggt-agtgagg aaaatctcta gca

The optimal secondary structure:


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