Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 934
Accession number AB287368
Name p05JPDR7065B46
Sampling year 2005

AB287368 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 227 nt 3' terminus

The primary sequence:

cgagccctca gatgctgcat ataagcagct gctttt-gcct gtactgggtc tctctggtta gaccagatct gagcctggga gctctctggc tagctaggga acccactgct taagcctcaa taaagcttgc cttgagtgct tcaagtagtg tgtgcccatc tgttgtgtga ctctggtagc tagagatccc tcagatatct ttagtccgtg tggaaaaatc tctagca

The optimal secondary structure:

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