Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2352
Accession number FJ614935
Name 99MHI12_5015
CountrySouth Korea (Africa)
Sampling year 1999

FJ614935 isolate has foldings of [DIS region] [PBS region] [Core poly(A) site] [123nt 3' terminus] [USE domain, TAR, polyA] [227nt 3' terminus] [Complete poly(A) region] [USE, TAR, polyA] .

The region encompassing 227 nt 3' terminus

The primary sequence:

-tagccctcag acgctgcata taagcagctg ctcttcgcct gtactggggt cttcttgcta gaccagattt gagcctggga gctctttgac tagcagggga acccactgct taagcttcaa taaagcttgc cttgagtgct tcaagtagtg tgtgcccgtc tgttgtgtga ctctggtaac tagagatccc tcagaccatt atagcttgag ta-aaaatctc tagca

The optimal secondary structure:

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