Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 534
Accession number AJ866553
Name 00IC-10092
CountryCote d'Ivoire
Sampling year 2000

AJ866553 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:

ctaaccctca gatgctgcat ataagcagcc gcttttcgct tgtactgggt ctctcttggt agaccagatc -gagcctggga gctctctggc tagcgaggga acccactgct tgaagcctca ataaagcttg ccttgagtgc tgaaagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagaccac tctagacgaa gta-aaaatct ctagca

The optimal secondary structure:

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