Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1857
Accession number AY610989
Name 02SP79321
CountrySpain (Equatorial Guinea)
Sampling year 2002

AY610989 isolate has foldings of [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 gaagctgcat ataagcagct gctttccgcc tgtgctgggt ctctctggtt agaccagatc tgagcctggg mgctctctgg ctagctaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc tataagtagt gtgtgcccat ctgttgtgtg actctgggta ctagagatcc ctcagaccac tctagacggt gta-aaaatct ctagca

The optimal secondary structure:

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