Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2237
Accession number EF370225
Name 03KJin9b_2883s1
CountrySouth Korea
Sampling year 2003

EF370225 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:

cgagccctca gatgctgcat aaaagcagct gctttctgcg tgtacggggt ctctctggtt agaccagatc tgagcctggg agctctctgg ctggctaggg aacccactgc ttaagcctca ataaagcttg cctggagtgc tttaagtagg gggtgcccgt ctgtggtggg actctggtaa ctagagatcc ctcagaccat tttagtcagt gtggaaaatc tctagca

The optimal secondary structure:

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