Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 3328
Accession number GU595162
Name 50612
Sampling year 2001

GU595162 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:

cgaccctaca gacgctgcat ttagccaccc gctttcgccc tgtacgggtt ctctctagta agcccagatc tgaccccggg agctctctgc ctggctagga aacccactgc ttaagcctca ataaagcttg ccttgagtgc tccaagtagt gtgtgcccgt ctgttgtgta actctggtaa ctagagatcc ctcagactat cttagtcagt gtgaaaaatc tctagca

The optimal secondary structure:

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