Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 3149
Accession number HM067749
Name sh52
Sampling year 2006

HM067749 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 gaagctgcat ataagcagcc gcttctcgcc tgtactgggt ctctcttgtt agaccagatc tgagcctggg agctctctgg ctagcagggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttcaagtagt gtgggcccgt ctgttgtgtg actctggtaa ctagagatcc ctcaggacca ctctagacag tgta-aaaatc tctagca

The optimal secondary structure:

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