Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2301
Accession number EU938105
Name 04RU1121
Sampling year 2004

EU938105 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 gatgctgcat ataagcagct gcttttcgct cggtactggg tctctctggt tagaccagat c-gagcctggg agctctctgg ctagctaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttaaagtagt gtgtgcccgt ctgttgtatg actctggtaa ctagagatcc ctcagaccac tctaggcggt gta-aaaatct ctagca

The optimal secondary structure:

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