Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2302
Accession number EU938106
Name 04RU1122
Sampling year 2004

EU938106 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 gcttttcgcc tgtactaggg tctctctggt tagaccagat c-gagcctggg agctctctgg ctagctaggg aacccactgg ttaagcctca ataaagcttg ccttgagtgc tttaagtagt gtgtgcccgt ctggtgtatg actctggtaa ctagagatcc cttagaccac tttaggcggt gtaaaaatct tctagca

The optimal secondary structure:

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