Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2059
Accession number AY610999
Name 01SP36729
CountrySpain (Liberia)
Sampling year 2001

AY610999 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 ataagcagcc gcttctcgcc tgtactgggt ctcttttgct aaaccagatt taagcctggg agctctctaa ctagcagaga aacccactgc ttaagcctca ataaagcttg ccttaagtgc ttcaagtagt gtgtgcccgt ctgttgtgta actctagtaa ctaaaaatcc ctcaaaccac tataaactgt gt--aaaatctc tagca

The optimal secondary structure:

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