Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2057
Accession number AY610997
Name 03SP118828
CountrySpain (Equatorial Guinea)
Sampling year 2003

AY610997 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 gaagctgcat ataagcagcc gcttctcgcc tgtactgggt ctctcttggt agaccagat-t gagcctggga gctctctggc tatcggggga acccactgct taagcctcaa taaagcttgc cttgagtgct ctaagtagtg tgtgcccgtc tgttgtgtga ctctggtaac tagagatccc tcagaccact ctagactgag ta-aaaatctc tagca

The optimal secondary structure:

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