Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2280
Accession number EU938084
Name 97RU246
Sampling year 1997

EU938084 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 tgtactgggt ctctctggtt agaccaaatc -gagcctggga gttctctggt tagttaggga acccctggtt taaccctcat aaaagttggc ctggagggtt ttaagtagtg tgtgcccgct ggttgtataa ctctggaaac taaaaatccc tcaaaccact ctaagcgggg aa-aaattctc tagca

The optimal secondary structure:

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