Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2331
Accession number FJ614901
Name 03LKD2_4073
CountrySouth Korea (Ghana)
Sampling year 2003

FJ614901 isolate has foldings of [DIS region] [PBS region] [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 ataagccgcc gcttctcgcc tgtactaggt ctctcttgct agaccagatc tgagcctagg agctctctgg ctaggg-gaga acccgctgct taagcctcaa taaagcttgc cttgagtgct taaagtagtg ggtgcccgtc tgttgtgtga ctctggtaac tagaaatccc tcagaccact ctagactgcg ta-aaaatctc tagca

The optimal secondary structure:

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