Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2333
Accession number FJ614908
Name 04LKD7_4080
CountrySouth Korea (Ghana)
Sampling year 2004

FJ614908 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:

ctacccctcc tatgctgcat ataagcagcc gcttctcgcc tgtactaggt ctctcttgct agaccagatc tgagcctagg agctctctgg ctag-tggaga acccgctgct taagcctcaa taaagcttgc cttgagtgct taaagtagtg tgtgcccgtc tgttgtgtga ctctggtaac tagagatccc tcagaccact ctagactgcg ta-aaaatctc tagca

The optimal secondary structure:

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