Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2384
Accession number FJ614961
Name 08MHI1_4366
CountrySouth Korea (Africa)
Sampling year 2008

FJ614961 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:

ctagcccaca gacgctgcat ataagcagct gcttctcgcc tgtactgggt ctctcttgct agaccaaatt tgagcctggg agctctctga ctagcaggag gaacccactg cttaagcctc aataaagctt gccttgagtg cttcaagtag tgtgtgcccg tcggttgtgt gactctggta actagagatc cctcagacca ttatagcttg agta-aaaatc tctagca

The optimal secondary structure:

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