Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 3153
Accession number EU047697
Name 03HSJ9_3524s1
CountrySouth Korea
Sampling year 2003

EU047697 isolate has foldings of [PBS region] [Core poly(A) site] [123nt 3' terminus] [USE domain, TAR, polyA] [USE region] [227nt 3' terminus] [USE, TAR, polyA] .

The region encompassing 227 nt 3' terminus

The primary sequence:

cgagccctca aatgctgcat ataagcagct gctttctgcc tgtactgggt ctctctggtt agaccagatc tgagcctggg agctctctgg ctagctaggg aacccactgc ttaagcctca ataaaagctt gccttgagtg cttcaagtag tgtgtgcccg tctgttgtgt -acacagcaaa cagcagccag gtcagccaaa attaccctat agtgcaaaac atccaggg

The optimal secondary structure:

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