Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2310
Accession number EU938114
Name 02RU872
Sampling year 2002

EU938114 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 gctttttgcc tgtactgggt ctctctggtt agaccagatc -gagcctggga gctctctggc tagctaggga acccactgct taagcctca-t aaagcttgcc ttgagtgctt tgagtagtgt gtgcccgtct gttgtatgac tctggtaact agagatccct cagaccactc taggcggtgt a-aaaatctct agca

The optimal secondary structure:

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