Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1999
Accession number AY610968
Name 03SP93329
CountrySpain (Thailand)
Sampling year 2003

AY610968 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:

ctagccctca gttgctgcat aaaagcagcc gcttttcgct tgtactgggt ctctcttgtt agaccagatc -gagcccggga gctctctgac tagcaaggga acccactgct taagcctcaa taaagcattg ccttgagtgc cctaaagtgg tgtgtgccca tctgtgtaaa ggactctggt aactagagat ccctctagac cacatcttag --actgagtaaa aatctctagc a

The optimal secondary structure:

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