Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 3139
Accession number EF370231
Name 06KJin1_2679
CountrySouth Korea
Sampling year 2006

EF370231 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:

cgaaccctta ggtggtgcat aaaagcgggt gctttt-gcct gtattgggtc tctctggtta gaccagatct gagcctggga gctctctggc tgagtaggga acccactgtt taagcctcaa taaagcttgc gttgagtgct ttaagtagtg tgtgcccgtt tgttgtgtga ctctggtaac tagagatccc tcagaccctt -------------------------a

The optimal secondary structure:

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