Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 165
Accession number AJ302646
Name 99SE-MP1299
SubtypeGroup O
Sampling year 1999

AJ302646 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:

ctaaccctca gatgctgcat ataagcagcc gcttaccgct tgtaccgggt ctcggttaga gaaccaggtc tgagcccggg agctccctgg cctctagctg aacccgctgc ttaacgctca ataaagcttg ccttgagtga g--aagcagtgt gtgctcatct gttc---gaccct ggtatctaga gatccctcag atcacgtaga ctgaggcaga aaatctctag ca

The optimal secondary structure:

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