CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 666
Accession number AM000053
Name 97CD.KCC2
SubtypeA4
CountryDRC
Sampling year 1997
PatientKCC2

AM000053 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 ataagcagct gctttctgct tgtactgggt ctctcttgat agaccagata -gagcctggga gctctctggc tagcaaggga acccactgct taagcctcaa taaaagcttg ccttgagtgc ttcaagtggt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagaccac cttag-cagag tgaaaaatct ctagca

The optimal secondary structure:


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