CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 111
Accession number AJ288981
Name 97SE1078
SubtypeCRF06_cpx
CountrySenegal
Sampling year 1997
Patient1078

AJ288981 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 USE region

The primary sequence:

gctggggagt ggctaaccct aagatgctgc ataaaagcag ccgcttctcg cttgtactgg gtctctcttg ctagaccaga tttgagcctg ggagctctct gactagcagg ggaacccact gcttaagcct caataaagct tgccttgagt gctttaagta gtgt

The optimal secondary structure:


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