CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2088
Accession number AF196751
Name 97CM21
SubtypeCRF02_AG
CountryCameroon
Sampling year 1997

AF196751 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 USE region

The primary sequence:

gttggggagt ggctaaccct cagaagctgc atataagcag ccgcttctcg cctgtactgg gtctctcttg ctagaccaga tttgagcctg ggagctctct gactagctag ggaacccact gcttaagcct caataaagct tgccttgagt gcttcaagta gtgt

The optimal secondary structure:


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