CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 340
Accession number AY535659
Name EE0359
SubtypeCRF06_cpx
CountryEstonia
Sampling year 2001
Patient359

AY535659 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 ggcgaaccct aagatgctgc atagaagcag ccgcttctcg cttgtactgg gtctctcttg ctagaccaga tttgagcctg ggagctctct gactagcagg ggaacccact gcttaggcct caataaagct tgccttgagt gcttcaagta gtgt

The optimal secondary structure:


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