CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2051
Accession number AY610990
Name 03SP110939
SubtypeG
CountrySpain (Equatorial Guinea)
Sampling year 2003
Patient110939

AY610990 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:

gctggggagt ggctaaccct cagaagctgc atataagcag ccgcttctcg cctgtactgg gtctctcttg ctagaccaga tttgagcctg ggagctctct ggctagtagg ggaacccact gcttaagcct caataaagct tgccttgagt gcttcaagta gtgt

The optimal secondary structure:


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