CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2043
Accession number AY610983
Name 03SP106196
SubtypeG
CountrySpain (Nigeria)
Sampling year 2003

AY610983 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 cagatgctgc atataagcag ctgcttctcg cctgtactgg gtctctcttg ctagaccaga tttgagcctg ggagctctct gactagcagg ggaacccact gcttaagcct caataaagct tgccttgagt gcttcaagta gtgt

The optimal secondary structure:


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