CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2042
Accession number AY610982
Name 03SP105211
SubtypeCRF11_cpx
CountrySpain (Cameroon)
Sampling year 2003

AY610982 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, TAR, polyA

The primary sequence:

agcagccgct ctttgcttgt actaggtctc tctagttaga ccagatctga gcctaagagc tctctggcta gctaaggaac ccactgctta agcttcaata aagcttgcct taagtgcttt aagtagtgt

The optimal secondary structure:


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