CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1999
Accession number AY610968
Name 03SP93329
SubtypeCRF01_AE
CountrySpain (Thailand)
Sampling year 2003
Patient93329

AY610968 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 123 nt 3' terminus

The primary sequence:

cactgcttaa gcctcaataa agcattgcct tgagtgccct aaagtggtgt gtgcccatct gtgtaaagga ctctggtaac tagagatccc tctagaccac atcttag--act gagtaaaaat ctctagca

The optimal secondary structure:


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