CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1982
Accession number AF405199
Name 99ZM096M
SubtypeC
CountryZambia
Sampling year 1999
Patient096M

AF405199 isolate has foldings of [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:

actggg-agtg gctaaccctc agatgctgca tataagcagc tgcttttcgc ctgtactggg tctctctagg tagaccagat ctgagcctgg gagctctctg gctatctggg gaacccactg cttaagcctc aataaagctt gccgtgagtg ctataagtag tgt

The optimal secondary structure:


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

STCU 2008-2010
Institute of Molecular Biology and Genetics 2008-2012