CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 340
Accession number AY535659
Name EE0359
SubtypeCRF06_cpx
CountryEstonia
Sampling year 2001
Patient359

AY535659 isolate has foldings of [DIS region] [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 Complete poly(A) region

The primary sequence:

cgaaccctaa gatgctgcat agaagcagcc gcttctcgct tgtactgggt ctctcttgct agaccagatt tgagcctggg agctctctga ctagcagggg aacccactgc ttaggcctca ataaagcttg ccttgagtgc ttcaagtagt gtgtgcccgt ctgttgtgtg actctggtaa

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