CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1996
Accession number AY610965
Name 98SP7030
SubtypeCRF11_cpx
CountrySpain (Cameroon)
Sampling year 1998

AY610965 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 cagaagctgc ataaaagcag ccgctttc-gc ctgtactggg tctctctagt tagaccagat ctgagcccgg gagctctctg gctagctagg gaacccactg cttaagcctc aataaagctt gccttgagag cttcaagtag 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