CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2041
Accession number AY610981
Name 03SP100609
SubtypeCRF02_AG
CountrySpain (Cameroon)
Sampling year 2003

AY610981 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 227 nt 3' terminus

The primary sequence:

ctaaccctca gatgctgcat ataagcagcc gcttttcgcc tgtactaagt ctctcttgct agaccagatt taagcctaag agctctctag ctagtaaaag aacccactgc ttaagcctca ataaaagctt gccttgagtg cttcaagtag tgtgtgcccg tctggtgttt gactctggta actagagatc cctcagacta aaagctagac tgtgtaaaaa tctctagca

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