Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2267
Accession number EF380390
Name 164284_01
CountrySpain (Cameroon)
Submitted to NCBI 2007

EF380390 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 tgtactaggt ctctcttgct agaccagatt tgagcctagg agctctctag ctagtagagg aacccactgc ttaagcctca ataaaagctt gccttaagtg cttcaagtag tgtgtgcccg tctagtgttt gactctggta actagagatc cctcagacta aaagctagac tgtgtaaaaa tctctagca

The optimal secondary structure:

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