Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2265
Accession number EF380386
Name 39124_02
CountrySpain (Cameroon)
Submitted to NCBI 2007

EF380386 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 tgtactgggt ctctcttgct agaccagatt tgagcctggg agctctctgg ctagtggagg aacccactgc ttaagcctca ataaaagctt gccttgagtg cttcaagtag tgtgtgcccg tctggtgttt gactctggta actagagatc cctcagacta aaagctagac tgtgtaaaaa tctctagaca

The optimal secondary structure:

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