Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2269
Accession number EF380393
Name 00110777
CountrySpain (Equatorial Guinea)
Submitted to NCBI 2007

EF380393 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:

ccaaccctca gatgctgcat ataagcagct gctctttgcc tgtactgggt ctctctggtt agaccagatt tgagcctgag agctctctgg ctagctaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc tttgagtacg tgtgtgcccg tctgttgttt gactctggta actagagatc cctcagacct ctttagtcag tgtggaaaat ctctgagcca

The optimal secondary structure:

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