Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2522
Accession number U73094
Name TW358_1
Submitted to NCBI 1996

U73094 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:

gcagccctca gatgctgcat gtaagcagct gctttttgcc tgtacggggt ctctctagtt agaccagatc tgagcctggg agctctctgg ctagctaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttgcaagtag tgtgtgcccg tctgttgtgt gagtgtggta actagagatc cctcagacct ttctagtcag tgtggaaaat ctctagca

The optimal secondary structure:

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