CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 296
Accession number AJ508597
Name 00NE36
Subtype0206
CountryNiger
Sampling year 2000

AJ508597 isolate has foldings of [DIS region] [PBS region] [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 Core poly(A) site

The primary sequence:

ctgggtctct ctcgctagac cagatttgag cctgggagct ctctgactag caggagaacc cactgcttaa gcctcaataa agcttgcctt gagtgcttca agtagtgtgt gcccgtctgt tgtgtgactc tggtaa

The optimal secondary structure:


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