CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1494
Accession number AF254706
Name NT42_3
SubtypeC
CountryTanzania
Sampling year 1996
Patient42

AF254706 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 DIS SD and Psi hairpins

The primary sequence:

ggactcggct tgctgaagtg cactcggcaa gaggcgagag -cggcgactgg tgagtacgcc aaattttact tgactagcgg aggctagaag gagag

The optimal secondary structure:


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