CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 584
Accession number AY835749
Name 5096-86 clone np2
SubtypeB
CountryUSA
Sampling year 1986
Patient5096

AY835749 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 tgctgaagcg cgcgcagcaa gaggcgaggg gcggcgactg gtgagtacgc caaaattttt gactagcgga ggctagaagg agaga

The optimal secondary structure:


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