CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 3133
Accession number AY610964
Name 03SP103959
SubtypeA1
CountrySpain (Equatorial Guinea)
Sampling year 2003
Patient103959

AY610964 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 Complete poly(A) region

The primary sequence:

ctaaccctca gaagctgcat ataagcagcc gcttttcgct tgtactgggt ctctcttgtt agaccagatc -gagcctggga gctctctgga actagcgagg gaacccactg cttaagcctc aataaagctt gccttgagtg cct-aagtagt gtgtgcccgt ctgttgtaag actctggtaa

The optimal secondary structure:


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