CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2287
Accession number EU938091
Name 00RU672
SubtypeA
CountryRussia
Sampling year 2000

EU938091 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:

ctaaccctca gatgctgcat ataagcagct gcttttcgcc tgtactgggt ctctctggtt agaccagatc -gagcctggaa gctctctggc tagctaggga acc-actgctt aagcctcaat aaagcttgcc ttgagtgctt taagtagtgt gtgcccgtct gttgtatgac tctggtaact agagatcctt cagacactct -aggcggtgta -aaaatctcta gca

The optimal secondary structure:


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