CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2288
Accession number EU938092
Name 97RU207
SubtypeA
CountryRussia
Sampling year 1997

EU938092 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 USE region

The primary sequence:

gttggggagt ggctaaccct cagatgctgc atataagcag ctgcttttcg cctgtactgg gtctctctgg ttagaccaga tc-gagcctgg aagctctctg gttagctagg gaacccactg cttaagcctc aataaagctt gccttgaggg ctttaagtag ggg

The optimal secondary structure:


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