CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2309
Accession number EU938113
Name 98RU340
SubtypeA
CountryRussia
Sampling year 1998

EU938113 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:

gttgaggagt ggctaaccct cagatgctgc atataagcag ctgcttttcg cctgtactag gtctctctgg gtagaccaga tc-gagcctgg gagctctctg gctagctaag gaacccactg cttaagcctc aataaagctt ggcttgagtg gtttaagtag tgg

The optimal secondary structure:


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