CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 850
Accession number EF036528
Name Fj052
SubtypeCRF01_AE
CountryChina
Sampling year 2005
PatientFj052

EF036528 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 227 nt 3' terminus

The primary sequence:

ccaaccctca gatgctgcat aaaagcagcc gcttctcgct tgtactgggt ctctcttggt agaccagatc -gagcccggga gctctctggc tagcaaggga acccactgct taaagcctca ataaagcttg ccttgagtgc ttgaagtggt gtgtgcccgt ctgtgtttgg actctggtaa ctagagatcc ctcagaccac tctagactaa gta-aaaatct ctagca

The optimal secondary structure:


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