CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2387
Accession number FJ614965
Name 08MHI4_4658
SubtypeCRF02_AG
CountrySouth Korea (Africa)
Sampling year 2008
PatientMHI

FJ614965 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:

ctagccctca gacgctgcat ataagcagct gcttctcgcc tgtactaggt ctctcttgct agaccagatt tgagcctagg agctctctga ctagcagagg aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttcaagtagt gtgtgcccgt ctgttgtgtg actctagtaa ctagagatcc ctcagaccat tctagcttga gta-aaaatct ctagca

The optimal secondary structure:


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