CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2338
Accession number FJ614916
Name 06LKD11_4096
SubtypeCRF02_AG
CountrySouth Korea (Ghana)
Sampling year 2006
PatientLKD

FJ614916 isolate has foldings of [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 PBS domain

The primary sequence:

tgttgtgtga ctctggtaac tagagatccc tcagaccact ctagactgcg ta-aaaatctc tagcagtggc gtccgaacag ggaccggaag ttaataggga ctcgaaagcg aaagtt---ccag agaagctctc tcgacgcagg gac

The optimal secondary structure:


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

STCU 2008-2010
Institute of Molecular Biology and Genetics 2008-2012