CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 538
Accession number AJ866557
Name 01IC-PCI123
Subtype02GK
CountryCote d'Ivoire
Sampling year 2001
PatientPCI123

AJ866557 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:

ctaaccctca gatgctgcat ataagcagcc gcttctcgcc tgtactgggt ctctcttgct agaccagatt tgagcctggg agctctctga ctagcagagg aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttcaagtagt gtgtgcccgt ctgttgtgtg actctggtta ctagagatcc ctcagaccac tctagactgt gta-aaaatct ctagca

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