CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 109
Accession number AJ288982
Name 95ML127
SubtypeCRF06_cpx
CountryMali
Sampling year 1995

AJ288982 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:

ctaaccctaa actgctgcat aaaagcagcc gcttctcgct tgtactgggt ctctcttgct agaccagatt tgagcctggg agctctctga ctagcagggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttacagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagaccac gctaggcggt gt--aaaatctc tagca

The optimal secondary structure:


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