CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1934
Accession number AF096653
Name TZB0020
SubtypeA
CountryTanzania
Sampling year 1996
Patient20

AF096653 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 227 nt 3' terminus

The primary sequence:

ctaaccctca gatgctgcat ataagcagct gctttttgcc tgtactgggt ctctcttgtt agaccagata -gagcctggga gctctctggc tagcgaggga acccactgct taagcctcaa taaagcttgc cttgagtgac tcaagcagtg tgtgcccgtc tgttgtctga ctctggtaac tagagatccc tcagaccacg gtagactgtg taaaaaatct ctagca

The optimal secondary structure:


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