CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1968
Accession number AF239646
Name PAIR18_INFANT
SubtypeC
CountryTanzania
Sampling year 1996
Patient18-baby

AF239646 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:

ccagccctca g-tgctgcata taagcagctg cttttcgctt gtactgggtc tctctaggta gaccagattt gagcctggga gctctctggc catctaggga acccactgct taaagcctca ataaagcttg ccttgagtgc tctaagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagactct ttt-gtcagtg tggaaaatct 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