CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 238
Accession number AF411967
Name 99ZACM9
SubtypeC
CountrySouth Africa
Sampling year 1999
PatientCM9

AF411967 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:

ccagccctca gatgctgcat ataagcagct gcttttcgcc tgtactgggt ctctctaggt agaccagatc tgagcccggg agctctctgg ctatctaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc tctaagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagaccct ttttggtagt gtggaaaatc tctagca

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