CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 311
Accession number AY228556
Name 99ZATM10
SubtypeC
CountrySouth Africa
Sampling year 1999
PatientTM10

AY228556 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:

tcaaccctca gatgctgcat ataagcagct gcttttcgct tgtacggggt ctctctaggt agaccagatc tgagcccggg agctctctgg ctatctaggg aacccactgc ttaagcctca ataaagcttg ccttgagcgc tctgagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagaccct ttgtggtagt gtggaaaatc tctagca

The optimal secondary structure:


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