CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1513
Accession number AF254726
Name E33_3
SubtypeC
CountryTanzania
Sampling year 1996
Patient33

AF254726 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 gcttttcgcc tgtactgggt ctctctaggt ggaccagatc tgagcctggg cgctctctgg ctacctaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc tctgagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagacctt tttggt-agtg tggaaaatct ctagca

The optimal secondary structure:


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