Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 3459
Accession number EF125630
Name AS1M24ltrc2C
Sampling year 2004

EF125630 isolate has foldings of [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:

cgagccctca gatgctgcat ataagcagct gctttctgcc tgtactgggt ctctctggtt agaccagatc tgagcctggg agctctctgg ctgactaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc tttaagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagaccat tttagtcagt gtggaaaatc tctagca

Isolates with identical sequences of region:

EF125628(#3457) EF125629(#3458)

The optimal secondary structure:

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