CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2564
Accession number U81459
Name VE6NEF
SubtypeB
CountryVenezuela
Sampling year 1991
Patient6

U81459 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:

cgagccctca gatgctgcat ataagcagcc gctttttgcc tgtactgggt ctctctagct agaccagatc tgagcctggg agctctctgg ctaactaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttcaagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagacctc tgtagtcagt gtggaaaatc tctagca

The optimal secondary structure:


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