Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2396
Accession number FJ614978
Name 00NYR11_4240
CountrySouth Korea
Sampling year 2000

FJ614978 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:

ctaaccctca gatgctgcat ataagcagcc gcttctcgcc tgtactgggt ctctcttgct aaaccagat-t gagcctggga gctctctgac tagtaaaggg caccctgtgc ttaaccctca aaaaagcttg ccttgagtgc ttcaagtagt gtgcccccct ctgttgtgag actctggtaa ctagagatcc ctcagaccac tctagactgt gtgaaaaatc tctagca

The optimal secondary structure:

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