Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2405
Accession number FJ614994
Name 04HAS1_4193
CountrySouth Korea
Sampling year 2004

FJ614994 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:

ctagccctca gaagctgcat ataagcagcc gcttctcgcc tgtactgggt ctctcttgct agaccagatc tgagcctggg agctctctga ctagcagggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttcaagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagactgt tcgagactaa gtg-aaaatct ctagca

Isolates with identical sequences of region:

FJ614995(#2406) FJ614998(#2409) FJ614999(#2410) FJ615001(#2412) FJ615002(#2413)

The optimal secondary structure:

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