Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 780
Accession number AB253657
Name pJPDR1873AE47
Submitted to NCBI 2006

AB253657 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 aaaagcagcc gcttttcgct tgtactgggt ctctcttgat tagaccaggt c-gagcccggg agctctctgg ctagcaaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttaaagtggt gtgtgcccat ttgtgtcagg actctggtaa ctagagatcc ctcagaccac tctagactga gta-aaaatct ctagca

Isolates with identical sequences of region:

AB253647(#770) AB253648(#771) AB253651(#774) AB253658(#781)

The optimal secondary structure:

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