Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 3464
Accession number EU807770
Name Progressor_20
Submitted to NCBI 2008

EU807770 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 gctttgcgcc tgtactgggt ctctctagct ggaccagatc tgagcctggg agctctctgg ctaactaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttcaagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagaccaa attagtcagt gtggaaaatc tctagca

Isolates with identical sequences of region:

EU807771(#3465) EU807772(#3466) EU807773(#3467) EU807774(#3468)

The optimal secondary structure:

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