Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 896
Accession number AB253718
Name pJPDR5032AE05
Submitted to NCBI 2006

AB253718 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:

ttaaccctca gatgctgcat aaaagcagcc gcttttcgct tgttctgggt ctctcttgtt agaccaggtc -gagcccggga gctctctggc tagcagggga acccactgct taaagcctca ataaagcttg ctttgagtgc ttaaagtggt gtgtgcccat ctgtgttagg actctggtaa ctagagatcc ctcagaccac tctagactga gta-aaaatct ctagca

Isolates with identical sequences of region:

AB253717(#895) AB253719(#897) AB253720(#898) AB253721(#899) AB253722(#900) AB253723(#901) AB253724(#902) AB253725(#903)

The optimal secondary structure:

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