CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2709
Accession number AB480045
Name 194AG29
Subtype02D
CountryGhana
Sampling year 2003

AB480045 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 gatgctgcat ataagcagcc gctttctgct tgtactgggt ctctctggtt agaccagatc tgagcctggg agctctctgg ctaactgggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc cttaagtagt gtgtgcccat ctgttgtgtg actctggtaa ctagagatcc ctcagacctt tgtagtcact gtagaaaatc tctagca

The optimal secondary structure:


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