Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1084
Accession number AX455917
Name TV001
CountryUSA South Africa
Submitted to NCBI 2002

AX455917 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:

tcaaccctca gatgctgcat ataagcagct gcttttcgcc tgtactgggt ctctctcggt agaccagatc tgagcctggg agccctctgg ctatctaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc tttaagtagt gtgtgcccat ctgttgtgtg actctggtaa ctagagatcc ctcagaccct ttgtggtagt gtggaaaatc tctagca

Isolates with identical sequences of region:

AY047308(#3184) AY162223(#239) BD437615(#1090)

The optimal secondary structure:

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