CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 3184
Accession number AY047308
Name TV001C8_5
SubtypeC
CountrySouth Africa
Sampling year 1998
PatientTV001

AY047308 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 Complete poly(A) region

The primary sequence:

tcaaccctca gatgctgcat ataagcagct gcttttcgcc tgtactgggt ctctctcggt agaccagatc tgagcctggg agccctctgg ctatctaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc tttaagtagt gtgtgcccat ctgttgtgtg actctggtaa

Isolates with identical sequences of region:

AX455917(#1084) AY162223(#239) BD437615(#1090)

The optimal secondary structure:


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