CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1977
Accession number AF239655
Name TZB0021 I9LTR
SubtypeD
CountryTanzania
Sampling year 1996
Patient9-baby

AF239655 isolate has foldings of [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 Complete poly(A) region

The primary sequence:

ctaaccctca gatgctgcat ataagcagct gctttttgcc tgtactgggt ctctcttgtt agaccagatt tgagcctgag agctctctgg ctagcgaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttcaagtagt gtgtgcccat ttgttgtg--ac tctggtaa

The optimal secondary structure:


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