CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1979
Accession number AF239657
Name TZB0017 I6LTR
SubtypeAD
CountryTanzania
Sampling year 1996
Patient6-baby

AF239657 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 USE region

The primary sequence:

gttggggagt ggctaaccct cagatgctgc atataagcag ctgcttttcg cctgtactgg gtctctcttg ttagaccaga tttgagcctg agagctctct ggctagctag ggaacccact gcttaagcct caataaagct tgccttgagt gcttcaagta gtgt

Isolates with identical sequences of region:

AF096643(#1925)

The optimal secondary structure:


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