CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 676
Accession number AY586548
Name Cu85
SubtypeG
CountryCuba
Sampling year 1999
PatientCU85

AY586548 isolate has foldings of [DIS region] [PBS region] [Core poly(A) site] [123nt 3' terminus] [USE domain, TAR, polyA] [227nt 3' terminus] [Complete poly(A) region] [USE, TAR, polyA] .

The region encompassing Complete poly(A) region

The primary sequence:

--agcccccaga tgctgcatat aagcagccgc ttctcgcctg tastgggtct ctcttgctag accagatttg agcctgggag ctctctgact agcaggggaa cccactgctt aagcctcaat aaagcttgcc ttgagtgctt gaagtagtgt gtgcccgtct gttgtgtgac tctggtaa

The optimal secondary structure:


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