CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 3297
Accession number HM067748
Name nx2
SubtypeCRF08_BC
CountryChina
Sampling year 2006

HM067748 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 gctttgcgcc tgtaccgggt ctct-tagtta gaccagatct gagcctggga gctctctggc tagctagg-aa cccactgctt aagcctcaat aaagcttgcc ttgagtgctc tgagcagtgt gtgcccatct gttgtgtgac tctggtaact agagatccct cagacccttg tgg-cagtgtg gaaaatctct agca

The optimal secondary structure:


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