CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1998
Accession number AY610967
Name 03SP100655
SubtypeA
CountrySpain (Mozambique)
Sampling year 2003

AY610967 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 USE region

The primary sequence:

gtttgggagt ggcttaccct cagaatgctg catataagca gctgcttttc gcctgtactg ggtctctctt gttggaccag ata-gagcctg ggagctctct ggctagcaag ggaacccact gcttaagcct caataaaagc ttgccttgag tgcttcaagt agtgt

The optimal secondary structure:


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