CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2000
Accession number AY610969
Name 03SP93328
SubtypeCRF01_AE
CountrySpain (Thailand)
Sampling year 2003
Patient93328

AY610969 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 Core poly(A) site

The primary sequence:

ctgggtctct cttgttagac cagatc-gagc ccgggagctc tctgactagc aagggaaccc actgcttaag cctcaataaa gcttgccttg agtgcctaaa gtggtgtgtg cccatctgtg taaaggactc tggtaa

The optimal secondary structure:


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