CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 877
Accession number AB253699
Name pJPDR1236AEE40
SubtypeCRF01_AE
CountryJapan
Submitted to NCBI 2006
Patient1236

AB253699 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 123 nt 3' terminus

The primary sequence:

cactgcttaa agcctcaata aagcttgcct tgagtgcttg aagtggtgtg tgcccatctg tgttaggact ctggtaacta gagatccctc agaccactct agactgagta -aaaatctcta gca

Isolates with identical sequences of region:

AB052604(#1060) AB253695(#873) EF036527(#849)

The optimal secondary structure:


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