CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 880
Accession number AB253702
Name pJPDR1236AEE48
SubtypeCRF01_AE
CountryJapan
Submitted to NCBI 2006
Patient1236

AB253702 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:

ttaaccctca gatgctgcat aaaagcagcc gcttttcgct tgtactgggt ctctcttgct agaccaggtc -gagcccggga gctctctggc tagcagggga acccactgct taaagcctca ataaagcttg ccttgagtgc ttaaagtggt gtgtgcccgt ctgtgttagg actctggtaa ctagagatcc ctcagaccac tctagactga gta-aaaatct ctagca

Isolates with identical sequences of region:

AB253692(#870) AB253693(#871) AB253696(#874) AB253701(#879)

The optimal secondary structure:


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

STCU 2008-2010
Institute of Molecular Biology and Genetics 2008-2012