CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 939
Accession number AB286849
Name p04JPDR5782C12
SubtypeCU
CountryJapan
Sampling year 2004
Patient5782

AB286849 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 USE region

The primary sequence:

actggg-agtg gctgaccctc agatgctgca tataagcagc tgcttttcgc ttgtactggg tctctctagt tggaccagat ctgagcctgg gagctctctg gctaactggg gaacccactg cttaagcctc aataaagctt gccttgagtg ctctgagcag tgt

Isolates with identical sequences of region:

AB286850(#940)

The optimal secondary structure:


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