CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1096
Accession number DD033495
Name patent seq
SubtypeCRF08_BC
CountryJapan
Submitted to NCBI 2004
CommentsPatent

DD033495 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 gtcaaccctc agatgctgca tataagcagc tgcttttcgc ctgtactggg tctctctagt tagaccagat ctgagcctgg gagctctctg gctagctagg gaacccactg cttaagcctc aataaagctt gccttgagtg ctctgagcag tgt

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