CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1348
Accession number AF413960
Name 98UA0116 clone 4-ltr
SubtypeA1
CountryUkraine
Sampling year 2000
PatientUA0116

AF413960 isolate has foldings of [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:

gttggggagt ggctaaccct cagatgctgc atataagcag ctgcttttcg cctgtactgg gtctctctgt ttagaccaga tc-gagcctgg gagctctctg gctagctagg gaacccactg cttaagcctc aataaagctt gccttgagtg ctttaagtag 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