CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2040
Accession number AY610980
Name 03SP99405
SubtypeCRF02_AG
CountrySpain (Equatorial Guinea)
Sampling year 2003

AY610980 isolate has foldings of [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:

ctaaccctca gatgctgcat ataagcagct gcttctcgct tgtactgggt ctctcttgct ggaccagatt tgagcctggg agctctctgg ctag-tagaga acccactgct taagcctcaa taaagcttgc cttgagtgct ttaagtagtg tgtgcccgtc tgttgtgtga ctctggtaac tagagatccc tcagaccact ctagactgtg ta-aaaatctc tagca

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