CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2038
Accession number AY610978
Name 03SP91571
SubtypeCRF11_cpx
CountrySpain (Equatorial Guinea)
Sampling year 2003

AY610978 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:

ttaaccctca gatgctgcat aaaagcagcc gcttttcgcc tgtactgggt ctctctagtt ggaccagatc tgagcccggg agctctctgg ctagctaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttcaagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagacc-tt ttagtcagtg tggaaaatct ctagca

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