CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1822
Accession number AY610971
Name 03SP97646
SubtypeB
CountrySpain (Switzerland)
Sampling year 2003

AY610971 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 227 nt 3' terminus

The primary sequence:

cgagccctca gatgctgcat ataagcagct gctttgtgcc tgtacggggt ctctctggtt agaccagatc tgagcctggg agctctctgg ctgactaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttcaagtagt gtgtgcccgt catgttgtgt gac-ctggtaa ctagagatcc ctcaaaccct tttagtcagt gtggaaaaat ctctagca

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