CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2279
Accession number EU938083
Name 03RU1028
SubtypeA
CountryRussia
Sampling year 2003

EU938083 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 gcttttcgcc tgtgctgggt ctctctggtt agaccagata -gagcctggga gctctctggc tagctaggga acccactgct taagcctcaa taaagcttgc cttgagtgat ttaagtagtg tgtgcccgtc tgttgtgtga ctctggtaac tagagatccc tcagaccact ctaggcggag ta-aaaatctc tagca

The optimal secondary structure:


The suboptimal structures within ΔΔG ≤ 4 kcal/mole of the minimum free energy