Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2291
Accession number EU938095
Name 04RU1077
Sampling year 2004

EU938095 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 tgtactgggt ctctctggtt agaccagatc -gagcctggga gctctctggc tagctaggga acccactgct taagcctcaa taaagcttgc cttgagtgct ttaagtagtg tgtgcccgtc tgttgtatga ctctggtaac tagagatccc tcagaccact ctaggcggtg ta-aaaatctc tagca

Isolates with identical sequences of region:

EU938086(#2282) EU938087(#2283) EU938094(#2290) EU938098(#2294) EU938102(#2298) EU938104(#2300) EU938107(#2303) EU938109(#2305)

The optimal secondary structure:

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