Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 240
Accession number AY162224
Name TV002 clone 12/5_1
CountrySouth Africa
Sampling year 1998

AY162224 isolate has foldings of [DIS region] [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:

ccagccctca gatgctgcat ataagcagcg gcttttcgcc tgtactgggt ctctctaggt agaccagatc cgagcctggg agctctctgt ctatctgggg aacccactgc ttaggcctca ataaagcttg ccttgagtgc tctaagtagt gtgtgcccat ctgttgtgtg actctggtaa ctctggtaac tagagatccc tcagaccctt tgtggtagtg tggaaaatct ctagca

Isolates with identical sequences of region:

AX455929(#1085) BD437626(#1091)

The optimal secondary structure:

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