CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 16
Accession number M38431
Name NY5CG
SubtypeB
CountryUSA
Sampling year 1984
PatientNY5

M38431 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 USE, TAR, polyA

The primary sequence:

agcagctgct ttttgcctgt actgggtctc tctggttaga ccagatctga gcctgggagc tctctggcta gctagggaac ccactgctta agcctcaata aagcttgcct tgagtgctac aagtagtgt

Isolates with identical sequences of region:

AB287369(#935) AB287370(#936)

The optimal secondary structure:


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