CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 288
Accession number AY423382
Name 671-00T93
SubtypeB
CountryNetherlands
Sampling year 2000
PatientH671

AY423382 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 PBS domain

The primary sequence:

tgttatgtga ctctggtaac tagagatccc tcagaccaat ttagtcagtg tggaaaatct ctagcagtgg cgcccgaaca gggacttgaa agcgaaagta aaaccagagg agatctctcg acgcaggac

The optimal secondary structure:


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