CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 794
Accession number AB253671
Name pJPDR3730AE08
SubtypeCRF01_AE
CountryJapan
Submitted to NCBI 2006
PatientNH2000-001

AB253671 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:

ctaaccctca gatgctgcat aaaagcagcc gcttttcgct tgtactgggt ctctcttgtt agaccaggtc -gagcccggga gctctctggc tagcagggga acccactgct taagcctcaa taaagcttgc cttgagtgct taaagtggtg tgtgcccatt tgtgtcagga ctctggtaac tagagatccc tcagaccact ctagactgag ta-aaaatctc tagca

Isolates with identical sequences of region:

AB253638(#761) AB253645(#768) AB253665(#788) AB253666(#789) AB253667(#790) AB253669(#792) AB253670(#793) AB253672(#795) AB253676(#799) AB253678(#801) AB253679(#802) AB253680(#803)

The optimal secondary structure:


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