CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 873
Accession number AB253695
Name pJPDR1236AEC41
SubtypeCRF01_AE
CountryJapan
Submitted to NCBI 2006
Patient1236

AB253695 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:

agcagccgct tttcgcttgt actgggtctc tcttgttaga ccaggtc-gag cccgggagct ctctggctag caagggaacc cactgcttaa agcctcaata aagcttgcct tgagtgcttg aagtggtgt

Isolates with identical sequences of region:

AB052609(#1065) AB220945(#728) AB253683(#861) AB253699(#877)

The optimal secondary structure:


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