CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 876
Accession number AB253698
Name pJPDR1236AEE03
SubtypeCRF01_AE
CountryJapan
Submitted to NCBI 2006
Patient1236

AB253698 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:

tgtgttagga ctctggtaac tagagatccc tcagaccact ctagactgag ta-aaaatctc tagcagtggc gcccgaacag ggacttgaaa gtgaaagtta atagggactc gaaagcgaaa gtt---ccagaga agttctctcg acgcaggac

Isolates with identical sequences of region:

AB052601(#1057) AB052612(#1068) AB220944(#727) AB253423(#906) AB253426(#909) AB253427(#910) AB253681(#859) AB253682(#860) AB253683(#861) AB253684(#862) AB253685(#863) AB253686(#864) AB253688(#866) AB253689(#867) AB253690(#868) AB253691(#869) AB253692(#870) AB253693(#871) AB253694(#872) AB253695(#873) AB253696(#874) AB253697(#875) AB253699(#877) AB253700(#878) AB253701(#879) AB253702(#880) AB485655(#2664)

The optimal secondary structure:


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

STCU 2008-2010
Institute of Molecular Biology and Genetics 2008-2012