CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 803
Accession number AB253680
Name pJPDR3730AE31
SubtypeCRF01_AE
CountryJapan
Submitted to NCBI 2006
PatientNH2000-001

AB253680 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:

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

Isolates with identical sequences of region:

AB253635(#758) AB253636(#759) AB253640(#763) AB253642(#765) AB253643(#766) AB253659(#782) AB253660(#783) AB253662(#785) AB253663(#786) AB253665(#788) AB253666(#789) AB253667(#790) AB253668(#791) AB253669(#792) AB253670(#793) AB253671(#794) AB253672(#795) AB253673(#796) AB253674(#797) AB253675(#798) AB253676(#799) AB253677(#800) AB253678(#801) AB253679(#802)

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