CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 3319
Accession number GU733714
Name I-1
SubtypeB
CountryUSA
Sampling year 2009
Patientpatient(36090)

GU733714 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 region

The primary sequence:

actggggagt ggcgagccct cagatgctgc atataagcag ctgctttttg cctgtactgg gtctctctgg ttagaccaga tctgagcctg ggagctctct ggctagctag ggaacccact gcttaagcct caataaagct tgccttgagt gcttcaagta gtgt

Isolates with identical sequences of region:

AB480696(#2721) AF042101(#123) AF102212(#3582) AF196714(#1285) DQ848479(#3645) DQ848481(#3647) DQ848486(#3652) DQ848488(#3654) DQ848490(#3656) DQ854716(#972) GU733713(#3313) GU733715(#3320) GU733716(#3321) GU733717(#3322) M38429(#15) M58176(#3735) M58178(#3737) M58179(#3738) M58184(#3069) M58186(#3743) M58194(#3750) M58196(#3752) M58198(#3754) M58204(#3760) M58212(#3767) M58215(#3770) M58228(#3783) U39362(#1101) U63538(#3077) U80520(#2539) U80525(#2544) U80527(#2546) U80539(#2558) U81454(#2559) U81456(#2561) U81477(#2582)

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