CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1888
Accession number EU047693
Name 01HSJ_3145_3496
SubtypeB
CountrySouth Korea
Sampling year 2001
PatientHSJ

EU047693 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 domain, TAR, polyA

The primary sequence:

cgagccctca gatgctgcat ataagcagct gctttctgcc tgtactgggt ctctctggtt agaccagatc tgagcctggg agctctctgg ctaactaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttcaagtagt gt

Isolates with identical sequences of region:

AF042106(#48) AF075719(#32) DQ287288(#3474) DQ287289(#3293) DQ287290(#3302) DQ287291(#3303) DQ287292(#3304) DQ287293(#3305) DQ287294(#3306) DQ287306(#3001) DQ287310(#2993) EF370172(#2226) EF370173(#2227) EF370176(#1451) EF370177(#1452) EF370180(#1454) EF370181(#1455) EF370211(#2233) EF370294(#2256) EU047600(#2270) EU047603(#1623) EU047606(#1600) EU047610(#1813) EU047611(#1814) EU047612(#1815) U37267(#3072)

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