CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1945
Accession number AF239623
Name PAIR8_MOTHER
SubtypeD
CountryTanzania
Sampling year 1996
Patient8-mother

AF239623 isolate has foldings of [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:

actggg-agtg gctaaccctc agatgctgca tataagcagc tgctttttgc ctgtactggg tctctcttgt tagaccagat ttgagcctga gagctctctg gctaactagg gaacccactg cttaagcctc aataaagctt gccttgagtg cttcaagtag tgt

Isolates with identical sequences of region:

AF239624(#1946)

The optimal secondary structure:


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