CESSHIV-1 DATABASE

Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 6
Accession number M93259
Name YU-10
SubtypeB
CountryUSA
Sampling year 1986
PatientYU

M93259 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:

tgttgtgtga ctctggtaac tagagatccc tcagaccctt ttagtcagtg tggaaaatct ctagcagtgg cgcccgaaca gggacttgaa agcgaaagga aaaccagagg agctctctcg acgcaggac

Isolates with identical sequences of region:

AF042100(#122) EU047603(#1623) M93258(#7)

The optimal secondary structure:


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