CESSHIV-1 database

General information on HIV-1 isolate

# 2782

Accession number	GQ452298
Name	HIV whole-genome vector AA1305#18
Subtype
Country	USA
Submitted to NCBI	2009
Comments	Vector

GQ452298 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 Core poly(A) site

The primary sequence:

ctgggtctct ctggttagac cagatctgag cctgggagct ctctggctaa ctagggaacc cactgcttaa gcctcaataa agcttgcctt gagtgctcaa agtagtgtgt gcccgtctgt tgtgtgactc tggtaa

Isolates with identical sequences of region:

AF003887(#1069) AF070521(#23) AF286365(#87) AX032749(#1082) AY835748(#583) AY835749(#584) AY835750(#585) AY835751(#606) AY835752(#581) AY835753(#607) AY835754(#586) AY835755(#587) AY835756(#588) AY835757(#589) AY835758(#608) AY835759(#590) AY835760(#591) AY835761(#609) AY835762(#592) AY835763(#593) AY835764(#594) AY835765(#610) AY835766(#611) AY835767(#595) AY835768(#582) AY835769(#596) AY835770(#597) AY835771(#598) AY835772(#612) AY835773(#599) AY835774(#600) AY835775(#601) AY835776(#613) AY835777(#602) AY835778(#603) AY835779(#604) AY835780(#605) AY835781(#614) BD238372(#1088) CS272319(#1092) DD153311(#1097) DD153312(#1098) DD334642(#3480) DJ491764(#3481) DM111087(#2820) EF420987(#1043) EU659803(#3025) EU659805(#3027) EU659806(#3028) M19921(#1100)

The optimal secondary structure:

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