CESSHIV-1 database

General information on HIV-1 isolate

# 15

Accession number	M38429
Name	JRCSF
Subtype	B
Country	USA
Sampling year	1986
Patient	JR

M38429 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, TAR, polyA

The primary sequence:

agcagctgct ttttgcctgt actgggtctc tctggttaga ccagatctga gcctgggagc tctctggcta gctagggaac ccactgctta agcctcaata aagcttgcct tgagtgcttc aagtagtgt

Isolates with identical sequences of region:

AB287371(#937) AB480694(#2719) AB480696(#2721) AB565478(#3284) AB565479(#3285) AF042101(#123) AF102210(#3580) AF102212(#3582) AF196714(#1285) AF538304(#1077) AF538307(#1080) AY851681(#2102) D86069(#1095) DQ848479(#3645) DQ848481(#3647) DQ848484(#3650) DQ848486(#3652) DQ848488(#3654) DQ848490(#3656) DQ854716(#972) EF370277(#2250) EF370278(#2251) EF370317(#1763) EF370379(#3017) EU047622(#1824) EU047656(#1859) GU733713(#3313) GU733714(#3319) GU733715(#3320) GU733716(#3321) GU733717(#3322) M58176(#3735) M58178(#3737) M58179(#3738) M58184(#3069) M58185(#3742) M58186(#3743) M58194(#3750) M58196(#3752) M58198(#3754) M58204(#3760) M58207(#3763) M58212(#3767) M58215(#3770) M58228(#3783) U12055(#11) U21135(#29) 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