LOCUS
DEFINITION
ACCESSION
VERSION
KEYWORDS
SOURCE
ORGANISM
REFERENCE
AUTHORS
JOURNAL
REFERENCE
AUTHORS
TITLE
JOURNAL
REFERENCE
AUTHORS
TITLE
JOURNAL
MEDLINE
REFERENCE
AUTHORS
TITLE
JOURNAL
MEDLINE
REFERENCE
AUTHORS
JOURNAL
REFERENCE
AUTHORS
JOURNAL
REFERENCE
AUTHORS
TITLE
JOURNAL
MEDLINE
COMMENT
SIVMM251
10277 bp ss-RNA
VRL
29-NOV-2000
Simian (macaque) immunodeficiency virus, complete genome; isolate
Mm251, proviral DNA.
M19499 M15897 M16125 M24614 Y00294
M19499.1 GI:334657
env protein; envelope-associated protein; gag polyprotein; nef
protein; pol polyprotein; rev protein; tat protein; vif protein;
vpr protein; vpx protein.
Simian immunodeficiency virus.
Simian immunodeficiency virus
Viruses; Retroid viruses; Retroviridae; Lentivirus; Primate
lentivirus group.
1 (bases 5731 to 10277)
Hirsch,V.M.
Unpublished
2 (bases 809 to 1677; 5731 to 10249)
Hahn,B.H., Kumar,P., Taylor,M.E., Arya,S.K. and Shaw,G.M.
Human retrovirses, cancer and AIDS: approach to prevention and
therapy
Unpublished
3 (bases 6078 to 10249)
Hirsch,V., Riedel,N. and Mullins,J.I.
The genome organization of STLV-3 is similar to that of the AIDS
virus except for a truncated transmembrane protein
Cell 49 (3), 307-319 (1987)
87187627
4 (bases 506 to 5975; 6319 to 10125)
Franchini,G., Gurgo,C., Guo,H.G., Gallo,R.C., Collalti,E.,
Fargnoli,K.A., Hall,L.F., Wong-Staal,F. and Reitz,M.S. Jr.
Sequence of simian immunodeficiency virus and its relationship to
the human immunodeficiency viruses
Nature 328 (6130), 539-543 (1987)
87287229
5 (bases 7757 to 8090; 8108 to 8225; 8237 to 8625; 8706 to 8898)
Kestler,H.W.
Unpublished
6 (bases 1 to 10249)
Donahue,P.R., Kornfeld,H., Gallo,M.V. and Mullins,J.I.
Unpublished
7 (sites)
Kestler,H.W. III., Li,Y., Naidu,Y.M., Butler,C.V., Ochs,M.F.,
Jaenel,G., King,N.W., Daniel,M.D. and Desrosiers,R.C.
Comparison of simian immunodeficiency virus isolates
Nature 331 (6157), 619-622 (1988)
88122665
[7] sites.
Kestler et al. [7], (Nature 331, 619-622 (1988)) present strong
evidence that the isolates previously referred to as STLV-III AGM
([4], [3], [1]) and HTLV-IV ([2]) are not authentic, but were
derived from cell cultures infected with SIV MAC-251. The
reference
sequence for this entry is from unpublished (1988), with
exception
of bases
10250-10277 which are from [1].
the vpr coding region has been annotated to end near where the
gene
ends in the SIVMM142 sequence.
A base change from 'a' at
position
6443 in SIVMM142 to 't' at corresponding position 6418 in the
SIVMM251 sequence results in the coding sequence ending 4 amino
acids earlier than it does in SIVMM142. Also, the variation
marked
at position 6377 ('aa' in K6W, 'aga' in K78) implies different
amino acid sequences for those isolates from that point onward in
vpr.
The tat start is annotated in agreement with the site in [2]
(also
agrees with HIV2ROD) sequence rather than at the site marked in
[3]
for the K78 sequence.
The start codon for rev is marked at position 6504 in accordance
with reference [3] for the K78 sequence. This position also
agrees
with the rev start in the SIVMM142 sequence. However, [2]
annotates
the rev start at position 6354. Both of these start sites are in
the same frame. The sequence annotation shows two alternate 3'
splice junction sites at 8743 and 8785. See reference [3]. Clean
copy of sequence unpublished (1988) kindly provided by H.W.
Kestler
to the
EMBL data library (25-FEB-1988). Computer-readable copy of
sequence
unpublished (1988) kindly provided by J.Mullins (12-SEP-1988). An
internal stop codon is present in the env cds at positions
8782-8784 in unpublished (1988) and 8785-8787 in [4],[3],[1],
[2],unpublished (1988).
unpublished (1988) has shown proviral clone BK28 to be
biologically
active,
causing persistent lymphadenopathy and death in one out of four
rhesus monkeys 17 months after infection. BK28 was originally
called HTLV-4 (Nature 326, 610-613 (1987)), but it has since been
found to correspond to SIVMM251. The K6W sequence [4], which was
derived from isolate Mm251, contains about 25 frame shifts in
gag-pol relative to this sequence.
A single base insertion at position 9678 results in a frame-shift
in the nef coding region. The nef coding region in [4] would
produce a protein about 36 residues longer than that produced by
the other isolates.
Author [7] address Kestler H.W., Harvard Medical School, New
England Regional Primate Research Center, Department of
Microbiology, One Pine Hill Drive, Southborough, Mass. 01772,
USA.
[7] submitted (25-FEB-1988) to the EMBL data library by. Complete
source information:
Simian (macaque) immunodeficiency virus proviral DNA, SIV mac
isolate K6W, clones lambda-16, 27, 35, and 11 [4]; and SIV mac
isolate K78, clones K2-10 and K2-5 [3], [1]; HTLV4/PK82 and
HTLV4/PK190 proviral DNA clones [2]; SIV mac integrated proviral
DNA isolate 251, clone lambda 251 unpublished (1988); proviral
DNA,
isolate Mm251,
clone BK28 unpublished (1988).
Location/Qualifiers
1..10277
/organism="Simian immunodeficiency virus"
/proviral
/isolate="Mm251"
/db_xref="taxon:11723"
LTR
1..806
/note="5' LTR"
misc_binding
428..437
/note="putative"
/bound_moiety="Sp1 III"
misc_binding
439..448
/note="putative"
/bound_moiety="Sp1 II"
misc_binding
450..459
/note="putative"
/bound_moiety="Sp1"
repeat_region
506..682
/note="R repeat 5' copy"
prim_transcript 507..10125
/note="genomic mRNA"
prim_transcript 507..10125
/note="tat, rev, nef subgenomic mRNA"
variation
517..519
/note="cgg in unpublished (1988); gc in [4]"
/replace="gc"
variation
617..618
/note="tg in unpublished (1988); t in [4]"
/replace="t"
variation
668
/note="g in unpublished (1988); gc in [4]"
/replace="gc"
variation
694
/note="g in unpublished (1988); c in [4]"
/replace="c"
variation
779
/note="a in unpublished (1988); g in [4]"
/replace="g"
variation
806
/note="a in unpublished (1988); agt in [4]"
/replace="agt"
misc_binding
810..827
/bound_moiety="Lys-tRNA primer"
variation
825..826
/note="ac in [4],unpublished (1988); gac in [2]"
/replace="gac"
variation
843..844
/note="ga in [2],unpublished (1988); agaa in [4]"
/replace="agaa"
variation
858..859
/note="ct in [2],unpublished (1988); cct in [4]"
/replace="cct"
variation
870
/note="a in [4],unpublished (1988); g in [Unpublished
(1987) UCLA Symposia on Molecular and Cellular Biology]"
/replace="g"
FEATURES
source
variation
variation
variation
variation
variation
CDS
895..897
/note="gac in [4],unpublished (1988);
/replace="gc"
919
/note="g in [2],unpublished (1988); a
/replace="a"
966..968
/note="gtt in [4],unpublished (1988);
/replace="gt"
1009..1011
/note="atc in [2],unpublished (1988);
/replace="ac"
1014
/note="g in [4],unpublished (1988); a
/replace="a"
1041..2561
/note="gag polyprotein"
/codon_start=1
/protein_id="AAB59905.1"
/db_xref="GI:334660"
gc in [2]"
in [4]"
gt in [2]"
ac in [4]"
in [2]"
/translation="MGARNSVLSGKKADELEKIRLRPGGKKKYMLKHVVWAANELDRF
GLAESLLENKEGCQKILSVLAPLVPTGSENLKSLYNTVCVIWCIHAEEKVKHTEEAKQ
IVQRHLVVETGTAETMPKTSRPTAPSSGRGGNYPVQQIGGNYVHLPLSPRTLNAWVKL
IEEKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIRDIINEEAADWDLQH
PQPAPQQGQLREPSGSDIAGTTSSVDEQIQWMYRQQNPIPVGNIYRRWIQLGLQKCVR
MYNPTNILDVKQGPKEPFQSYVDRFYKSLRAEQTDAAVKNWMTQTLLIQNANPDCKLV
LKGLGVNPTLEEMLTACQGVGGPGQKARLMAEALKEALAPVPIPFAAAQKRGPRKPIK
CWNCGKEGHSARQCRAPRRQGCWKCGKMDHVMAKCPDRQAGFLGLGPWGKKPRNFPMA
QVHQGLTPTAPPEDPAVDLLKNYMQLGKQQRESREKPYKEVTEDLLHLNSLFGGDQ"
variation
1056
/note="t in [2],unpublished (1988); g
/replace="g"
variation
1083
/note="g in [4],unpublished (1988); a
/replace="a"
variation
1190
/note="g in [2],unpublished (1988); c
/replace="c"
variation
1365
/note="g in [4],unpublished (1988); a
/replace="a"
variation
1396
/note="c in [4],unpublished (1988); t
/replace="t"
variation
1435
/note="g in [4],unpublished (1988); a
/replace="a"
variation
1619
in [4]"
in [2]"
in [4]"
in [2]"
in [2]"
in [2]"
variation
variation
variation
variation
variation
variation
CDS
/note="g in [2],unpublished (1988); a in [4]"
/replace="a"
1848
/note="g in unpublished (1988); a in [4]"
/replace="a"
1882
/note="c in unpublished (1988); t in [4]"
/replace="t"
1905
/note="g in unpublished (1988); a in [4]"
/replace="a"
2156..2158
/note="cgc in unpublished (1988); gcg in [4]"
/replace="gcg"
2170
/note="t in unpublished (1988); c in [4]"
/replace="c"
2189..2190
/note="ga in unpublished (1988); ac in [4]"
/replace="ac"
<2216..5386
/note="NH2-terminus uncertain"
/codon_start=1
/product="pol polyprotein"
/protein_id="AAB59906.1"
/db_xref="GI:334661"
/translation="VLELWEGGTLCKAMQSPKKTGMLEMWKNGPCYGQMPRQTGGFFR
PWSMGKEAPQFPHGSSASGADANCSPRGPSCGSAKELHAVGQAAERKQREALQGGDRG
FAAPQFSLWRRPVVTAHIEGQPVEVLLDTGADDSIVTGIELGPHYTPKIVGGIGGFIN
TKEYKNVKIEVLGKRIKGTIMTGDTPINIFGRNLLTALGMSLNLPIAKVEPVKVTLKP
GKVGPKLKQWPLSKEKIVALREICEKMEKDGQLEEAPPTNPYNTPTFAIKKKDKNKWR
MLIDFRELNRVTQDFTEVQLGIPHPAGLAKRKRITVLDIGDAYFSIPLDEEFRQYTAF
TLPSVNNAEPGKRYIYKVLPQGWKGSPAIFQYTMRHVLEPFRKANPDVTLVQYMDDIL
IASDRTDLEHDRVVLQLKELLNSIGFSTPEEKFQKDPPFQWMGYELWPTKWKLQKIEL
PQRETWTVNDIQKLVGVLNWAAQIYPGIKTKHLCRLIRGKMTLTEEVQWTEMAEAEYE
ENKIILSQEQEGCYYQEGKPLEATVIKSQDNQWSYKIHQEDKILKVGKFAKIKNTHTN
GVRLLAHVIQKIGKEAIVIWGQVPKFHLPVERDVWEQWWTDYWQVTWIPEWDFISTPP
LVRLVFNLVKDPIEGEETYYTDGSCNKQSKEGKAGYITDRGKDKVKVLEQTTNQQAEL
EAFLMALTDSGPKTNIIVDSQYVMGIITGCPTESESRLVNQIIEEMIKKSEIYVAWVP
AHKGIGGNQEIDHLVSQGIRQVLFLEKIEPAQEEHDKYHSNVKELVFKFGLPRIVARQ
IVDTCDKCHQKGEAIHGQVNSDLGTWQMDCTHLEGKIVIVAVHVASGFIEAEVIPQET
GRQTALFLLKLAGRWPITHLHTDNGANFASQEVKMVAWWAGIEHTFGVPYNPQSQGVV
EAMNHHLKNQIDRIREQANSVETIVLMAVHCMNFKRRGGIGDMTPAERLINMITTEQE
IQFQQSKNSKFKNFRVYYREGRDQLWKGPGELLWKGEGAVILKVGTDIKVVPRRKAKI
IKDYGGGKEVDSSSHMEDTGEAREVA"
variation
2277
/note="g in unpublished (1988); a in [4]"
/replace="a"
variation
2336
/note="g in unpublished (1988); a in [4]"
/replace="a"
variation
2717
/note="a in unpublished (1988); g in [4]"
/replace="g"
variation
2747
/note="g in unpublished (1988); a in [4]"
/replace="a"
variation
2858
/note="a in unpublished (1988); g in [4]"
/replace="g"
variation
3053
/note="g in unpublished (1988); c in [4]"
/replace="c"
variation
3083
/note="g in unpublished (1988); ga in [4]"
/replace="ga"
variation
3103..3104
/note="ag in unpublished (1988); a in [4]"
/replace="a"
variation
3648
/note="g in unpublished (1988); t in [4]"
/replace="t"
variation
3702
/note="a in unpublished (1988); c in [4]"
/replace="c"
variation
3839
/note="t in unpublished (1988); a in [4]"
/replace="a"
variation
3878
/note="g in unpublished (1988); a in [4]"
/replace="a"
variation
3971..3973
/note="tgg in unpublished (1988); gta in [4]"
/replace="gta"
variation
4131
/note="g in unpublished (1988); t in [4]"
/replace="t"
variation
4218
/note="a in unpublished (1988); t in [4]"
/replace="t"
variation
4231..4237
/note="agaacag in unpublished (1988); gaca in [4]"
/replace="gaca"
variation
4261
/note="a in unpublished (1988); g in [4]"
variation
variation
variation
variation
variation
variation
variation
variation
variation
variation
variation
variation
variation
variation
variation
variation
variation
variation
variation
/replace="g"
4268
/note="t in unpublished (1988); a in [4]"
/replace="a"
4271
/note="c in unpublished (1988); ta in [4]"
/replace="ta"
4283..4284
/note="ac in unpublished (1988); a in [4]"
/replace="a"
4302
/note="c in unpublished (1988); g in [4]"
/replace="g"
4318..4320
/note="ttc in unpublished (1988); att in [4]"
/replace="att"
4324..4325
/note="at in unpublished (1988); agt in [4]"
/replace="agt"
4348..4350
/note="atg in unpublished (1988); tt in [4]"
/replace="tt"
4405..4407
/note="aaa in unpublished (1988); a in [4]"
/replace="a"
4413..4415
/note="aaa in unpublished (1988); gg in [4]"
/replace="gg"
4439..4442
/note="caca in unpublished (1988); ttag in [4]"
/replace="ttag"
4470..4474
/note="accac in unpublished (1988); gtcca in [4]"
/replace="gtcca"
4490
/note="a in unpublished (1988); t in [4]"
/replace="t"
4786..4790
/note="aagac in unpublished (1988); a in [4]"
/replace="a"
4804
/note="t in unpublished (1988); tc in [4]"
/replace="tc"
4832
/note="a in unpublished (1988); tat in [4]"
/replace="tat"
4850..4851
/note="ga in unpublished (1988); cag in [4]"
/replace="cag"
4870
/note="c in unpublished (1988); a in [4]"
/replace="a"
4892
/note="g in unpublished (1988); a in [4]"
/replace="a"
4911
/note="a in unpublished (1988); ag in [4]"
variation
CDS
/replace="ag"
4921..4922
/note="tg in unpublished (1988); t in [4]"
/replace="t"
5316..5960
/note="vif protein"
/codon_start=1
/protein_id="AAB59907.1"
/db_xref="GI:334662"
/translation="MEEEKRWIAVPTWRIPERLERWHSLIKYLKYKTKDLQKVCYVPH
FKVGWAWWTCSRVIFPLQEGSHLEVQGYWHLTPERGWLSTYAVRITWYSRNFWTDVTP
DYADILLHSTYFPCFTAGEVRRAIRGEQLLSCCKFPRAHRYQVPSLQYLALKVVSDVR
SQGENPTWKQWRRDNRRGLRMAKQNSRGDKQRGSKPPTKGADFPGLAKVLGILA"
variation
5560
/note="t in unpublished (1988); c in [4]"
/replace="c"
variation
5598..5599
/note="aa in unpublished (1988); gac in [4]"
/replace="gac"
variation
5632
/note="a in unpublished (1988); g in [4]"
/replace="g"
variation
5639
/note="a in unpublished (1988); tc in [4]"
/replace="tc"
variation
5660..5662
/note="ttg in unpublished (1988); t in [4]"
/replace="t"
variation
5737
/note="a in [4],[2],unpublished (1988); g in [1]"
/replace="g"
CDS
5788..6126
/note="vpx protein"
/codon_start=1
/protein_id="AAB59908.1"
/db_xref="GI:334663"
/translation="MSDPRERIPPGNSGEETIGEAFEWLNRTVEEINREAVNHLPREL
IFQVWQRSWEYWHDEQGMSQSYVKYRYLCLMQKALFMHCKKGCRCLGEGHGAGGWRPG
PPPPPPPGLA"
variation
5817..5818
/note="tg in [4],[2],unpublished (1988); aa in [1]"
/replace="aa"
variation
5877
/note="g in [4],[2],unpublished (1988); a in [1]"
/replace="a"
variation
5895
/note="a in [2],unpublished (1988); g in [4],[1]"
/replace="g"
variation
5968
/note="g in [4],[2],unpublished (1988); a in [1]"
/replace="a"
variation
6070
variation
CDS
/note="g in [2],unpublished (1988); a in [1]"
/replace="a"
6078
/note="a in [3],[1],unpublished (1988); g in [2]"
/replace="g"
6127..6420
/note="vpr protein"
/codon_start=1
/protein_id="AAB59909.1"
/db_xref="GI:334664"
/translation="MEERPPENEGPQREPWDEWVVEVLEELKEEALKHFDPRLLTALG
NHIYNRHGDTLEGAGELIRILQRALFMHFRGGCNHSRIGQPGGGNPLSTIPPS"
variation
6143
/note="c in [2],unpublished (1988); t in [3],[1]"
/replace="t"
variation
6250
/note="g in [3],[1],unpublished (1988); a in [2]"
/replace="a"
CDS
join(6278..6573,8785..8884)
/note="tat protein"
/codon_start=1
/protein_id="AAB59910.1"
/db_xref="GI:334658"
/translation="METPLREQENSLESSNERSSCILEADATTPESANLGEEILSQLY
RPLEACYNTCYCKKCCYHCQFCFLKKGLGICYEQSRKRRRTPKKAKANTSSASNNRLI
PNRTRHCQPEKAKKETVEKAVATAPGLGR"
variation
6377..6378
/note="aa in [4],unpublished (1988); aga in [3],[1],
[2]"
/replace="aga"
variation
6493
/note="g in [4],[2],unpublished (1988); a in [3],[1]"
/replace="a"
variation
6499
/note="a in [3],[1],[2],unpublished (1988); t in [4]"
/replace="t"
CDS
join(6504..6573,8785..9041)
/note="rev protein"
/codon_start=1
/protein_id="AAB59911.1"
/db_xref="GI:334659"
/translation="MSSHEREEELRKRLRLIHLLHQTIDSYPTGPGTANQRRQRRRRW
RRRWQQLLALADRIYSFPDPPTDTPLDLAIQQLQNLAIESIPDPPTNTPEALCDPTKG
SRSPQD"
intron
6574..8784
/note="rev and tat,[3]"
/number=2
intron
6574..8742
/note="tat, rev, nef subgenomic mRNA intron 2
(alternate),
[3]"
intron
6574..8742
intron
CDS
variation
variation
variation
variation
variation
variation
variation
variation
variation
variation
variation
variation
variation
/note="rev and tat (alternate),[3]"
/number=2
6574..8784
/note="tat, rev, nef subgenomic mRNA intron 2,[3]"
6580..9225
/note="envelope polyprotein (in-frame stop at 8785, [4],
[3],[1],[2],["
/codon_start=1
/pseudo
6592..6593
/note="gg in [4],[2],unpublished (1988); aa in [3],[1]"
/replace="aa"
7009
/note="a in [4],[2],unpublished (1988); t in [3],[1]"
/replace="t"
7097
/note="c in [4],[2],unpublished (1988); a in [3],[1]"
/replace="a"
7174
/note="g in [4],[2],unpublished (1988); a in [3],[1]"
/replace="a"
7209
/note="g in [4],[3],[1],unpublished (1988); a in [2]"
/replace="a"
7239
/note="a in unpublished (1988); g in [4],[3],[1],[2]"
/replace="g"
7565
/note="g in [4],[2],unpublished (1988); a in [3],[1]"
/replace="a"
7569
/note="g in [4],[2],unpublished (1988); a in [3],[1]"
/replace="a"
7588
/note="a in [3],[1],[2],unpublished (1988); c in [4]"
/replace="c"
7592
/note="a in [3],[1],[2],unpublished (1988); c in [4]"
/replace="c"
7638
/note="g in [4],[2],unpublished (1988); a in [3],[1]"
/replace="a"
7743
/note="g in [4],[3],[1],unpublished (1988); a in [2]"
/replace="a"
7826
/note="g in [4],[2],unpublished (1988),unpublished
(1988);
variation
a in [3],[Unpublished (1987) Cancer Biol Dept, Harvard
School of Pub."
/replace="a"
7865
/note="g in [4],[2],unpublished (1988),unpublished
(1988);
a in [3],[Unpublished (1987) Cancer Biol Dept, Harvard
School of Pub."
/replace="a"
variation
variation
variation
variation
variation
7894
/note="a in [4],[3],[1],unpublished (1988),unpublished
(1988); g in [Unpublished (1987) UCLA Symposia on
Molecular and Cellular"
/replace="g"
8021
/note="g in [4],[3],[1],unpublished (1988); a in [2],
[Unpublished"
/replace="a"
8061
/note="g in [3],[1],[2],unpublished (1988),unpublished
(1988); a in [Nature 328, 539-543"
/replace="a"
8100
/note="t in [4],[3],[1],unpublished (1988); c in [2]"
/replace="c"
8184
/note="g in [4],[2],unpublished (1988),unpublished
(1988);
variation
a in [3],[Unpublished (1987) Cancer Biol Dept, Harvard
School of Pub."
/replace="a"
8214
/note="g in [4],[2],unpublished (1988),unpublished
(1988);
variation
variation
a in [3],[Unpublished (1987) Cancer Biol Dept, Harvard
School of Pub."
/replace="a"
8223
/note="g in [3],[1],[2],unpublished (1988),unpublished
(1988); c in [Nature 328, 539-543"
/replace="c"
8229..8231
/note="gac in [3],[1],[2],unpublished (1988); cag in
[4]"
variation
variation
variation
/replace="cag"
8294
/note="a in [3],[1],[2],unpublished (1988),unpublished
(1988); g in [Nature 328, 539-543"
/replace="g"
8326
/note="c in [3],[1],[2],unpublished (1988),unpublished
(1988); t in [Nature 328, 539-543"
/replace="t"
8360
/note="g in [4],[2],unpublished (1988),unpublished
(1988);
variation
variation
a in [3],[Unpublished (1987) Cancer Biol Dept, Harvard
School of Pub."
/replace="a"
8386
/note="a in [3],[1],[2],unpublished (1988),unpublished
(1988); g in [Nature 328, 539-543"
/replace="g"
8403
/note="a in unpublished (1988); g in [4],[3],[1],[2],
[Unpublished"
variation
variation
/replace="g"
8407
/note="g in [4],[3],[1],unpublished (1988),unpublished
(1988); a in [Unpublished (1987) UCLA Symposia on
Molecular and Cellular"
/replace="a"
8587
/note="g in [4],[2],unpublished (1988),unpublished
(1988);
variation
variation
misc_feature
variation
misc_feature
variation
CDS
a in [3],[Unpublished (1987) Cancer Biol Dept, Harvard
School of Pub."
/replace="a"
8601
/note="g in [4],[3],[1],unpublished (1988),unpublished
(1988); a in [Unpublished (1987) UCLA Symposia on
Molecular and Cellular"
/replace="a"
8782
/note="c in [4],[3],[1],[2],unpublished (1988); t in
[Unpublished"
/replace="t"
8782..8784
/note="in-frame stop in env cds unpublished (1988)"
8785
/note="t in [4],[3],[1],[2],unpublished (1988); c in
[Unpublished"
/replace="c"
8785..8787
/note="in-frame stop in env cds [4],[3],[1],[2],
unpublished (1988)"
9019
/note="g in unpublished (1988); a in [4],[3],[1],[2]"
/replace="a"
9059..9802
/note="nef protein"
/codon_start=1
/protein_id="AAB59912.1"
/db_xref="GI:334665"
/translation="MGGAISMRRSKPAGDLRQKLLRARGETYGRLLGEVEDGSSQSLG
GLGKGLSSRSCEGQKYNQGQYMNTPWRNPAEEKEKLAYRKQNMDDIDEEDDDLVGVSV
RPKVPLRAMTYKLAIDMSHFIKEKGGLEGIYYSARRHRILDMYLEKEEGIIPDWQDYT
SGPGIRYPKTFGWLWKLVPVNVSDEAQEDERHYLMQPAQTSKWDDPWGEVLAWKFDPT
LAYTYEAYARYPEELEASQACQRKRLEEG"
variation
9133
/note="a in unpublished (1988); g in [4] [3],[1],[2]"
/replace="g"
variation
9204
/note="g in [3],[1],[2],unpublished (1988); a in [4]"
/replace="a"
variation
9224
/note="g in [3],[1],[2],unpublished (1988); a in [4]"
/replace="a"
variation
9289
variation
LTR
variation
variation
/note="a in [3],[1],unpublished (1988); g in [4],[2]"
/replace="g"
9352
/note="a in [4],[2],unpublished (1988); c in [3],[1]"
/replace="c"
9444..10249
/note="3' LTR"
9474
/note="a in [4],[3],[1],unpublished (1988); g in [2]"
/replace="g"
9498..9508
/note="aaaaggaagaa in [3],[1],[2],unpublished (1988); a
in
variation
variation
variation
variation
variation
variation
variation
variation
[4]"
/replace="a"
9677..9678
/note="tg in [3],[1],[2],unpublished (1988); t in [4]"
/replace="t"
9691..9692
/note="ag in unpublished (1988),[3],[1],[2]; ga in [4]"
/replace="ga"
9702
/note="t in [4],[3],[1],unpublished (1988); c in [2]"
/replace="c"
9714
/note="t in [4],[2],unpublished (1988); c in [3],[1]"
/replace="c"
9738
/note="c in unpublished (1988); t in [4],[3],[1],[2]"
/replace="t"
9754
/note="g in unpublished (1988); gt in [4],[3],[1],[2]"
/replace="gt"
9836
/note="g in [4],[2],unpublished (1988); a in [3],[1]"
/replace="a"
9852..9853
/note="ta in unpublished (1988); ca in [4],[3],[1]; cg
in
repeat_region
variation
[2]"
/replace="cg"
9949..10125
/note="R repeat 3' copy"
9959..9962
/note="gcgg in [3],[1],[2],unpublished (1988); ggc in
[4]"
variation
variation
variation
polyA_signal
/replace="ggc"
9972
/note="c in [4],[3],[1],unpublished (1988); t in [2]"
/replace="t"
10019
/note="g in [4],[2],unpublished (1988); a in [3],[1]"
/replace="a"
10061..10063
/note="ggg in [3],[1],[2],unpublished (1988); gg in [4]"
/replace="gg"
10102..10107
variation
variation
variation
variation
variation
variation
variation
/note="mRNA polyadenylation signal"
10111
/note="g in [3],[1],[2],unpublished (1988); gc in [4]"
/replace="gc"
10188..10189
/note="aa in [3],[1],unpublished (1988); gg in [2]"
/replace="gg"
10192..10193
/note="cc in [3],[1],unpublished (1988); ccc in [2]"
/replace="ccc"
10222
/note="a in [3],[1],unpublished (1988); g in [2]"
/replace="g"
10227
/note="c in [2],unpublished (1988); t in [3],[1]"
/replace="t"
10231
/note="a in [3],[1],unpublished (1988); g in [2]"
/replace="g"
10239
/note="a in [3],[1],unpublished (1988); g in [2]"
/replace="g"
3451 a
1941 c
2581 g
2304 t
BASE COUNT
ORIGIN
1 tggaagggat
61 aagaaggcat
121 agacatttgg
181 atgagaggca
241 aggttctagc
301 acccagaaga
361 cgcaagaggc
421 tccacaaggg
481 atatcactgc
541 tgggaggttc
601 agcacttggc
661 taaagctgcc
721 gtcaactcgg
781 aaaccgaagc
841 gagactcctg
901 gtgctcctat
961 ctccggttgc
1021 ataataagat
1081 atgaattaga
1141 tagtatgggc
1201 aagaaggatg
1261 atttaaaaag
1321 tgaaacacac
1381 cagcagaaac
1441 attacccagt
1501 taaatgcctg
1561 ttcaggcact
1621 gagaccatca
1681 gggacttgca
1741 cagatattgc
1801 agaaccccat
1861 gtgtcagaat
1921 ttcagagcta
ttattacagt
cataccagat
ctggctatgg
ttatttaatg
gtggaagttt
gttggaagca
cttcttaaca
gatgttatgg
atttcgctct
tctccagcac
cagtgctggg
attttagaag
tactcggtaa
aggaaaatcc
agtacggctg
aaaggcgcgg
aggtaagtgc
agagtgggag
aaaaattagg
agcaaatgaa
tcaaaaaata
cctttataat
tgaggaagca
tatgccaaaa
acaacaaata
ggtaaaattg
gtcagaaggc
agcggctatg
gcacccacaa
aggaacaact
accagtaggc
gtataaccca
tgtagacagg
gcaagaagac
tggcaggatt
aaattagtcc
cagccagctc
gatccaactc
agtcaggcct
tggctgacaa
ggaggagccg
gtattcagtc
tagcaggtag
cagagtggct
taagccagtg
taagaagacc
ctagcagatt
agtgaaggca
gtcggtacca
aacacaaaaa
atgggcgcga
ctacgacccg
ttagatagat
ctttcggtct
actgtctgcg
aaacagatag
acaagtagac
ggtggtaact
atagaggaaa
tgcaccccct
cagattatca
ccagctccac
agttcagtag
aacatttaca
acaaacattc
ttctacaaaa
atagaatctt
acacctcagg
ctgtaaatgt
aaacttccaa
tagcctacac
gtcagaggaa
gagggaaact
gtcgggaaca
gctctgcgga
agcctgggtg
ccacgcttgc
tgtgttccca
ctggtctgtt
ggcgcccgaa
gtaagggcgg
gacggcgtga
agaaatagct
gaaactccgt
gcggaaagaa
ttggattagc
tagctccatt
tcatctggtg
tgcagagaca
caacagcacc
atgtccacct
agaaatttgg
atgacattaa
gagatattat
aacaaggaca
atgaacaaat
ggagatggat
tagatgtaaa
gcttaagagc
agacatgtac
accaggaatt
atcagatgag
gtgggatgac
ttatgaggca
gaggttagaa
cgctgagata
cccactttct
gaggctggca
ttccctgcta
ttgcttaaag
tctctcctag
aggacccttt
caggacttga
caggaaccaa
ggagcgggag
gtcttgttat
cttgtcaggg
aaagtacatg
agaaagcctg
agtgccaaca
cattcacgca
cctagtggtg
atctagcggc
gccattaagc
agcagaagta
tcagatgtta
aaatgaggag
gcttagggag
ccagtggatg
ccaactgggg
acaagggcca
agaacaaaca
ttagaaaagg
agatacccaa
gcacaggagg
ccttggggag
tatgctagat
gaaggctaac
gcagggactt
tgatgtataa
gattgagccc
gactctcacc
acctcttcaa
tcgccgcctg
ctgctttgag
aggagagtga
ccacgacgga
aggaggaggc
ccaggaaggg
aagaaagcag
ttgaagcatg
ttggagaaca
ggctcagaaa
gaagagaaag
gaaacaggaa
agaggaggaa
ccgagaacat
gtgccaggat
aattgtgtgg
gctgcagatt
ccgtcaggat
tacagacaac
ttgcaaaaat
aaagagccat
gatgcagcag
1981
2041
2101
2161
2221
2281
2341
2401
2461
2521
2581
2641
2701
2761
2821
2881
2941
3001
3061
3121
3181
3241
3301
3361
3421
3481
3541
3601
3661
3721
3781
3841
3901
3961
4021
4081
4141
4201
4261
4321
4381
4441
4501
4561
4621
4681
4741
4801
4861
4921
4981
5041
5101
5161
5221
5281
5341
taaagaattg
tgctgaaggg
tagggggacc
cagtgccaat
ggaattgtgg
gctggaaatg
ttttaggcct
aggggctgac
tgcagttggg
atttgctgca
acagcctgta
gttaggtcca
agaatacaaa
aggggacact
aaatcttccc
accaaaattg
tgaaaagatg
ccccacattt
ggaactaaat
aggactagca
acctctagat
agagccagga
catcttccaa
gaccttagtc
tgacagggta
agagaaattc
atggaagttg
gaagttagta
tctctgtagg
ggcagaagca
ttaccaagaa
ttataaaatt
tacacatacc
aatagtgatc
acagtggtgg
gccaccacta
ctattataca
agataggggc
agaagcattt
acaatatgtt
ccaaataata
caaaggtata
tctcttcttg
aaaagaattg
ctgtgataaa
gacttggcaa
agctagtgga
atttctgtta
taactttgcc
tggggtacca
aaatcaaata
agttcattgc
attaattaac
atttaaaaat
tgagctattg
agtacccaga
cagttcccac
gatgactcaa
gctgggtgtg
aggacagaag
cccttttgca
gaaggaggga
tggaaaaatg
tggtccatgg
gccaactgct
caagcagcag
cctcaattct
gaagtattat
cattataccc
aatgtaaaaa
ccgattaaca
atagctaagg
aagcagtggc
gaaaaggatg
gccataaaga
agggtcactc
aaaaggaaaa
gaagaattta
aaacgataca
tacactatga
cagtatatgg
gttttacagc
caaaaagatc
caaaagatag
ggagtattaa
ttaattagag
gaatatgagg
ggcaagccat
caccaagaag
aatggagtta
tggggacagg
acagactatt
gtaagattag
gatggatcat
aaagacaaag
ctcatggcat
atgggaataa
gaagaaatga
ggaggaaacc
gaaaagatag
gtattcaaat
tgtcatcaga
atggactgta
ttcatagaag
aaattggcag
tcgcaagaag
tacaatccac
gatagaatca
atgaatttta
atgatcacta
tttcgggtct
tggaaagggg
agaaaggcta
atggaggata
acactgctga
aatcccaccc
gctagattaa
gcagcccaga
cactctgcaa
gaccatgtta
ggaaagaagc
cccccagagg
agagaaagca
ctctttggag
tggatacagg
caaaaatagt
tagaagtttt
tttttggtag
tagagcctgt
cattatcaaa
gtcagttgga
aaaaagataa
aggactttac
ggattacagt
ggcagtacac
tttataaggt
gacatgtgct
atgacatctt
taaaggaact
ccccatttca
agttgccaca
attgggcagc
gaaaaatgac
aaaataagat
tagaagccac
acaaaatact
gactattagc
tcccaaaatt
ggcaggtaac
tcttcaatct
gtaataaaca
taaaagtgtt
tgacagactc
taacaggatg
ttaaaaagtc
aagaaataga
agccagcaca
ttggattacc
aaggagaagc
cccatctaga
cagaagtaat
gcagatggcc
taaagatggt
agagtcaggg
gggaacaagc
aaagaagggg
cagaacaaga
attacagaga
aaggagcagt
aaattatcaa
ccggagaggc
ttcaaaatgc
tagaagaaat
tggcagaagc
agaggggacc
ggcaatgcag
tggccaaatg
cccgcaattt
acccagctgt
gagagaagcc
gagaccagta
ggctgatgat
aggaggaata
aggcaaaagg
gaatttgcta
aaaagtcacc
agaaaagata
ggaagctccc
gaacaaatgg
agaagtccaa
actggatata
tgcctttact
tctgcctcag
agaacccttc
aatagctagt
cttaaatagc
atggatgggg
aagagagacc
tcaaatttat
tctaacagag
aattctcagt
ggtaataaag
gaaagtagga
acatgtaata
ccacttacca
ctggataccg
agtgaaggac
gtcaaaagaa
agaacagact
agggccaaag
ccctacagaa
agaaatttat
ccacctagtt
agaagaacat
cagaatagtg
tatacatggg
aggaaaaata
tccacaagag
tattacacat
tgcatggtgg
agtagtggaa
aaattcagta
aggaataggg
aatacaattt
aggcagagat
catcttaaag
agattatgga
tagagaggtg
taacccagat
gctgacggct
cctgaaagag
aagaaagcca
agccccaaga
cccagacaga
ccccatggct
ggatctgcta
ttacaaggag
gtcactgctc
tctattgtaa
ggaggtttta
attaaaggga
acagctctgg
ttaaagccag
gttgcattaa
ccgaccaatc
agaatgctga
ttaggaatac
ggtgatgcat
ttaccatcag
ggatggaagg
aggaaggcaa
gacaggacag
atagggttct
tacgaattgt
tggacagtga
ccaggtataa
gaagttcagt
caggaacaag
agtcaggaca
aaatttgcaa
cagaaaatag
gttgagaggg
gagtgggatt
cctatagagg
gggaaagcag
actaatcaac
acaaatatta
tcagagagca
gtagcatggg
agtcagggga
gataaatacc
gccagacaga
caggtaaatt
gtcatagttg
acaggaagac
ctacacacag
gcagggatag
gcaatgaatc
gaaaccatag
gatatgactc
caacaatcaa
caactgtgga
gtagggacag
ggaggaaaag
gcatagcctc
tgcaagctag
tgtcaaggag
gccctcgcac
attaagtgtt
agacagggat
caggcgggtt
caagtgcatc
aagaactaca
gtgacagagg
atattgaagg
caggaataga
ttaatactaa
caatcatgac
ggatgtctct
gaaaggttgg
gagaaatctg
catacaacac
tagattttag
cacaccctgc
atttctccat
taaataatgc
ggtcaccagc
atccagatgt
acctggaaca
ctaccccaga
ggccgacaaa
atgatataca
aaaccaaaca
ggactgagat
aaggatgtta
atcagtggtc
agataaagaa
gaaaggaagc
atgtatggga
ttatctcaac
gagaagaaac
gatatatcac
aagcagaatt
tagtagattc
ggctagttaa
taccagcaca
ttagacaagt
atagtaatgt
tagtagacac
cagatctagg
cagtacatgt
agacagcact
ataatggtgc
agcacacctt
accacctgaa
tattaatggc
cagcagaaag
aaaactcaaa
agggacccgg
acattaaggt
aggtggatag
ataaaatatc
5401
5461
5521
5581
5641
5701
5761
5821
5881
5941
6001
6061
6121
6181
6241
6301
6361
6421
6481
6541
6601
6661
6721
6781
6841
6901
6961
7021
7081
7141
7201
7261
7321
7381
7441
7501
7561
7621
7681
7741
7801
7861
7921
7981
8041
8101
8161
8221
8281
8341
8401
8461
8521
8581
8641
8701
8761
tgaaatataa
gggcatggtg
tacaagggta
taacctggta
tgcatagcac
aacaactgct
agtacttagc
aacagtggag
ataaacagag
tcttgggaat
ttgtgtttaa
gaaggacacg
gcataaatgg
tgggtagtgg
ttgctaactg
ggagaactca
cactccagaa
ggcgtgctat
taaaaaggga
ggctaaggct
ctgcttatcg
gtcttttatg
aatagggata
gcccttaatg
gaggacgtat
tgcattacta
acaacaataa
aatgagacta
ataagctgta
acttggtact
tgctacatga
gatactatta
acaaattatt
atgatggaga
acttatattt
aatctaacaa
tctggattgg
tttggaggaa
aggtatactg
ccggaagtta
tggtttctaa
agaaggaatt
aaaaatgttt
ctcatagcaa
gtggcagaac
ggcttggccc
ggggtctttg
gcgtcgttga
caacagctgt
acaaagaacc
ctaaatgctt
gcaagtctaa
ttcttggagg
atgtatgaat
tcttggataa
atagtgatct
tcttccccac
aactaaagat
gacctgcagc
ttggcatttg
ctcaaggaac
ttatttccct
gtcttgctgc
actaaaagta
aagagacaat
aggcagtaaa
actggcatga
tgcaaaaggc
gggcaggagg
aagaaagacc
aggttctgga
cacttggtaa
ttagaatcct
tcggccaacc
aacacatgct
ttggggatat
aatacatctt
ccatcttgct
gtgtaccagc
cttggggaac
ttacagaaag
ggcaactctt
tgagatgcaa
caacagcagc
gttcttgtat
aattcaccat
ctacagattt
atcactgtaa
gatttaggta
caggctttat
cacagacttc
actggcatgg
tgaaatgtag
ttttccactc
aatggaagga
gaactaacaa
ccttcatgtg
attgggtaga
acgtgccgtg
atttgcctcc
acatagattg
tgtatcgatt
ccacagatgt
tgctagggtt
cgctgaccgc
tggacgtggt
tccagactag
ggggatgtgc
caccagactg
aaaatataac
tacaaaagtt
agtatataca
atatagtaca
cctcttattt
ctacaaaagg
agagtaatct
acaccagaaa
ttttggacag
tgctttacag
aagttcccga
gtaagcgatg
aggagaggcc
ccacctacca
tgaacaaggg
tttatttatg
atggagacca
tccagaaaat
agaattgaaa
tcatatctat
ccaacgagcg
tgggggagga
attgtaaaaa
gttatgagca
ctgcatcaaa
tttaagtgtc
ttggaggaat
aactcagtgc
ctttgatgct
tgagacctca
taaaagtgag
accaacatca
agctcagaat
gacagggtta
ggtttgtgaa
cacttctgtt
ttgtgcacct
gcctaaatgt
tacttggttt
tagggataat
aagaccagga
acaaccaatc
tgcaataaaa
tactgataaa
gacaaattgc
ggatagggat
tcatattaga
aagagaggga
gactgatgga
ggagttggga
gaagaggtac
cttgggtttt
tcagtcccgg
caagagacaa
ggtcactgcc
gtttagacaa
gaacaatgat
agccctccta
gaatagctgg
atatggaatt
aatgctagct
ccagtagact
tttgctatgt
tccccctaca
gagggtggct
atgtaacacc
cgggagaagt
gagctcatag
tcagatccca
ttcgaatggc
agggagctga
atgtcacaaa
cattgcaaga
ggacctcctc
gaaggcccac
gaagaagctt
aatagacatg
ctcttcatgc
aatcctctct
gtgttgctac
gtcacgaaag
caagtaagta
tatgggatct
gcgacaattc
ctaccagata
tgggagaata
ataaagcctt
acagatagat
gcaccagtat
aattgcacag
aaaagagaca
caagggaata
atccaagaat
ccaggttatg
tctaaggtgg
ggctttaatg
aggactataa
aataagacag
aatgataggc
gaggtgaaac
atcaatttaa
agaggagagt
gtaactaccc
caaataatca
gacctcacgt
aaccaaacta
gattataaat
actactggtg
ctcgcaacgg
actttattgg
caagaattgt
atcgagaagt
gtctgccaca
acttggcaag
gaagaggcac
gatgtgtttg
tatgtagttg
aagttaaggc
catacccaac
gccccatttt
ggaaggaagc
cagtacttat
agactatgca
gagaagggcc
gtaccaggta
gggagagaat
taaacagaac
ttttccaggt
gctatgtaaa
aaggctgtag
ctcctccccc
aaagggaacc
taaaacattt
gagacaccct
attttagagg
caactatacc
cattgccagt
agaagaagaa
tgggatgtct
attgtactca
ccctcttctg
atggtgatta
cagtcacaga
gtgtaaaatt
ggggattgac
cagaaaaaat
gcttggaaca
agacaaagga
gcactgataa
cttgtgacaa
ctttgcttag
tggtctcttc
gaactagagc
ttagtttaaa
ttttaccagt
caaagcaggc
agaccattgt
cggctcctgg
tcctctactg
agaggccaaa
acacttggca
gtaactccac
gtatcaccat
tagtagagat
gcacctcaag
caggttctgc
ctgggatagt
tgcgactgac
acttaaagga
ctactgtacc
agtgggagcg
aaattcaaca
gcaattggtt
taggagtaat
aggggtatag
aggacccggc
aaggtcggat
catttagaag
gcagtgagga
gacattttac
atcaggggag
ccaagcctac
cccacctgga
agtagaggag
ttggcaaagg
atacagatac
atgtctaggg
tccaggacta
atgggatgaa
tgatcctcgc
tgagggagca
cggatgcaac
gccctcttga
tttgttttct
ctccgaaaaa
tgggaatcag
atatgtcaca
tgcaaccaag
ttcagaattg
acaggcaata
atccccatta
aaaatcatca
agacatggtc
agagcaaatg
gtacaatgaa
tgaaagcaga
acattattgg
atgtaatgac
atgcacaagg
agaaaataga
taagtattat
caccattatg
atggtgttgg
caaacatccc
aggaggagat
taaaatgaat
ggaacggcat
taaagtaggc
agtgaccagt
gagtgcagag
cactccgatt
aaataaaaga
aatgggcgcg
gcagcaacag
cgtctgggga
ccaggcgcag
atggccaaat
aaaggttgac
agagaagaac
tgaccttgct
actgttaaga
gccagtgttc
actgccaacc
8821
8881
8941
9001
9061
9121
9181
9241
9301
9361
9421
9481
9541
9601
9661
9721
9781
9841
9901
9961
10021
10081
10141
10201
10261
agagaaggca
atagaatata
aactgcagaa
tctgcgaccc
gggtggagct
gcgggcgcgt
atccctagga
tcaggggcag
atacagaaaa
agtgaggcca
ttttataaaa
cttagacatg
aggaccagga
tgtatcagat
caagtgggat
cacttatgag
gaagaggtta
actcgctgag
acacccactt
ggagaggctg
gtgttccctg
tgcttgctta
ccatctctcc
gttaggaccc
taatatagga
aagaaggaga
ttcatttcct
ccttgctatc
tacgaagggt
atttccatga
ggagagactt
ggattaggca
tatatgaata
caaaatatgg
aaagttcccc
gaaaaggggg
tacttagaaa
attagatacc
gaggcacagg
gacccttggg
gcatatgcta
gaagaaggct
atagcaggga
tcttgatgta
gcagattgag
ctagactctc
aagacctctt
tagtcgccgc
tttctgcttt
gagacct
cggtggagaa
gatccgccaa
gagagcatac
tcgagaagtc
ggcggtccaa
atgggagact
agggcttgag
ctccatggag
atgatataga
taagagcaat
gactggaagg
aggaagaagg
caaagacatt
aggatgagag
gagaggttct
gatacccaga
aaccgcaaga
ctttccacaa
taaatatcac
ccctgggagg
accagcactt
caataaagct
ctggtcaact
gagaaaccga
ggcggtggca
ctgatacgcc
cagatcctcc
ctcaggactg
gccggctgga
cttaggagag
ctcacgctct
aaacccagct
tgaggaagat
gacttacaaa
gatttattac
catcatacca
tggctggcta
gcattattta
agcgtggaag
agagttggaa
ggccttctta
ggggatgtta
tgcatttcgc
ttctctccag
ggccagtgct
gccattttag
cggtactcgg
agcaggaaaa
acagctcctg
tcttgacttg
aaccaatact
aactgaccta
gatctgcgac
gtggaagatg
tgtgagggac
gaagaaaaag
gatgacttgg
ttggcaatag
agtgcaagaa
gattggcagg
tggaaattag
atgcagccag
tttgatccaa
gcaagtcagg
acatggctga
tggggaggag
tctgtattca
cactagcagg
gggcagagtg
aagtaagcca
taataagaag
tccctagcat
gccttggcag
gctattcagc
ccagaggctc
cctacaatat
agaaactctt
gatcctcgca
agaaatacaa
aaaaattagc
taggggtatc
atatgtctca
gacatagaat
attacacctc
tccctgtaaa
ctcaaacttc
ctctagccta
cctgtcagag
caagagggaa
ccggtcggga
gtcgctctgc
tagagcctgg
gctccacgct
gtgtgtgttc
accctggtct
gaagatggac
//
6
n
above report in format
g
1
334657
Save
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