ID   M25381; SV 1; linear; genomic RNA; STD; VRL; 9474 BP.
XX
AC   M25381; M25729;
XX
DT   20-DEC-1990 (Rel. 26, Created)
DT   14-NOV-2006 (Rel. 89, Last updated, Version 8)
XX
DE   Feline immunodeficiency virus complete genome.
XX
KW   complete genome; env protein; gag protein; long terminal repeat;
KW   pol protein.
XX
OS   Feline immunodeficiency virus
OC   Viruses; Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus.
XX
RN   [1]
RP   1-355
RX   DOI; 10.1073/pnas.86.7.2448.
RX   PUBMED; 2928341.
RA   Olmstead R.A., Barnes A.K., Yamamoto J.K., Hirsch V.M., Purcell R.H.,
RA   Johnson P.R.;
RT   "Molecular cloning of feline immunodeficiency virus";
RL   Proc. Natl. Acad. Sci. U.S.A. 86(7):2448-2452(1989).
XX
RN   [2]
RP   1-9472
RX   DOI; 10.1073/pnas.86.15.5743.
RX   PUBMED; 2762293.
RA   Talbott R.L., Sparger E.E., Lovelace K.M., Fitch W.M., Pedersen N.C.,
RA   Luciw P.A., Elder J.H.;
RT   "Nucleotide sequence and genomic organization of feline immunodeficiency
RT   virus";
RL   Proc. Natl. Acad. Sci. U.S.A. 86(15):5743-5747(1989).
XX
RN   [3]
RP   1-9474
RX   DOI; 10.1073/pnas.86.20.8088.
RX   PUBMED; 2813380.
RA   Olmsted R.A., Hirsch V.M., Purcell R.H., Johnson P.R.;
RT   "Nucleotide sequence analysis of feline immunodeficiency virus: genome
RT   organization and relationship to other lentiviruses";
RL   Proc. Natl. Acad. Sci. U.S.A. 86(20):8088-8092(1989).
XX
RN   [4]
RP   7175-7182
RA   Elder J.H.;
RT   ;
RL   Unpublished.
XX
DR   MD5; 4e85fd5fba1de36d375617d692fddeb7.
DR   EuropePMC; PMC104329; 10438892.
DR   EuropePMC; PMC109955; 9696827.
DR   EuropePMC; PMC1143723; 15956574.
DR   EuropePMC; PMC114918; 11333894.
DR   EuropePMC; PMC1262595; 16227303.
DR   EuropePMC; PMC136364; 12097574.
DR   EuropePMC; PMC149757; 12584357.
DR   EuropePMC; PMC1622752; 17038183.
DR   EuropePMC; PMC1642619; 16971429.
DR   EuropePMC; PMC1847453; 17376229.
DR   EuropePMC; PMC1866009; 17192306.
DR   EuropePMC; PMC2045550; 17670835.
DR   EuropePMC; PMC2244644; 17971219.
DR   EuropePMC; PMC2270836; 18251995.
DR   EuropePMC; PMC2397500; 18315870.
DR   EuropePMC; PMC2453118; 18559113.
DR   EuropePMC; PMC2519550; 18550661.
DR   EuropePMC; PMC2603253; 19075221.
DR   EuropePMC; PMC2789563; 18279991.
DR   EuropePMC; PMC2821968; 19896220.
DR   EuropePMC; PMC2898260; 20444897.
DR   EuropePMC; PMC2987497; 20732330.
DR   EuropePMC; PMC3169092; 18689668.
DR   EuropePMC; PMC3347033; 22590677.
DR   EuropePMC; PMC3439265; 22632459.
DR   EuropePMC; PMC369484; 14747582.
DR   EuropePMC; PMC3706335; 23800358.
DR   EuropePMC; PMC371036; 15016897.
DR   EuropePMC; PMC3721975; 20210778.
DR   EuropePMC; PMC3812036; 24204263.
DR   EuropePMC; PMC3835772; 24298557.
DR   EuropePMC; PMC3999937; 24642186.
DR   EuropePMC; PMC4176367; 25147212.
DR   EuropePMC; PMC4180853; 25699660.
DR   EuropePMC; PMC4304674; 23800540.
DR   EuropePMC; PMC4327927; 25613718.
DR   EuropePMC; PMC4361796; 25535323.
DR   EuropePMC; PMC4373062; 25808580.
DR   EuropePMC; PMC4702554; 26491161.
DR   EuropePMC; PMC4908968; 26887496.
DR   EuropePMC; PMC5074269; 26935128.
DR   EuropePMC; PMC5110171; 27630243.
DR   EuropePMC; PMC5249086; 28107367.
DR   EuropePMC; PMC5432859; 28331087.
DR   EuropePMC; PMC545975; 15510684.
DR   EuropePMC; PMC5754089; 29300759.
DR   EuropePMC; PMC5827384; 29263270.
DR   EuropePMC; PMC5894237; 29636069.
DR   EuropePMC; PMC5899207; 29467316.
DR   EuropePMC; PMC5977254; 29772651.
DR   GOA; P20885.
DR   InterPro; IPR018582; Envelope_glycop_lentivirus.
DR   RFAM; RF01834; fiv_FSE.
DR   UniProtKB/Swiss-Prot; P20885; REV_FIVPE.
XX
CC   [4] revision. [2] sequence kindly provided in computer-readable
CC   form by John Elder, Scripps Institute, La Jolla, CA. [3] sequence
CC   kindly provided in computer-readable form by Robert Olmstead,
CC   NIAID, NIH, Bethesda, MD. [1] contains the LTR sequence from the
CC   complete genome in [3]. The sequence from [3] is shown (with
CC   differences from [2]); the substantive difference from [2] is at
CC   position 6123 where the latter possesses an early stop codon in
CC   orf2, which is thought to encode the transactivator protein. Clone
CC   34TF10 is, nevertheless, biologically active as described in [2]. A
CC   difference earlier reported at 7175-7182 turns out to have been a
CC   typo [2,4]. Orf1 is weakly homologous (PLSEARCH) with the Q orf of
CC   visna and has no detectable similarity to the vif protein of HIV
CC   and SIV. This is consistent with the clustering of FIV with the
CC   ungulate lentiviruses [2],[3]. Several 'urfs' are identified by [2]
CC   and [3] of which only orf3, possibly analogous to the L orf of
CC   visna, is annotated below; a small, possibly associated, orf is
CC   found at 8955-9170. For a fuller discussion of the reading frames,
CC   see [2] and [3]. NCBI gi: 323933
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..9474
FT                   /organism="Feline immunodeficiency virus"
FT                   /strain="Petaluma"
FT                   /mol_type="genomic RNA"
FT                   /clone="34TF10"
FT                   /clone="FIV-14"
FT                   /db_xref="taxon:11673"
FT   repeat_region   1..355
FT                   /standard_name="5' LTR"
FT                   /rpt_type=LONG_TERMINAL_REPEAT
FT   variation       12
FT                   /replace="t"
FT                   /citation=[3]
FT   variation       12
FT                   /replace="c"
FT                   /citation=[2]
FT   variation       122
FT                   /replace="t"
FT                   /citation=[2]
FT   variation       122
FT                   /replace="c"
FT                   /citation=[3]
FT   variation       146
FT                   /replace="t"
FT                   /citation=[2]
FT   variation       146
FT                   /replace="g"
FT                   /citation=[3]
FT   repeat_region   217..281
FT                   /note="R repeat 5' copy"
FT   misc_binding    357..377
FT                   /bound_moiety="unspecified"
FT                   /note="primer binding site"
FT   variation       373..374
FT                   /note="replace (373,'ag')"
FT                   /citation=[3]
FT   variation       373..374
FT                   /note="replace (373,'a')"
FT                   /citation=[2]
FT   variation       498..501
FT                   /note="ggac in [3]; agca in [2]"
FT   CDS             628..1980
FT                   /codon_start=1
FT                   /gene="gag"
FT                   /product="gag protein"
FT                   /db_xref="GOA:P16087"
FT                   /db_xref="InterPro:IPR000721"
FT                   /db_xref="InterPro:IPR001878"
FT                   /db_xref="InterPro:IPR008916"
FT                   /db_xref="InterPro:IPR008919"
FT                   /db_xref="InterPro:IPR012344"
FT                   /db_xref="InterPro:IPR036875"
FT                   /db_xref="PDB:2N1R"
FT                   /db_xref="PDB:4IC9"
FT                   /db_xref="PDB:4ICA"
FT                   /db_xref="PDB:5DCK"
FT                   /db_xref="PDB:5NA2"
FT                   /db_xref="PDB:5XMF"
FT                   /db_xref="PDB:5XMM"
FT                   /db_xref="UniProtKB/Swiss-Prot:P16087"
FT                   /protein_id="AAB59936.1"
FT                   /translation="MGNGQGRDWKMAIKRCSNVAVGVGGKSKKFGEGNFRWAIRMANVS
FT                   TGREPGDIPETLDQLRLVICDLQERREKFGSSKEIDMAIVTLKVFAVAGLLNMTVSTAA
FT                   AAENMYSQMGLDTRPSMKEAGGKEEGPPQAYPIQTVNGVPQYVALDPKMVSIFMEKARE
FT                   GLGGEEVQLWFTAFSANLTPTDMATLIMAAPGCAADKEILDESLKQLTAEYDRTHPPDA
FT                   PRPLPYFTAAEIMGIGLTQEQQAEARFAPARMQCRAWYLEALGKLAAIKAKSPRAVQLR
FT                   QGAKEDYSSFIDRLFAQIDQEQNTAEVKLYLKQSLSIANANADCKKAMSHLKPESTLEE
FT                   KLRACQEIGSPGYKMQLLAEALTKVQVVQSKGSGPVCFNCKKPGHLARQCREVKKCNKC
FT                   GKPGHVAAKCWQGNRKNSGNWKAGRAAAPVNQMQQAVMPSAPPMEEKLLDL"
FT   variation       1575
FT                   /gene="gag"
FT                   /note="g in [3]; a in [2]"
FT   variation       1840
FT                   /gene="gag"
FT                   /note="g in [3]; c in [2]"
FT   variation       1977
FT                   /gene="gag"
FT                   /note="a in [3]; g in [2]"
FT   variation       2028
FT                   /note="g in [3]; a in [2]"
FT   variation       2033
FT                   /note="c in [3]; t in [2]"
FT   CDS             2251..5243
FT                   /partial
FT                   /codon_start=3
FT                   /gene="pol"
FT                   /product="pol polyprotein"
FT                   /db_xref="GOA:P16088"
FT                   /db_xref="InterPro:IPR000477"
FT                   /db_xref="InterPro:IPR001037"
FT                   /db_xref="InterPro:IPR001584"
FT                   /db_xref="InterPro:IPR001969"
FT                   /db_xref="InterPro:IPR001995"
FT                   /db_xref="InterPro:IPR002156"
FT                   /db_xref="InterPro:IPR003308"
FT                   /db_xref="InterPro:IPR008181"
FT                   /db_xref="InterPro:IPR010659"
FT                   /db_xref="InterPro:IPR010661"
FT                   /db_xref="InterPro:IPR012337"
FT                   /db_xref="InterPro:IPR017856"
FT                   /db_xref="InterPro:IPR018061"
FT                   /db_xref="InterPro:IPR021109"
FT                   /db_xref="InterPro:IPR029054"
FT                   /db_xref="InterPro:IPR033704"
FT                   /db_xref="InterPro:IPR034170"
FT                   /db_xref="InterPro:IPR036157"
FT                   /db_xref="InterPro:IPR036397"
FT                   /db_xref="InterPro:IPR036862"
FT                   /db_xref="PDB:1B11"
FT                   /db_xref="PDB:1DUT"
FT                   /db_xref="PDB:1F7D"
FT                   /db_xref="PDB:1F7K"
FT                   /db_xref="PDB:1F7N"
FT                   /db_xref="PDB:1F7O"
FT                   /db_xref="PDB:1F7P"
FT                   /db_xref="PDB:1F7Q"
FT                   /db_xref="PDB:1F7R"
FT                   /db_xref="PDB:1FIV"
FT                   /db_xref="PDB:2FIV"
FT                   /db_xref="PDB:2HAH"
FT                   /db_xref="PDB:3FIV"
FT                   /db_xref="PDB:3OGP"
FT                   /db_xref="PDB:3OGQ"
FT                   /db_xref="PDB:4FIV"
FT                   /db_xref="PDB:4MQ3"
FT                   /db_xref="PDB:4PA1"
FT                   /db_xref="PDB:5FIV"
FT                   /db_xref="PDB:6FIV"
FT                   /db_xref="UniProtKB/Swiss-Prot:P16088"
FT                   /protein_id="AAB59937.1"
FT                   /translation="VLEDNSLIQPLLGRDNMIKFNIRLVMAQISDKIPVVKVKMKDPNK
FT                   GPQIKQWPLTNEKIEALTEIVERLEREGKVKRADPNNPWNTPVFAIKKKSGKWRMLIDF
FT                   RELNKLTEKGAEVQLGLPHPAGLQIKKQVTVLDIGDAYFTIPLDPDYAPYTAFTLPRKN
FT                   NAGPGRRFVWCSLPQGWILSPLIYQSTLDNIIQPFIRQNPQLDIYQYMDDIYIGSNLSK
FT                   KEHKEKVEELRKLLLWWGFETPEDKLQEEPPYTWMGYELHPLTWTIQQKQLDIPEQPTL
FT                   NELQKLAGKINWASQAIPDLSIKALTNMMRGNQNLNSTRQWTKEARLEVQKAKKAIEEQ
FT                   VQLGYYDPSKELYAKLSLVGPHQISYQVYQKDPEKILWYGKMSRQKKKAENTCDIALRA
FT                   CYKIREESIIRIGKEPRYEIPTSREAWESNLINSPYLKAPPPEVEYIHAALNIKRALSM
FT                   IKDAPIPGAETWYIDGGRKLGKAAKAAYWTDTGKWQVMELEGSNQKAEIQALLLALKAG
FT                   SEEMNIITDSQYVINIILQQPDMMEGIWQEVLEELEKKTAIFIDWVPGHKGIPGNEEVD
FT                   KLCQTMMIIEGDGILDKRSEDAGYDLLAAKEIHLLPGEVKVIPTGVKLMLPKGYWGLII
FT                   GKSSIGSKGLDVLGGVIDEGYRGEIGVIMINVSRKSITLMERQKIAQLIILPCKHEVLE
FT                   QGKVVMDSERGDNGYGSTGVFSSWVDRIEEAEINHEKFHSDPQYLRTEFNLPKMVAEEI
FT                   RRKCPVCRIRGEQVGGQLKIGPGIWQMDCTHFDGKIILVGIHVESGYIWAQIISQETAD
FT                   CTVKAVLQLLSAHNVTELQTDNGPNFKNQKMEGVLNYMGVKHKFGIPGNPQSQALVENV
FT                   NHTLKVWIRKFLPETTSLDNALSLAVHSLNFKRRGRIGGMAPYELLAQQESLRIQDYFS
FT                   AIPQKLQAQWIYYKDQKDKKWKGPMRVEYWGQGSVLLKDEEKGYFLIPRRHIRRVPEPC
FT                   ALPEGDE"
FT   variation       2288
FT                   /gene="pol"
FT                   /note="a in [3]; g in [2]"
FT   variation       2464
FT                   /gene="pol"
FT                   /note="g in [3]; a in [2]"
FT   variation       2490
FT                   /gene="pol"
FT                   /note="c in [3]; t in [2]"
FT   variation       2580
FT                   /gene="pol"
FT                   /note="c in [3]; t in [2]"
FT   variation       2631
FT                   /gene="pol"
FT                   /note="t in [3]; c in [2]"
FT   variation       2735
FT                   /gene="pol"
FT                   /note="a in [3]; g in [2]"
FT   variation       3733
FT                   /gene="pol"
FT                   /note="a in [3]; g in [2]"
FT   variation       3743
FT                   /gene="pol"
FT                   /note="a in [3]; t in [2]"
FT   variation       3812
FT                   /gene="pol"
FT                   /note="g in [3]; a in [2]"
FT   variation       4202
FT                   /gene="pol"
FT                   /note="g in [3]; a in [2]"
FT   variation       4211
FT                   /gene="pol"
FT                   /note="c in [3]; t in [2]"
FT   variation       4271
FT                   /gene="pol"
FT                   /note="c in [3]; t in [2]"
FT   variation       4493
FT                   /gene="pol"
FT                   /note="a in [3]; g in [2]"
FT   variation       4540
FT                   /gene="pol"
FT                   /note="g in [3]; t in [2]"
FT   variation       4706
FT                   /gene="pol"
FT                   /note="c in [3]; t in [2]"
FT   variation       4891
FT                   /gene="pol"
FT                   /note="g in [3]; a in [2]"
FT   CDS             5236..5991
FT                   /codon_start=1
FT                   /note="ORF 1;  NCBI gi: 323936"
FT                   /db_xref="GOA:P16089"
FT                   /db_xref="InterPro:IPR008668"
FT                   /db_xref="UniProtKB/Swiss-Prot:P16089"
FT                   /protein_id="AAB59938.1"
FT                   /translation="MSEEDWQVSRRLFAVLQGGVNSAMLYISRLPPDEREKYKKDFKKR
FT                   LFDTETGFIKRLRKAEGIKWSFHTRDYYIGYVREMVAGSTTSLSLRMYIYISNPLWHSQ
FT                   YRPGLKNFNKEWPFVNMWIKTGFMWDDIEKQNICIGGEVSPGWGPGMVGIAIKAFSCGE
FT                   RKIEATPVMIIRGEIDPKKWCGDCWNLMCLRNSPPKTLQRLAMLACGVPAKKWRGCCNQ
FT                   RFVSPYRTPADLEVIQSKPSWNLLWSGEL"
FT   variation       5332
FT                   /note="g in [3]; a in [2]"
FT   variation       5497
FT                   /note="t in [3]; c in [2]"
FT   variation       5559
FT                   /note="t in [3]; c in [2]"
FT   variation       5986
FT                   /note="t in [3]; c in [2]"
FT   CDS             5992..6228
FT                   /codon_start=1
FT                   /note="ORF 2;  NCBI gi: 323937"
FT                   /db_xref="GOA:Q66013"
FT                   /db_xref="UniProtKB/Swiss-Prot:Q66013"
FT                   /protein_id="AAB59939.1"
FT                   /translation="MEDIIVLFNRVTEKLEKELAIRIFVLAHQLERDKAIRLLQGLFWR
FT                   YRFKKPRVDYCLCWWCCKFYYWQLQSTLSITTA"
FT   variation       6000
FT                   /note="c in [3]; a in [2]"
FT   variation       6123
FT                   /note="g in [3]; a in [2]"
FT   variation       6149
FT                   /note="t in [3]; c in [2]"
FT   variation       6179
FT                   /note="a in [3]; g in [2]"
FT   variation       6238
FT                   /note="g in [3]; t in [2]"
FT   variation       6245..6248
FT                   /note="attt in [3]; ttt in [2]"
FT   CDS             6266..8836
FT                   /codon_start=1
FT                   /gene="env"
FT                   /product="envelope polyprotein"
FT                   /db_xref="GOA:P16090"
FT                   /db_xref="InterPro:IPR000328"
FT                   /db_xref="InterPro:IPR018582"
FT                   /db_xref="UniProtKB/Swiss-Prot:P16090"
FT                   /protein_id="AAB59940.1"
FT                   /translation="MAEGFAANRQWIGLEEAEELLDFDIATQMSEEGPLNPGVNPFRVP
FT                   GITEKEKQNYCNILQPKLQDLRNEIQEVKLEEGNAGKFRRARFLRYSDESVLSLVHAFI
FT                   GYCIYLGNRNKLGSLRHDIDIEAPQEECYNNREKGTTDNIKYGRRCCLGTVTLYLILFI
FT                   GIIIYSQTTNAQVVWRLPPLVVPVEESEIIFWDCWAPEEPACQDFLGAMIHLKAKTNIS
FT                   IREGPTLGNWAREIWATLFKKATRQCRRGRIWKRWNETITGPSGCANNTCYNVSVIVPD
FT                   YQCYLDRVDTWLQGKINISLCLTGGKMLYNKVTKQLSYCTDPLQIPLINYTFGPNQTCM
FT                   WNTSQIQDPEIPKCGWWNQMAYYNSCKWEEAKVKFHCQRTQSQPGSWFRAISSWKQRNR
FT                   WEWRPDFESKKVKISLQCNSTKNLTFAMRSSGDYGEVTGAWIEFGCHRNKSKLHAEARF
FT                   RIRCRWNVGSNTSLIDTCGNTQKVSGANPVDCTMYSNKMYNCSLQNGFTMKVDDLIMHF
FT                   NMKKAVEMYNIAGNWSCTSDLPSSWGYMNCNCTNSSSSYSGTKMACPSNRGILRNWYNP
FT                   VAGLRQSLEQYQVVKQPDYLVVPEEVMEYKPRRKRAAIHVMLALAAVLSIAGAGTGATA
FT                   IGMVTQYHQVLATHQEAVEKVTEALKINNLRLVTLEHQVLVIGLKVEAMEKFLYTAFAM
FT                   QELGCNQNQFFCKIPPELWTRYNMTINQTIWNHGNITLGEWYNQTKDLQQKFYEIIMDI
FT                   EQNNVQGKKGIQQLQKWEDWVGWIGNIPQYLKGLLGGILGIGLGVLLLILCLPTLVDCI
FT                   RNCIHKILGYTVIAMPEVEGEEIQPQMELRRNGRQCGMSEKEEE"
FT   variation       6306
FT                   /gene="env"
FT                   /note="t in [3]; c in [2]"
FT   variation       6430
FT                   /gene="env"
FT                   /note="c in [3]; t in [2]"
FT   variation       6548
FT                   /gene="env"
FT                   /note="a in [3]; c in [2]"
FT   CDS             6712..6918
FT                   /codon_start=1
FT                   /gene="env"
FT                   /note="ORF 3;  NCBI gi: 323939"
FT                   /db_xref="InterPro:IPR009588"
FT                   /db_xref="UniProtKB/TrEMBL:Q66014"
FT                   /protein_id="AAB59941.1"
FT                   /translation="MLPRNGDFVPDFIYRNNNIFTDNQRSGSMETSTISSPSRRIRNNF
FT                   LGLLGTRRTRLSGLSWGNDTSKS"
FT   variation       6739
FT                   /gene="env"
FT                   /note="c in [3]; t in [2]"
FT   variation       6753
FT                   /gene="env"
FT                   /note="t in [3]; c in [2]"
FT   variation       6758
FT                   /gene="env"
FT                   /note="a in [3]; g in [2]"
FT   variation       6764
FT                   /gene="env"
FT                   /note="a in [3]; g in [2]"
FT   variation       6779
FT                   /gene="env"
FT                   /note="a in [3]; g in [2]"
FT   variation       6782..6783
FT                   /gene="env"
FT                   /note="aa in [3]; gg in [2]"
FT   variation       7175..7182
FT                   /gene="env"
FT                   /note="acaggagg in [3]; caggagga in [2]"
FT   variation       7381
FT                   /gene="env"
FT                   /note="a in [3]; g in [2]"
FT   variation       7484
FT                   /gene="env"
FT                   /note="g in [3]; a in [2]"
FT   variation       7512..7513
FT                   /gene="env"
FT                   /note="ag in [3]; ca in [2]"
FT   variation       7618
FT                   /gene="env"
FT                   /note="a in [3]; c in [2]"
FT   variation       7625
FT                   /gene="env"
FT                   /note="g in [3]; a in [2]"
FT   variation       7670
FT                   /gene="env"
FT                   /note="a in [3]; g in [2]"
FT   variation       7704..7708
FT                   /gene="env"
FT                   /note="aaaaa in [3]; caaat in [2]"
FT   variation       7750
FT                   /gene="env"
FT                   /note="t in [3]; c in [2]"
FT   variation       7808..7810
FT                   /gene="env"
FT                   /note="atg in [3]; gta in [2]"
FT   variation       7824..7828
FT                   /gene="env"
FT                   /note="aaaag in [3]; caaaa in [2]"
FT   variation       7996
FT                   /gene="env"
FT                   /note="g in [3]; a in [2]"
FT   variation       8054
FT                   /gene="env"
FT                   /note="g in [3]; c in [2]"
FT   variation       8129
FT                   /gene="env"
FT                   /note="g in [3]; a in [2]"
FT   variation       8222
FT                   /gene="env"
FT                   /note="g in [3]; a in [2]"
FT   variation       8238
FT                   /gene="env"
FT                   /note="a in [3]; g in [2]"
FT   variation       8329
FT                   /gene="env"
FT                   /note="g in [3]; a in [2]"
FT   variation       8377
FT                   /gene="env"
FT                   /note="t in [3]; c in [2]"
FT   variation       8394
FT                   /gene="env"
FT                   /note="c in [3]; t in [2]"
FT   variation       8548..8550
FT                   /gene="env"
FT                   /note="gaa in [3]; aac in [2]"
FT   variation       8588
FT                   /gene="env"
FT                   /note="g in [3]; a in [2]"
FT   repeat_region   9120..9474
FT                   /rpt_type=LONG_TERMINAL_REPEAT
FT                   /note="3' LTR"
FT   variation       9131
FT                   /note="t in [3]; c in [2]"
FT   variation       9241
FT                   /note="c in [3]; t in [2]"
FT   variation       9265
FT                   /note="g in [3]; t in [2]"
FT   repeat_region   9336..9400
FT                   /note="R repeat 3' copy"
XX
SQ   Sequence 9474 BP; 3571 A; 1370 C; 2119 G; 2414 T; 0 other;
     tgggatgagt attggaaccc tgaagaaata gaaagaatgc ttatggacta gggactgttt        60
     acgaacaaat gataaaagga aatagctgag catgactcat agttaaagcg ctagcagctg       120
     cctaaccgca aaaccacatc ctatggaaag cttgctaatg acgtataagt tgttccattg       180
     taagagtata taaccagtgc tttgtgaaac ttcgaggagt ctctttgttg aggacttttg       240
     agttctccct tgaggctccc acagatacaa taaatatttg agattgaacc ctgtcgagta       300
     tctgtgtaat cttttttacc tgtgaggtct cggaatccgg gccgagaact tcgcagttgg       360
     cgcccgaaca gggacttgat tgagagtgat tgaggaagtg aagctagagc aatagaaagc       420
     tgttaagcag aactcctgct gacctaaata gggaagcagt agcagacgct gctaacagtg       480
     agtatctcta gtgaagcgga ctcgagctca taatcaagtc attgtttaaa ggcccagata       540
     aattacatct ggtgactctt cgcggacctt caagccagga gattcgccga gggacagtca       600
     acaaggtagg agagattcta cagcaacatg gggaatggac aggggcgaga ttggaaaatg       660
     gccattaaga gatgtagtaa tgttgctgta ggagtagggg ggaagagtaa aaaatttgga       720
     gaagggaatt tcagatgggc cattagaatg gctaatgtat ctacaggacg agaacctggt       780
     gatataccag agactttaga tcaactaagg ttggttattt gcgatttaca agaaagaaga       840
     gaaaaatttg gatctagcaa agaaattgat atggcaattg tgacattaaa agtctttgcg       900
     gtagcaggac ttttaaatat gacggtgtct actgctgctg cagctgaaaa tatgtattct       960
     caaatgggat tagacactag gccatctatg aaagaagcag gtggaaaaga ggaaggccct      1020
     ccacaggcat atcctattca aacagtaaat ggagtaccac aatatgtagc acttgaccca      1080
     aaaatggtgt ccatttttat ggaaaaggca agagaaggac taggaggtga ggaagttcaa      1140
     ctatggttta ctgccttctc tgcaaattta acacctactg acatggccac attaataatg      1200
     gccgcaccag ggtgcgctgc agataaagaa atattggatg aaagcttaaa gcaactgaca      1260
     gcagaatatg atcgcacaca tccccctgat gctcccagac cattacccta ttttactgca      1320
     gcagaaatta tgggtatagg attaactcaa gaacaacaag cagaagcaag atttgcacca      1380
     gctaggatgc agtgtagagc atggtatctc gaggcattag gaaaattggc tgccataaaa      1440
     gctaagtctc ctcgagctgt gcagttaaga caaggagcta aggaagatta ttcatccttt      1500
     atagacagat tgtttgccca aatagatcaa gaacaaaata cagctgaagt taagttatat      1560
     ttaaaacagt cattgagcat agctaatgct aatgcagact gtaaaaaggc aatgagccac      1620
     cttaagccag aaagtaccct agaagaaaag ttgagagctt gtcaagaaat aggctcacca      1680
     ggatataaaa tgcaactctt ggcagaagct cttacaaaag ttcaagtagt gcaatcaaaa      1740
     ggatcaggac cagtgtgttt taattgtaaa aaaccaggac atctagcaag acaatgtaga      1800
     gaagtgaaaa aatgtaataa atgtggaaaa cctggtcatg tagctgccaa atgttggcaa      1860
     ggaaatagaa agaattcggg aaactggaag gcggggcgag ctgcagcccc agtgaatcaa      1920
     atgcagcaag cagtaatgcc atctgcacct ccaatggagg agaaactatt ggatttataa      1980
     attataataa agtaggtact actacaacat tagaaaagag gccagaaata ctcatatttg      2040
     taaatggata tcctataaaa tttttattag acacaggagc agatataaca attttaaata      2100
     ggagagattt tcaagtaaaa aattctatag aaaatggaag gcaaaatatg attggagtag      2160
     gaggaggaaa gagaggaaca aattatatta atgtacattt agagattaga gatgaaaatt      2220
     ataagacaca atgtatattt ggtaatgttt gtgtcttaga agataactca ttaatacaac      2280
     cattattagg gagagataat atgattaaat tcaatattag gttagtaatg gctcaaattt      2340
     ctgataagat tccagtagta aaagtaaaaa tgaaggatcc taataaagga cctcaaataa      2400
     aacaatggcc attaacaaat gaaaaaattg aagccttaac agaaatagta gaaagactag      2460
     aaagagaagg gaaagtaaaa agagcagatc caaataatcc atggaataca ccagtatttg      2520
     ctataaaaaa gaaaagtgga aaatggagaa tgctcataga ttttagagaa ttaaacaaac      2580
     taactgagaa aggagcagag gtccagttgg gactacctca tcctgctggt ttacaaataa      2640
     aaaaacaagt aacagtatta gatatagggg atgcatattt caccattcct cttgatccag      2700
     attatgctcc ttatacagca tttactttac ctagaaaaaa taatgcggga ccaggaagga      2760
     gatttgtgtg gtgtagtcta ccacaaggct ggattttaag tccattgata tatcaaagta      2820
     cattagataa tataatacaa ccttttatta gacaaaatcc tcaattagat atttaccaat      2880
     atatggatga catttatata ggatcaaatt taagtaaaaa ggagcataaa gaaaaggtag      2940
     aagaattaag aaaattacta ttatggtggg gatttgaaac tccagaagat aaattacagg      3000
     aagaaccccc atatacatgg atgggttatg aattacatcc attaacatgg acaatacaac      3060
     agaaacagtt agacattcca gaacagccca ctctaaatga gttgcaaaaa ttagcaggaa      3120
     aaattaattg ggctagccaa gctattccag acttgagtat aaaagcatta actaacatga      3180
     tgagaggaaa tcaaaaccta aattcaacaa gacaatggac taaagaagct cgactggaag      3240
     tacaaaaggc aaaaaaggct atagaagaac aagtacaact aggatactat gaccccagta      3300
     aggagttata tgctaaatta agtttggtgg gaccacatca aataagttat caagtatatc      3360
     agaaggatcc agaaaagata ctatggtatg gaaaaatgag tagacaaaag aaaaaggcag      3420
     aaaatacatg tgatatagcc ttaagagcat gctataagat aagagaagag tctattataa      3480
     gaataggaaa agaaccaaga tatgaaatac ctacttctag agaagcctgg gaatcaaatt      3540
     taattaattc accatatctt aaggccccac ctcctgaggt agaatatatc catgctgctt      3600
     tgaatataaa gagagcgtta agtatgataa aagatgctcc aataccagga gcagaaacat      3660
     ggtatataga tggaggtaga aagctaggaa aagcagcaaa agcagcctat tggacagata      3720
     caggaaagtg gcaagtgatg gaattagaag gcagtaatca gaaggcagaa atacaagcat      3780
     tattattggc attaaaagca ggatcagagg agatgaatat tataacagat tcacaatatg      3840
     ttataaatat tattcttcaa caaccagata tgatggaggg aatctggcaa gaagttttag      3900
     aagaattgga gaagaaaaca gcaatattta tagattgggt cccaggacat aaaggtattc      3960
     caggaaatga ggaagtagat aagctttgtc aaacaatgat gataatagaa ggggatggga      4020
     tattagataa aaggtcagaa gatgcaggat atgatttatt agctgcaaaa gaaatacatt      4080
     tattgccagg agaggtaaaa gtaataccaa caggggtaaa gctaatgttg cctaaaggat      4140
     attggggatt aataatagga aaaagctcga tagggagtaa aggattggat gtattaggag      4200
     gggtaataga cgaaggatat cgaggtgaaa ttggagtaat aatgattaat gtatcaagaa      4260
     aatcaatcac cttaatggaa cgacaaaaga tagcacaatt aataatattg ccttgtaaac      4320
     atgaagtatt agaacaagga aaagtagtaa tggattcaga gagaggagac aatggttatg      4380
     ggtcaacagg agtattctcc tcttgggttg acagaattga ggaagcagaa ataaatcatg      4440
     aaaaatttca ctcagatcca cagtacttaa ggactgaatt taatttacct aaaatggtag      4500
     cagaagagat aagacgaaaa tgcccagtat gcagaatcag aggagaacaa gtgggaggac      4560
     aattgaaaat agggcctggt atctggcaaa tggattgcac acactttgat ggcaaaataa      4620
     ttcttgtggg tatacatgtg gaatcaggat atatatgggc acaaataatt tctcaagaaa      4680
     ctgctgactg tacagttaaa gctgtcttac aattgttgag tgctcataat gttactgaat      4740
     tacaaacaga taatggacca aattttaaaa atcaaaagat ggaaggagta ctcaattaca      4800
     tgggtgtgaa acataagttt ggtatcccag ggaacccaca gtcacaagca ttagttgaaa      4860
     atgtaaatca tacattaaaa gtttggattc ggaaattttt gcctgaaaca acctccttgg      4920
     ataatgcctt atctctcgct gtacatagtc tcaattttaa aagaagaggt aggataggag      4980
     ggatggcccc ttatgaatta ttagcacaac aagaatcctt aagaatacaa gattattttt      5040
     ctgcaatacc acaaaaattg caagcacagt ggatttatta taaagatcaa aaagataaga      5100
     aatggaaagg accaatgaga gtagaatact ggggacaggg atcagtatta ttaaaggatg      5160
     aagagaaggg atattttctt atacctagga gacacataag gagagttcca gaaccctgcg      5220
     ctcttcctga aggggatgag tgaagaagat tggcaggtaa gtagaagact ctttgcagtg      5280
     ctccaaggag gagtaaatag cgctatgcta tacatatcta ggctacctcc ggatgaaaga      5340
     gaaaagtata aaaaagactt caagaaaaga ctttttgaca cagaaacagg atttataaag      5400
     agactacgga aagctgaagg aataaaatgg agctttcata ctagagatta ttacatagga      5460
     tatgtcagag aaatggtggc aggatccact acatcattaa gtctaaggat gtatatatat      5520
     ataagtaacc cactatggca ttctcagtat cgtccaggtt tgaaaaattt caataaggaa      5580
     tggccttttg taaatatgtg gataaaaaca ggatttatgt gggatgatat tgaaaaacaa      5640
     aatatttgta taggaggaga agtttcacca ggatggggac cagggatggt aggtatagca      5700
     ataaaagctt ttagttgtgg cgaaagaaag attgaggcta ctcctgtaat gattataaga      5760
     ggagaaatag atccaaaaaa atggtgcgga gattgttgga atttaatgtg tcttagaaac      5820
     tcacctccaa agactttaca aagactcgct atgttggcgt gtggcgtgcc ggctaagaag      5880
     tggcgaggat gctgtaatca acgctttgtt tctccttaca gaacgcctgc tgatttagag      5940
     gtcattcaat ccaagcccag ctggaacctg ttatggtcgg gagaattatg aatggaagac      6000
     ataatagtat tattcaatag ggtcactgag aaactagaaa aagaattagc tatcagaata      6060
     tttgtattag cacatcaatt agaaagggac aaagctatta gattactaca aggattattt      6120
     tggagatata gatttaagaa accccgagta gattattgtt tatgttggtg gtgttgcaaa      6180
     ttctattatt ggcagttgca atctacatta tcaataacta ctgcttagaa atatttagat      6240
     taatatttca tttgcaacaa taagaatggc agaaggattt gcagccaata gacaatggat      6300
     aggactagaa gaagctgaag agttattaga ttttgatata gcaacacaaa tgagtgaaga      6360
     aggaccacta aatccaggag taaacccatt tagggtacct ggaataacag aaaaagaaaa      6420
     gcaaaactac tgtaacatat tacaacctaa gttacaagat ctaaggaacg aaattcaaga      6480
     ggtaaaactg gaagaaggaa atgcaggtaa gtttagaaga gcaagatttt taaggtattc      6540
     tgatgaaagt gtattgtccc tggttcatgc gttcatagga tattgtatat atttaggtaa      6600
     tcgaaataag ttaggatctt taagacatga cattgatata gaagcacccc aagaagagtg      6660
     ttataataat agagagaagg gtacaactga caatataaaa tatggtagac gatgttgcct      6720
     aggaacggtg actttgtacc tgattttatt tataggaata ataatatatt cacagacaac      6780
     caacgctcag gtagtatgga gacttccacc attagtagtc ccagtagaag aatcagaaat      6840
     aattttttgg gattgttggg caccagaaga acccgcctgt caggactttc ttggggcaat      6900
     gatacatcta aaagctaaga caaatataag tatacgagag ggacctacct tggggaattg      6960
     ggctagagaa atatgggcaa cattattcaa aaaggctact agacaatgta gaagaggcag      7020
     aatatggaaa agatggaatg agactataac aggaccatca ggatgtgcta ataacacatg      7080
     ttataatgtt tcagtaatag tacctgatta tcagtgttat ttagatagag tagatacttg      7140
     gttacaaggg aaaataaata tatcattatg tctaacagga ggaaaaatgt tgtacaataa      7200
     agttacaaaa caattaagct attgtacaga cccattacaa atcccactga tcaattatac      7260
     atttggacct aatcaaacat gtatgtggaa tacttcacaa attcaggacc ctgaaatacc      7320
     aaaatgtgga tggtggaatc aaatggccta ttataacagt tgtaaatggg aagaggcaaa      7380
     agtaaagttt cattgtcaaa gaacacagag tcagcctgga tcatggttta gagcaatctc      7440
     gtcatggaaa caaagaaata gatgggagtg gagaccagat tttgaaagta aaaaggtgaa      7500
     aatatctcta cagtgcaata gcacaaaaaa cctaaccttt gcaatgagaa gttcaggaga      7560
     ttatggagaa gtaacgggag cttggataga gtttggatgt catagaaata aatcaaaact      7620
     tcatgctgaa gcaaggttta gaattagatg tagatggaat gtagggagta atacctcgct      7680
     cattgataca tgtggaaaca ctcaaaaagt ttcaggtgcg aatcctgtag attgtaccat      7740
     gtattcaaat aaaatgtaca attgttcttt acaaaacggg tttactatga aggtagatga      7800
     ccttattatg catttcaata tgaaaaaggc tgtagaaatg tataatattg ctggaaattg      7860
     gtcttgtaca tctgacttgc catcgtcatg ggggtatatg aattgtaatt gtacaaatag      7920
     tagtagtagt tatagtggta ctaaaatggc atgtcctagc aatcgaggca tcttaaggaa      7980
     ttggtataac ccagtggcag gattacgaca atccttagaa cagtatcaag ttgtaaaaca      8040
     accagattac ttagtggtcc cagaggaagt catggaatat aaacctagaa ggaaaagggc      8100
     agctattcat gttatgttgg ctcttgcagc agtattatct attgccggtg cagggacggg      8160
     ggctactgct atagggatgg taacacaata ccaccaagtt ctggcaaccc atcaagaagc      8220
     tgtagaaaag gtgactgaag ccttaaagat aaacaactta agattagtta cattagagca      8280
     tcaagtacta gtaataggat taaaagtaga agctatggaa aaatttttgt atacagcttt      8340
     cgctatgcaa gaattaggat gtaatcaaaa tcaatttttc tgcaaaatcc ctcctgagtt      8400
     gtggacaagg tataatatga ctataaatca aacaatatgg aatcatggaa atataacttt      8460
     gggggaatgg tataaccaaa caaaagattt acaacaaaag ttttatgaaa taataatgga      8520
     catagaacaa aataatgtac aagggaagaa agggatacaa caattacaaa agtgggaaga      8580
     ttgggtagga tggataggaa atattccaca atatttaaag ggactattgg gaggtatctt      8640
     gggaatagga ttaggagtgt tattattgat tttatgttta cctacattgg ttgattgtat      8700
     aagaaattgt atccacaaga tactaggata cacagtaatt gcaatgcctg aagtagaagg      8760
     agaagaaata caaccacaaa tggaattgag gagaaatggt aggcaatgtg gcatgtctga      8820
     aaaagaggag gaatgatgaa gtatctcaga cttattttat aagggagata ctgtgctgag      8880
     ttcttccctt tgaggaaggt atgtcatatg aatccatttc gaatcaaatc aaactaataa      8940
     agtatgtatt gtaaggtaaa aggaaaagac aaagaagaag aagaaagaag aaagccttca      9000
     agaggatgat gacagagtta gaagatcgct tcaggaagct atttggcacg acttctacaa      9060
     cgggagacag cacagtagat tctgaagatg aacctcctaa aaaagaaaaa agggtggact      9120
     gggatgagta ttggaaccct gaagaaatag aaagaatgct tatggactag ggactgttta      9180
     cgaacaaatg ataaaaggaa atagctgagc atgactcata gttaaagcgc tagcagctgc      9240
     ctaaccgcaa aaccacatcc tatggaaagc ttgctaatga cgtataagtt gttccattgt      9300
     aagagtatat aaccagtgct ttgtgaaact tcgaggagtc tctttgttga ggacttttga      9360
     gttctccctt gaggctccca cagatacaat aaatatttga gattgaaccc tgtcgagtat      9420
     ctgtgtaatc ttttttacct gtgaggtctc ggaatccggg ccgagaactt cgca            9474
//