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LOCUS KF527090 4682 bp RNA linear VRL 02-SEP-2013
DEFINITION HIV-1 isolate 4419_311 from Malawi pol protein (pol) gene, partial
cds; and vif protein (vif), vpr protein (vpr), tat protein (tat),
rev protein (rev), vpu protein (vpu), envelope glycoprotein (env),
and nef protein (nef) genes, complete cds
ACCESSION KF527090
VERSION KF527090.1 GI:534805114
KEYWORDS .
SOURCE Human immunodeficiency virus 1 (HIV-1)
ORGANISM Human immunodeficiency virus 1 Viruses; Retro-transcribing viruses;
Retroviridae; Orthoretrovirinae; Lentivirus; Primate lentivirus
group
REFERENCE 1 (bases 1 to 4682)
Show all sequences for reference 1
AUTHORS Permar,S.R., Salazar,M.G., Gao,F., Cai,F., Learn,G.H., Kalilani,L.,
Hahn,B.H., Shaw,G.M. and Salazar-Gonzalez,J.F.
TITLE Clonal amplification and maternal-infant transmission of
nevirapine-resistant HIV-1 variants in breast milk following
single-dose nevirapine prophylaxis
JOURNAL Retrovirology 10, 88 (2013)
PUBMED 23941304
REFERENCE 2 (bases 1 to 4682)
Show all sequences for reference 2
AUTHORS Permar,S., Salazar,M., Gao,F., Cai,F., Learn,G., Kalilani,L.,
Hahn,B., Shaw,G. and Salazar-Gonzalez,J.
TITLE Direct Submission
JOURNAL Submitted (06-AUG-2013) Medicine, University of Alabama at
Birmingham, 720 20th Street South, Birmingham, AL 35294, USA
COMMENT Annotation information was provided by the author. Some of the
information does not have GenBank feature identifiers and is being
provided in the comment section. Information in this section is
searchable in HIV Database at Los Alamos (hiv.lanl.gov).;
##HIVDataBaseData-START## Patient code 714904419 Sample city
Blantyre Patient Cohort CHAVI 009 Patient sex M Risk factor MB
Viral load 1210000 Patient health status acute infection Sample
timepoint 12 weeks of age Sample tissue plasma Culture method
uncultured Amplification Strategy single genome amplification
Patient comment Postnatally infected infant via breastfeeding
##HIVDataBaseData-END##
FEATURES Location/Qualifiers
source 1..4682
/organism="Human immunodeficiency virus 1"
/mol_type="genomic RNA"
/isolate="4419_311"
/host="Homo sapiens"
/db_xref="taxon:11676"
/country="Malawi"
/collection_date="15-Aug-2008"
/note="plasma sample taken at 12 weeks of age when first
detected HIV DNA PCR positive; subtype: C"
gene <1..173
/gene="pol"
CDS <1..173
/gene="pol"
/codon_start="3"
/transl_table="1"
/product="pol protein"
/protein_id="AGU35811.1"
/db_xref="GI:534805115"
/translation="PIWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKVKIIKDYGKQMA
GADCVAGRQDED"
gene 118..696
/gene="vif"
CDS 118..696
/gene="vif"
/codon_start="1"
/transl_table="1"
/product="vif protein"
/protein_id="AGU35812.1"
/db_xref="GI:534805116"
/translation="MENRWQVLIVWQVDRMRIRTWNSLVKHHMYVSRRAHGWFYRHHY
ESRHPKISSEVHIPLGEARLVIKTYWGLQTGEREWHLGHGVSIEWRLRRYSTQVDPGL
ADQLIHMHYFDCFADSAIRKAILGHIVIPRCDYQAGHNKVGSLQYLALTALIKPKKRK
PPLPSVRKLVEDRWNNPQKTRGRRGNHTMNGH"
gene 636..926
/gene="vpr"
CDS 636..926
/gene="vpr"
/codon_start="1"
/transl_table="1"
/product="vpr protein"
/protein_id="AGU35813.1"
/db_xref="GI:534805117"
/translation="MEQPPEDQGPQREPYNEWTLEILEELKQEAVRHFPIPWLHNLGQ
YIYETYGDTWAGVEAIIKILQQLLFIHFRIGCQHSRIGILRQRRARNGANRS"
gene 907..3536
/gene="tat"
CDS join(907..1121,3446..3536)
/gene="tat"
/codon_start="1"
/transl_table="1"
/product="tat protein"
/protein_id="AGU35814.1"
/db_xref="GI:534805118"
/translation="MEPIDPKLEPWNHPGSKPKTACNNCYCKCCSYHCLVCFQTKGLG
ISYGRKKRRQRRRAPPSSEDHQNPISKQPLPQARGDPTGSEESKKKVESKTETDPFD"
gene 1046..3693
/gene="rev"
CDS join(1046..1121,3446..3693)
/gene="rev"
/codon_start="1"
/transl_table="1"
/product="rev protein"
/protein_id="AGU35815.1"
/db_xref="GI:534805119"
/translation="MAGRSGDSDEGLLQAVRIIKILYQSNPYPKPEGTRQARKNRRRR
WRARQRQIHSISERILSTCLGRPAEPVPLPLPPIERLSIGDSENGGNSGTQQSQGTTE
GVGSP"
gene 1135..1395
/gene="vpu"
CDS 1135..1395
/gene="vpu"
/codon_start="1"
/transl_table="1"
/product="vpu protein"
/protein_id="AGU35816.1"
/db_xref="GI:534805120"
/translation="MSSLIEKVDYRVGIAALIIALLIAIVVWIIVYIEYRKLLRQRKI
DWLVERIRERAEDSGNESEGDIEELATMGDMGHLRLLDGVDL"
gene 1313..3883
/gene="env"
CDS 1313..3883
/gene="env"
/codon_start="1"
/transl_table="1"
/product="envelope glycoprotein"
/protein_id="AGU35817.1"
/db_xref="GI:534805121"
/translation="MRVRGILRSWQPWGIWGILGFWMVLTCSVLGNLWVTVYYGVPVW
KEAKTTLFCASDAKAYEREMHNVWATHACVPTDPNPQELVLENVTENFNMWKNDMVDQ
MHEDIISLWDQSLKPCVKLTPLCVTLDCKNSTENITDSRNITDNGERKNCSFNITTEI
KDKKQNVYALFYKLDIVPLHEDNSSYYRLINCNTSAITQACPKVSFDPIPIHYCAPAG
YAILKCNNKTFNGTGPCHNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSKDLTDN
AKIIIVHLNKSVEINCTRPGNNTRKSIRIGPGQTFYAPNGIIGNIRKAHCNIKGKQWN
ETLIKVGEKLAELFPNKIIKFNSSSGGDLEITTHSFNCGGEFFYCDTSGLFNGTYNPN
DTTSNSSSLNNITLTLPCKIKQVINMWQGVGKAIYAPPIAGNITCRSNITGLLLLRDG
GTTNDTEEIFRPGGGDMRDNWRSELYKYKVVEIKPLGVAPTKAKRRVVEREKRAVGIG
AVLLGFLGAAGSTMGAASITLTVQARQLLSGIVQQQSNLLRAIEAQQHMLQLTVWGIK
QLQARVLAIERYLKDQQLLGIWGCSGKLICTTSVPWNDSWSHNKSLQDIWDNMTWMQW
DKEINNYTSTIYRLLEESQNQQEKNEQDLLALDSWQNLWNWFSISKWLWYIKIFIMIV
GGLIGLRIIFAVLSIVNRVRQGYSPLSFQTLTPSPRGPDRLGRIEEEGGEQDRDRSIR
LVSGFLALAWDDLRSLCLFLYHRLRDFLLVIARTVEILGRSSLRGLQRGWEALKYLGN
LVQYWGSEIKKSAINLFDTIAIAVAEGTDRIIEIIQRIYRAICNIPVRIRQGFEAALL
"
gene 3885..4508
/gene="nef"
CDS 3885..4508
/gene="nef"
/codon_start="1"
/transl_table="1"
/product="nef protein"
/protein_id="AGU35818.1"
/db_xref="GI:534805122"
/translation="MGGKWSKSSPFGWPAVRERMRQTVPAAEGVGAASQDLDKRGALT
INNTPSNNEACAWLQAQEEEEEVGFPVRPQVPLRPMTFKGAFDLSFFLKEKGGLEGLI
YSRKRQEILDLWVYNTQGYFPDWQNYTPGPGVRYPLTFGWCFKLVPVDPKEVEEANEG
ENNCLLHPMSLHGMEDEEREVLKWVFDSRLAHRHVAREKHPEYYKDC"
BASE COUNT 1627 a 823 c 1133 g 1099 t
ORIGIN
1 accctatttg gaaaggacca gccaaactac tctggaaagg tgaaggggca gtagtaatac
61 aagataacag tgacataaag gtagtaccaa ggaggaaagt aaaaatcatt aaggactatg
121 gaaaacagat ggcaggtgct gattgtgtgg caggtagaca ggatgaggat tagaacatgg
181 aatagtttag taaagcacca tatgtatgtg tcaaggagag ctcatggatg gttttacaga
241 catcattatg aaagcagaca tccaaaaata agttcagaag tacacatacc attaggggag
301 gctaggttag taataaaaac atattggggt ttgcaaacag gagaaagaga atggcacttg
361 ggtcatggag tctccataga atggagattg agaagatata gtacacaagt agaccctggc
421 ctggcagatc agctaattca tatgcattat tttgattgtt ttgcagactc tgccataaga
481 aaagccatat taggacacat agttattcct aggtgtgact atcaagcagg acacaataag
541 gtaggatctc tacaatactt ggcactgaca gcattgataa aaccaaaaaa gagaaagcca
601 cctctgccta gtgttaggaa attagtagag gatagatgga acaaccccca gaagaccagg
661 ggccgcagag ggaaccatac aatgaatgga cactagagat tctagaggaa ctcaagcagg
721 aagctgtcag acactttcct ataccatggc tccataactt aggacaatat atttatgaaa
781 cctatggaga tacttgggca ggagtcgaag ctataataaa aatactgcaa caactactgt
841 tcattcattt cagaattgga tgccaacata gcagaatagg cattttgaga cagagaagag
901 caagaaatgg agccaataga tcctaaacta gagccttgga accatccagg aagtaaacct
961 aaaactgctt gtaacaattg ttattgtaaa tgttgtagct accattgtct agtttgcttt
1021 cagacaaaag gcttaggcat ttcctatggc aggaagaagc ggagacagcg acgaagggct
1081 cctccaagca gtgaggatca tcaaaatcct atatcaaagc agtaagtata tgtaatgtca
1141 agtttaatag aaaaagtaga ttatagagta ggaatagcag cattaataat agcattactt
1201 atagcaatag ttgtgtggat catagtatat atagaatata ggaaattgtt aagacaaagg
1261 aaaatagact ggttagttga aagaattagg gaaagagcag aagacagtgg caatgagagt
1321 gagggggata ttgaggagtt ggcaaccatg ggggatatgg ggcatcttag gcttttggat
1381 ggtgttgact tgtagtgtac tagggaactt gtgggtcaca gtctattatg gggtacctgt
1441 gtggaaagaa gcaaaaacta ctctattctg tgcatcagat gctaaagcat atgagagaga
1501 aatgcacaat gtctgggcta cacatgcctg tgtgcccaca gaccccaacc cacaagaact
1561 ggttttggaa aatgtaacag aaaattttaa catgtggaaa aatgacatgg tagatcagat
1621 gcatgaggat ataatcagtt tatgggatca aagcctaaaa ccatgtgtaa agctgactcc
1681 actctgtgtc actttagatt gtaaaaatag tactgaaaat attactgata gcaggaatat
1741 tacagataat ggagaaagga aaaattgctc ttttaatata accacagaaa taaaagataa
1801 gaaacagaac gtgtatgcac ttttttataa acttgatata gtaccacttc atgaggacaa
1861 cagttcctac tatagactaa taaattgtaa tacctcagcc ataacacaag cctgtccaaa
1921 ggtctctttt gacccaattc ctatacacta ttgtgcacca gctggttatg cgattctaaa
1981 gtgtaataat aagacattca atgggacagg accatgccat aatgtcagca cagtacaatg
2041 tacacatgga attaagccag tggtatcaac tcaactactg ttaaatggta gcctagcaga
2101 agaagagata ataattagat ctaaagatct gacagacaat gccaaaataa taatagtaca
2161 ccttaataag tctgtagaga ttaattgtac aagacccggc aacaatacaa gaaaaagtat
2221 aaggatagga ccaggacaaa cattctatgc accaaatgga ataataggaa acataagaaa
2281 agcacattgt aacattaagg gaaagcagtg gaatgaaact ttaataaagg taggggaaaa
2341 attagcagaa ctcttcccta ataaaataat aaagtttaat tcatcctcag gaggggatct
2401 agaaattaca acacatagct ttaattgtgg aggagaattt ttctattgcg atacatcagg
2461 attgtttaat ggcacataca atcctaatga tacaacaagt aattcaagct cacttaacaa
2521 catcacactc acactcccat gcaaaataaa gcaagttata aacatgtggc agggggtagg
2581 aaaagcgata tatgcccctc ccattgcagg aaacataaca tgtagatcaa atatcacagg
2641 actactattg ctacgtgatg gaggaactac aaatgacaca gaagagatat tcagacctgg
2701 aggaggagat atgagggaca attggagaag tgaattatat aaatacaaag tggtagaaat
2761 taagccattg ggagtagcac ccactaaggc aaaaaggaga gtggtggaga gagaaaaaag
2821 agcagtggga ataggagctg tactccttgg gttcttagga gcggcaggaa gcactatggg
2881 cgcggcgtca ataacgctga cggtacaggc cagacaactg ttgtctggta tagtgcaaca
2941 gcaaagcaat ttgctgaggg ctatagaggc gcaacagcat atgttgcaac tcacggtctg
3001 gggcattaag cagctccagg ctagagtcct ggccatagaa agatacctaa aggatcaaca
3061 gctcctagga atttggggct gctctggaaa actcatctgc accacttctg tgccttggaa
3121 tgacagttgg agtcataata aatctctaca agatatttgg gataacatga cctggatgca
3181 gtgggataaa gaaattaata attacacaag cacaatatac aggttacttg aggaatcaca
3241 aaaccagcag gaaaaaaatg aacaagattt attagcattg gacagttggc aaaatctgtg
3301 gaattggttc agcatatcaa aatggctgtg gtatataaaa atattcataa tgatagtagg
3361 aggcttgata ggtttaagga taatttttgc tgtgctttct atagtgaata gagttaggca
3421 gggatactca cctttgtcgt ttcagaccct taccccaagc ccgaggggac ccgacaggct
3481 cggaagaatc gaagaagaag gtggagagca agacagagac agatccattc gattagtgag
3541 cggattctta gcacttgcct gggacgacct gcggagcctg tgcctcttcc tctaccaccg
3601 attgagagac tttctattgg tgatagcgag aacggtggaa attctgggac gcagcagtct
3661 caggggacta cagagggggt gggaagccct taaatatctg ggaaaccttg tgcagtattg
3721 gggttcagag ataaaaaaga gtgctattaa tctatttgat accatagcca tagcagtagc
3781 tgagggaaca gataggatta tagaaataat acaaagaatt tatagagcta tctgcaacat
3841 acctgtgaga ataagacagg gctttgaagc agctttgcta taaaatggga ggcaagtggt
3901 caaaaagcag cccatttgga tggcctgctg taagagagag aatgaggcaa actgtgccag
3961 cagcagaggg agtcggagca gcatctcaag acttagataa acgtggagca cttaccatca
4021 acaacacacc cagcaataat gaggcttgtg cctggctgca agcacaagag gaggaagaag
4081 aagtaggctt tccagtcaga cctcaggtgc ctttaagacc aatgactttt aagggagcat
4141 ttgatctcag cttcttttta aaagaaaagg ggggactgga agggttaatt tactctagga
4201 aaaggcaaga aatccttgat ttgtgggtct ataacacaca aggctatttc cctgattggc
4261 aaaactacac accgggacca ggggtcagat atccactgac ctttggatgg tgcttcaagc
4321 tagtaccagt tgaccccaag gaggtagaag aggccaacga aggagaaaac aactgtttgc
4381 tacaccctat gagcctacat ggaatggagg acgaagaaag agaagtatta aagtgggtgt
4441 ttgacagtcg cctagcacac agacacgtgg cccgcgagaa acatccggag tattacaaag
4501 actgctgaca cagaagggac tttccgctgg gactttccac cggggcgttc caggaggagg
4561 ggtctgggcg ggactaggga gtggccaacc ctcagatgct gcatataagc agctgctttt
4621 cgcctgtact gggtctctct aggtagacca gatctgagcc tgggagctct ctggccttct
4681 ag
//
last modified: Tue May 31 10:56 2022