From: GenBank-Updates@genbank.bio.net
Newsgroups: bionet.molbio.genbank.updates
Subject: Avian leukemia virus ALV-RSA genome.
Date: 29 Jul 92 10:01:10 GMT
Distribution: bionet
Checksum: 05356    17

LOCUS       ALVCG        7286 bp ss-RNA             VRL       29-JUL-1992
DEFINITION  Avian leukemia virus ALV-RSA genome.
ACCESSION   M37980
KEYWORDS    capsid protein; complete genome; envelope polyprotein; integrase;
            matrix protein; nucleocapsid protein; polymerase; protease;
            reverse transcriptase; surface protein; trans-acting factor;
            transmembrane protein.
SOURCE      Avian leukemia virus RNA.
  ORGANISM  Avian leukosis virus
            Viridae; ss-RNA enveloped viruses; Positive strand RNA virus;
            Retroviridae; Oncovirinae; Type C oncovirus group;
            Avian type C oncoviruses.
REFERENCE   1  (bases 1 to 7286)
  AUTHORS   Bieth,E. and Darlix,J.-L.
  TITLE     Complete nucleotide sequence of a highly infectious avian leukosis
            virus
  JOURNAL   Nucleic Acids Res. 20, 367-367 (1992)
  STANDARD  full staff_entry
COMMENT     Draft entry and computer-readable sequence for [Unpublished (1990)]
            kindly submitted
            by E.Bieth, 24-AUG-1990.
               CRBGC du CNRS
               118 route de Narbonne
               31062 Toulouse Cedex
               France
FEATURES             Location/Qualifiers
     CDS             join(372..388,5069..6872)
                     /product="envelope protein"
                     /gene="env"
                     /codon_start=1
                     /translation="MEAVIKAFLTGYPGKTSKKDSKEKPLATSKKDPEKTPLLPTRVN
                     YILIIGVLVLCEVTGVRADVHLLEQPGNLWITWANRTGQTDFCLSTQSATSPFQTCLI
                     GIPSPISEGDFKGYVSDNCTTLGTDRLVSSADFTGGPDNSTTLTYRKVSCLLLKLNVS
                     MWDEPHELQLLGSQSLPNITNIAQISGITGGCVGFRPQGVPWYLGWSRQEATRFLLRH
                     PSFSKSTEPFTVVTADRHNLFMGSEYCGAYGYRFWNMYNCSQVGRQYRCGNARSPRPG
                     LPEIQCTRRGGKWVNQSQEINESEPFSFTVNCTASSLGNASGCCGKAGTILPGKWVDS
                     TQGSFTKPKALPPAIFLICGDRAWQGIPSRPVGGPCYLGKLTMLAPKHTDILKVLVNS
                     SRTGIRRKRSTSHLDDTCSDEVQLWGPTARIFASILAPGVARAQALREIERLACWSVK
                     QANLTTSFLGDLLDDVTSIRHAVLQNRAAIDFLLLAHGHGCEDVAGMCCFNLSDHSES
                     IQKKFQLMKEHVNKIGVDSDPIGSWLRGLFGGIGEWAVHLLKGLLLGLVVILLLVVCL
                     PCLLQIVCGNIRKMINNSISYHTEYKKLQKACGQPESRIV"
     CDS             join(372..387,674..1029)
                     /product="trans-acting factor"
                     /gene="trans-acting factor"
                     /codon_start=1
                     /translation="MEAVIREGGSLPQVRSASRNQQRSGESTKGRKWEKQLRSEMRRW
                     RRRKWPHLKPLAHPAISAEQLLAVIAPQPRPLLLLMWGVVCILPWRGWESSRARGVTH
                     LGGRNSQGRSQGTRVWPLGRP"
     5'UTR           1..371
     misc_feature    1..21
                     /note="5' terminal redundancy"
     misc_feature    1
                     /note="CAP site"
     RBS             10..41
     misc_feature    22..101
                     /note="U5 region"
     repeat_unit     91..101
                     /rpt_type=TERMINAL
                     /note="5'imperfect repeat"
     protein_bind    102..120
                     /bound_moiety="primer"
     misc_feature    102..371
                     /note="leader sequence"
     misc_feature    210..270
                     /note="dimer promoting sequence"
     misc_feature    218..248
                     /note="encapsidation element"
     RBS             331..371
     mat_peptide     372..2477
                     /rpt_type=3'imperfect terminal repeat
                     /product="matrix protein"
                     /gene="MAp19"
                     /codon_start=1
     protein_bind    423..440
                     /bound_moiety="nucleocapsid"
     protein_bind    502..511
                     /bound_moiety="nucleocapsid"
     misc_feature    512..540
                     /note="dimer linkage structure"
     misc_feature    536..556
                     /note="dimer linkage structure"
     misc_feature    701..792
                     /note="negative splicing regulator"
     protein_bind    805..818
                     /bound_moiety="nucleocapsid"
     misc_feature    817..876
                     /note="enhancer domain"
     mat_peptide     837..902
                     /gene="p2"
                     /codon_start=1
     protein_bind    880..897
                     /bound_moiety="nucleocapsid"
     mat_peptide     903..1088
                     /gene="p10"
                     /codon_start=1
     mat_peptide     1836..2102
                     /product="nucleocapsid protein"
                     /gene="NCp12"
                     /codon_start=1
     protein_bind    1941..1948
                     /bound_moiety="nucleocapsid"
     mat_peptide     2103..2474
                     /product="protease"
                     /gene="PRp15"
                     /codon_start=1
     protein_bind    2388..2400
                     /bound_moiety="nucleocapsid"
     CDS             2495..5182
                     /product="polymerase"
                     /gene="pol"
                     /codon_start=1
                     /translation="TVALHLAIPLKWKPDHTPVWIDQWPLPEGKLVALTQLVEKELQL
                     GHIEPSLSCWNTPVFVIRKASGSYRLLHDLRAVNAKLVPFGAVQQGAPVLSALPRGWP
                     LMVLDLKDCFFSIPLAEQDREAFAFTLPSVNNQAPARRFQWKVLPQGMTCSPTICQLV
                     VGQVLEPLRLKHPSLRMLHYMDDLLLAASSHDGLEAAGEEVISTLERAGFTISPDKIQ
                     REPGVQYLGYKLGSTYVAPVGLVAEPRIATLWDVQKLVGSLQWLRPALGIPPRLMGPF
                     YEQLRGSDPNEAREWNLDMKMAWREIVQLSTTAALERWDPALPLEGAVARCEQGAIGV
                     LGQGLSTHPRPCLWLFSTQPTKAFTAWLEVLTLLITKLRASAVRTFGKEVDILLLPAC
                     FREDLPLPEGILLALRGFAGKIRSSDTPSIFDIARPLHVSLKVRVTDHPVPGPTAFTD
                     ASSSTHKGVVVWREGPRWEIKEIADLGASVQQLEARAVAMALLLWPTTPTNVVTDSAF
                     VAKMLLKMGQEGVPSTAAAFILEDALSQRSAMAAVLHVRSHSEVPGFFTEGNDVADSQ
                     ATFQAYPLREAKDLHTALHIGPRALSKACNISMQQAREVVQTCPHCNSAPALEAGVNP
                     RGLGPLQIWQTDFTLEPRMAPRSWLAVTVDTASSAIVVTQHGRVTSVAAQHHWATAIA
                     VLGRPKAIKTDNGSCFTSKSTREWLARWGIAHTTGIPGNSQGQAMVERANRLLKDKIR
                     VLAEGDGFMKRIPTSKQGELLAKAMYALNHFERGENTKTPIQKHWRPTVLTEGPPVKI
                     RIETGEWEKGWNVLVWGRGYAAVKNRDTDKVIWVPSRKVKPDVTQKDEVTKKDEASPL
                     FAGISDWIPWEDEQEGLQGETASNKQERPGEDTLAANES"
     mat_peptide     2495..5179
                     /product="reverse transcriptase beta-subunit"
                     /gene="reverse transcriptase beta-subunit"
                     /codon_start=1
     mat_peptide     2495..4210
                     /product="reverse transcriptase alpha-subunit"
                     /gene="reverse transcriptase alpha-subunit"
                     /codon_start=1
     protein_bind    2950..2964
                     /bound_moiety="nucleocapsid"
     mat_peptide     4211..5179
                     /product="integrase"
                     /gene="INp32"
                     /codon_start=1
     protein_bind    4747..4758
                     /bound_moiety="nucleocapsid"
     mat_peptide     5244..6260
                     /product="surface protein"
                     /gene="SU"
                     /codon_start=1
     protein_bind    5712..5727
                     /bound_moiety="nucleocapsid"
     protein_bind    6187..6201
                     /bound_moiety="nucleocapsid"
     mat_peptide     6261..6869
                     /product="transmembrane protein"
                     /gene="TM"
                     /codon_start=1
     protein_bind    6414..6425
                     /bound_moiety="nucleocapsid"
     repeat_unit     7037..7047
                     /rpt_type=TERMINAL
                     /note="3'imperfect repeat"
BASE COUNT     1752 a   1768 c   2114 g   1652 t
ORIGIN
        1 gccatttgac cattcaccac attggtgtgc acctgggttg atggccggac cgttgattcc
       61 ctgacgacta cgagcacctg catgaagcag aaggcttcat ttggtgaccc cgacgtgata
      121 gttagggaat agtggtcggc cacagacggc gtggcgatcc tgtctccatc cgtctcgtct
      181 atcgggaggc gagttcgatg accctggtgg agggggctgc ggcttaggga ggcagaagct
      241 gagtaccgtc ggagggagct ccagggcccg gagcgactga cccctgccga gaactcagag
      301 ggtcgtcgga agacggagag tgagcccgac gaccacccca ggcacgtctt tggtcggcct
      361 gcggatcaag catggaagcc gtcattaagg tgatttcgtc cgcgtgtaaa acctattgcg
      421 ggaaaatctc tccttctaag aaggaaatag gggccatgtt gtccctgtta caaaaggaag
      481 ggttgcttat gtctccctca gatttatatt ccccggggtc ctgggatccc atcactgcgg
      541 cgctctccca gcgggcaatg gtacttggga aatcgggaga gttaaaaacc tggggattgg
      601 ttttgggggc attgaaggcg gctcgagagg aacaggttac atctgagcaa gcaaagtttt
      661 ggttgggatt agggggaggg agggtctctc ccccaggtcc ggagtgcatc gagaaaccag
      721 caacggagcg gcgaatcgac aaaggggagg aagtgggaga aacaactgcg cagcgagatg
      781 cgaagatggc gccggagaaa atggccacac ctaaaaccgt tggcacatcc tgctatcagt
      841 gcggaacagc tactggctgt aattgcgcca cagcctcggc ccctcctcct ccttatgtgg
      901 ggagtggttt gtatccttcc ctggcggggg tgggagagca gcagggccag gggggtgaca
      961 caccttgggg ggcggaacag ccaagggcgg agccagggca cgcgggtctg gcccctgggc
     1021 cggccctgac tgactgggca aggatcaggg aggagcttgc gagtacaggt ccgcccgtgg
     1081 tggccatgcc tgtagtgatt aagacagagg gacccgcctg gacccctctg gagccaaaat
     1141 tgatcacaag actggctgat acggtcagga ccaagggctt acgatccccg atcactatgg
     1201 cagaagtgga agcgctcatg tcctccccgt tgctgccgca tgacgtcacg aatctaatga
     1261 gagtgatttt aggacctgcc ccatatgcct tatggatgga cgcttgggga gtccaactcc
     1321 agacggttat agcggcagcc actcgcgacc cccgacaccc agcgaacggt caagggcggg
     1381 gggaacggac taacttggat cgattaaagg gcttagctga tgggatggtg ggcaacccac
     1441 agggtcaggc cgcattatta agaccggggg aattggttgc tattacggcg tcggctctcc
     1501 aggcgtttag agaagttgcc cggctggcgg aacctgcagg tccatgggcg gacatcacgc
     1561 agggaccatc tgagtccttt gttgattttg ccaatcggct tataaaggcg gttgaggggt
     1621 cagatctccc gccttccgcg cgggctccgg tgatcattga ctgctttagg cagaagtcac
     1681 agccagatat tcagcagctt atacgggcag caccctccac gctgaccacc ccaggagaga
     1741 taatcaaata tgtgctagac aggcagaaga ttgcccctct tacggatcaa ggcatagccg
     1801 cggccatgtc gtctgctatc cagcccttag ttatggcagt agtcaataga gagagggatg
     1861 gacaaactgg gtcgggtggt cgtgcccgag ggctctgcta cacttgtgga tccccgggac
     1921 attatcaggc gcagtgcccg aaaaaacgaa agtcaggaaa cagccgtgag cgatgtcagc
     1981 tgtgtgacgg gatgggacac aacgctaaac agtgcagaag gcgggatggc aaccagggcc
     2041 aacgcccagg aaaaggcctc tcttcggggt cgtggcccgt ctctgagcag cctgccgtct
     2101 cgttagcgat gacaatggaa cataaagatc gccccttggt tagggtcatt ctgactaaca
     2161 ctgggagtca tccggtcaaa cagcgttcgg tgtatatcac cgcgctgttg gactctggag
     2221 cggacatcac tattatttca gaggaggact ggcccaccga ttggccagtg atggaggccg
     2281 cgaacccgca gatccatggg ataggagggg gaattcccat gcgaaaatcc cgggatatga
     2341 tagaggtggg ggttattaac cgagacgggt ctttggagcg acccctgctc ctcttccccg
     2401 cagtagctat ggttagaggg agtatcctag gaagagattg tctgcagggc ctagggctcc
     2461 gcttgacaaa tttataggga gggccactgt tcttactgtt gcgctacatc tggctattcc
     2521 gctcaaatgg aagccagacc acacgcctgt gtggattgac cagtggcccc ttcctgaagg
     2581 taaacttgta gcgctaacgc aattagtgga aaaagaatta cagttaggac atatagaacc
     2641 ttcacttagt tgttggaaca cacctgtctt tgtgatccgg aaggcttccg ggtcttatcg
     2701 cttattgcat gacttgcgcg ctgttaacgc caagcttgtt ccttttgggg ccgtccaaca
     2761 gggggcgcca gttctctccg cgctcccgcg tggctggccc ctgatggtcc tagacctcaa
     2821 ggattgcttc ttttctattc ctcttgcgga acaagatcgc gaagcttttg catttacgct
     2881 cccctctgtg aataaccagg cccccgctcg aagattccaa tggaaggtct tgccccaagg
     2941 gatgacctgt tctcccacta tctgtcagtt ggtggtgggt caggtacttg agcccttgcg
     3001 actcaagcac ccatctctgc gcatgttgca ttatatggat gatcttttgc tagccgcctc
     3061 aagtcatgat gggttggaag cggcagggga ggaggttatc agtacattgg aaagagccgg
     3121 gttcaccatt tcgcctgata agatccagag ggaacccgga gtacaatatc ttgggtacaa
     3181 gttaggcagt acgtatgtag cacccgtagg cctggtagca gaacccagga tagccacctt
     3241 gtgggatgtt caaaagctgg tggggtcact tcagtggctt cgcccagcgt taggaatccc
     3301 gccacgactg atgggcccct tctatgagca gttacgaggg tcagatccta acgaggcgag
     3361 ggaatggaat ctagacatga aaatggcctg gagagagatc gtacagctta gcaccactgc
     3421 tgccttggaa cgatgggacc ctgccctgcc tttggaggga gcggtcgcta ggtgtgaaca
     3481 gggggcaata ggggtcctgg gacagggact gtccacacac ccaaggccat gtttgtggtt
     3541 attctccacc caacccacca aggcgtttac tgcttggtta gaagtgctca cccttttgat
     3601 tactaagcta cgcgcttcgg cagtgcgaac ctttggcaag gaggttgata tcctcctgtt
     3661 gcctgcatgc tttcgggagg accttccgct cccggagggg atcctgttag cccttagggg
     3721 gtttgcagga aaaatcagga gtagtgacac gccatctatt tttgacattg cgcgtccact
     3781 gcatgtttct ctgaaagtga gggtcaccga ccaccctgta ccgggaccca ctgcctttac
     3841 cgacgcctcc tcaagcaccc ataaaggggt ggtagtctgg agggagggcc caaggtggga
     3901 gataaaagaa atagctgatt tgggggcaag tgtacaacaa ctggaagcac gcgctgtggc
     3961 catggcactt ctgctgtggc cgacaacgcc cactaatgta gtgactgact ccgcgtttgt
     4021 cgcgaaaatg ttactcaaga tgggacagga gggagtcccg tctacagcgg cggcttttat
     4081 tttagaggat gcgttaagcc aaaggtcagc catggccgcc gttctccacg tgcggagtca
     4141 ttctgaagtg ccagggtttt tcacagaagg aaatgacgtg gcagatagcc aagccacctt
     4201 tcaagcgtat cccttgagag aggctaaaga tcttcatact gctctccata ttggaccccg
     4261 cgcgctatcc aaagcgtgta atatatctat gcagcaggct agggaggttg ttcagacctg
     4321 cccgcattgt aattcagccc ctgcgttgga ggccggggta aaccctaggg gtttgggacc
     4381 cctacagata tggcagacag actttacgct tgagcctaga atggcccccc gttcctggct
     4441 cgctgttact gtggataccg cctcatcggc gatagtcgta actcagcatg gccgtgtcac
     4501 atcggttgct gcacaacatc attgggccac ggctatcgcc gttttgggaa gaccaaaggc
     4561 cataaaaaca gataatgggt cctgtttcac gtctaaatcc acgcgagagt ggctcgcgag
     4621 atgggggata gcacacacca ccgggattcc gggtaattcc cagggtcaag ctatggtaga
     4681 gcgggccaac cggctcctga aagataagat ccgtgtgctt gcggaggggg acggctttat
     4741 gaaaagaatc cccaccagca aacaggggga actactagcc aaggcaatgt atgccctcaa
     4801 tcactttgag cgcggtgaaa acacaaaaac accgattcaa aaacactgga gacctaccgt
     4861 tcttacagaa ggacccccgg ttaaaatacg aatagagaca ggggagtggg aaaaaggatg
     4921 gaatgtgctg gtctggggac gaggttatgc agctgtgaaa aacagggaca ctgataaggt
     4981 tatttgggta ccctctcgga aagttaaacc ggatgtcacc caaaaggatg aggtgactaa
     5041 gaaagatgag gcgagccctc tttttgcagg catttctgac tggataccct gggaagacga
     5101 gcaagaagga ctccaaggag aaaccgctag caacaagcaa gaaagacccg gagaagacac
     5161 ccttgctgcc aacgagagtt aattatattc tcattattgg tgtcctggtc ttgtgtgagg
     5221 ttacgggggt aagagctgat gtccacttac tcgagcagcc agggaacctt tggattacat
     5281 gggccaaccg tacaggccaa acggattttt gcctctctac acagtcagcc acctcccctt
     5341 ttcaaacatg tttgataggt atcccgtccc ctatttccga aggtgatttt aagggatacg
     5401 tctctgataa ttgcaccacc ttgggaactg atcggttagt ctcgtcagcc gactttactg
     5461 gcggacctga caacagtacc accctcactt atcggaaggt ctcatgcttg ttgttaaagc
     5521 tgaatgtctc tatgtgggat gagccacatg aactacagct gttaggttcc cagtctctcc
     5581 ctaacattac taatattgct cagatttccg gtataaccgg gggatgcgta ggtttcagac
     5641 cacaaggggt tccttggtat ctaggttggt ctagacagga ggccacgcgg tttctcctta
     5701 gacacccctc tttctctaaa tccacggaac cgtttacggt ggtgacagcg gataggcaca
     5761 atctttttat ggggagtgag tactgcggtg catatggcta cagattttgg aacatgtata
     5821 actgctcaca ggtggggcgg cagtaccgct gtggtaatgc gcgcagcccc cgcccgggtc
     5881 ttcctgaaat ccagtgtaca aggagaggag gcaaatgggt taatcaatca caggaaatta
     5941 atgagtcgga gccgttcagc tttacggtga actgtacagc tagtagtttg ggtaatgcca
     6001 gtgggtgttg cggaaaagca ggcacgattc tcccgggaaa gtgggtcgac agcacacaag
     6061 gtagtttcac caaaccaaaa gcgctaccac ccgcaatttt cctcatttgt ggggatcgcg
     6121 catggcaagg aattcccagt cgtccggtag ggggcccctg ctatttaggc aagcttacca
     6181 tgttagcacc taagcataca gatattctca aggtgcttgt caattcatcg cggacaggta
     6241 taagacgtaa acgaagcacc tcacacctgg atgatacatg ctcagatgaa gtgcagcttt
     6301 ggggtcctac agcaagaatc tttgcatcta tcttagcccc gggggtagca cgtgcgcaag
     6361 ccttaagaga aattgagaga ctagcctgtt ggtccgttaa acaggctaac ttgacaacat
     6421 cattcctcgg ggacttattg gatgatgtca cgagtattcg acacgcggtc ctgcagaacc
     6481 gagcggctat tgacttcttg cttctggctc acggccatgg ctgtgaggac gttgccggaa
     6541 tgtgttgttt caatctgagt gatcacagtg agtctataca gaagaagttc cagctaatga
     6601 aggaacatgt caataagatc ggcgtggaca gcgacccaat cggaagttgg ctgcgaggat
     6661 tattcggggg aataggggaa tgggccgttc atttgctgaa aggactgctt ttggggcttg
     6721 tagttatttt gttgctagta gtgtgcctgc cttgcctttt gcaaatcgta tgcggtaaca
     6781 tcagaaagat gattaataac tccatcagct accacacgga atataagaag ctgcaaaagg
     6841 cctgtgggca gcctgaaagc agaatagtat aaggcagtac atgggtggtg gtatagcgct
     6901 tgcgagtcgg gttgtaacgg ggcatggctt aactaagggg actatggcat gtataggcgc
     6961 aaagcggggc ttcggttgta cgcggttagg agtcccctca ggatatagta gtttcgcttt
     7021 tgcataggga gggggaaatg tagtcttatg caatactctt gtagtcttgc aacatggtaa
     7081 cgatgagtta gcaacatgcc ttacaaggag agaaaaagca ccgtgcatgc cgattggtgg
     7141 aagtaaggtg gtacgatcgt gccttattag gaaggcaaca gacgggtctg acatggattg
     7201 gacgaaccac tgaattccgc attgcagaga tattgtattt aagtgcctag ctcgatacaa
     7261 taaacgccat ttgaccattc accaca
//