Subject: RE: New natural transposable element of D. melanogaster
Dear Gillian,
I am sending you as an attached file the information you requested about
Pilgrim.
Subsequent to the submission of our manuscript for publication (two months
later, to be more precise), another manuscript was submitted by others
(Bowen and McDonald, Genome Research 11, 1527-1540, 2001), which reported a
similar phylogenetic characterization for several members of the mdg1
lineage ot the Ty3/gypsy group. In their report, the element wolfman is
identical to Pilgrim, and therefore both names should be considered
synonyms.
Yours sincerely,
Horacio
Dr. Horacio F. Naveira
Dep. Biol. Cel. y Molec.
Univ. A Coruña
campus da Zapateira s/n
15071 A Coruña
Spain
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DEFINITION Drosophila melanogaster Pilgrim retrotransposon inserted
at genomic clone AC007146 (nucleotides
115349-122693)
LTR 1..506
/standard_name='5' LTR'
CDS 1229..1456
/gene='sORF'
/note='homologous to sORFs from 412, mdg1, blood and
Stalker'
/translation='MGWFGSDDSQTKDNTANVVNNVKIVDHTEDIQALWVLLLILTIT
SVAQFLLTLYIKHNKILKRRYMSRANNLDRV'
CDS 1531..2851
/gene='ORF1'
/note='gag homologous gene'
/translation='MRTGNYIVPHNFHVVDDNFPIPGDGIVGIDFIKTFNCQLDFTTE
SDFFILRPNNIKQAIQIPIFHNIDNTEITIPSRCEVIRQITVSSVDNQILIPNQEIED
GVFVGNSISDSKNTYIRILNTTNSNKILNVNKINFEPLTSYKIADLNDSIRAESILSR
LKKNFPSAHKKMLTELCSQYTDIFGLETEPITTNKFYKQKIRLRDDEPSYIKNYRTPH
SQQAEISRQVTKLIEDKIVEPAVSEYNSPLLLVPKKSLPDSKEKKWRLVIDYRQINKK
LLADKFPLPRIDDILDQLGRAKYFSCLDLMSGFHQIELEEDSRNITSFSTSSGSYRFT
RLPYGLKIAPNSFQRMMTMAFTGLEPSQAFLYMDDLIVIGCSEKHMTKNLTNVFELCR
KNNLKLHPDKCSFFMSEVTFLGHKCTDKGILPDDTKYDAIQRYPVPTDADSARRFVAF
CNYYRRFIQNFADYSRHITRLCKKNVKFEWTADCQHAFEHLKKQLMNPTLLKYPDFSK
EFCIITDASKEACGAVLTQNYNGIHLPVAYASRSFTKGESNKSTTEQELSAIHWAINH
FKPYIYGRHFTVKTDHRPLTYLFSMVNPSSKLTRMRLDLEEYEFTVEYLKGKDNYVAD
ALSRITIDQLKNISKQVLKVTTRNQSRQESCAGKGNKNDKVELPKQTTQEASKPKVYG
VINNDEVRKVVTLHVNNMICFFKHEKKITARYNVEDLYINGTLDLGQFFHRLEKQAGM
HNINQLKMAPWENIFDNISIDTFKKMGNKTLKLLRVALLNPVTLVNTKKEKEAILSTH
HDDPTQGGHAGITKTLARIKRHYFWKGMTREITEYIRKCPKCQKAKIMKHTKTPLSIT
ETPISAFDRVIVDTIGPLPKSENGNEYAVTLICDLTKYLVTIPIANKSANTVAKAIFE
SFVLKFGPMKTFISDMGTEYRNSIIKDLCKYLKVENITSSAHHHQTVGTVERSHRTFN
EYIRSYISVDKTDWDVWIKYFEFCFNTTPSMAHNYCPYELIFGKTCNLPKHFNSTDRI
EPIYNIEDYPKESKYRLEVAYNRARIMLEEQKKKNKELYDLKLNDISISIGDKVLLKN
ETGHKLDFKYTGPYTVVKIEERDNIVISNDKKKPQTVHKDRLKLFSS'
CDS 2787..6479
/gene='ORF2'
/note='pol homologous gene'
/codon_start=1
/translation='MRTGNYIVPHNFHVVDDNFPIPGDGIVGIDFIKTFNCQLDFTTE
SDFFILRPNNIKQAIQIPIFHNIDNTEITIPSRCEVIRQITVSSVDNQILIPNQEIED
GVFVGNSISDSKNTYIRILNTTNSNKILNVNKINFEPLTSYKIADLNDSIRAESILSR
LKKNFPSAHKKMLTELCSQYTDIFGLETEPITTNKFYKQKIRLRDDEPSYIKNYRTPH
SQQAEISRQVTKLIEDKIVEPAVSEYNSPLLLVPKKSLPDSKEKKWRLVIDYRQINKK
LLADKFPLPRIDDILDQLGRAKYFSCLDLMSGFHQIELEEDSRNITSFSTSSGSYRFT
RLPYGLKIAPNSFQRMMTMAFTGLEPSQAFLYMDDLIVIGCSEKHMTKNLTNVFELCR
KNNLKLHPDKCSFFMSEVTFLGHKCTDKGILPDDTKYDAIQRYPVPTDADSARRFVAF
CNYYRRFIQNFADYSRHITRLCKKNVKFEWTADCQHAFEHLKKQLMNPTLLKYPDFSK
EFCIITDASKEACGAVLTQNYNGIHLPVAYASRSFTKGESNKSTTEQELSAIHWAINH
FKPYIYGRHFTVKTDHRPLTYLFSMVNPSSKLTRMRLDLEEYEFTVEYLKGKDNYVAD
ALSRITIDQLKNISKQVLKVTTRNQSRQESCAGKGNKNDKVELPKQTTQEASKPKVYG
VINNDEVRKVVTLHVNNMICFFKHEKKITARYNVEDLYINGTLDLGQFFHRLEKQAGM
HNINQLKMAPWENIFDNISIDTFKKMGNKTLKLLRVALLNPVTLVNTKKEKEAILSTH
HDDPTQGGHAGITKTLARIKRHYFWKGMTREITEYIRKCPKCQKAKIMKHTKTPLSIT
ETPISAFDRVIVDTIGPLPKSENGNEYAVTLICDLTKYLVTIPIANKSANTVAKAIFE
SFVLKFGPMKTFISDMGTEYRNSIIKDLCKYLKVENITSSAHHHQTVGTVERSHRTFN
EYIRSYISVDKTDWDVWIKYFEFCFNTTPSMAHNYCPYELIFGKTCNLPKHFNSTDRI
EPIYNIEDYPKESKYRLEVAYNRARIMLEEQKKKNKELYDLKLNDISISIGDKVLLKN
ETGHKLDFKYTGPYTVVKIEERDNIVISNDKKKPQTVHKDRLKLFSS'
LTR 6840..7345
/standard_name='3' LTR'
BASE COUNT 2933 a 1304 c 1288 g 1830 t
ORIGIN
1 tgtaatgtgc acacatatcg aataagcact gtatcaaatc agaacattgg gaacaatcac
61 attgtagcac ttttgcaaca atgtttatgt aagacttttc agttcccagg catatcttga
121 gtgctcagca atctgaccac acaagaatgc tattcagacc agaagtgcag agtcagcata
181 attagcatgc gcgactgctc gatctttatg tccacatgac tctcttagac agcggcgctc
241 tcgctgccaa agttaagtac ataagagcaa agcaacgtct ctgccgacgg cctctctgcc
301 ggcgcagacg gattgcattt ggctagcttg gactcttcta gaccaagtac aaggcagtcg
361 taaaggagtc gtcaaagagc cttcaacatg tcctaattga atattaatga gtcttaacag
421 aagttacaat tttactgata tcatactgaa tctctatttc aataaaagta atataaagaa
481 cacaaaaatg cattacaatt attacatggc gaccgtgaca tggtcactta agcctgtaaa
541 acaataataa aaagaaatat ataaaagtta aaatgcgaac agtgaccatt aaaaaataaa
601 attgtgacaa ttgatcaaac ccagacgaca acagaagccg caaactggag gactctgctc
661 ctatcgagca aagggacgca cctactctac aagaggcact agaggtgtgt ccaaacgatg
721 gaccacgccc actcacaata gctgagtata gggcaagaag acagccgaaa ccaaaaataa
781 agaagaaaag aagcggcaaa aggatcaagc ttcttcaaca acggagatta ataaaggacc
841 taataaagac ggcaactacg gaggaagaga aaactaacca agccaaaaat ctggaagcga
901 ttgaagccaa attgtgcagt ggtgcgcaat aacgcagttg aggctgtatt taataccaat
961 gccccaatct gccttaatat taaaaataca tacctcaagc cgatgcgtga aaacgctgct
1021 tgaaaaatac taatctctgt taggctttta ctaaaaacat gtgtacggta ttgaattata
1081 tagagcaaaa cattgtaaac cgtacacatg ccctctaact aactttttct tggacagaca
1141 tacgtgtagg gagaaattat agcaatatac aatttttaat caaaatttaa taaataaata
1201 aataataata atcgttcaat taacaactat gggttggttc ggatctgacg atagtcagac
1261 caaagacaac acggctaatg tcgtgaacaa cgtcaaaatt gtagatcaca cagaagatat
1321 tcaagcactg tgggttttac tcctaatttt gacaattaca agtgtggccc agttccttct
1381 gacgttgtac ataaaacaca acaaaatatt aaaaagaaga tatatgagta gggcgaataa
1441 tctagacagg gtttaaaaga aaaaaaaaaa atatatttta aagaatgagt atataaatat
1501 atactaacaa gtaggaatat ataaaatagt atggaatgga acgagttatg taaaaacata
1561 acaagaataa gaaacgaatt tgaaaaatct cataaatgtt tgtcgcaaaa tagacctatt
1621 ttaggaccga caacaaagaa acatgcaaat attctggtaa attccttcaa cgaagcacga
1681 atactagtgt atgataacaa ggaaagacta aatccagatc attggtctca ggtatcgaaa
1741 gttctcataa aacttagatc gaacttgtta tctgtaaaat tgaaacttgg tttggatata
1801 tcaataccaa ccattttaaa ttcgccaata aaaatagaat cggacgaaca aacagaaaca
1861 gaaatagaag acgaagattt aaacaactta acaattccag ctatattaac actagctgaa
1921 ttgacggagg aagaattggc tgagtcagac atagaagaaa cagaaacaaa atctgtcatc
1981 atggtggacg aagcagctgc ccagagggca tacataaaag acatttcaac ggcgattccg
2041 gaatttgacg gtaaaaagat caatttgcgt agatttatca cggcaatcaa gttggttaac
2101 ctgactaagg gaccacatga agctattgcc attgaagtga ttaaatcaaa aataatcgga
2161 acaacactct atagagtaca gaatgaagtt acaattgatg ccataatcag gaaattagaa
2221 gaagtggtcg taggagaaac aacggacgta gtaagagcaa aaatggcaaa tgtttaccaa
2281 aaaggtaaaa cagccacaca atttacaaat gaaattgaaa acctacgcaa gtctcttgaa
2341 tcttcatata tagatgaagg attgcaacca gaacatgcta tcaaatttag cacaaaggaa
2401 gcaatcaata caatgacaaa gaattgcgat catggaaaac tgaaagcaat cctagaggca
2461 ggaacattta agacaatgga cgaagcaata agtaaataca tccattgcag cactgagatg
2521 acaggaagtg caagttccgt tttgttttac aagagaggac aaggaagtta caccagaggt
2581 aactaccgag gacgaggaaa tggtcgaggt ggtaataata gaaataatta taaccagaac
2641 accggccaat acaacaactt taataattat aacaatagca atggcagagg acgaggagga
2701 tatagagaat ataactacca gaacagaggc ggtggtaact ataacaacca aaaccgcaat
2761 ttctcaagtt atagccaaaa tggtaatgtc agacatgcac aaggcacgtc ggaaaaccag
2821 caggctccct tagggcatca agaacagtaa aacaaaaggt tcataccatc aatcttaatc
2881 taaatatttt cattaaagta aaaaatgaac acacaaataa gatacttaca tttctagtag
2941 acacaggcgc cgatatatca gtcattaaag aaaactcaga tgaacttttg aatcttgatc
3001 ataataatat aacacaaatt acaggaattg gaaagggttc aataaattca ataggtttaa
3061 cacttctcga gatgagaacc ggtaactata tagtaccgca caattttcat gttgtggacg
3121 acaattttcc gatccctggt gacggaatag ttggaatcga cttcataaaa acattcaatt
3181 gccaattaga ttttactaca gaaagtgatt ttttcattct aagaccaaac aatattaaac
3241 aagcgataca aataccaatt tttcataata tcgataacac tgagataacc ataccatctc
3301 gttgtgaggt tattaggcaa attaccgtaa gttcggtgga taaccaaatt ctaataccca
3361 atcaggaaat agaagatggt gtatttgtcg gaaattcgat atcagattca aaaaacacgt
3421 acatccgaat actaaacaca actaacagca ataaaatttt aaatgtaaac aaaatcaatt
3481 ttgaaccatt aactagctac aaaatagcag acctaaacga ctccataaga gccgaatcaa
3541 ttttaagcag attaaagaaa aactttccat ctgcacataa gaaaatgttg actgaactgt
3601 gttcacaata tactgatatt tttggattgg agacagagcc aatcactaca aataaatttt
3661 acaaacaaaa gataagattg agagatgatg aaccaagcta tattaagaac tatagaacac
3721 cccattcaca acaagccgaa atatcgagac aggtaactaa attaatagaa gacaagatag
3781 tagaaccagc tgtatctgaa tacaatagcc cattattgct agttccaaag aaatccttac
3841 cggattcaaa agaaaaaaaa tggcgtttag tgatagacta tcgccaaata aataaaaagt
3901 tgttagctga caagttcccc ttgccaagaa tagatgacat acttgatcaa ttaggccgag
3961 caaaatattt ctcgtgcctg gatcttatgt cgggattcca tcaaatagag ttagaagaag
4021 attctcgaaa tataacatcc ttttctacga gcagtggctc ttatcgcttc acgcgactac
4081 catacggatt aaaaatagct ccaaattcct ttcaacgaat gatgacaatg gcatttacag
4141 gtctggaacc atctcaagca tttctgtaca tggatgactt aattgtcata ggctgttctg
4201 aaaaacacat gaccaagaat cttacaaatg tttttgaact atgcaggaaa aacaacctca
4261 aactgcatcc agataagtgc tcatttttca tgagtgaagt cacttttctt ggacacaaat
4321 gtactgataa aggcatattg cctgacgata ctaaatatga tgctatacag agatatccag
4381 ttcctactga cgcagacagt gccagaagat tcgtagcatt ttgtaactat tatagacgtt
4441 ttatacaaaa ttttgcagat tattcccgtc acataacaag attatgtaag aaaaatgtaa
4501 agttcgaatg gacagctgat tgccagcatg ccttcgaaca cctgaaaaaa caactaatga
4561 atccaacttt gctgaaatac cccgacttta gcaaagagtt ctgtattata actgatgcaa
4621 gcaaagaggc atgcggagcg gtactgaccc agaactataa tggtatccat ttgccagtag
4681 cttatgcatc ccgtagcttc actaagggtg agagcaacaa gtcaacaaca gagcaagagt
4741 tgtcagcaat acattgggcg ataaatcatt tcaaaccata tatatatggt agacacttca
4801 ccgtcaaaac agatcacaga ccgttaacat acttgttctc gatggttaat ccaagctcaa
4861 aactgaccag aatgaggctt gatttagaag aatatgaatt tactgtggaa tatcttaagg
4921 gaaaagacaa ttacgtagca gatgcgttat ccagaataac catcgaccaa ctaaaaaata
4981 tatccaaaca agtacttaaa gtcactacaa gaaatcaaag tagacaggaa tcctgcgcag
5041 gaaaaggaaa taaaaatgat aaagtagaat tgcctaagca aactactcaa gaagcttcta
5101 agcccaaagt atacggagtc attaataatg acgaagtacg caaagtagtg acattgcatg
5161 taaataatat gatatgtttt tttaaacatg aaaaaaaaat tactgcaaga tacaacgttg
5221 aagatttgta tattaatgga actctcgact taggtcaatt tttccacagg cttgaaaagc
5281 aggccggtat gcataatatc aatcaactta aaatggcacc gtgggaaaat atctttgata
5341 acatttcaat agatacattt aagaaaatgg gcaataaaac attaaaacta ttaagagtag
5401 cgctactcaa cccggtgacc ttagtgaata caaagaaaga aaaagaagca atcctgtcta
5461 cacaccacga cgatccaaca caaggaggac acgcaggcat tacaaaaacc ctggccagga
5521 ttaaaagaca ttacttttgg aaaggtatga ctcgggaaat aacagagtac atacggaaat
5581 gtccaaaatg ccaaaaagct aaaattatga aacacacaaa aactccttta tcaattacag
5641 agacaccaat aagcgcattt gacagagtca tagtggatac gataggtcca ctaccaaagt
5701 cagaaaacgg taatgaatat gctgttacac ttatatgcga cctgacaaaa tatttggtaa
5761 ccattccaat cgcaaataaa agcgcaaata cagtagcgaa agcaatattt gaatcctttg
5821 tactaaagtt cggtccaatg aagacgttca tttcggacat gggaactgaa tacagaaatt
5881 caattatcaa agacttatgc aaatacctga aagtagaaaa tataacttct tcagcacacc
5941 atcatcagac ggtaggaaca gtggaaagaa gtcatagaac ttttaacgaa tacatccggt
6001 catacatatc ggttgataaa actgactggg acgtatggat aaaatatttc gaattttgtt
6061 ttaatactac accatctatg gcacataatt attgtccata tgagttgatt ttcggtaaaa
6121 catgcaattt accaaagcat tttaatagca cggatagaat agaacccatt tataatatag
6181 aagactatcc taaagaaagt aaatataggt tagaagtagc atataacaga gcaagaatta
6241 tgctcgaaga acagaagaaa aagaataaag aattatatga cttaaaatta aacgatataa
6301 gtatatcaat aggagataag gtgttattaa aaaacgaaac cggacataaa ttagatttca
6361 aatatactgg accatatacg gtagtaaaga ttgaagaaag ggataatata gtaatatcaa
6421 atgataagaa aaaaccacaa acggtacata aggataggtt aaaattgttt agttcttaaa
6481 aaaaaaaaat aaataatatg gtggccacca gcaaaaaaaa aaaatatata tagagaaaag
6541 agttaacccc acataagtgc attgaatgta agaaaacatt tttcttttat catctttgat
6601 ggttgaacga ttataaacta aaaatttgaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa
6661 accaaaaaaa aacccccaag aacacgtatg tttgtacaaa atgttcctta aatttcctta
6721 acattaaaat tacttcctta aaaaaaaaaa aaaaaaaaaa aaaaaaaaat atatatatat
6781 aaaattttta attataaaat aacttcataa aattacgtta ttttccaaaa ggagggagat
6841 gtaatgtgca cacatatcga ataagcactg tatcaaatca gaacattggg aacaatcaca
6901 ttgtagcact tttgcaacaa tgtttatgta agacttttca gttcccaggc atatcttgag
6961 tgctcagcaa tctgaccaca caagaatgct attcagacca gaagtgcaga gtcagcataa
7021 ttagcatgcg cgactgctcg atctttatgt ccacatgact ctcttagaca gcggcgctct
7081 cgctgccaaa gttaagtaca taagagcaaa gcaacgtctc tgccgacggc ctctctgccg
7141 gcgcagacgg attgcatttg gctagcttgg actcttctag accaagtaca aggcagtcgt
7201 aaaggagtcg tcaaagagcc ttcaacatgt cctaattgaa tattaatgag tcttaacaga
7261 agttacaatt ttactgatat catactgaat ctctatttca ataaaagtaa tataaagaac
7321 acaaaaatgc attacaatta ttaca
//
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