CC ********************************************************************
CC                                                                    *
CC   REPBASE UPDATE                                                   *
CC   (C) 1997-2004  Genetic Information Research Institute            * 
CC   All rights reserved                                              *
CC                                                                    *
CC   A REFERENCE COLLECTION OF CIONA INTESTINALIS REPETITIVE ELEMENTS *
CC   RELEASE 1.0.3; NOVEMBER 2004                                     *
CC                                                                    *
CC ********************************************************************
XX
ID   DNA1_CI   repbase; DNA; CIN; 536 BP.
CC   DNA1_CI DNA
XX
AC   ;
XX
DT   07-JUL-2003 (Rel. 1.00, Created)
DT   07-JUL-2003 (Rel. 1.00, Last updated, Version 1)
XX
DE   Nonautonomous DNA transposon DNA1_CI - a consensus.
XX
KW   Nonautonomous DNA transposon, hAT superfamily; TTAA target
KW   site duplication; DNA1_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-536
RC   [1]  (bases 1 to 536)
RA   Kapitonov V.V., Jurka J.;
RT   "DNA1_CI, a family of nonautonomous
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 99 (2003)
XX
CC   There are ~100 DNA1_CI elements in the 
CC   C. intestinalis genome, they are 99% identical to the consensus.
CC   DNA1_CI i flanked by 19-bp terminal inverted repeats.
CC   Putative classification: piggyBac (based on the TTAA target site 
CC   duplications).
XX
CC   [1] (Consensus)
XX
SQ   Sequence 536 BP; 191 A; 104 C; 106 G; 134 T; 1 other;
     agggcctaaa cacaccccaa atgtacttcg ctttaatcga tagagtgtgt ttttctaatt        60
     ccaacgacac cttacttgtt ttaatcggtt ctgtataacc aaagatattc cagctcaaac       120
     accgtgaaat tcaaaaaact gatttgaaag ttgcgtggcg aaaaaaattg agaagtgtac       180
     tacccacgtg acaaacacgt macaaaattg ttgaagcgtg gccgctctca ttcagaaagg       240
     cgagaggcag tgttttcagc gaaaaacgag agaacaaaaa aaacgcaaaa aagcacaaaa       300
     aaaacgcagg tttcgctttt acgaatgaat cagtcacgtg actagtacgt tcctacgtca       360
     caatcacgga gctcgtagta aaaaaaagat agcgctagag atcactgttt gaggacgaat       420
     atctccgcct atactggacc aattttaata agcaaagtat ttttggaatc aataaaacgg       480
     tcgctttatg aatttaccat aaaaaataaa agtgacgtgg ggtgtgttta ggccct           536
//
ID   Gypsy3-LTR_CI repbase; DNA; CIN; 564 BP.
CC   Gypsy3-LTR_CI DNA
XX
AC   ;
XX
DE   Nonautonomous DNA transposon Gypsy3-LTR_CI - a consensus.
XX
KW   Nonautonomous DNA transposon, mariner/Tc1 superfamily; 4-bp target
KW   site duplication; Gypsy3; Gypsy3-LTR_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-564
RC   [1]  (bases 1 to 564)
RA   Kapitonov V.V., Jurka J.;
RT   "Gypsy3-LTR_CI, a long terminal repeat of the Gypsy3_CI family
RT   of Gypsy-like retrotransposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 100 (2003)
XX
CC   Gypsy3-LTR_CI is a long terminal repeat of the Gypsy3_CI LTR 
CC   retrotrasposon. There are ~100 Gypsy3-LTR_CI elements in the 
CC   C. intestinalis genome. They are ~95% identical to the consensus
CC   sequence, and represent several subfamilies that are even younger.
CC   The Gypsy3-I_CI internal sequence is not known yet, 
CC   although ~50-bp PBS encoded by it is 90% identical to the
CC   Gypsy2_CI PBS.
XX
CC   [1] (Consensus)
XX
SQ   Sequence 564 BP; 167 A; 145 C; 108 G; 144 T; 0 other;
     tgttgcaact cgacgcctaa agtgacgtca cataacccaa tcccaatact tcattaatca        60
     atgtcaacac tgcggatacg acttatctca tgggagactt tcccatgaaa acaaaccccc       120
     cgttgaacga ggttaatgat atcccgttca gccgatgaca ggcccaaatc gattcccttt       180
     tatcgcatga cgtcacactg ctgtcacgtg attctgtccg gtatataatt cgccttttcc       240
     ctaacacaat aactaataac gagaactacc caactaacac cactatcggc actgagacct       300
     cgaggtcagt ctaggttcat ggcgggctct tacgagcctt tgcccagccg tcaagtaagc       360
     ttttgcccga taccgtatcg tgtacttgta taccagaaaa aggaataaaa catagcaaga       420
     tatcatgaac tgtttggttt ctggttataa aagcaattag tactacagta gatatagcac       480
     cccgctgaag cctgtatatg aagtcggatc agcacggagt catataaccc aaccagcgat       540
     cctgtatatt cagtgggggc tata                                              564
//
ID   HAT1_CI   repbase; DNA; CIN; 2774 BP.
CC   HAT1_CI DNA
XX
AC   ;
XX
DT   07-JUL-2003 (Rel. 1.00, Created)
DT   07-JUL-2003 (Rel. 1.00, Last updated, Version 1)
XX
DE   Autonomous DNA transposon HAT1_CI - a consensus.
XX
KW   Nonautonomous DNA transposon, hAT superfamily; 8-bp target
KW   site duplication; transposase; BED zinc finger; HATN1_CI; HAT1_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-2774
RC   [1]  (bases 1 to 2774)
RA   Kapitonov V.V., Jurka J.;
RT   "HAT1_CI, a family of autonomous hAT
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 101 (2003)
XX
CC   HAT1_CI is a family of autonomous elements related to the 
CC   hAT superfamily. There are ~10 HAT1_CI elements in the 
CC   C. intestinalis genome, they are 97% identical to the consensus.
CC   The consensus was reconstructed from 5 copies, therefore
CC   a transposase encoded by HAT1_CI is not completely reconstructed.
CC   The draft version of the HAT1_CIp transposase is 575-aa long
CC   (positions 617-2314). The N-terminal portion of HAT1_CIp (pos.
CC   8-54) includes a BED zinc finger.
CC   HAT1_CI is flanked by 15-bp terminal inverted repeats (1 mismatch).
CC   The HAT1_CIp transposase was also involved in propagation of the 
CC   HATN1_CI nonautonomous element.
CC
CC   HAT1_CIp:
CC   MQSSRHKSKVWEYFSVEKGAVNCLLCKLNLSQGSTDTKKKNTTNLWSHLRVNHQKEYQESQKQILIEHKG
CC   QPTLEESFNQVRRWSNIDPRSKELDRIILEMMATDNRPFALVTAPGFQRLMAKAEPRYQLKSEKYYRTDM
CC   LDQVYCLVEKKIRELLCVENAGHFLSFTSDCWTGSTESLMSLTVHFIDTEWNRRQAILNAKAMMGSHTGQ
CC   YVSEIFKTMLQHWQINENRVFLVLRDSGSNMIKGMKLIDMPSLSCFAHTLQLVIEDGIKTQRTVINILAR
CC   LRKIATHFNHSVLAKQKLQDIQEQISVPKHTILQSVATRWNSSLDMLKECWSKEEHXLFMKVIMEQSHVP
CC   PVMNGNXLKIXLIHCLEPFKTITLEMSKSNACLSIILPNICALRLLLKNVGPKSRGIQTMRGEMLTSLEK
CC   RFLTIEQNKEVVMACMLDPRFKTKVMSPLSSQQGKEWILEEINNQNSSSPQPKKICLQAQSSSAAAHEPQ
CC   RSCLDAVFESLLGSSSIESGPTHELAQYLGEPVQKKNTDPHLWWKNNSCRFPSLEATARKYLSAPPTSIP
CC   SERLFSEIGNIYDLR
XX
CC   [1] (Consensus)
XX
SQ   Sequence 2774 BP; 938 A; 479 C; 558 G; 799 T; 0 other;
     tagagcacga ccgattatcg gttagccgat atatcggccg cattttaggt gatttaccga        60
     ttatcggcaa gagcataaaa tggccgatat tatcggtgca aagtaacccg atgacatgcg       120
     tacgtccgca ttaatacaga gcgttaactc aatcgtaaac gtaattcaac tcgttcgtaa       180
     caatgtaacg tattaaacta ggtcaaagcg tctgatcacg cgtccaccgc atgtcatgtt       240
     tatcaggcgc gtgtaacgtc gaggttactt taggtcactt acgcgtctct ttgagcgaga       300
     tacacaaacg gtcacttacg cgtctcttta agcgtaatac acaaacaaac tgcattggcg       360
     cgatacatac tatgtttgtt tgatggaata cagcgtttag ttaaaacaaa atataatata       420
     aataactaat taattaaaat atgaacatcc atgcagtttt actgcgcatg ttgtgccagg       480
     taaagacgta ggttgctagc ctgtgtcgtc ataaactaac ttgtttgcaa tatgactttt       540
     ggtcaagtca gtgtggcttg cctcattttt actttgagag tttactgttt gcattgaata       600
     aagttttaaa acggtaatgc agtcttctcg acataagagt aaggtctggg aatattttag       660
     tgtggaaaaa ggggctgtca actgcttatt gtgtaaacta aatttaagtc agggatcaac       720
     agacacaaaa aagaaaaata caacaaatct ttggtcgcat ttgagggtaa atcatcaaaa       780
     agaatatcaa gagtcgcaaa aacaaatatt aatagaacat aaaggtcagc caacattgga       840
     agaatctttc aatcaagtta ggaggtggag taacatagat ccaagatcaa aagaattaga       900
     cagaatcatt ttggaaatga tggctacaga caacaggccc tttgccttag tcactgcacc       960
     tggcttccag agactaatgg caaaagctga accaaggtat cagctcaaaa gcgaaaaata      1020
     ttatagaacc gatatgcttg atcaagttta ttgtttggtt gaaaaaaaga taagagaatt      1080
     gctatgtgtg gaaaacgctg gacactttct gtcatttaca agtgactgct ggactggttc      1140
     gacagaaagt ttaatgagcc ttacagtgca cttcattgat acagaatgga accgccgcca      1200
     agccatttta aatgctaagg caatgatggg ttcacacact ggtcagtatg ttagcgaaat      1260
     ctttaagaca atgttacagc actggcagat taatgaaaat agagtgtttt tagtgctaag      1320
     agatagtgga tcaaatatga ttaagggaat gaaattgata gacatgccaa gtttgagttg      1380
     ttttgctcat acattgcaat tggtcataga ggatgggata aaaacacaac gaacagtgat      1440
     caacattttg gcaaggttaa ggaaaattgc tacacatttc aatcattctg tattggccaa      1500
     acagaaactc caggacatac aagagcaaat atcagtacca aaacatacaa tattacaatc      1560
     tgttgcaaca agatggaact cctctctgga catgttgaaa gaatgttgga gcaaagaaga      1620
     gcattgactg tttatgaaag tgataatgga acaatctcat gtccctccag tgatgaatgg      1680
     aaattaattg aaaatttaat tgatacactg tcttgagcca ttcaaaacaa ttactttgga      1740
     aatgagcaaa agtaatgctt gcctatccat aattttgcca aatatttgtg cattaagact      1800
     gcttttaaaa aatgttggtc ctaaaagtag agggatacaa acgatgagag gggaaatgtt      1860
     aacgagcctt gaaaaaagat ttttaacaat agaacaaaac aaagaggtag tgatggcgtg      1920
     tatgctggac ccaaggttta aaaccaaagt gatgtcacca ctctcttcac aacaagggaa      1980
     agaatggatt cttgaagaaa taaataatca aaactcgtct tcaccacagc caaagaagat      2040
     ttgcttgcaa gcccaaagca gcagtgctgc agctcacgag ccacaacgga gttgcttgga      2100
     tgctgtgttt gagagcttgc ttggttcaag ttctattgaa tctggtccaa ctcatgaact      2160
     tgcacaatat ttaggtgaac cagtgcaaaa gaaaaataca gacccacatt tatggtggaa      2220
     gaataatagt tgtcgttttc cttctttgga agctacagca aggaaatact tgagtgcacc      2280
     ccccacttca attccaagtg aacggctctt cagcgaaatt ggaaacattt acgatcttcg      2340
     ctaactggaa taaatgcaga gaaactctca tttttacatg acaatcttag gctactaaat      2400
     tggaactacc tttaaacaat gcaagaggta aataagtaca gtttctggaa ttaaagacat      2460
     ggaaagtttc tacctatact gttattaaat gttttttcct ttatttgttt ttaaattttc      2520
     ggttattttc cttgttgtca gtacaaacca actggttttc tgtgactgta tgtgacatgt      2580
     tctttttgcc ataaaatttc atttgaaact gaaaaaatgg taaattaaca ggcagtttga      2640
     tttcatcagc ttcaccggcg tttcagttta taatcagtta agttttttag cgccgttaaa      2700
     atatcggtta tcggcaactt caatttgtaa aatatcggta tcggtttgaa aaaagcaata      2760
     tcggtcgggc tcta                                                        2774
//
ID   HAT2_CI   repbase; DNA; CIN; 2677 BP.
CC   HAT2_CI DNA
XX
AC   AABS01000165.1;
XX
DT   07-JUL-2003 (Rel. 1.00, Created)
DT   07-JUL-2003 (Rel. 1.00, Last updated, Version 1)
XX
DE   Autonomous hAT-like DNA transposon HAT2_CI - a fossilized copy.
XX
KW   Nonautonomous DNA transposon, hAT superfamily; 
KW   transposase; BED zinc finger; HATN4_CI; HAT2_CI.
XX
OS   Ciona intestinalis
CC   sea squirt
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-2677
RC   [1]  (bases 1 to 2677)
RA   Kapitonov V.V., Jurka J.;
RT   "HAT2_CI, a family of autonomous hAT
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 102 (2003)
XX
CC   HAT2_CI is a family of autonomous elements related to the 
CC   hAT superfamily. HAT2_CI encodes a 604-aa HAT2_CIp transposase
CC   (positions 422-2233). The N-terminal portion of HAT2_CIp (pos.
CC   4-44) includes a BED zinc finger.
CC   HAT2_CI is flanked by 12-bp terminal inverted repeats.
CC   The HAT2_CIp transposase was also involved in propagation of
CC   HATN4_CI nonautonomous elements. HAT2_CI and HATN4_CI share
CC   common ~80-bp 5' and ~250-bp 3' termini, respectively. 
CC
CC   HAT2_CIp:
CC   MPVSNVWQWFSKSESDVSCKLCSKGFSLRCSTTTLKYHLQSSHKDKLAGASGPSSSGSSESDVLVQSDIR
CC   QYQVRPKLSDDESRRIDVLVSSFMWRDMRPFHIVEGQGFRDLVHGLNHQYKIKHRSTYQAITERTYKSAK
CC   SFLLDVLQHANYMGITTDMWTSIRNDSYITVTVHWITDDWKMQHGVLTTECMTEANTAENLSLRLTDVLA
CC   EYRITSNKISATVTDNGRNIKKAVDLLDDWTQLSCFAHTLQLCVKAGLDIPAVSRMRAGARRLVNHFKHS
CC   SKATAALREKQFSLRPGETVLDLITECPARWNSTFDMFDRLLLLQWCIRAVLTDFKITKPSVASSLQMSS
CC   TQWDLCQSLVHVLKPLKIATTMMSASKYPSIPWIYPVLFTLQKKLESCDIDSGATAHCKTAIREQIDKRF
CC   FASNWHRNLPVLASVLDPRYKFLKFIDNDATRQEVYDHLKGQITEFAAKYSDFEQHLQSESTNEAHTFDP
CC   FEELCGKDTKKQTVVAPEDEIKAYLREPAQPSDSDPLQWWKLNAARLPTMSLMARFYFCIPATSVPSECI
CC   PATSVPSESVFSSAGHIVNAKRASLTPANVNMLVFLNKNAHMII
XX
DR   GENBANK; AABS01000165.1.
CC   Positions   23356   26032  Accession No AABS01000165.1  GenBank
XX
SQ   Sequence 2677 BP; 819 A; 541 C; 548 G; 769 T; 0 other;
     tagggctgtg gattttcgcc tttttttgtt aaccgttaac cgttcagttt taaccggtta        60
     accggttaac cgatacaaga ttagctgttg cttaaaacag cgtagtgaga tacgctgtgt       120
     gtcataaatg gggactttta aagcgtggcg gcaatttgtc cttgattggc atcaagcgcg       180
     tggctgaccg gatttatatt gcaacacatg tgcgcacacg aggcaaccta aacaaattct       240
     tatcatttaa ggttttgacg tgatgcatgt taccatggtt atttaaagat attgcaccat       300
     ctttagaata cattcctcta taaatacgtc ataataactt ttatacgatc ataaacacca       360
     gtctataaca aacccacaca tttttttgct gcgtgtcagt tattaaattg tatgcaacaa       420
     tatgccggtt tcgaatgttt ggcagtggtt tagcaagagc gaatcagatg tttcgtgtaa       480
     gttgtgcagc aaaggattta gtttacgttg ttctaccaca acattaaagt atcacctaca       540
     atctagccat aaggacaagt tagcaggtgc aagtggaccc tctagttctg gatcgtccga       600
     atctgatgtt ttagttcagt cagatattcg tcagtatcaa gtgcgaccaa aactatcaga       660
     cgatgaatcg cggcgtattg atgtgttggt gtcgtcattt atgtggagag acatgcgtcc       720
     atttcatatt gtggaagggc aaggatttag agatcttgtt catggcctca atcatcaata       780
     taaaataaaa cacagatcga catatcaggc aatcactgaa cgtacataca agagtgctaa       840
     atctttttta ctagacgttt tgcagcatgc caactatatg ggaataacaa cggatatgtg       900
     gacttcaatt cgcaacgaca gttacatcac agtaaccgtt cattggatta ctgatgattg       960
     gaaaatgcaa cacggcgttc ttactacaga gtgcatgacg gaggcaaata ccgctgaaaa      1020
     cctttctcta aggttaaccg atgtattggc ggaatataga attacatcta acaaaataag      1080
     cgcaactgta actgacaatg gcagaaatat aaaaaaggct gtagatctat tggatgactg      1140
     gacccaattg tcgtgttttg cacacaccct acaactttgc gttaaagcgg gtctcgatat      1200
     tcctgcagta tcaagaatgc gagctggagc acggcgactt gttaaccact ttaaacattc      1260
     atcaaaagca actgcagcac tacgtgaaaa gcagttctca ctgcgaccag gcgaaactgt      1320
     tctggactta attacagagt gtccagctcg ttggaacagc acattcgaca tgttcgaccg      1380
     cctgcttttg cttcaatggt gcattagagc tgtattaacc gacttcaaaa taacaaaacc      1440
     ctcagttgct tcatctctac aaatgtcaag cacacaatgg gacctctgcc aatcacttgt      1500
     tcatgttttg aaaccattaa aaatagcaac aacaatgatg tcagcaagca aatacccgtc      1560
     cattccctgg atttacccag tgttattcac gctgcagaag aaactggagt cttgcgatat      1620
     tgacagtggt gcaaccgctc attgcaaaac agctatacga gaacaaattg ataaacgttt      1680
     ttttgcatct aactggcata ggaatttgcc tgttttagca tcagtattgg atccgcgata      1740
     taagtttctc aaatttatag acaatgatgc cacaaggcaa gaagtgtacg accatcttaa      1800
     aggacaaatc acagagtttg cggctaaata ttctgatttc gaacaacatc ttcaaagtga      1860
     aagtacaaac gaagcgcata catttgaccc ctttgaggaa ttgtgtggga aagatacgaa      1920
     gaagcaaaca gtggtcgcac cagaagacga aattaaggca tatttacgcg aacctgcgca      1980
     gccatcagac tctgatccgc tacagtggtg gaagcttaac gcagcgcgtc tacctacaat      2040
     gtcgcttatg gcccgtttct acttctgtat accagcaaca agtgtcccat ctgaatgtat      2100
     accagcaaca agtgtcccat ctgaatcggt ctttagtagt gcgggccata tagtaaatgc      2160
     aaaacgggcg tcacttactc ctgcaaatgt aaacatgcta gtgtttttaa acaaaaatgc      2220
     acatatgatc atttaactat actctgcaaa gattgtaaat agcagttaag attgtaaata      2280
     gcagtttgta acgtgttgac attttaaatg gtgtttggaa atcttcaatt gaatgtgaaa      2340
     tacactcttt ctattaattt ttcttttatt ttttatgact attcatgacg tggcaggttc      2400
     gtggttgcgc aagagaaaaa atagttcacc tgaggtatta acaatcgaga ttgataacgc      2460
     aatcgctgtt agaggagtgc tcgatcaaag ccacagcgtc gcttatcgcg aagctacaat      2520
     caacgaacgc ggacgcgcgt ttcgtgtaaa taatacattg cttaatataa gtgtgtgcgg      2580
     atgacgtcat aattcggtta acgactcgaa ctttttgtta gcggttaacc gaatagtttc      2640
     ggttaaccgg ttaaccgtta acttttccac agcccta                               2677
//
ID   HAT3_CI   repbase; DNA; CIN; 2502 BP.
CC   HAT3_CI DNA
XX
AC   AABS01000855.1;
XX
DT   07-JUL-2003 (Rel. 1.00, Created)
DT   07-JUL-2003 (Rel. 1.00, Last updated, Version 1)
XX
DE   Autonomous hAT-like DNA transposon HAT3_CI - a fossilized copy.
XX
KW   Nonautonomous DNA transposon, hAT superfamily; 8-bp TSD; 
KW   transposase; HATN5_CI; HAT3_CI.
XX
OS   Ciona intestinalis
CC   sea squirt
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-2502
RC   [1]  (bases 1 to 2502)
RA   Kapitonov V.V., Jurka J.;
RT   "HAT3_CI, a family of autonomous hAT
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 103 (2003)
XX
CC   HAT3_CI is a family of autonomous elements related to the 
CC   hAT superfamily. HAT3_CI encodes a 428-aa remnant of the HAT3_CIp 
CC   transposase (positions 661-1944).
CC
CC   HAT3_CIp:
CC   PEDSGQGRNCCVLSHQSRPCRAQERWQKVVKEAFLEAADSLFNNFNNKTKIVKSIEEVQLSRSTITRRCE
CC   VMAVDVEEQLGKDVDLCQFFFLQFDESTDMVDVAELRVFLRMVFEDMSAKEELLTILPLKRHTRGEDIFN
CC   TFKEFVNEKKLPLCKLISITTDGAPAVIGRTNGFIALCKQSESFPDFLNYHCLIHQQALCCNILNMKEVM
CC   DVAVKIVCSIRARSLQRRLFRAHLEENDFQHTDLLLQTNVRWLSRAKYLARFIELLLEIKTFLRLSNRVE
CC   YHTKLDDHQWLLDLSFLTDLTGELNVLNIELQGKDKDVANMMSSVNTFKSKLQLISSRLQRDDLRNFPYM
CC   QAELLRQGKRVTQLKTACYKEQVQRILLEFERRFADFSSIEPVVLCVTHLLQVLMLVASLPKSNHFLAWK
CC   SPLLRKKF
CC
CC   HAT3_CI is flanked by 15-bp terminal inverted repeats (4 
CC   mismatches) and 8-bp target site duplications.
CC   The nonautonomous HATN5_CI is a deletion derivate
CC   of an autonomous element 80% identical to HAT3_CI.
CC
XX
DR   GENBANK; AABS01000855.1.
CC   Positions   10081  7580  Accession No AABS01000855.1  GenBank
XX
SQ   Sequence 2502 BP; 725 A; 482 C; 589 G; 706 T; 0 other;
     catgggtgtg caaccggcca ccgcgtctac cggtagtcat cggaggtcga ctgcgaggga        60
     tgtaaaaaaa aaatctgctg tgactttcag ttattcgcct aattaccaaa tcgttaatat       120
     tttcaacttt gtacaaaaat acgctgtaat tagccatgtt aggggcagtt acgttcctgt       180
     atactcaggc agaaaaatat tcaagatggc ggctgctatg gcataagaat cgggaaacaa       240
     tagcgatgat ttgcctgtaa cttagtctgc atgatttgta cactagtaag tcactgtgcc       300
     ttgatctaat tatttttgaa taaatcctcc aaaatttgga cgcttactaa ttttttgaga       360
     acctaaaggt taacgatcgc cacaaatgtg ggaatggctg agaaaaaacg agccaaaatt       420
     taccatttta acgctgaaag ggaggtagat tatttttttg tttattcgta ttcaaagcct       480
     gtatgtttaa tttgcaatgc aacggggggg ggggttggca agaaaatcaa atctggtgcg       540
     gcactttaga acagtacaca ggtgctatga gagggatttt cctgcaaaat cccaactccg       600
     cgcccctaaa gtgagggact tgaaggcaca gcttgtagca cggcagtcca tttttactaa       660
     cctgaagact cagggcaagg ccgcaactgt tgcgtcctat cgcatcagtc acgtccttgc       720
     cgagcacaag aaagatggca aaaggttgtg aaagaagctt ttcttgaggc agcggatagt       780
     cttttcaaca acttcaacaa taaaacgaag atcgtgaagt ctattgaaga agtgcaactc       840
     tcccgtagta ccatcacaag gcgatgtgag gtaatggctg tggatgtgga ggagcaattg       900
     gggaaggatg ttgacttatg tcagttcttt ttcctgcaat tcgacgagtc gactgatatg       960
     gtggatgtgg cggaattgcg tgttttcctc aggatggttt tcgaagacat gagcgccaag      1020
     gaggagctac tcaccatttt gccattaaaa cgacacacca gaggtgaaga tatttttaat      1080
     actttcaagg aatttgtaaa cgagaaaaag ctgccgcttt gcaagcttat ctctattaca      1140
     actgatggcg cacctgctgt gataggccgc accaacgggt tcattgcact gtgcaaacaa      1200
     agtgaatcgt tcccggattt cttgaattat cattgtttaa ttcaccaaca agcgctgtgc      1260
     tgtaacattt taaatatgaa agaagtgatg gacgttgcgg tgaagattgt gtgttcaatt      1320
     cgagccagga gtttgcagag gagacttttt cgtgcccact tagaggagaa tgattttcag      1380
     cacacagatt tgctgcttca gacaaatgtc aggtggttaa gtagagctaa atatttggcc      1440
     agatttatag agctgttgct tgaaatcaag acctttctga gactttcgaa tcgtgtggaa      1500
     tatcatacaa agctagatga ccaccagtgg cttttagatt tatcttttct cacggatctc      1560
     actggcgagc ttaatgtttt aaatatagag ctgcagggta aggataaaga tgtagccaac      1620
     atgatgagtt ccgtaaatac atttaaaagc aagctacagc tgatatcaag caggctgcag      1680
     cgtgatgacc tgcgcaactt tccttacatg caagcagaac tactacgtca aggcaaacgt      1740
     gtgacacagc ttaaaacggc atgttataaa gagcaggttc agcggatatt attagagttt      1800
     gaaaggcgtt ttgctgactt ttcatccatc gagcctgtag ttttatgtgt tactcattta      1860
     ctgcaagtat tgatgttggt tgcatcgctg ccaaaatcga atcacttttt ggcttggaaa      1920
     tctccgctct tgaggaagaa gttctgaagt tgcagaatga catagaaata aaagccagat      1980
     cagattctgc tcaacctgga tagcacgtgg tgttctgaag atttctaggg gaggggaagt      2040
     atcccaatct tcgaatatgt gccttaaatc tgacagctct ttttggatca acttatttgc      2100
     atgagtcggc tttcccgcac atgaatatca tcaagtcaaa gtacagatca acaatgactg      2160
     atgctcacct tgcaaccagc ttctacactc ctgactatga gaagctagcc tccacggctc      2220
     agtgtcagat atcccactaa aacagaaagt gccgtatgcc actgcctctg tgtatgtgtg      2280
     acgtttttcg tttgttgctg attaaaaaca tgccaattag ttttgccaag tcatttatta      2340
     acgcgctgta gttgtttaga caagggaaaa acgcatacaa gagttatttc ggcatacgca      2400
     ggaaatatga gaggtcctgc gaaattgacg ctggctggta gaccgcgtga gaatggttag      2460
     ttgaaaagta gatcttgggt caaaaaaggt tgggcacgcc tg                         2502
//
ID   HAT4N_CI  repbase; DNA; CIN; 449 BP.
CC   HAT4N_CI DNA
XX
AC   ;
XX
DT   07-JUL-2003 (Rel. 1.00, Created)
DT   07-JUL-2003 (Rel. 1.00, Last updated, Version 1)
XX
DE   Nonautonomous DNA transposon HAT4N_CI - a consensus.
XX
KW   Nonautonomous DNA transposon, hAT superfamily; 8-bp target
KW   site duplication; HAT4_CI; HAT4N_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-449
RC   [1]  (bases 1 to 449)
RA   Kapitonov V.V., Jurka J.;
RT   "HAT4N_CI, a family of nonautonomous hAT
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 104 (2003)
XX
CC   HAT4N_CI is a family of nonautonomous elements related to the 
CC   hAT superfamily. There are several hundred HAT4N_CI elements in the 
CC   C. intestinalis genome, they are 95% identical to the consensus.
CC   This element is a internal deletion derivate of the HAT4_CI
CC   autonomous transposon.
CC   HAT4N_CI has 21-bp terminal inverted repeats.
XX
CC   [1] (Consensus)
XX
SQ   Sequence 449 BP; 147 A; 72 C; 68 G; 161 T; 1 other;
     tagggatgca cattacagaa tttcgaatcc atgagattcg aatccttttg tattcgaatc        60
     taattacggg attcggtatt ctgtttaatg acgtcattac acgtcatctc atatactata       120
     ttaacaattt ttgaaactta ttaattttga aaaaaaatat ttttgtgttt gtgggacttt       180
     cgagagtaaa cgtttcgtaa cgtcttttca tagcctgcta tacgtttcat gacgcaaaaa       240
     ctacccaata gtacaatttt tgatcatttt acagctcatg atccaacaag gctgctatga       300
     aagagtcaat aaactgactt wtgtgggtaa aattattttt tcctataaat ataaaaagat       360
     tcgaaattct agattcggaa ttctagattc gaaataaagt attctaggat atcctagaat       420
     acctaattat tctgtaatgt gcatcccta                                         449
//
ID   HAT4_CI   repbase; DNA; CIN; 3569 BP.
CC   HAT4_CI DNA
XX
AC   AABS01001724.1;
XX
DT   07-JUL-2003 (Rel. 1.00, Created)
DT   07-JUL-2003 (Rel. 1.00, Last updated, Version 1)
XX
DE   Autonomous hAT-like DNA transposon HAT4_CI - a fossilized copy.
XX
KW   Nonautonomous DNA transposon, hAT superfamily; 
KW   transposase; BED zinc finger; HAT4N_CI; HAT4_CI.
XX
OS   Ciona intestinalis
CC   sea squirt
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-3569
RC   [1]  (bases 1 to 3569)
RA   Kapitonov V.V., Jurka J.;
RT   "HAT4_CI, a family of autonomous hAT
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 105 (2003)
XX
CC   HAT4_CI is a family of autonomous elements related to the 
CC   hAT superfamily. 
CC   It encodes a 607-aa hAT transposase, HAT4_CIp (5 exons,
CC   695-918, 1077-1099, 1214-1626, 1685-2399,2454-2902).
CC   The N terminal portion of HAT4_CIp is the BED zinc finger.
CC
CC   HAT4_CIp: 
CC   MKDSIMKRGRKLSSDVWEHFSPPNVENKVKCNYCHATLSYCQSTGSLMKHLKQKHPFTSL
CC   TRSEEGDSPSPSTSQLSVGETSIGDLRPINLVEGENFQALIKHLAPGYNIPSRMTFMRKL
CC   KQSLEICKAKIRDELSNANSIALTTDLWSSIRMQSFIGVTAHVISKDSAELRNFVLATKE
CC   VLEESHTGENIVEWIESILVDYHVSPAKIVGIVTDNGSNMRCVKEAVAIGPIKSAIGAAR
CC   HLVVYFCQSAKASAALRSQQTRSGDNCDLILDVPTRWNSTYAMVKRLCRLQWMVRQVLCD
CC   TSITPRTKAMHLELKDANWVILQQLIDVLAPIKTASDYIEGDQYVTLGSARTKAMHLELK
CC   DANWVILQQLIDVLAPIKTASDYIEGDQYVTLGSALPLIKSLAEKYNSNQGLETLQTPSH
CC   TSIMQAKSTMELSIKRRFPLFFANTGSMAPHPFFTKQHVRDELETEITTEGLDANETTQL
CC   RNTAKTRSQTSNDNPELCLQSILQCGVENAASSDDSIEEDCVAAEVSKYLKDKTACTDPL
CC   VWWKNKKSEYPQLYLLILKYLCIPATSASSERCFSSAGLTATALWSRLTGEHLEALNILH
CC   CNRTLLH
CC
CC   The nonautonomous HAT4N_CI is a deletion derivate
CC   of HAT4_CI.
XX
DR   GENBANK; AABS01001724.1.
CC   Positions   928  4496  Accession No AABS01001724.1  GenBank
XX
SQ   Sequence 3569 BP; 1128 A; 622 C; 690 G; 1129 T; 0 other;
     tatttttgtg tttgtgggac tttcgagagt aaacgtttcg taacgtcttt tcatagcctg        60
     ctatacgttt catggcgcat aaactaccca atagtacaat ttttgatcat tgctatgaaa       120
     gggtcaataa actgactttc gaatttctag attcgaaata aattattcta ggatatccta       180
     gaatacctaa ttattctgta atgtgcatcc ctagttcgat ggtaaggtga agtccagata       240
     aagacagatg gtcatgttta aaatttttaa aataattggc aggcagttcg atggtaaggt       300
     gaagtccaga taaagacaga tggtcatgtt tataattttt aaaataattg gcaggcagtt       360
     cgatggtaag gtgaagtcag ataaagacag atggtcatgt taaaatttca aaataattgg       420
     caaaactcca gaatacaaga ggaactgtaa ttgggagaaa gggatcaaag tgggtagtaa       480
     agtgggatat tgatggcaca gtaacgtttt tcaacgtttt tttaaagtta aaatttagtt       540
     gttgactacc tcactgatca tttatttgcg aagcgttttg cacccctttt gtctgacgtc       600
     atttacattt aacggttgac tgcacaattg ttgcaccact tcacggcgtt cgcgcaacgt       660
     ctgttttgaa gttttttacc gcagttttgg tttaatgaaa gatagcatta tgaagcgtgg       720
     aagaaagtta tcaagcgatg tttgggagca tttttcacca ccaaatgttg aaaataaagt       780
     taaatgcaat tattgccatg caaccctgag ttactgtcaa agtacaggta gtctcatgaa       840
     gcacttaaaa cagaaacatc cgtttacaag cttgacccga tcagaggaag gggacagccc       900
     aagcccatca acatcacagt aagtgggata gtaaagaata aatttttgat tttgttacct       960
     agtctgcatt aacttacttc atctaaattt ttccaattga atgtgaatga atttacttag      1020
     tttcatagtt tgaactgtta tgtaataaca gctgatttaa aattttgttt gcacagatta      1080
     tctgtcggag aaacatcaag tagttctgct ggatcaccag ctgttcggca aaggcggctg      1140
     gatacttatg tgcacaggcc acttacccca caacaagctg agtgaataac aaattgtata      1200
     tttactgtca tagttggtga cttaagacct attaatcttg ttgaaggtga aaacttccaa      1260
     gccctaatta aacatttagc tcctggatac aatattccca gcagaatgac ttttatgaga      1320
     aagcttaaac aatctttgga aatttgcaaa gccaaaatcc gtgatgaatt atctaatgca      1380
     aatagtattg ctttaaccac agatctatgg tcaagcataa ggatgcaatc atttattggt      1440
     gtaacagctc atgtcattag caaagattca gctgaattgc gtaattttgt tctggctacc      1500
     aaggaggttc tagaagaaag ccacactggt gaaaacattg tggaatggat agaaagtata      1560
     ttggtggatt accatgtgtc accagctaag atcgtgggga ttgttactga taacggttcc      1620
     aacatggtaa atgcttgtga aaaactaaat gataagcatc cgatgcatgg cgcatacttt      1680
     gcagcgatgt gtaaaagagg cagttgcaat tggccccatt aaatccgcta ttggagctgc      1740
     tagacatctg gtggtctatt tctgccagtc ggccaaagca tcagcagcac tccgttcaca      1800
     acagacccgt tctggtgata attgtgattt gattttggat gttcccacca ggtggaattc      1860
     aacctatgca atggttaaaa gactttgccg gctgcagtgg atggtaagac aggtgttgtg      1920
     tgacacatcc ataacaccaa gaacaaaagc tatgcatctt gaactgaaag atgctaactg      1980
     ggttattttg cagcaattaa ttgatgtgct tgccccaatt aaaaccgctt cagactatat      2040
     tgaaggagat cagtatgtta cccttggatc tgcaagaaca aaagctatgc atcttgaact      2100
     gaaagatgct aactgggtta ttttgcagca attaattgat gttcttgccc caattaaaac      2160
     cgcttcagac tatattgaag gagatcagta tgttaccctt ggatctgctt tgccacttat      2220
     aaaaagttta gccgaaaaat ataacagcaa ccaaggttta gaaacacttc aaacacctag      2280
     tcataccagc attatgcaag caaaatcaac aatggaactg tctataaaaa gacgttttcc      2340
     tttgtttttt gcaaacaccg gtagtatggc cccccatcca tttttcacaa agcaacatgg      2400
     ttgaacccaa tgtaccaaag caatgtattt tacaaaactt ttggggtctc aagtgagaga      2460
     cgagcttgaa accgaaataa caacagaagg cttagatgca aatgaaacta ctcaattaag      2520
     aaatacagct aaaacaagat cacagacatc caatgataat ccagaactgt gcttacaaag      2580
     cattcttcaa tgtggagtgg aaaatgctgc aagcagcgat gattcaatag aggaagactg      2640
     tgttgcagca gaagtatcta aatatttgaa agataaaaca gcttgcactg atcctttggt      2700
     gtggtggaag aataaaaaat ctgaatatcc gcagctctac ctattaattt taaaatattt      2760
     atgtatccca gctacatcag cctcatcgga aaggtgcttt tctagtgcag gcttaactgc      2820
     cactgcgctc tggtctcgtt taaccggtga acaccttgaa gccttaaaca ttttacattg      2880
     caacagaaca ctacttcatt gaacatgttt tgattgtttt catttttttg tacttgttta      2940
     tgtttttatt tcatttcata cctctttaag tttttcttgc aaaaagccta cttgtgttat      3000
     ttttttggta cttttaatac aagacttaat gtaatatatg cctttatggc tcctctcggt      3060
     ataaaatctt caataaaatt aaaattttca taccgagagg agccataaaa gcatatattg      3120
     tgttatttac atactgtggt ttaaagagga tgtaattgca caatttttgt tctcttattc      3180
     atttcgtacc tttctagtta attcagcaaa ctgcaacttt aataaagtga tttatattgg      3240
     tacaaattga tttggtctaa taaataaata aggattcgaa attctagatt cgaaataaag      3300
     tattctagga tatcctagaa tacctaatta ttctgtaatg tgcatcccat aaagtagtcc      3360
     tacagctgca ggtcgttttt ataaagcagt cctacagttg caggtcgttt ttataaagta      3420
     gtcttacagt tgtaggtctt tttataaagc agtcttacag ttgtaggtct ttttataaag      3480
     tagtcctaca gctgcaggtc gtttttataa agtagtctta cagctgcagg tcgtttttat      3540
     aaagcagtct tacagctgca ggtcgtttt                                        3569
//
ID   HAT5N_CI  repbase; DNA; CIN; 945 BP.
CC   HAT5N_CI DNA
XX
AC   ;
XX
DT   07-JUL-2003 (Rel. 1.00, Created)
DT   07-JUL-2003 (Rel. 1.00, Last updated, Version 1)
XX
DE   Nonautonomous DNA transposon HAT5N_CI - a consensus.
XX
KW   Nonautonomous DNA transposon, hAT superfamily; 8-bp target
KW   site duplication; HAT5; HAT5N_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-945
RC   [1]  (bases 1 to 945)
RA   Kapitonov V.V., Jurka J.;
RT   "HAT5N_CI, a family of nonautonomous hAT-like
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 106 (2003)
XX
CC   There are ~50 HAT5N_CI elements in the 
CC   C. intestinalis genome, they are ~85% identical to the consensus.
CC   HAT5N_CI has ~100-bp degenerative terminal inverted repeats.
CC   HAT5N_CI elements are flanked by 8-bp target site duplications.
CC   HAT5N_CI is a nonautonomous derivate of the HAT5 transposon.
CC   They share common ~100-bp 5' and ~140-bp 3' termini, respectively.
CC   The 23-bp CGTGCGTCGTAGTTTGACCTTTA minisatellite is present in HAT5N.
XX
CC   [1] (Consensus)
XX
SQ   Sequence 945 BP; 215 A; 196 C; 209 G; 324 T; 1 other;
     tagaggtcga ccgatatatc ggttcaccga tattatcggc cgatatttac gttctaccga        60
     taatcggtat cggtaaaaaa gcgccgatat ttcaccgata tataaatagt tcgtgcgaag       120
     cgacgtgcgt cctacttgac ctttacgtgt gttcgtagtt taacgtccac gtgcctcgta       180
     ctttagcctt cacgtgcgtc gtagtttaac gtccacgtgc gtcatagttt gacctttacg       240
     tgcgtcgtat ttatgcsttt acgagcgtgg tagtttaacg tccacgtgcg tcgtagtttg       300
     acctttacgt gcgtcgtagt ttgaccttta cgtgcgtcgt agtttaacct ttacgtgcgt       360
     cgtagtttaa ccttcacgtg cgtcgtagtt tgacctttac gtgcgtcgta gtttgacctt       420
     tacgtgcgtc gtagtttgac ctttacgtgc gtcgtagttt tgacctttac gtgcgtcgta       480
     gtttaacctt tacgtgcgtc gtagtttaac gtccacgtgc gtcgtagttt aacgtccacg       540
     tgtgcgtcgt agtttaacgt ccacgtgcgt catagtttaa cgtccacgtg cgttgtattt       600
     caacgtctac gtgcgttgta gtttaacgtc cacgtgcgtc atagtataac gttcacgcgc       660
     gttgtagttt agcgttcatg tgcgtcctag ttttgtacaa aagcaacata tttggagtta       720
     cctattaaga acatgcagac ttcctaaaaa agtgatgacc aaccattttt tctctataat       780
     aacttgcaat atcttgaata caggtattaa ttttgattaa tactgatcat ttcatatgtt       840
     tcgctatagt gtcaaatatc ggtaaaatat cggtatcggt atcggtaaaa gctaaaaata       900
     tcggtatcgg tatcggtgga aaaaattgat atcggtcggt ctcta                       945
//
ID   HAT5_CI   repbase; DNA; CIN; 2211 BP.
CC   HAT5_CI DNA
XX
AC   AABS01000231.1;
XX
DT   07-JUL-2003 (Rel. 1.00, Created)
DT   07-JUL-2003 (Rel. 1.00, Last updated, Version 1)
XX
DE   Autonomous hAT-like DNA transposon HAT5_CI - a fossilized copy.
XX
KW   Nonautonomous DNA transposon, hAT superfamily; 8-bp TSD;
KW   transposase; BED zinc finger; HAT5N_CI; HAT5_CI.
XX
OS   Ciona intestinalis
CC   sea squirt
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-2211
RC   [1]  (bases 1 to 2211)
RA   Kapitonov V.V., Jurka J.;
RT   "HAT5_CI, a family of autonomous hAT
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 107 (2003)
XX
CC   HAT5_CI is a family of autonomous elements related to the 
CC   hAT superfamily. 
CC   It encodes a 608-aa hAT transposase, HAT5_CIp (pos. 256-2079).
CC   The N-terminal portion of HAT5_CIp (pos. 10-55) is the BED zinc finger.
CC
CC   HAT5_CIp: 
CC   MSAIAKVSSSKVWDYFNVSEGSVKCQLCKNLVSQGSTSSAQKNTSNLWSHLRSKHREVEVYEQAHCHKIG
CC   KSSKVVQPTLFQSFDNSRKWSNTDGRSRNLDKLIIEMIATDIQPFSVTNDIGFKRLLATAEPRYNLKDEK
CC   YYRTEMLPKVHLKVVDKIKNMLKEENAGESLSFTTDCWSGSTESLMSLTAHFIDNQWKRKQLVLSVKSMS
CC   ESHTGDYIGKVFLDILSQWEIDRSRVLLVLRDSGANVVKGMRVADVSDFSCCAHTMQLIIKEGIESQRVV
CC   IDIVAKLKRCATHFNHSTLAKKRLHAIQNQVGLPVHSIIQAIPTRWNSTLHMLRRMLEQKHALSIYASEY
CC   GHFSLPNTYEWELVAKLVALLIPFETITLEISHSEASASCILPSIAVLKALLQSDNEATFGIGTIKGTMC
CC   ESLLRRYCNVENVKPVVIACLLDPRFKDKPFSSEIVLGRAKDWLINEVKEQDQGEEPVAAKKQKQSSDSE
CC   NDLLSNLYKNVLGQGSTDNNECESTDVQTEINKYLSEPLIDRSTGHPLDWWKNNETRFVILAKLARKYLN
CC   PPPSSVPSERDFSTIGNIYEDKRSRLTGEHAEQLCFLYYNLHLLEYNY
CC
CC   The nonautonomous HAT5N_CI is a derivate of the HAT5_CI transposon.
CC   They share common ~100-bp 5' and ~140-bp 3' termini, respectively.
XX
DR   GENBANK; AABS01000231.1.
CC   Positions  115974  113764  Accession No AABS01000231.1  GenBank
XX
SQ   Sequence 2211 BP; 752 A; 372 C; 473 G; 614 T; 0 other;
     tagaggtcga ccgatatatc gtttcaccga tattatcggc cgatatttac gttctaccga        60
     taatcggtat cggtaaaaaa gcaccgatat ataaattgtt cgagcgatgt gcgtatgcga       120
     atataacgaa gagaagagag aggggaaaag gctagagaaa aaagaaaaag gcgccgtgac       180
     gttgaagcgt aagcgcgcga aacaaaccac gcgaaataga ttaccgcata tcgttagtat       240
     aataaaactt gcaagatgag tgccattgcg aaagtttcct ctagcaaagt ttgggattat       300
     tttaatgttt cggaaggttc agttaagtgc caactgtgta agaacttggt cagtcaaggt       360
     tccacttctt ctgctcagaa aaatacaagt aacctatggt cacatttgcg tagtaagcac       420
     agagaagtag aagtgtatga acaagcgcac tgccataaaa taggcaaaag ttcaaaggtc       480
     gtgcagccta cactgtttca gtcgtttgac aatagtagaa agtggtctaa tacagatggt       540
     cggtccagaa atttggataa gctgataatt gagatgatag ctacagatat acagccattt       600
     tcagtcacaa atgacatagg attcaaacgt cttctggcga ctgcagagcc aaggtacaat       660
     cttaaagatg aaaagtatta cagaacagaa atgttgccta aagttcacct gaaagttgtt       720
     gataaaatta aaaatatgct caaagaagaa aatgcaggag agagtttgtc atttactaca       780
     gattgttggt caggttcaac tgaatctctt atgagtttaa cagctcattt tattgacaat       840
     caatggaaga gaaagcaact agttttgtca gtaaagtcaa tgtcggagtc tcacacagga       900
     gattacatag gtaaagtgtt cttggacatt cttagccagt gggaaattga cagaagtcgt       960
     gtgttgcttg ttttacgtga cagtggtgct aatgttgtca aaggcatgag ggtagcagat      1020
     gtttcagatt tcagctgctg tgcacatacc atgcaattaa taataaaaga gggtatagaa      1080
     tctcaaagag tcgtaattga tattgtggca aagcttaaac gctgtgccac acacttcaat      1140
     cattcaacac ttgcaaagaa acggctacat gcaattcaaa accaagttgg tttgccggtt      1200
     cattcaatta tacaggcaat cccaacaaga tggaattcaa ctctacatat gttgcgtagg      1260
     atgttggaac agaagcatgc tctcagcata tatgcaagtg agtatggtca ttttagttta      1320
     ccaaatacat atgagtggga acttgtcgcc aaattagttg ctttattgat accctttgag      1380
     acgataacgt tggagattag tcattctgaa gcttccgcat catgcatact acccagtatt      1440
     gcagtactta aagctcttct acaaagtgat aatgaagcaa catttgggat tggtactata      1500
     aaaggaacca tgtgtgaaag cctgttaaga agatattgta atgttgaaaa tgttaaacca      1560
     gtggtgattg cttgcctcct ggatccccga ttcaaagaca aaccattttc atcagagatt      1620
     gtcttaggta gagctaagga ttggttaatt aatgaagtta aggaacaaga ccaaggagaa      1680
     gaaccagtgg cagcaaagaa gcaaaaacaa tccagtgata gtgagaatga cctattgtcc      1740
     aatttgtaca aaaatgtctt aggtcaagga tctactgata acaatgagtg tgaatcaaca      1800
     gatgttcaaa cagaaattaa taaatatctt tcagaaccac ttattgatcg gtctaccgga      1860
     catccactgg attggtggaa aaataatgaa actcgttttg tcattctagc caaactagct      1920
     agaaaatatt taaatccacc gccttcttct gtgccaagtg aacgagattt tagcacaatt      1980
     ggaaatatat atgaagataa aagaagccgc ctcactggcg aacacgcaga acaactttgt      2040
     ttcctgtact ataacttgca tttgctcgaa tacaattatt aaatcagatt tagattgatt      2100
     attttcattt gtttcgctag tgtaaaaata tcggtaaaat atcggtatcg gtgaaagcta      2160
     aaaatatcgg tatcggtatc ggtggaaaaa attgatatcg gtcggtctct a               2211
//
ID   HATN1_CI  repbase; DNA; CIN; 611 BP.
CC   HATN1_CI DNA
XX
AC   ;
XX
DT   07-JUL-2003 (Rel. 1.00, Created)
DT   07-JUL-2003 (Rel. 1.00, Last updated, Version 1)
XX
DE   Nonautonomous DNA transposon HATN1_CI - a consensus.
XX
KW   Nonautonomous DNA transposon, hAT superfamily; 8-bp target
KW   site duplication; HAT1_CI; HATN1_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-611
RC   [1]  (bases 1 to 611)
RA   Kapitonov V.V., Jurka J.;
RT   "HATN1_CI, a family of nonautonomous hAT
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 108 (2003)
XX
CC   HATN1_CI is a family of nonautonomous elements related to the 
CC   hAT superfamily. There are ~50 HATN1_CI elements in the 
CC   C. intestinalis genome, they are 97% identical to the consensus.
CC   This element is a internal deletion derivate of the HAT1_CI
CC   autonomous transposon.
CC   HATN1_CI has 15-bp terminal inverted repeats (1 mismatch).
XX
CC   [1] (Consensus)
XX
SQ   Sequence 611 BP; 199 A; 109 C; 117 G; 186 T; 0 other;
     tagagcacga ccgattatcg gttagccgat atatcggccg catttttggt gatttaccga        60
     ttatcggcaa gggcaaaaaa cggccgatat tatcggcgct aagtaaccag acggccagca       120
     acgtgcgtac gtaagaatta atgcagagcg atagcttgtt cataaacgta aactcactcg       180
     tatacctaat tcaactcgtt cgtaaaaatc taacgtatta aactaggtca aagcgtctga       240
     tcacgcgtcc accgcatgtc atgtttatca ggcgcgtgta acgtcgaggt tactttaggt       300
     cacttacgcg tctttacgcg tcaacgtgat acacaaataa actgcattag ctgataaata       360
     taatgtttgt ttaatggaag ggaggtaaaa tttatttgaa aaaattacaa attaaccaat       420
     taagtaatta caagttcact aataactaat taataataat taagcctgtt agttgatttt       480
     tattagctat atcagatttt tccgttttaa tcagtcaagt tttttaggtg cattaaaata       540
     tcggttatcg gcaactgaaa tttacaaaat atcggtatcg gtttgaaaaa agcaatatcg       600
     gtcgggctct a                                                            611
//
ID   HATN2_CI  repbase; DNA; CIN; 1649 BP.
CC   HATN2_CI DNA
XX
AC   ;
XX
DT   07-JUL-2003 (Rel. 1.00, Created)
DT   07-JUL-2003 (Rel. 1.00, Last updated, Version 1)
XX
DE   Nonautonomous DNA transposon HATN2_CI - a consensus.
XX
KW   Nonautonomous DNA transposon, hAT superfamily; 8-bp target
KW   site duplication; HATN2_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-1649
RC   [1]  (bases 1 to 1649)
RA   Kapitonov V.V., Jurka J.;
RT   "HATN2_CI, a family of nonautonomous hAT
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 109 (2003)
XX
CC   HATN2_CI is a family of nonautonomous elements related to the 
CC   hAT superfamily. There are ~100 HATN2_CI elements in the 
CC   C. intestinalis genome, they are 98% identical to the consensus.
CC   There are also several hundred elements that are 65-85% identical 
CC   to HATN2_CI and represent several young subfamilies related to it.
CC   HATN2_CI i flanked by 14-bp terminal inverted repeats (1 mismatch).
XX
CC   [1] (Consensus)
XX
SQ   Sequence 1649 BP; 488 A; 313 C; 352 G; 494 T; 2 other;
     tagggatgtg ctgaagttga aaaagctcgg gttcgccgag cgccgagctt caacgaaaag        60
     ctcggcacga gcccgagccc gagcacctat gacgtcatca aggagaaagg cgtacgagaa       120
     tgcgttccta ttcagccgaa aagcgccgct aatcaaaata atacagaaca cgtggtttgc       180
     ggttaaagac gcgtctcgct tttcrtaatt cctactgttg caaaatgtaa aattcataca       240
     aaaaatattt aattaaaaaa ttatttataa ctgttacagc cagtggcgca actagcaagt       300
     tcaaaaaggg gtctgtcata cagataatta cgtcaaatca acgttatctc tgaagcgata       360
     taaacgcttt agatattggt cttgcacact aatatatcta ttctacttta tgcggtaaat       420
     taggaccaat attacattat ttatactaaa ttagaaacgt ctttttaata aatgaaacat       480
     tggtgtaagt tttacgcatg ttcatcttgg ataatgtaac gattatttac gtcagaataa       540
     ctttgataaa cctttacgat cgttacatca caaacgagat tgttggaaaa caatcgtgtt       600
     ttattcgctt ccatacgatc tgtagtttgt gtataatttt tgtttctgat gattagttta       660
     aatgcaggta aatcgcgatt atgtgaattt taattggtgc aaatataaga gcgaggagcg       720
     acgctatcag taaattggaa ccaacataaa ttgtaatatg atattacaaa gtatcgtccc       780
     ggtcgagctt ggacagaagc caaaaaacat cgtttgatgg caccgcacga gaaccagagt       840
     ttcattacgt catttttcac gagaataaat tcacaacgat tgcttcgttt gttacgtgtg       900
     gaatgtatgc taccgcatgc gtcttccttt atttcatacg ccggcgcaga gtgtaaaaat       960
     gtgacgctga tacacgatgt tttgatctcg tggttggttg ggctgccaac ttgggcagtg      1020
     ggcacattcc tcccgattgt tatattataa aacgtcataa ttaatagtta cgttgcgata      1080
     ggacacgtga cgtaacaatt gaatgaaaaa ttgttcvaat tccaagcgaa ggaatgttat      1140
     attgaatgca acgcgtgtgt gtgcgtctta gcactttctg gctgcgtgcg tgtctgcggt      1200
     aaaggtggct taggggttgc aaaaccctgt ggttgcaaaa cagcccccgt ggttgcagca      1260
     atttatatta tttcattata aaaaagttta agagtttttg gctttttatt taaaatgtga      1320
     tacgaaaaca ttgggcgctc gtgtaattcg acacctgctg taattcgata cgggcaaatt      1380
     cgctgacgtt gcgattcgtt acttgcgaga gagcaaattc acaacgaacg aaaaataatt      1440
     aaagagaaag ctacgctgac tagtctcgtt atctcctctt agtagcttca cttttttcat      1500
     ttttaatatt ttttcgctct cgcgtgcaac attatagcaa tagcataagg ctcggcgctc      1560
     ggcccagttt tcagccgagc gccgagcgtc aaaaaaggag acgctcgggc acgagctttt      1620
     gagttcgggc tcggctcggc acatcccta                                        1649
//
ID   HATN3_CI  repbase; DNA; CIN; 287 BP.
CC   HATN3_CI DNA
XX
AC   ;
XX
DT   07-JUL-2003 (Rel. 1.00, Created)
DT   07-JUL-2003 (Rel. 1.00, Last updated, Version 1)
XX
DE   Nonautonomous DNA transposon HATN3_CI - a consensus.
XX
KW   Nonautonomous DNA transposon, hAT superfamily; 8-bp target
KW   site duplication; HATN3_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-287
RC   [1]  (bases 1 to 287)
RA   Kapitonov V.V., Jurka J.;
RT   "HATN3_CI, a family of nonautonomous hAT
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 110 (2003)
XX
CC   HATN3_CI is a family of nonautonomous elements related to the 
CC   hAT superfamily. There are ~100 HATN3_CI elements in the 
CC   C. intestinalis genome, they are 98% identical to the consensus.
CC   There are also several hundred elements that are 65-85% identical 
CC   to HATN3_CI and represent several young subfamilies related to it.
CC   HATN3_CI i flanked by 16-bp terminal inverted repeats.
XX
CC   [1] (Consensus)
XX
SQ   Sequence 287 BP; 85 A; 57 C; 57 G; 88 T; 0 other;
     cagcggttcc caaactgggg tccatacagc agtttcagag ggtccgcaat gaagcaatga        60
     ttgtgatcca aaaccaaacc aaacattgat gagttaattg cagcaaaaca agtgcaccca       120
     tcccattaaa cagcttaccg tatttgatag tttttgcttt ttctttcatt ggtgtggttt       180
     ttgcattttt cctatagcat tctttgattt ttatagggcc gcgaaatatc aaaataattg       240
     caaagggtcc accaggcaaa atttttagaa aagtttggga accgctg                     287
//
ID   HATN4_CI  repbase; DNA; CIN; 718 BP.
CC   HATN4_CI DNA
XX
AC   ;
XX
DT   07-JUL-2003 (Rel. 1.00, Created)
DT   07-JUL-2003 (Rel. 1.00, Last updated, Version 1)
XX
DE   Nonautonomous DNA transposon HATN4_CI - a consensus.
XX
KW   Nonautonomous DNA transposon, hAT superfamily; 8-bp target
KW   site duplication; HATN4_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-718
RC   [1]  (bases 1 to 718)
RA   Kapitonov V.V., Jurka J.;
RT   "HATN4_CI, a family of nonautonomous hAT
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 111 (2003)
XX
CC   HATN4_CI is a family of nonautonomous elements related to the 
CC   hAT superfamily. There are ~100 HATN4_CI elements in the 
CC   C. intestinalis genome, they are 98% identical to the consensus.
CC   HATN4_CI i flanked by 12-bp terminal inverted repeats.
XX
CC   [1] (Consensus)
XX
SQ   Sequence 718 BP; 209 A; 147 C; 135 G; 226 T; 1 other;
     tagggctgtg gattttccct atttttgttt aaccgttaac cgttcagttt taaccggtta        60
     accggttaac cgatacaagt gtaatcctaa taaaagcgtc ttgtttatcg cttttctttc       120
     gcgaatttaa aggcaacttt acgacgaacg tatggactat gcttgcaata cacgggcaaa       180
     cgttcttaac gttaaagtaa tgctttctta ttcatattca aacctgtttt aaarcacctg       240
     ccgtctaaat aatcaacgtg tgaattgcaa ttatgacgca gttattaacg tgtgaattgc       300
     tattatgtcg taatcaattg ccaggtcaaa caatcgctat tatgatgcaa tgaatccacg       360
     tgtgaatgcc tgctttttcg taataaacac gctgcttggc tgaggaaaac atttaagttg       420
     tgtattacac caatataatg ttgcaaaact agttagcctg cggtattaac aatcaagatt       480
     gatggcgtaa tcgccgttgt agggcacgat caaagcaaca gcgtccctgc gcactctgtc       540
     ttattgcaaa acaacaatca acgaacacga acacgtgcct ttcgtgtaaa taagacagat       600
     attgatatac gtttatgccc tatgacgtca tagttcggtt aacgacttga acttttcgtt       660
     agcggttaac cgaataggtt cggttaaccg gttaaccgtt aacttttcca cagcccta         718
//
ID   HATN5_CI  repbase; DNA; CIN; 904 BP.
CC   HATN5_CI DNA
XX
AC   ;
XX
DT   07-JUL-2003 (Rel. 1.00, Created)
DT   07-JUL-2003 (Rel. 1.00, Last updated, Version 1)
XX
DE   Nonautonomous DNA transposon HATN5_CI - a consensus.
XX
KW   Nonautonomous DNA transposon, hAT superfamily; NNNTANNN target
KW   site duplication; HATN5_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-904
RC   [1]  (bases 1 to 904)
RA   Kapitonov V.V., Jurka J.;
RT   "HATN5_CI, a family of nonautonomous hAT
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 112 (2003)
XX
CC   HATN5_CI is a family of nonautonomous elements related to the 
CC   hAT superfamily. There are ~50 HATN5_CI elements in the 
CC   C. intestinalis genome, they are 98% identical to the consensus.
CC   HATN5_CI has 15-bp terminal inverted repeats. HATN5_CI is 
CC   characterized by the target site specificity, its copies are
CC   flanked by the NNNTANNN target site duplications.
XX
CC   [1] (Consensus)
XX
SQ   Sequence 904 BP; 277 A; 172 C; 200 G; 254 T; 1 other;
     caggcgtgcc caacccgtcg accgcggtct accggtagtc cgcggaccta tctcaggtcg        60
     accgcgacag gtgtaataaa aaaaatcaaa aaatctgctg tggcgttata attgccaaat       120
     cattaatttt atcaatactt tgtacaaaaa atacggaccg tgttaagagg gcgtacctgt       180
     acggcagcag gcaaaaaatc caagatgacg actactatga cgtaacaatc ggaacaatgg       240
     cgattatttt acaataattt ccttaacctg gtctgcatga tttgtacact agtaactctc       300
     tgtgcttcaa actaagtatt tttgactata ttccccaaaa ttttgatcct ttccgacttt       360
     tgacaagcga tcgcaacaaa cgttagtagc atggcagaga gataacgagc caagacctat       420
     cattttawcg ctaaatagga ggacgattat tttttcctgt ttattcgtat tcaaagcctg       480
     tttgtttaat atgcaacgca acggtaccgt agggcaaaaa aagcaaatca ggagcagcac       540
     tttagaacgg tacacggggc tatgagaggg attttcctgc aaaaacacaa ctaagctccg       600
     ctaaagatga cgtgtgaggt gtgacgcaac aattgtatgt gtgacgtttt tcgtttgttg       660
     catattaaaa acatttcagt tagttttggt aacgaagtca ttgaaatttg tgtagtaatt       720
     aaagtagttt tgttgctgat aagttaaaac catgagcatg gttcattgaa ccgctgcagt       780
     tgcttataca ggggataaac gcatacaaga gatatttcgg catacgttga cgctagctgg       840
     tagaccgcgt gcagttggtt agttgaaaag tagatcttgg gtcaaaaaag gttgggcacg       900
     cctg                                                                    904
//
ID   HATN6_CI  repbase; DNA; CIN; 307 BP.
CC   HATN6_CI DNA
XX
AC   ;
XX
DT   07-JUL-2003 (Rel. 1.00, Created)
DT   07-JUL-2003 (Rel. 1.00, Last updated, Version 1)
XX
DE   Nonautonomous DNA transposon HATN6_CI - a consensus.
XX
KW   Nonautonomous DNA transposon, hAT superfamily; gtcTAnac target
KW   site duplication; HATN6_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-307
RC   [1]  (bases 1 to 307)
RA   Kapitonov V.V., Jurka J.;
RT   "HATN6_CI, a family of target specific nonautonomous hAT
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 113 (2003)
XX
CC   HATN6_CI is a family of nonautonomous elements related to the 
CC   hAT superfamily. There are ~50 HATN6_CI elements in the 
CC   C. intestinalis genome, they are 96% identical to the consensus.
CC   HATN6_CI has 15-bp terminal inverted repeats. HATN6_CI is 
CC   characterized by the target site specificity, its copies are
CC   flanked by the gtcTAnac target site duplications.
XX
CC   [1] (Consensus)
XX
SQ   Sequence 307 BP; 89 A; 62 C; 62 G; 94 T; 0 other;
     cagtgctctt caaccttttt tgggttggtg aacccctaaa gttgttgcga caaactcatg        60
     cacccctgat tgctttaacg taaaactaat gacgtttcgc aattcccagt gatgcaagat       120
     atagaattca tataaaaaaa actgtagaaa agtggctaaa tttgttaaaa atgttcaaaa       180
     ctgagtatta ttgctgaaaa ttgttgaagt ttgtgatgca cccttgtata cccttttgta       240
     ctggtgcacc cctggcatat tttgatgcac cctagggtgc accgtgcaca ccggttgaag       300
     agcactg                                                                 307
//
ID   MarinerN1_CI repbase; DNA; CIN; 1357 BP.
CC   MarinerN1_CI DNA
XX
AC   ;
XX
DT   07-JUL-2003 (Rel. 1.00, Created)
DT   07-JUL-2003 (Rel. 1.00, Last updated, Version 1)
XX
DE   Nonautonomous DNA transposon MarinerN1_CI - a consensus.
XX
KW   Nonautonomous DNA transposon, mariner/Tc1 superfamily; TA target
KW   site duplication; Cimi-1; MarinerN1_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-1357
RC   [1]  (bases 1 to 1357)
RA   Kapitonov V.V., Jurka J.;
RT   "MarinerN1_CI, a family of nonautonomous mariner/Tc1
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 115 (2003)
XX
CC   MarinerN1_CI is a family of nonautonomous elements related to the 
CC   mariner/Tc1 superfamily. There are ~100 MarinerN1_CI elements in the 
CC   C. intestinalis genome. The consensus sequence was reconstructed from
CC   70 copies, which are 94% identical to it.
CC   MarinerN1_CI shares similar 48-bp and 33-bp 5' and 3' termini with
CC   Cimi-1. MarinerN1_CI has 28-bp terminal inverted repeats (3 mismatches).
CC   The compact ~120-Mb C. intestinalis genome is a heaven for mariner/Tc1
CC   DNA transposons, they constitute over 5% of the whole genome. 
XX
CC   [1] (Consensus)
XX
SQ   Sequence 1357 BP; 475 A; 211 C; 188 G; 481 T; 2 other;
     tagtacaatg ggggaagatg ggacacttaa gcacatattg ccaaatattt ccaaaatcaa        60
     aatagatgac ggtttttggg taataccacg aattagtact atcattcctt tattaattga       120
     caccaattta ataaaatata ataaaacaca cgaggagtta tttagcgatc cgcacaacar       180
     gtgaaatttt acaaattcga aaacacacag gataagatgg gacagtttaa aatcattgtt       240
     aattttgatt attaagtgta tttataaata ggaatatacg taaataacac gaaataatac       300
     tgtacgcttt gaaaattaag tctaaacatt ctttttcttg ccctactccg gcttactgct       360
     atagttttta acatgttacc tattacatta tattattgca taacaattgg tattgtttga       420
     acgacaatgg gtaatgttcg aacatcaatg gataaatatt gtatcctaca aatgtatatg       480
     aacttgtaat aacagaaaat tgatwataac tattgataaa gtttttattt ttgctacaaa       540
     ttgggtatta ctactctgtt tttggcacaa gccacttctt ataaattatc accaagtgca       600
     aatgaccaaa tttcgaatat attttcaaaa tattatcttt ttattatatc agtatcttat       660
     agttgaataa cccctgaggt ataaattact aaattaaaag caaatctttc aaagtttggc       720
     aatgaaaaca tacaaaacta caatgtgggg gaagatggga ctctaaattg aaatatattt       780
     acattagcag tattctgcaa cttgtagtta acctaccgag tttaacaggc tgtgctagtt       840
     tctttgccat gtaaacttca tatatataac gttaaaccga tatttttttt gttgttttta       900
     tctcaaatta aagtcatatt gacccctgcc tattttcttc atgcttatat ctcagtgttt       960
     ttttttacaa aactaaaact agttttatga gacaaaatca aactgtacga aatattcaag      1020
     gttgttttat gaagctatga aactagttta atcgttcgca cacgcaaact aaaaaaattc      1080
     attggcttta ctatgattta gcgagcatta aaaaatagca ccttactatt tcgcattttt      1140
     tttacctgtt caaagtatac tgtttctatt ttacatattt tttttaatat ttaaaaacag      1200
     taatcagctt tgacgggcgt tttataaagt cgtgataata ctgtcgaata attctgtaac      1260
     cttattttcc tgattatcat taaatggggg tccgtaaaaa gaaaattaaa aaaaaagtct      1320
     cgtctgacaa agtgtcccat cttcccccac cctacta                               1357
//
ID   P-N1_CI   repbase; DNA; CIN; 1036 BP.
CC   P-N1_CI DNA
XX
AC   ;
XX
DE   Nonautonomous DNA transposon P-N1_CI - a consensus.
XX
KW   Nonautonomous DNA transposon, P superfamily; 8-bp target
KW   site duplication; P-N1_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-1036
RC   [1]  (bases 1 to 1036)
RA   Kapitonov V.V., Jurka J.;
RT   "P-N1_CI, a family of nonautonomous P-like
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 116 (2003)
XX
CC   There are ~100 P-N1_CI elements in the C. intestinalis genome, 
CC   they are 97% identical to the consensus, and are characterized
CC   by 8-bp target site duplications.
CC   P-N1_CI is flanked by 30-bp terminal inverted repeats, and it
CC   has subterminal inverted repeats (pos. 88-106 and 978-996).
CC   Putative classification - P superfamily of DNA transposons.
XX
CC   [1] (Consensus)
XX
SQ   Sequence 1036 BP; 346 A; 196 C; 168 G; 326 T; 0 other;
     caaagttagt atagaccaag ttaggaaacg gattgtaaaa caacgagtct tgttatccat        60
     tgtctcgcgt ctatgacgtc atagtcgcca ccattacgga gcccacggca tagcatttta       120
     tcattgctgg gtgctgtttt tcgtttaaat attgcgattt tttaaaaacc aagcacttct       180
     gcgcgtaaaa atggctttct actaatgtta tatcttatca caataataaa cctcacaaaa       240
     ataatcaact tttattgaac actcaatcga ttaaagagta aaaaaacaga aaatatcaag       300
     tttactaacc aaaaacataa aagaacatgt ttaaaatata aaaatacaaa caaaaacgca       360
     taacattacc ataaactggt gtatctagct gcagttttgc atgtaaattg ccgtgatttt       420
     actttttggc tcacaaactt aacacgtata cccggcaacg aaacttaagg tatctttgta       480
     aaatttgcct aatatcgaag tgacattgag gaaaacaata ctgagttact atttttggtc       540
     ctctgcttga attagtaagc taccttttct gcgttccggg tctttatgaa atcggaaaac       600
     gcgaacacct tatctgctag tacttaagca gtttggagct gcatgtccac tcatgttgga       660
     ttataaatgt agtaaagaat ggctctgtag attcgtaggt atgatcatat actattatgt       720
     aaactaagct gattgctgct agtcttaatc gccaacgtaa agtaccctgt taaaccacac       780
     tgtacgccga aaaccagtca aaatattaat ttacttcaca ttaattccta gatttaatat       840
     tatataacaa gatttatatt agaaattata ttttaaatgt taaaacaacc gctatacgtg       900
     ttttctagct ttgtatcgct tacaagaact aaatgaacac atgccgacca tgcatttgta       960
     taggcgattc acgctctgtg ggctccgtaa tggcggacac gagcgccgtt tcctaacttg      1020
     gtctatacta actttg                                                      1036
//
ID   P-N2_CI   repbase; DNA; CIN; 494 BP.
CC   P-N2_CI DNA
XX
AC   ;
XX
DE   Nonautonomous DNA transposon P-N2_CI - a consensus.
XX
KW   Nonautonomous DNA transposon, P superfamily; 8-bp target
KW   site duplication; P-N2_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-494
RC   [1]  (bases 1 to 494)
RA   Kapitonov V.V., Jurka J.;
RT   "P-N2_CI, a family of nonautonomous P-like
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 117 (2003)
XX
CC   There are ~100 P-N2_CI elements in the C. intestinalis genome, 
CC   they are 97% identical to the consensus, and are characterized
CC   by 8-bp target site duplications.
CC   P-N2_CI is flanked by 29-bp terminal inverted repeats.
CC   Putative classification - P superfamily of DNA transposons.
XX
CC   [1] (Consensus)
XX
SQ   Sequence 494 BP; 165 A; 81 C; 87 G; 160 T; 1 other;
     cacagaaata aaaaagaata gaacgcgcat ctctaatgtc ggtaaaggag agagcatgat        60
     acactctctc tttttcacga ctcgttcccg tttactatwg tagtcaatgg aagccagggc       120
     gttttatgta gtttttcttc gttttttgac ttaatttaag tttataggga aaaataacta       180
     tttccaaaca tatatatatt tctaacaaac cgtttgtttg aacgttttta attaaattta       240
     taaaataatt aattttccta aacaagcgct aaagtgtaag cgttaaccta ccaaaaacta       300
     aactggccta ataaactgga atagttagtg tagtttttaa aataaacagc taaaacctcc       360
     taaaatcact gtgcgcctat cttttacaat ggagaccaag cgaaatgggg acggagttgg       420
     cggtcacgtg aatagaaaaa agaatatatc acggttttgg gaagttgcgc gttctactct       480
     tttttatttc tgtg                                                         494
//
ID   piggyBac1N_CI repbase; DNA; CIN; 633 BP.
CC   piggyBac1N_CI DNA
XX
AC   ;
XX
DT   07-JUL-2003 (Rel. 1.00, Created)
DT   07-JUL-2003 (Rel. 1.00, Last updated, Version 1)
XX
DE   Nonautonomous DNA transposon piggyBac1N_CI - a consensus.
XX
KW   Nonautonomous DNA transposon, piggyBac superfamily; TTAA target
KW   site duplication; transposase; piggyBac1_CI; piggyBac1N_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-633
RC   [1]  (bases 1 to 633)
RA   Kapitonov V.V., Jurka J.;
RT   "piggyBac1N_CI, a family of nonautonomous piggyBac
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 118 (2003)
XX
CC   piggyBac1N_CI is a family of nonautonomous elements related to the 
CC   piggyBac superfamily. The consensus was reconstructed from 10 copies
CC   98% identical to it. piggyBac1N_CI elements are flanked by the
CC   TTAA target site duplications, and have 13-bp terminal inverted repeats.
CC   The piggyBac1N_CI family was derived from an autonomous element 
CC   similar to piggyBac1_CI. 
XX
CC   [1] (Consensus)
XX
SQ   Sequence 633 BP; 173 A; 115 C; 120 G; 225 T; 0 other;
     cactttcggc gccaatctac gtatatatac gtttaagtaa caatggttcg cggtgccatc        60
     acacgtatat atacgtttta ccattttttc attgttacga gtgccgcgtt gcatttaaac       120
     taatagtaaa ccacgtatat atacgtacgc tcgatctagg ctgcattgag actaaatgcg       180
     aacgtctgct ttgagattac gttatttttg accaattagc ttgtgactct gcgatcagct       240
     gtttctgacg atttcaagta tattttacgc aatattacta gtttacaatg tttcactgct       300
     gccactgctg gaataattac ggataatggt tcaaacttca atgatttagt gtctgatcat       360
     tacaattatg atgttgtgaa gttttgtttt gtccaattct tattcttacg gctctgaaga       420
     aaagtgaagt tatggataca ttggtagtga tgttatacgt ccacacaaac gggataacat       480
     ggatatgtca ctgtttcttg gattcctgtt gcttactgtt gtataatttg caactttcaa       540
     ttgcaattca tggcttattt aaaatttaat aaaatccaaa attcgtgcgg cacccagtgt       600
     ccgattgttc aaattagtgc ggcgccgaaa gtg                                    633
//
ID   piggyBac1_CI repbase; DNA; CIN; 2216 BP.
CC   piggyBac1_CI DNA
XX
AC   ;
XX
DT   07-JUL-2003 (Rel. 1.00, Created)
DT   07-JUL-2003 (Rel. 1.00, Last updated, Version 1)
XX
DE   Autonomous DNA transposon piggyBac1_CI - a consensus.
XX
KW   Nonautonomous DNA transposon, piggyBac superfamily; TTAA target
KW   site duplication; transposase; piggyBac1N_CI; piggyBac1_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-2216
RC   [1]  (bases 1 to 2216)
RA   Kapitonov V.V., Jurka J.;
RT   "piggyBac1_CI, a family of autonomous piggyBac
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(6) p. 119 (2003)
XX
CC   piggyBac1_CI is a family of autonomous elements related to the 
CC   hAT superfamily. The consensus was reconstructed from 5 copies.
CC   It encodes a 773-aa piggyBac1_CIp transposase (positions 263-1981).
CC   A zinc finger is present at the C-terminus of piggyBac1_CIp.  
CC   piggyBac1_CI has 13-bp terminal inverted repeats and is
CC   flanked by the TTAA target site duplications.
CC   A piggyBac1_CIp-like transposase was also involved in propagation 
CC   of the piggyBac1N1_CI nonautonomous element.
CC
CC   piggyBac1_CIp:
CC   MFSATAAAEILMDAGSDLSDLESDHDEDDNVGSFIVPNVADISDSDSESSDDSLPPPPPPANVWKSSITQ
CC   QSLNSFLGEHGPSSHACVSNDDSPLEYFRLIFTDELLTLVVEETNRYAAQYLQKTPLSSKSRAHNWKPVD
CC   AEELSLFLGLTLLTGIVHKRGKLESYWSKNSMIETPFFGKCMSRNRYQAITGFLHFNDNEKLAENNDNDK
CC   LYKVRPVYDLIVARWKALYNLGEHISIDEGMMKWRGRLGFRVYNKDKPIKYGIKSYILADSHSHYCWNLD
CC   MYHRVQKTLKETVSQILTSKCHFLWHSLYMDNFYNSVSMSQMLLAFQIHSVGTLRSNRGEPREIRTPPNQ
CC   MKKGDIIARQNQSVTVLAWKDKRVVKAISTKHDASVTTITRRQRRGGEKESVEKPVCIADYNLHMSGVDQ
CC   VDQMISYYPCHRKSLKWTKKVFFYFMTISVHNAYILYKSKSSAKSCKTLYSFILTLVSQLCQQDRLQPQI
CC   DDENLAGPPPKSPRIDSTKRLKGGFKKHVIALYLQLKKRQQRKDHVVRAWKTVAERTRYYCAYCNVPLCV
CC   IPCFTKYHACAEF
XX
CC   [1] (Consensus)
XX
SQ   Sequence 2216 BP; 688 A; 442 C; 436 G; 650 T; 0 other;
     cactttcggc gccatcctac gtaaatatac gtttaagcaa caatggttcg cggtgccatc        60
     acacgtaaat atacgtttta caattttttc tttgttacga gtgccgcgtt gcgtttaaac       120
     taatagtaaa ccacgtatat atacgtacgc gcgatctagg ctgcattgag actaaaactg       180
     aagtctgcta cgagactatt ctttttcgat cagctgtctg ctacactttc acataaaaaa       240
     aatactttct acataatcca caatgttttc cgctactgct gctgctgaaa tactcatgga       300
     tgctggttca gacttgagcg atttagagtc tgaccatgac gaagatgaca acgtgggcag       360
     ttttattgta cccaatgttg cggatatttc cgattccgat agtgaatcta gtgatgattc       420
     cctaccacca ccaccaccac ctgcaaacgt ctggaagtca tccatcaccc aacaatcttt       480
     gaactccttt ttgggagagc acggtccatc ctctcacgct tgtgtcagta atgacgatag       540
     cccattagaa tattttagac tgatatttac tgacgaactt ttgaccttgg ttgttgagga       600
     gaccaatcgg tatgctgctc agtaccttca aaaaacgcct ctttcctcca agtctagagc       660
     acataattgg aaaccggttg atgctgagga attgtctttg tttcttgggc ttactctgct       720
     aactggcata gtccataaac gtggaaaact ggagtcttat tggagcaaaa attcgatgat       780
     tgagacgcca ttttttggta aatgtatgtc cagaaaccga taccaagcca tcaccggatt       840
     tttacatttc aatgataacg aaaaacttgc ggaaaataat gataatgata agctatacaa       900
     agttcgtccc gtttatgatc tgatcgttgc taggtggaag gctttatata acttgggcga       960
     acacatttcc attgatgaag gtatgatgaa gtggaggggc aggcttgggt ttagagtgta      1020
     taacaaagat aagccaataa aatatggaat aaaatcatac attttagctg attcacattc      1080
     acactactgc tggaacttag atatgtacca ccgagttcaa aaaacattga aagaaactgt      1140
     ttcgcaaata ttgacatcga aatgccactt tttatggcac agcttgtata tggacaattt      1200
     ctacaacagt gtttccatga gtcaaatgct tcttgcgttt caaatacact ccgtgggaac      1260
     actgcgcagc aacagggggg aaccacgtga aattcggact ccaccaaatc aaatgaaaaa      1320
     gggggacatc attgcgaggc aaaatcaaag tgttacggtt ctagcttgga aagataaaag      1380
     ggtggtaaag gctatttcaa caaagcatga tgcttctgtc acaacaatca caagacgaca      1440
     gagaagaggg ggtgaaaagg aatcggtgga gaaaccagta tgcattgcgg actacaatct      1500
     gcatatgtct ggagtggacc aggtagatca gatgatttct tattatcctt gccaccgtaa      1560
     atcgctcaaa tggaccaaga aagttttttt ttattttatg acgattagtg ttcataatgc      1620
     atacatttta tacaaatcca aatcttcggc aaaatcttgc aaaaccctat acagcttcat      1680
     tttgacactt gtaagccaac tgtgtcagca ggacagactg caacctcaaa tagatgatga      1740
     gaacctggct ggtccaccac ccaagtcacc acgcatcgat tcaacaaaac ggctgaaagg      1800
     aggtttcaag aaacacgtca tcgcgttgta cctccaacta aaaaaaaggc agcagcgcaa      1860
     agaccatgtc gtgcgtgcat ggaaaacggt tgcagaaagg acacgatatt attgtgcata      1920
     ctgcaatgta ccgctttgtg taataccatg cttcacaaaa tatcatgcat gtgctgaatt      1980
     ttaaataaaa aaaatatttt cgtttttttt gttttttttt cgtttttttt tcgttttttt      2040
     tttgtttaat ttcgttttat ctttcttttc tttccttttt taacaattat ttcgtggaat      2100
     tttaaataaa atattgaatt ttgttcgaat tgtcgcataa aaaaaaaaaa aaaaattgat      2160
     gaaaaagtgc ggcaccgcgc gaccaaacgt tccaaaacaa agcggcgccg aaagtg          2216
//
ID   Merlin1_CI repbase; DNA; CIN; 1791 BP.
CC   Merlin1_CI DNA
XX
AC   ;
XX
DT   05-AUG-2003 (Rel. 1.0, Created)
DT   05-AUG-2003 (Rel. 1.0, Last updated, Version 1)
XX
DE   DNA transposon Merlin1_CI - a consensus.
XX
KW   DNA transposon, Merlin/IS1016 superfamily; 9-bp TSD; Merlin1m_CI;
KW   Merlin1_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-1791
RC   [1]  (bases 1 to 1791)
RA   Feschotte C., Wessler S.R.;
RT   "Merlin1_CI, a family of Merlin/IS1016-like
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(5) p. 93 (2003)
XX
CC   The Merlin1_CI family is one of the founding members of a new 
CC   superfamily of eukaryotic DNA transposons related to the IS1016 
CC   group of bacterial insertion sequences. There are at least 3 copies 
CC   of Merlin1_CI containing large ORFs in the C. intestinalis draft 
CC   genome sequence (WGS assembly 1.0, 116.7 Mb). The sequence below 
CC   is a consensus constructed from these 3 copies. Merlin1_CI has been
CC   recently active because the three copies are ~94-98% similar to the 
CC   consensus. Merlin1_CI are related and have probably provided the 
CC   transposase to a large family of nonautonomous elements (Merlin1m_CI, 
CC   see description in RR). The Merlin1_CI consensus sequence is 1791-bp 
CC   long with 155-bp TIRs (8 mismatches). It contains one predicted gene 
CC   (positions 518-1435), which can encode a 273-aa protein, Merlin1_CIp. 
CC   The C-terminal half of this protein has strong similarity with the 
CC   putative transposases of IS1016 from Haemophilus influenzae (and 
CC   related IS) and with ORFs from a wide range of eukaryotes, including 
CC   other ascidians (annotated transposase, GenBank AAM76104), nematodes, 
CC   flat worms, mosquito (described previously in the AF293351 GenBank locus
CC   as an IS1016-like insertion), zebrafish, Xenopus and humans. Many of 
CC   these ORFs are clearly parts of transposable elements. 
CC   Multiple alignments reveal that the most conserved domain 
CC   of these proteins contains a putative DDE motif  (D(60)D(36)E in 
CC   Merlin1_CIp). A HTH DNA-binding domain is predicted in the N-terminal 
CC   region of Merlin1_CIp. Thus, this protein is likely to represent the 
CC   Merlin1_CI transposase. Merlin1_CI elements create a 9-bp TSD upon 
CC   insertion, unlike most other members of the Merlin/IS1016, which 
CC   create an 8-bp TSD. There may be other lineages of Merlin transposases 
CC   in Ciona intestinalis. 
CC   
CC   Putative Merlin1_CIp transposase: 
CC   MQKDFEGENSESLPCIRCKSCGTYVSPRKNSFFAFMDNRNRANVKISYKQVMAILINWVQRVPVGTTQQ
CC   NYGFGAHTVTDWYNFCREMCMLGFSKREPMGGPNTIVEIDESLLRGKRKYNRAGIEGPWIFGMCHVTVD
CC   SEGARSTQEVRFFHVLRRDKQTLLPIIQNEVLPSTTIHSDQWAAYTGLDQLGYSHQSVNHSENFIDPQT
CC   GAHTQTIESTWHHMKTTLLRNMRGVEPELLDSYLAELWARKLYRDHAALLEKLFDWIVEAYPIRNI
XX
CC   [1] (Consensus)
XX
SQ   Sequence 1791 BP; 504 A; 380 C; 393 G; 508 T; 6 other;
     ggtaatcctg ccgctggtga ccagtgaaaa ttttggtctc aaaatgttcc ttacgtctct        60
     ctgatactcg ctgtatatat ttaaaaaaaa caaactcggg cgttcgtatc gaaaattaac       120
     tttgaaaatc cgcgaaaaac tgctgcgtca ccgtactcgc ctgtgctgaa caaaatcaac       180
     gaatatatgg ttacattatg acgtcacata gtagttacgt caaaatgatg gaaaatccgt       240
     tctgttacgt cataatacaa ccctaaatat atataccggt ccacgtgttg cgaaactcct       300
     ttttttgctc aaaattttaa cttgtactct ataacgatgg cattttttcc acacatgcaa       360
     gccattattg cggatgcaga caaattacaa ggttacttac tagaaaaaaa tcttatacgg       420
     ggtccatctt cttttgatcg atgcccgaac cgaagttgtc gcaagagtat actcttgttt       480
     ggggtagccg gcggagaccc ctgaacgcag caagctcatg caaaaagatt ttgagggcga       540
     gaactcagaa tctttgccgt gtattcgatg caaatcttgc ggcacgtatg tttccccgag       600
     aaaaaattca ttttttgcct ttatggataa ccggaaccgt gccaatgtta aaatcagcta       660
     taagcaggtt atggccattt taattaactg ggtgcaacgg gtacccgtcg gcacaacgca       720
     acagaactat ggttttggcg cacacacagt tactgattgg tataatttct gtcgagaaat       780
     gtgcatgctg ggatttagca agagagagcc catgggaggt ccaaacacga tcgtggaaat       840
     tgatgagtct cttcttcggg gcaagaggaa gtataaccgt ggcaggttac ttcgtggtga       900
     cgtccgagaa gacgatgtca atgacacgga cgatgaggac ctggtcgcgc atgtatctga       960
     cgcccgcaat tacggttcca ggatcgaagg accatggatt tttgggatgt gtcatgtcac      1020
     cgtcgactcg gaaggggcaa ggtctacaca agaagtgcgt ttttttcacg ttttaaggcg      1080
     tgataaacag accttgctcc caatcattca aaacgaagtc ctccccagta ccaccataca      1140
     ctccgatcaa tgggcagctt acactggatt ggaccagctc gggtattcgc accagtctgt      1200
     caatcacagc gagaacttca ttgatccgca gactggcgca cacacacaga ccattgagtc      1260
     cacgtggcac cacatgaaga cgacactact ccgcaatatg cgaggtgttg agcctgagtt      1320
     actggattcc tatttggcag agctttgggc aagaaagttg taccgcgacc acgccgcatt      1380
     attggagaag ctttttgact ggatcgttga agcttatccg atccgcaata tttaattttt      1440
     ttatttattt tttttatttt gaacagttct ttttagagct acgagccttc gggttcactt      1500
     ttaaacaagt atttatgaaa taagattagt tatttgcgct akttcacgca ataagacaag      1560
     ttttctattg tgacgtcata gttgtattgt gacgttaaaa acbgcctttt acttataggt      1620
     aaacaatatg gcgcatgcaa ttacggtgac gcagcagttt ttcgcagatt ttcaaagtta      1680
     attttcgata cgaacgcccg agtttttttt aaaatataca gcgagtatcw gggagwcgta      1740
     agraayattt tgagaccaaa attttcactg gtcaccagcg gcaggattac c               1791
//
ID   Merlin1m_CI repbase; DNA; CIN; 605 BP.
CC   Merlin1m_CI DNA
XX
AC   ;
XX
DT   05-AUG-2003 (Rel. 1.0, Created)
DT   05-AUG-2003 (Rel. 1.0, Last updated, Version 1)
XX
DE   Nonautonomous DNA transposon Merlin1m_CI - a consensus.
XX
KW   Nonautonomous DNA transposon, Merlin/IS1016 superfamily; 9-bp TSD; 
KW   Merlin1_CI; Merlin1m_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-605
RC   [1]  (bases 1 to 605)
RA   Feschotte C., Wessler S.R.;
RT   "Merlin1m_CI, a family of nonautonomous Merlin/IS1016-like
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(5) p. 96 (2003)
XX
CC   Merlin1m_CI is a family of nonautonomous elements related to the 
CC   Merlin1_CI family. There are ~250 Merlin_Ci1m elements in the C. 
CC   intestinalis draft genome sequence (WGS assembly 1.0, 116.7 Mb). 
CC   The sequence below is a consensus constructed from 20 copies 
CC   extracted from the database. Elements can be grouped into subfamilies
CC   that range in size from 400 to 700 bp and have 90-99% similarity to 
CC   the consensus. Some subfamilies have recently expanded because 
CC   they are very homogeneous in length and sequence. The Merlin1m_CI 
CC   consensus sequence is 605-bp long with 155-bp TIRs (5 mismatches). 
CC   The TIRs are almost identical to those of the Merlin_Ci1 consensus, 
CC   but the internal 295 bp are of unknown origin. Like Merlin1_CI, 
CC   Merlin1m_CI elements create a 9-bp TSD upon insertion. 
XX
CC   [1] (Consensus)
XX
SQ   Sequence 605 BP; 170 A; 109 C; 132 G; 184 T; 10 other;
     ggtaatactg ccgctggtga ccagtgaaaa ttttggtctc aaaatgttcc ttacgtctcc        60
     ctgatactcg ctgtataatt ttttttwaaa aaactcgggc gttcgtatcg aaaattaact       120
     ttgaaaatgc gcgaaatcgt gctgcgtcac cgtattttcc acacgagccg tcaaaggtta       180
     gattatkacg tcatagaatg cgtattacma cctttgattt cwacgttaca gattacgtaa       240
     tttgttagtt tttttrgatt tagrggttrs gggttaaamg taggggttag ggttgggtta       300
     agggttaggg cttggggttt tccctagcat aaaacagtgc gaaaaacaag attataacgt       360
     gctgtaacgt acgtaatatg tcactactgt gacgtaacat atcgctattg tgacgtaata       420
     aatcgttaac cttacgcaag tcaggcgaat tacggtgacg cagcacgttt tcgcgcattt       480
     tcaaagttaa ttttcgacac gaacgcccga gttttttcwa aaaaaaatta tacagcgggt       540
     atcagggaga cgtaaggaac attttgagac caaaattttc actggtcacc agcggcagta       600
     ttacc                                                                   605
//
ID   Cics-1    repbase; DNA; CIN; 298 BP.
CC   Cics-1 DNA
XX
AC   ;
XX
DE   tRNA-derived SINE - a consensus sequence
XX
KW   nonautonomous non-LTR retrotransposon; SINE; Cics-1.
XX
OS   Ciona intestinalis
CC   sea squirt
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-298
RC   [1]  (bases 1 to 298)
RA   Simmen M.W., Bird A.;
RT   "Sequence analysis of transposable elements in the sea squirt, Ciona
RT   intestinalis.";
RL   Mol. Biol. Evol. 17, 1685-1694 (2000)
XX
CC   [1] (Consensus)
XX
SQ   Sequence 298 BP; 87 A; 71 C; 73 G; 65 T; 2 other;
     gtccggcgcc gtggcaaagt ggttagcgcg cgtgcctcta acccagaggt aatgggttca        60
     aggctcgtcg ctgctaccat tgtgggcgta tgtgtccttg ggcaagacac ttaacggcaa       120
     ttgctccaac ccagtggtca ctaatgggtt gtccaaatta tcagccatac ataaaaaaaa       180
     aaaaaaaata atcacccaca aagttacata cgtggtaact cgtaagcngg cacgaggtgt       240
     atgaaacaga acacccgtgt tataacgact gtcgttttcc ngccacgcga ggataaag         298
//
ID   Cigr-1-I  repbase; DNA; CIN; 3736 BP.
CC   Cigr-1-I DNA
XX
AC   Z83760;
XX
DE   Internal portion of the Cigr-1 gypsy-like LTR retrotransposons - 
DE   a fossilized copy.
XX
KW   LTR retrotransposon; gypsy superfamily; protease
KW   reverse transcriptase; integrase; RNaseH; Cigr-1; Cigr-1-LTR; Cigr-1-I.
XX
OS   Ciona intestinalis
CC   sea squirt
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-3736
RC   [1]  (bases 1 to 3736)
RA   Simmen M.W., Bird A.;
RT   "Sequence analysis of transposable elements in the sea squirt, Ciona
RT   intestinalis.";
RL   Mol. Biol. Evol. 17, 1685-1694 (2000)
XX
CC   Cigr-1 is a gypsy-like LTR retrotransposon.
CC   Cigr-1-I is an internal portion of Cigr-1.
CC   Long terminal repeat is deposited as Cigr-1-LTR.
XX
DR   GENBANK; Z83760.
CC   Positions  34429  30694  Accession No Z83760  GenBank
XX
SQ   Sequence 3736 BP; 1099 A; 824 C; 847 G; 966 T; 0 other;
     tagtttaaat aaacaaggtc tcgacaattt atttaacata acaaatggat caaaagatac        60
     ttcgaccaaa ggagttgtcg gtggaaccct cgtcagtaga tgcagctaaa gtttttaagt       120
     tttggttacg gacggttgaa gatttcatat catcgctaag tgaaagtcaa agttcttcct       180
     cggcgattaa caagaagcgg atagtcataa gttgtttgtc gcccgatgtc tatccgtatg       240
     ttgaagaagc agaatcctat gaagagatta tccgaaccct ccgaagtgtc tacatcaaaa       300
     agaaaaacaa tatatattcg cgctatttgc ttctcagtag gcaacaatcg cctgaagaaa       360
     gtattccgga atacatacaa gaattaaagt cgctctcaag acaatgcgaa ttcactgcag       420
     tagaagccaa tcagtatcgg gaggaactga ctcgagatgc ctttattgac ggactttctt       480
     cttctgtcat ccgacagcgt ttactggagg tagattcctt ggacttgatg aaagcgtttg       540
     aacttgcgga tagtctggac cgtgcgcaga agtattccac atctatggga cgaaacgccg       600
     cacccacgcc gtcttatgct gcatctgccc cacagcacca acacgaacca aaacgatctg       660
     ccccacagca ccaatacgaa gaaactgtat gtcgacagca ggtccgaggt aaatgtatct       720
     tttgcggtgg ttttgcgcat agtcggacca attgtcccgc cagaaatgaa gactgtttta       780
     aatgtggaag acgcggacat ttctctagag catgccgaag tgcacgatat gggaaccgag       840
     ttaggatgat ggctatggat aagcaagatg aggatcagcc atatcttgct gtaatgcaaa       900
     ctccttcagt agtagctggg gcgccagatt gccttggtcc cgccgtggta gatgcgattg       960
     tgaaaggtca atccattaaa gttctcctcg attccggtgc ctccgataat ttcttgaaca      1020
     aaaaagtagc tcaccgactc aatttacgtg tagaaaagtc gtctgcggtt atcggcatgg      1080
     ccacaaatgg actatcagct acaactcaag gaagggcatc ggcttcaatc tctttgttgg      1140
     gacgtgatta cacaaacgtt ccattccagg tactagacgg tttgtgcgcg gatattatct      1200
     tgggtcacaa ttttatgtgt cggcattctg aagttatttt taaaatgaat ggcccgcgac      1260
     gtcctctgac gatccctcct ctccaaaaag cagtgttagg tcttttggct gcaaaagtag      1320
     accctcctga cctctttagg cacatgcggc caaactggaa accgctggta acccgatcac      1380
     gtcgatatag taaggaggat ctaggattca tcagccatga ggtgaaacgg ttgcttgaag      1440
     aggaaattat tgaaccatcc aattcaccat ggagagcaca ggttctggtg gctcgcgagg      1500
     gatcaaagaa accaaggatg gtaattgatt attcacaaac ggtgaatgta tttacagagc      1560
     tagacgccta tcccttgcca tcaatcgagt ccatagttaa caaggtgact caagataagg      1620
     tttactcctc cttggatctg agatctgcgt atcaccaaat cccgttgaaa gactcagatc      1680
     gacccttcac cgcctttgaa gcagaaggtc agttatatca gtacaaacgc ctaccttttg      1740
     gggtcacaaa tggagtatct gcgtttcaac gaataataaa tcgattcata caagacaatc      1800
     atttaaataa ggtatatgcg tatttggatg acataactgt tacaggagag acattggagg      1860
     agcatgatag aaatttaaag aaattgttag tggctgcgaa aaggcataat ctaaccatca      1920
     atgaagagaa gtccaaactt cgaatgacca gtattgactt tctcggctac cggatctctt      1980
     acggtgatgc acgtcctgat ccggaacgcc tacgccctct cctaaatcta ccgccaccag      2040
     atacaccccg agagttgaaa cgtattcaag gtatgtttgc ttattatgcg aaatggatct      2100
     cgaggttctc acacaaaata caacctttac tttgtataaa gaagtttcca ctaacaaaag      2160
     atgcacttgt ttgttttgaa accttaaaaa cagagctggc ggctgcaagc ttaggagcca      2220
     ttagaagtga agagccccta caagtcgaaa cggacgcatc ggattacgca attgctgcag      2280
     ttctttccca atccgggcgc ccagtggcgt acatgtctcg aactctaaac acgtgtgaac      2340
     ggaactatcc cgcgatcgag aaagaggcga cggcggtggt agaagcggtt cggaaatggt      2400
     cacattttct taaaggtaaa tcttttacgt tggttacgga ccagaggtct gtttcgttta      2460
     tgttcgacca aagaaaccgg ggtaaaataa aaaactccaa aattctaatg tggcgattag      2520
     agctgagtca gttcacctat gacatagttc atagaccggg acgtgataac ttcgtcccag      2580
     atgcgctgtc ccgagtgaat gctcttaatc gtgatttgaa ggaactccaa acgctgcaca      2640
     ataatctagg gcatccaggt ttttcaagat tgtaccactt tattaaaact cgtaatcttc      2700
     ccttctctag tgaagaagct aagattattt gtcggcaatg taaaacgtgc gccgaagtta      2760
     agccaaggtt ctacaaacca gcttctcgga atctgattaa agcaatgaga ccatgggaga      2820
     gattgagcat ggattttaaa ggacctgtca aaggtcgcaa tagctattta cttatcatcg      2880
     tcgatgagta tagccgcttc ccgtttgtat ttccttgtaa aagaatgact tccgcggttg      2940
     tcatacagtg tctcacgaat ttattttgtt tatttggctt tccagcttac gtacattcgg      3000
     atcgtggatt gtcgttcatc agccatgaag tgaaagtttt tctgacggag cgtgggattg      3060
     caaccagcaa atctacacca tatcaccctc aaggtaattc tcaatgcgaa cgcgtcaatc      3120
     aaaccatttg gagaactgtt aaactacttc tgcacgggaa acttatggcc gaggaacagt      3180
     gggaggaagt cttaccccag gcgcttcatg ccattcggtc tttggtgtgc ctagccacca      3240
     atgaaactcc acacgaacgt ttttttaatt tttccagacg ttcaatgaca gggacaacgc      3300
     tacccacatg gttgctgaca aaaggtcctg tgcttttgcg aagattcgta agaacgaagg      3360
     gtgatccgct atgtgaccag gtcgagttgt tggacgccaa ccctacatac gcgaacataa      3420
     gacatccgga tggacgggaa acgactgttt caacttctga cctcgccccg taccccagca      3480
     ttgagccaac ggatccggac agaaatgaac atgtaacgag tgaacgattc gaaactcagg      3540
     aagggaccgc caatgaacaa accggtgaca gtgaaagatc tgaaatcatc gaacccagca      3600
     acgaaacgac gtacgaggtg ccattacgtc gatcgacacg gcaaagaaaa gaaccccagc      3660
     gctacgggtt ttaaaccgcg tattaatcct gttatttgta ttgtaatttg ttaaaacaaa      3720
     attttgtggg gaagaa                                                      3736
//
ID   Cigr-1-LTR repbase; DNA; CIN; 245 BP.
CC   Cigr-1-LTR DNA
XX
AC   Z83760;
XX
DE   Long terminal repeat of the Cigr-1 gypsy-like LTR retrotransposons - 
DE   a fossilized copy.
XX
KW   LTR retrotransposon; gypsy superfamily; 
KW   Cigr-1; Cigr-1-I; Cigr-1-LTR.
XX
OS   Ciona intestinalis
CC   sea squirt
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-245
RC   [1]  (bases 1 to 245)
RA   Simmen M.W., Bird A.;
RT   "Sequence analysis of transposable elements in the sea squirt, Ciona
RT   intestinalis.";
RL   Mol. Biol. Evol. 17, 1685-1694 (2000)
XX
CC   Cigr-1 is a gypsy-like LTR retrotransposon.
CC   Cigr-1-LTR is a long terminal repeat of Cigr-1.
CC   Internal portion is deposited as Cigr-1-I.
XX
DR   GENBANK; Z83760.
CC   Positions  30693  30449  Accession No Z83760  GenBank
XX
SQ   Sequence 245 BP; 54 A; 47 C; 46 G; 98 T; 0 other;
     tgtgaagcat tccacaaacg gcaacactgt gtgcggcgcg cgccgctaat gattactttc        60
     gtgtgttcct tcttttgttc gccacgtttc accatttgtg ttaactcccg tctttcagtt       120
     gcagtgttac tgtttgaatt agcttactga gtttagtgat atcatttccg ttgttaattt       180
     aatctatatc taatattcta tttgtttaag gtcgtagtta cgttatgtta aataaagcct       240
     aagtt                                                                   245
//
ID   Cili-1    repbase; DNA; CIN; 420 BP.
CC   Cili-1 DNA
XX
AC   ;
XX
DE   Cili-1 is a non-LTR retrotransposon - a partial sequence.
XX
KW   non-LTR retrotransposon; L1 superfamily; Cili-1.
XX
OS   Ciona intestinalis
CC   sea squirt
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-420
RC   [1]  (bases 1 to 420)
RA   Simmen M.W., Bird A.;
RT   "Sequence analysis of transposable elements in the sea squirt, Ciona
RT   intestinalis.";
RL   Mol. Biol. Evol. 17, 1685-1694 (2000)
XX
DR   GENBANK; AJ226259.
CC   Positions    421  2  Accession No AJ226259    GenBank 
XX
SQ   Sequence 420 BP; 151 A; 88 C; 86 G; 95 T; 0 other;
     gtccctaaac tcaccacaga cgaatctaat agtattgaaa ccgaactctc ggagaacgag        60
     ctgttcagcg ctctgtgcca gataaaaaat aataaagcgc cgggtttaga tggtctgccg       120
     agcgaattct ataaaacttt ttggtcagat ataagcagca cgtttgcgaa caacgtaaaa       180
     tactcaatgg tgaaaggaac cctgagtgaa acacaacgga aaggagtgat aacgctgatc       240
     ccaaaatcaa cggaagaacc aattcacccg aataatctac gcccgatcac gctgcttaat       300
     gttgactata aaataatctc gaaagctatt aacgagaaaa ttaagatata tttgccctcg       360
     ctaataagtc cagaccagag tggcttcatc aagggtcggt atattggaga caatataaga       420
//
ID   Cili-2    repbase; DNA; CIN; 332 BP.
CC   Cili-2 DNA
XX
AC   ;
XX
DE   Cili-2 is a non-LTR retrotransposon - a partial sequence.
XX
KW   non-LTR retrotransposon; LOA superfamily; Cili-2.
XX
OS   Ciona intestinalis
CC   sea squirt
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-332
RC   [1]  (bases 1 to 332)
RA   Simmen M.W., Bird A.;
RT   "Sequence analysis of transposable elements in the sea squirt, Ciona
RT   intestinalis.";
RL   Mol. Biol. Evol. 17, 1685-1694 (2000)
XX
DR   GENBANK; AJ227045.
CC   Positions    1  332  Accession No AJ227045    GenBank 
XX
SQ   Sequence 332 BP; 91 A; 86 C; 83 G; 72 T; 0 other;
     catctgcata aacttaaaaa aagtgagagt cccatctgcc ctgtctgtga cgaggaagat        60
     gagacatcct ttcattatgt tggcatatgt ccagcatatg cgaacgcaag acgggagcat       120
     ctaaacttga ccgagctgtc aagggaagat ctcccatcca tcaccattaa agcccttgtc       180
     gcctaccttc ggggaagcgc caggctcctt aaactgggaa ggtccatgca gtagcacccc       240
     gggtgttggg gtaatgggtc aattatggcc taaatcctag ggcccatggc gtgccacgct       300
     gcgggacctc acccacatag aatagaatag aa                                     332
//
ID   Cimi-1    repbase; DNA; CIN; 193 BP.
CC   Cimi-1 DNA
XX
AC   ;
XX
DT   05-AUG-2003 (Rel. 1.0, Created)
DT   05-AUG-2003 (Rel. 1.0, Last updated, Version 1)
XX
DE   Cimi-1 is a nonautonomous mariner-like DNA transposon - consensus.
XX
KW   nonautonomous DNA transposon; mariner superfamily; Cimi-1.
XX
OS   Ciona intestinalis
CC   sea squirt
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-193
RC   [1]  (bases 1 to 193)
RA   Simmen M.W., Bird A.;
RT   "Sequence analysis of transposable elements in the sea squirt, Ciona
RT   intestinalis.";
RL   Mol. Biol. Evol. 17, 1685-1694 (2000)
XX
CC   [1] (Consensus)
XX
SQ   Sequence 193 BP; 59 A; 35 C; 42 G; 57 T; 0 other;
     tagtagggtg ggggaagatg ggacaccttt agcacataat atccaaatat cctgatcgtg        60
     ttttaaacaa ttaacaacgg tctatgggag tcgtgaggat acggttttat aattctttga       120
     atgttctttg tttactacca aatgggacga gaaaatagaa tgaaaaggtg tcccatcttc       180
     ccccacccta cta                                                          193
//
ID   Foldback1N_CI repbase; DNA; CIN; 2444 BP.
CC   Foldback1N_CI DNA
XX
AC   ;
XX
DT   05-AUG-2003 (Rel. 1.0, Created)
DT   05-AUG-2003 (Rel. 1.0, Last updated, Version 1)
XX
DE   Foldback1N_CI is a nonautonomous DNA transposon - consensus.
XX
KW   nonautonomous DNA transposon; Foldback1N_CI.
XX
OS   Ciona intestinalis
CC   sea squirt
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-2444
RC   [1]  (bases 1 to 2444)
RA   Simmen M.W., Bird A.;
RT   "Sequence analysis of transposable elements in the sea squirt, Ciona
RT   intestinalis.";
RL   Mol. Biol. Evol. 17, 1685-1694 (2000)
XX
DR   GENBANK; 1764010.
CC   Positions 18327  20770  Accession No 1764010     GenBank 
XX
SQ   Sequence 2444 BP; 828 A; 441 C; 407 G; 768 T; 0 other;
     ggtaccagat aatctcatac cgctgcaggt caccgttgcc tttttccttt gcgtttctct        60
     cgtttaacaa ttggttgatt atgtcgtcag ttaggtaact gtgtgtccca cgaataatat       120
     acgagtcaag agtctgacag ttgcaggtcg tttttttaaa gtagtcttac agtttcaggt       180
     cgtttttata cagtagtctt acagttgcag gtcgtttttg taaagtagtc tgacagttgc       240
     aggtcgtttt tataaagtag tcttacagtt gcaggtcgtt tttataaagt agtctgacag       300
     ttgcaggtcg tttttataaa gtagtcgtac agttgcaggt cgtttttata aagtagtctt       360
     acagttgcag gtcgtttttg taaagtagtc tggccgtttt tataaagtag tcgtacagtt       420
     gcaggtcgtt tttataaagt agtcgtacag ttgcaggtca tttttataaa tcagtcctac       480
     agttgcaggt cgtttttata aagtagtcgt acagttgcag gtcgttttta taaagtagtc       540
     ttacagttgc aggtcgtttt tgtaaagtag tctggccgtt tttataaagt agtcgtacag       600
     ttgcaggtcg tttttataaa gtagtcgtac agttgcaggt catttttata aatcagtcct       660
     acagttgcag gtcgttttta aaagcagtct tacagtccta cacagttttt ttgtttcatc       720
     tataaatttt gtaacatcat tccagtttgg atgcaattca caaatttgaa acagacacag       780
     ttacaaaatt tgatgttttt attttagaat tctgaaactt ttattacaaa attacctatt       840
     tgcattttac agatgtaaaa aatgtaaagt tcagtttggt tctaaagatg gtattccatt       900
     tgtttgtaaa tcctatacaa aactggaatg tcagcatttg gaccaaacag agcaattgaa       960
     actccatctg taaatatttg tggttcatga acttttccaa aacgctacac ctccacagtc      1020
     aactaacaga agattctttc caacaaaaaa acgacattag caatcactat cattgtatca      1080
     tattgcatat acaaagcaca agctgtcaaa aattgatgaa ccagatgatg ttcaattcct      1140
     ggtggtccca tggtgtcaac aaatcacctg aagatagcat atttccttta ggccgtacat      1200
     tgccagtgtc agtccgaaac agccagatag tgacatggtc attgctgatt ttcgcttgtt      1260
     ttattctaga aaaatatcaa agatgaacaa cagtgtatat ttacaactta caacacaagt      1320
     ttaaaattaa tgacttacga ttttgatctc tttttttatt tttaaagtgc ccagcggcac      1380
     cccctttgct tgggccgatt tgatcggaag tcgaaatttt gttccatcta aaaatttatg      1440
     caaaaaatgt attacacacc acaccctctc gcatgagaaa attgttaatg tatttgttgg      1500
     taagatataa ttaagagtac tataaaattg caaatataaa aaaatgataa taaaacatgc      1560
     ttttaaatac caacaacagt ggccaaatta aaacaaatac caataacagt ggccaatact      1620
     tacattttta aataacaatt tgattgtaac atatgttctg taataataat aaaaagaaac      1680
     ggttgggcaa tttaaacatc aacaaatata taattggaaa ttggaatgat attacaaaat      1740
     ttgtagatga aacaaaaaac tgtaagacta ctttataaaa acgacctgca actgtaagac      1800
     tactttataa aaacgacctg caactgtaag actactttat aaaaacgacc tgcaactgta      1860
     agactacttt acaaaaacga cctgcaactg taagactact ttacaaaaac gacctgcaac      1920
     tgtaagacta ctttataaaa acgacctgca actgtaagac tactttacaa aaacgacctg      1980
     caactgtcag actactttat aaaaacgaca tgcaactgtc agactacttt acaaaaacga      2040
     cctgcaactg taagactatt ttataaaaac gacctgcaac tgtaagacta ctttataaaa      2100
     acgcgacctg caactgtcag actactttat aaaaacgacc tgcaactgtc agactacttt      2160
     ataaaaacga cctgcaactg taagactact ttacaaaaac gacctgcaac tgtcagacta      2220
     ctttataaaa acgacctgaa actgtaagac tactttataa aaacgacctg aaactgtaag      2280
     actactttaa aaaaacgacc tgcaactgtc agactcttga ctcgtatatt attcgtgggc      2340
     acacagttac ccaactgacg acataatcaa ccaattgtta aacgagagaa acgcaaaaga      2400
     aaaaggcaac ggtgacctgc agcggtatga gattatctgg tacc                       2444
//
ID   Penelope1_CI repbase; DNA; CIN; 2803 BP.
CC   Penelope1_CI DNA
XX
AC   ;
XX
DT   06-NOV-2003 (Rel. 1.0, Created)
DT   06-NOV-2003 (Rel. 1.0, Last updated, Version 1)
XX
DE   Penelope-like non-LTR retrotransposon - a consensus.
XX
KW   non-LTR retrotransposon, Penelope superfamily; reverse transcriptase; 
KW   Penelope1_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-2803
RC   [1]  (bases 1 to 2803)
RA   Kapitonov V.V., Jurka J.;
RT   "Penelope1_CI, a family of Penelope-like non-LTR retrotransposons
RT   from the sea squirt Ciona intestinalis.";
RL   Repbase Reports 3:(10) p. 187 (2003)
XX
CC   Penelope1_CI is a family of non-LTR retrotransposons from the
CC   Penelope superfamily. Penelope1_CI encodes a 604-aa Penelope1_CIp 
CC   reverse transcriptase (pos. 1-2531, conceptual translation). 
CC   Penelope1_CI retrotransposons usually are 5' truncated. Therefore, 
CC   the consensus sequence is incomplete at its 5' end.
CC   Penelope1_CI is represented in the genome by approximately 1000 
CC   ~1kbp long 3'-end copies. They are 5% divergent from the consensus 
CC   sequence. The ~200-bp 3'-terminus is often repeated and forms 
CC   a palindromic structure.
CC
CC   Penelope1_CIp:
CC   MAWQIESSTGETLSNKDWVMNMSDKELTPAQSVLSLGLNFAVSPDNVPWKQIVASIEKGLVGQPLHIKSL
CC   LQSKLVGCIRSHKTTTTNVPKSYLAAIRELQXKDRSIVILSADKGNRAVVMNRTDYTAKLLELMKDARTY
CC   KKLARNPTPSLERKVNNYVXRLHREREVLSYSEFRQLHCTDGRTPQLYGLPKVHKPDIPLRAIVSFIGSP
CC   SYMLAKFLAKIVAPLIGNNSHHVRNSHEFAAEVRDMTIADGECLVSFDVVSLFTNVPIPLAMLVSGCVLT
CC   LHVLRFRVHSTNKCFGTAMGGSPISVVIANVVIETIEEDALATFMHPPRYWKRYVDDTFAIIAAEQLHPF
CC   LGIEESIQFTLERENEGKIAFLDVEVSRDEEGGMKTYVYRKPTHTNRYLSFWSAHPIEHKKAVVRSLKHR
CC   AEALVSDPLRLQDEMKFIKDGLRYNSYPPWMVKWKPTQKPKEVTPTIATLSLPYVPGLSDTLKRECLPIT
CC   VLRFNSKPHTTLRSLLSHPVENQATEPKGVVYLIPCGDCEEGVYIGETGRALKTRLKEHRRDVAAKDASK
CC   TALSKHSAVCNHRVAFENVQILERETDLTKRLFLETLHIHKHRECVNNKEQCTYFPTVYNNLI
XX
CC   [1] (Consensus)
XX
SQ   Sequence 2803 BP; 789 A; 643 C; 639 G; 732 T; 0 other;
     tggcaaattg aaagttccac tggtgaaaca ctctctaaca aggattgggt catgaatatg        60
     tccgataaag aacttacacc cgcgcagtcc gtattatctt taggattgaa tttcgccgta       120
     tcgcccgata atgtaccgtg gaagcagatc gtagcgtcca tagagaaggg cctcgtcgga       180
     caacccctgc acattaagtc acttttacaa agcaagttgg tgggatgcat tcgtagccat       240
     aagaccacaa ccaccaacgt ccctaaatca tacttagccg ctatacggga attacaaaaa       300
     gaccgttcga ttgttatatt atcggctgat aagggaaatc gtgcggtggt tatgaaccga       360
     acggattaca cagcgaaact tttggaactc ctgaaagacg ccagaaccta caagaagctg       420
     gctcggaatc cgactccttc cttagaacgt aaggtaaata attatgttcg acgtcttcgt       480
     gaggttctat cgtacagtga atttcggcag ctactgtacg gatgggagga caccccagtt       540
     aaagaaggcc tttgcaaggt tggagaaagt gttgaaccat agccttctga cgtcgcttgt       600
     ctgtcatgta aggagaggat caactcgaat cgttgcactg ggagtaaaaa agtgtgatga       660
     caacattgag agatggcgtg gcaaattgaa agttccactg gtgaaacact ctaacaagga       720
     ttgggtcatg aatatgtccg ataaagaact tacacccgcg cagtccgtat tatctttagg       780
     attgaatttc gccgtatcgc ccgataatgt accgtggaag cagatcgtag cgcatagaga       840
     agggcctcgt cggacaaccc ctgcacatta agtcactttt acaaagcaag ttggtgggat       900
     gcattcgtag ccataagacc acaaccacca acgtccctaa atcatactta gccgctatac       960
     gggaattaca aaaagaccgt tcgattgtta tattatcggc tgataaggga aatcgtgcgg      1020
     tggttatgaa ccgaacggat tacacagcca aacttttgga actcatgaaa gacgccagaa      1080
     cctacaagaa gctggctcgg aatccgactc cttccttaga acgtaaggta aataattatg      1140
     tttgacgtct tcacagggaa cgtgaggttc tatcgtacag tgaatttcgg cagctacact      1200
     gtacggatgg gaggacaccc caactgtatg gactaccgaa ggtccataaa ccagatatcc      1260
     cgttacgagc gattgtttct tttattggtt cgcctagcta tatgttggct aagtttctcg      1320
     ccaaaatcgt tgcccccttg attggaaata atagtcacca cgtcaggaat tcacatgagt      1380
     tcgcggccga ggtaagagac atgacaattg cagatggtga gtgtttagtt tcctttgatg      1440
     tggtttcctt attcaccaac gttccgatac ccctggcgat gttggtctcc ggttgtgtct      1500
     taacgctaca tgttttgcgt ttcagggtgc attctaccaa caaatgtttc ggtacagcga      1560
     tgggtggttc gcccatctct gtcgtcattg caaacgtcgt tattgagact attgaagagg      1620
     atgccctcgc tactttcatg caccctcctc gatactggaa gcgctacgtt gacgacactt      1680
     ttgccatcat tgcggcggaa caactccacc cttttctggg aatagaggag tccatccagt      1740
     ttaccctaga aagagagaac gaaggaaaaa tagcgttctt agatgttgag gtgagtcggg      1800
     acgaagaagg aggaatgaaa acctatgtat acaggaaacc tacccacact aatcgctatc      1860
     tatctttttg gtcagctcat ccgatcgaac ataaaaaagc ggtagtaagg tccctaaaac      1920
     acagagcaga ggctttggtg tccgatccac tacgtctaca agatgaaatg aaattcatta      1980
     aagacgggct tcggtacaac tcatacccgc cgtggatggt aaagtggaag ccaacacaga      2040
     aacccaaaga agtaacacct actattgcta ctttgagcct cccgtatgtc ccaggcctat      2100
     ccgacacttt aaagagaatg cttaccgatc acggtattaa ggtttattca aagccgcaca      2160
     caacgcttcg cagcctgtta tctcaccccg ttgagaatca ggcaactgag cccaaggggg      2220
     ttgtgtattt gattccctgt ggtgactgtg aggagggtgt gtacatcgga gaaacgggca      2280
     gagctctaaa aacgcgcttg aaagaacatc gccgagatgt cgcagcaaag gacgcgagca      2340
     agacggctct gtccaagcac tcagctgtat gtaatcaccg agtggcgttt gagaacgttc      2400
     aaattctcga acgggagacc gacttgacca aacggttgtt tttagagact ctacacattc      2460
     acaaacaccg agaatgtgtc aacaacaaag aacaatgcac ctatttcccc acagtttaca      2520
     acaacctgat ataaaatttt tttctgtttc cgatttttca cgtgactgcc gttgtgcgtt      2580
     tttgccctct caccgtctct tccttacagt gcccttatca cgttaatatc gcctttttct      2640
     caccttttct gcttttcgct tgttgtaact gttgcgtttc attccctgat gaagtctcgc      2700
     cgtatggcag acgaaacgtt ggaaatacac tatacgtttt tataccagat gagccactga      2760
     tatattgttt atactatgcc tggtagcaga agtaacagaa tat                        2803
//
ID   R2CIA_CI  repbase; DNA; CIN; 3721 BP.
CC   R2CIA_CI DNA
XX
AC   AB097121;
XX
DT   17-NOV-2004 (Rel. 1.0, Created)
DT   17-NOV-2004 (Rel. 1.0, Last updated, Version 1)
XX
DE   Ciona intestinalis retrotransposon R2Ci-A, complete sequence.
XX
KW   non-LTR retrotransposon; reverse transcriptase; R2CIA_CI.
XX
OS   Ciona intestinalis
CC   Ciona intestinalis
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea;
OC   Enterogona; Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-3721
RC   [1] 
RA   Kojima K.K., Fujiwara H.;
RT   "Cross-Genome Screening of Novel Sequence-Specific Non-LTR
RT   Retrotransposons: Various Multicopy RNA Genes and Microsatellites
RT   Are Selected as Targets";
RL   Mol. Biol. Evol. 21 (2), 207-217 (2004)
XX
DR   DR   Positions   1   3721  Accession No AB097121    Genbank
CC   Positions   1   3721  Accession No AB097121    Genbank
XX
SQ   Sequence 3721 BP; 923 A; 943 C; 1094 G; 760 T; 1 other;
     gactctctat ggtggtcgcc ttctcgtggc gagagtcgta attacctccg gcataactgc        60
     gagccctcac aaggctggca gggactgcgg gagcgaaacc aagaatcacc acgcccgggc       120
     gggctaactc cctgctcggg tgtaaagcga aaccaagaat caccacgccc gggcgggcta       180
     actccctgct cgggtgtaaa atattgttac agaaaataca aataagcaaa gggctgcggc       240
     ctctgccccg gctcacaata taaatatgcc cggttgccaa agcgtagtgg gctcggaatg       300
     ctcccagtgt gggagagttt ttaagaccgc ccgcggtttg agcgtacacc ggaggagtaa       360
     gcatcccgag gcataccacc gggaacatat cgccgcccct agagtgaagg ctcgttggtc       420
     cgaggaggag atgattctga tggctcagnc ggaggtgcaa gcgccagcag gtacacggtt       480
     catcaaccag tatctgcatg cgctatttcc gtctcgatcc cttgatgcca tcaagggagc       540
     cagaggcaag tccgcagctt ataagaagat cattctggag cagcggcttg cagcgctggt       600
     gcctgtaagt cctccaaatc agatcagcgg ggcggaaagc cctagccaac catccaacac       660
     ctcccaggag gtaagacagg atcctgagga gaggtctttg agacttcggg acgcgattga       720
     cttaggtcac ttgcgaaccg acttcgacat gactgcggtg aaccccggtc accccgaccc       780
     ggtaatacgg gaagagattg atcgggagtt cctgcgatgg ctcgaaccca accggcgcag       840
     acgcgggtat gcgaaagcga ctcgcattgc actgaacgcg ccgggaaagg tgaggcgaag       900
     ggcggagtac gccgctatgc agcgacaatg gaaaaccaag agaggtttgt gcgctaggga       960
     ggcgctcgag gggacttgga aaatccctgc gagaaccgtc tcgcttagtg atcaggaggc      1020
     tttttggagg cccctgatgg agagtcagtc aaagaacgat ctaagggagc cagccaaagt      1080
     gggggaaacc ctatgggggc tgttggatcc cataacaccg gacgaggttc ggcagatact      1140
     gggcagtatg tccagtaagg ctccggggcc ggacggccac cggctgtcgg atctcaggtc      1200
     catccctatc gatcaaatct gcagtcactt caatctgtgg ttgctggctg gctaccaacc      1260
     gaaagcgtta aggatgggtg agagctgtct catcccaaag gtgaaggatg cttctagacc      1320
     tcagcagttc cgacccatta ccctgggaag ctatgtaggc aggtgcctgc acaagtgtct      1380
     ggcatcccgt ttcgaacggg atctgcccat ttcgatcaga cagaaggctt tccgatgcat      1440
     ggacggagtt gcagagaacg tcatgatcct gaggagtgtc ttagacgatc acaagaagcg      1500
     acttgctgaa ttgaaccttg tgttccttga tgtaagcaag gcgtttgata gcgtatctca      1560
     ccgttccatc ctacatgctg ttaaaaggct gggcgttccg cccccgttac tcaaatacgt      1620
     tgaggagctg tacgctgact cggagacttt ccttcgaggt tccggcgaac tatcgccctc      1680
     gattaaagtt cgacggggtg taaagcaggg cgaaccgcta tccccccacc tgttcaatgc      1740
     agttatagac tgggcgctct cgtctctcga ccaatccttc ggggttacgg tcggagaagc      1800
     aagggttaat catctagctt ttgcggacga tatagtttta ctatcatctt cgcaacctgg      1860
     tttacaacga ctaatcgatc agctgaccac tcacctgggc gagtctggac tcagagtgaa      1920
     tagcacaaaa tcggcaagca ttcggattgc ggtcgatggc aagaacaaaa ggtgggtggt      1980
     ggatccgcgt gattcagttc acgtcggtgg tgtgaggata ccggctgtgg ccgtttcggg      2040
     ctcataccgg tacctcgggg ttaatatctc cgccgccggg atgcgggtgg atgcagcaga      2100
     cagtctagca agtaagttgg cgaatctctc gagggctcct ttaaagccgc agcagcgcct      2160
     gtacatttta tgtactcacc tgctaccttc gatctaccat cagctggtac tttcgagtac      2220
     tagcaagaaa tttctgaagt acctagacag gtgcgtgagg gtggcggtcc ggaggtggct      2280
     caggctacca aaggataccc ctaaagcata tttccacgca aagtgcaatg acggtgggct      2340
     cggggttccc gagctccagc gggtaatacc gcttcaaaag gccggccgtt ggctgaagat      2400
     gacgaggtcg caagatcccg tggtgcaggc tgcggtcgga ctggagtatt tccagaaact      2460
     gttggagcgc tggagtaccc ccgaattata tcagtggggg ggggggggca tcaccacaag      2520
     tgggcacctg gccgtcgcac aggctcgatc gctttattcc tcagtcaatg ggcggggtct      2580
     gaggcagtcg gggcttgtgt cgacccagtt tgactgggtg agaagcggct gtagcctact      2640
     aagtggcaga aactttatcg gagcgatgca gctgagagga aacctgctcg caactaaatt      2700
     acgtgcctcc aggggacgac ctagagtgga catatcatgc gattgttgcc gtacgccgga      2760
     atcgtctggc cacattcttc aggtctgccc aagaacctcc tggggagcgc gtattggccg      2820
     ccatgataac gtggccaaat tagtagcgag ggagagcgcg aaacgtcatt ggaaggtgat      2880
     acgtgagccg gccattccaa cgccggccgg tattcgccga cctgacctcg tgttttcaaa      2940
     aggggatact gcaatcgtag tcgatgtgac gatcgtgccc gataatgccg agctatcgga      3000
     tgcacacagc agtaaagtat cgtattacga taacggggcg atacgggggt gggtagccct      3060
     taatactggg gcaagtcaca tcacattttc aagcgtcaac aacaattgga gcgactgcat      3120
     ggcggaagaa tctaagcgaa tgctgaaact tggcctcggc ctccccaatt caatcagggg      3180
     gacgatctcc gcggttgttc tggagaaagg cttccacatg tacctctgct tcaagagggg      3240
     gacatttcga gctagctact gatgaaggga agctggatta aaacgtgagt agcaacgggc      3300
     cagaaactct gaggtaagcc acctcaatcc attatcaaat ggcgaaaggc gaaaagagtg      3360
     ggctaccgta agccgcatgg cgccgggtgg agaagcagaa ctccggccca acgtacgagg      3420
     gcatgaagcc cccaaacgta ggatccgggg caaaagcgca cccggcaaaa cgaatagccg      3480
     caaaagtagg tgtttaggcc gggcctcggg cctggccatc cttgcaagaa ggccaggcac      3540
     taggtggccg cccgacagcc acacggctaa gaacaaacaa ggcgcctggc gaagacgatt      3600
     aaacacaatc gatcctgatg ggtgtgatga acaccttcat aagacataca tataaggatg      3660
     gatcccgcca aggttaagcg gtagcttgat aactctaaaa gctataaaaa aaataaaaaa      3720
     a                                                                      3721
//
ID   R2CIB_CI  repbase; DNA; CIN; 3720 BP.
CC   R2CIB_CI DNA
XX
AC   AB097122;
XX
DT   17-NOV-2004 (Rel. 1.0, Created)
DT   17-NOV-2004 (Rel. 1.0, Last updated, Version 1)
XX
DE   Ciona intestinalis retrotransposon R2Ci-B, complete sequence.
XX
KW   non-LTR retrotransposon; reverse transcriptase; R2CIB_CI.
XX
OS   Ciona intestinalis
CC   Ciona intestinalis
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea;
OC   Enterogona; Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-3720
RC   [1] 
RA   Kojima K.K., Fujiwara H.;
RT   "Cross-Genome Screening of Novel Sequence-Specific Non-LTR
RT   Retrotransposons: Various Multicopy RNA Genes and Microsatellites
RT   Are Selected as Targets";
RL   Mol. Biol. Evol. 21 (2), 207-217 (2004)
XX
DR   DR   Positions   1   3720  Accession No AB097122    Genbank
CC   Positions   1   3720  Accession No AB097122    Genbank
XX
SQ   Sequence 3720 BP; 1161 A; 892 C; 868 G; 799 T; 0 other;
     cgacggtgaa ccaccttgtc gcggtgtaag agctttagtg tctcgaacaa gaaatagctt        60
     gtgtgctgtc cttctgggcg gtgcacatac ttcttaacct cccgaggcca tgccggcggg       120
     ggctttagcc cccggcaggt tttaccatgc cggacgggtt cgagaggtag aggccaaact       180
     aagagttcac cagcagactt cgcacgcggc tggccactgg ccgaagttta aacaacaggg       240
     ccgcatcttc ccaaactcaa tatatggtgt taagtgaacc gtgccgatgg gtgaatggcc       300
     atgggtaagt tggtctctaa cggtccttgt ggagaagtgg cgacccttca caatacttca       360
     gccttaccct atgcccgggc aacttagggt ggacgtatat ctcccgcgga aaacatctta       420
     tctcatggat aaaaatatat acgaaaacac tacttctcca ggagggggac cgctttgcgg       480
     tgagaagacg catcgttccg atgtgatcat ccctccaccg gggttcgccc cgtcgacgga       540
     cactgcttcc aatacattag gggaaaatgt ggatgcatct gcaaccacta gcagtgccaa       600
     cccattaagt caggaaccag gatggtgcga atcttgttcc aagctgttca aatcacaaag       660
     aggacttaga gtccaccaaa gatcaaaaca tccagagttg taccattctc agaatcaacc       720
     gcttccgcga tctaaagcac gatggagtga tgaggaaatg gttatctttg ctcgcgaaga       780
     aattgcaaat aggaagatcc gctttatcaa tcagcactta cacaaagtgt ttccacacag       840
     aacgctagag tcaattaaag ggttgagggg aaaaaacgta agatacgctc gcatcatggc       900
     tgaccttgag gcggaaatga cctctcagcc cgaagcagcc acaagcttgt gcaccgaaac       960
     atcagaaaat ctcgcttcta gcaatgttct gccccaaaca agaggatggg ctgaaaatct      1020
     cgtcgaaaat attgacacag cacatctggc aaaccttggg ccgttatccc agtttgaacc      1080
     tggtaaacca agcagcagta caaaagaggc tatcaacacc gagtacaacg actggatcag      1140
     caaatggctt ccctctggtg ctgctcatag agaaagaaga gcaaatccac cctcaactaa      1200
     gctaaatgct agagcaacaa ggaggctaca atacagtagg atccagaatc tctacaaatt      1260
     aaatcgttct gcctgcgccc aagaagtatt aagcggggct tggaaggtcc agtcgggcga      1320
     actgaacttg aaagaggtcc aaccgttttg ggaaaaaatg ttccggaaag aatccgccaa      1380
     ggacaggcgc aagcccaagc ccactggtga agtactctgg ggactgatgg agcctctaac      1440
     aattgccgag gtgggatcca ctctgaagtc aacgacacca tcagccccag gacccgacaa      1500
     gttaacacta gatggcgtaa agaggatacc cattgctgaa ctagtatccc attacaacct      1560
     atggttgtac gctggctacc aaccagaggg actgcgcgaa ggaataacca ccctaattcc      1620
     gaaaattaag ggtacgcgtg acccggctaa gctacgccca attacagtgt ctagctttat      1680
     ttgccgcatc ttccaccgat gtttggcaca acgaatggaa acctctcttc cattgggcga      1740
     aagacagaaa gctttccgca aggtcgatgg catctgtcat aatatttggt ccctaaggtc      1800
     tctaatacac aatagcaaag acaacttaaa agaactcaat ataacatttt tggacgtacg      1860
     aaaagcattt gactccatct cgcataaatc actgggcata gctgcagccc gccttggact      1920
     tcccccaccc ttgataacat acatctccaa cctttaccca aactgttcta ccaaattaaa      1980
     agtaaacgga aaaatatcaa aaccaattga agttcgtcga ggagtccgac aaggagaccc      2040
     actctccccg ctactgttta atgcagtaat ggattgggcc ctatctgaac tggacccaag      2100
     agtgggagta caaattgggg aacaacgaat aaaccatcta gcattcgccg atgatattat      2160
     tttggtctct tcaacaaaga tcggaatggt gtcctccatc aatacgttga gtcgccatct      2220
     ggcaaaatca ggcctcgaaa ttagcgctgg gaaagaagga aaatcagcta gtatggccat      2280
     cgttgttgat ggaaagaaaa agatgtggac agtagatccc cttcctaggt tcaaagtaaa      2340
     cagccagaaa attccggcac tgagtattac acaacagtat aagtatctgg ggataaacat      2400
     agatgcccaa ggggcaagaa atgatgcagc tcgaatcctt acagagggtc tagcagaatt      2460
     atctcgtgcc ccactgaagc cacaacagcg actatatctg cttcgggtgc atcttcttcc      2520
     gaaactgcaa cacggactgg ttttaagtag ttgtgcaaaa agagcgctaa catacctgga      2580
     caaaagtgta aggtctgcaa taagaagatg gcttacactt ccgaaggaca caccaacagc      2640
     cttttaccat gcgaaagcat gtgacggtgg actaggcatt acacgtttgg aacacacaat      2700
     accaatactc aaaagaaata gaatgatgaa gttgacattg tcagaggatc cagtgatcat      2760
     ggaacttgta aaattgacat actttacaaa tttactacac aaatactcaa atgtgaagct      2820
     gcttaactcc tggccagtaa cagacaaaga cagtctggcc cgtgccgaag cctccatgct      2880
     tcacacctct gtggatgggc gtggactaag caattgcagt gatgtcccgc gccaaagtga      2940
     ctgggtcaca aatggcgcgt cgctacttag tggtcgtgac tttattggag caataaaagt      3000
     gaggggcaac ctcttgccaa caaaggttag tgcggcacgt ggacggcaac gggagataac      3060
     atgcgactgc tgcagacgac cggagtcact gggccacatc ctgcagacct gccctagaac      3120
     atggggaccg agaatctcca ggcatgactc cctgttgaag cgagttcgga atcaggcatg      3180
     cttaaaaaac tggaccccga taatagagcc atcgatacca accaacatag gacttcgtcg      3240
     gccagacctc gttttggcca aaggtaacat cgcctttctt gtagatgcca ccgtggttgc      3300
     agacaatgcc aacatgcagt tgcaacacga agcaaaagtg gaaaagtaca acaactcaga      3360
     tataaaggaa tggataaaag tacactgccc aggggttgat gaagtgaggg taacgtcact      3420
     aactgcgaac tggcgcggtt gcttgtatgg aggttcagca tccttcctaa cagaagacct      3480
     gggactgcct aaagcagagt taagtctgct cagtgcaaag atcaatgaaa aaggatacta      3540
     cctttggtgt gctcactaca ggggaacagc aaggttgtgg aatcgaccgt taaggtcctg      3600
     acagtaatat gaaaacatca catctgaccg gcacagaatc accatgccgt aatgcaccca      3660
     actaaggatt ccaatgggta aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa      3720
//
ID   YURE_CI   repbase; DNA; CIN; 5198 BP.
CC   YURE_CI DNA
XX
AC   AB097133;
XX
DT   17-NOV-2004 (Rel. 1.0, Created)
DT   17-NOV-2004 (Rel. 1.0, Last updated, Version 1)
XX
DE   Ciona intestinalis retrotransposon YURECi.
XX
KW   non-LTR retrotransposon; reverse transcriptase; YURE_CI.
XX
OS   Ciona intestinalis
CC   Ciona intestinalis
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea;
OC   Enterogona; Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-5198
RC   [1] 
RA   Kojima K.K., Fujiwara H.;
RT   "Cross-Genome Screening of Novel Sequence-Specific Non-LTR
RT   Retrotransposons: Various Multicopy RNA Genes and Microsatellites
RT   Are Selected as Targets";
RL   Mol. Biol. Evol. 21 (2), 207-217 (2004)
XX
DR   DR   Positions   1   5198  Accession No AB097133    Genbank
CC   Positions   1   5198  Accession No AB097133    Genbank
XX
SQ   Sequence 5198 BP; 1108 A; 1515 C; 1337 G; 1238 T; 0 other;
     tcaatcaata aggaggtgtt ttctttggtc tgttgtttta tagtttaccg ttataatagt        60
     ctgttgtcct atagttttcc gtggtgtatt tctggtctac tatagttggt gcctctaaaa       120
     cattattata ccgaagagtg ctagcgattt ctattattaa ctcacccacc agtactgctg       180
     tgcatccacg cagcaccacg cctgccatca cgtacagtgc gcttgctgcc ttgtgttttg       240
     ttttgcagac accactggac gatagatggc gacttcgtct tcctccgttt catcggggaa       300
     tgttcagacc gaggtgcgtt gcgtctacca cggaaaagga gacttgttgc tggaatgccc       360
     agttgcccat tgccctagca tacaccccac agttgccaca atcacaaaac acttaaaaaa       420
     acatcacaca cctcaattcg aacagataac cactaaaaat ctcacaataa catatacatg       480
     cagtcaatgt agtttctcca ccaccggtct cacacaacac cacatatcca aacactacaa       540
     aacatgcaaa ggcgtgggcg ctgttcagga aggcaacaag ggtcgattct gctgccctgc       600
     atgcggtacc aggtgggctc ttttgtgtaa ggcacggcac cattttaata atgtccactt       660
     cgagtatgac acccctccaa ttgccgcttt ctctggcaca ccctataaac taaaaaaacg       720
     gaaatttaca attattaata aggccctaac atattcatgc cctctccccc tcaaccaact       780
     actttgccct ttgtggtcgt gctccctcac gatcttaaat aaacctcttt caagcgtgca       840
     gcaggaaacg gcacatggcg acggctcaca aggccagagt tatgttccaa ctcagttgcg       900
     gcaggtgctc agagcccgtt gccactgcgg aaaccctcca attggaaagg gccactgggc       960
     atcttgccaa gggaagcgac cactctcttc acctaagggt gggcgcagtt cgcccactcc      1020
     acctgctaat ctaaccctcc acttccttaa ctatctcccc ttccaacttc cctcacaaag      1080
     ctcctccccc caaagtagca ccctcgaccc tacggcctgt aaagctcgag tccccatccc      1140
     ctctttccta cgcggcgact gtgaagtcac ctttttcatc atcccctccg ttaattttta      1200
     tagaccctac ctctcctacc ccctcaggat gttctggcgt aaccgaacat cctccggtca      1260
     ctgttcccta caccgggtcg ttcgaggctt tgtccgagag cgactcgtcc cccatcctcg      1320
     gtcgaaatcg ccggcgagga ctccccttga attcctctgc gagttccggc tcgcgggggt      1380
     cttccccgat cctgggaagg tcgcgtccct tcgacccgta ccagctcccc ttacgctttg      1440
     cctttctcca ccagtcgctg gtccaatgat ttcctgtgag gaccacagcg cccccccttc      1500
     cgttcgctcg agctccccca ttcctaactc cccagcctcc gtaagctccg tggaggcgca      1560
     cttgtctgac ttgttagaca aagtgtcttc cggagaactg cggccgctgt cccccaccct      1620
     gccttcttca ggcttttttg gccctctgtt gccacccact ccccctcccc gacctacccc      1680
     ctcggccgaa aaggcatctc cttcaggcct ttcctaccta ccctgcagag aagtaaaaat      1740
     cgcgtccatt gcacggccat cccctgcctc acagagggtc ggctgcgacg cggaccgaac      1800
     agggccttcg ctgaacccta attatcagca aacctccccc ccgtctactc cgagtttctc      1860
     ccccatagtt agacccccta aattcccccg gtcgggcgcc aaagtaaatt ccaagtccaa      1920
     accccccggc gtccgaccac gccgtgccaa gccaattgag ccagggaccg agtcggcatc      1980
     acccgttgat gtcgacacta ttagtagttc ggttcaggaa ccttgtactc cagaaaacag      2040
     aaccccggaa tttttttatg agcgaaagtg gctcgtgagt attttaaata ttcacgagcg      2100
     ggagggatcc aatttttttc aatttaaccg ggatctggag tattggacgc agttgctttc      2160
     aggctcccag aagggaggac gcgcgaagcg tgcgtcctac aatcgtggtg cggcgaacca      2220
     agcgatgaaa aaccgcgatt ccggccgtaa ggatttcgat ccccggccgg tagcaggcca      2280
     cagtagtgga ggtggcaccg agctcggttc gcggccacga taccctaagg gcgcacgtct      2340
     tcgtgccgac ttctggaggg acatgaaagg gacggtccgt aagttacttg atggttcgaa      2400
     cggtgagcgt cgctgcggga ttcccctcga tatcatagag cggaaattcc ggcaagtatc      2460
     catgcccggc tggatagacc acagacggta cgcggccggc gcgtccccgt ccctagtaac      2520
     ccaagctgaa acggatgttg ccatcaccag tgaggaagtt gaggcggtcc tcagtggcct      2580
     aaacgttcag tccgctccgg gctcggatgg cctctcctat cgattttgga agggcctcga      2640
     tcctagtggt cgattgttgt catgcctttt cgaaatcgtt aggaggcatg gtcgtattcc      2700
     gggcgcgtgg ccgacttgta gcgtcatcct gctctgtaaa gatgctcagg gtgacgttca      2760
     ggacgtggga aactggagac cgatcaccat ctgccgcact ctgtacaaat tgtacgcggc      2820
     tgtgatcgcc agacgtattc agacttgggc gaaacagggc ggggtgctct cgcggctcca      2880
     gaaagggttc atgccagttg agggtgtgtt tgagcacgtc ttcatgttgg ataccgtcct      2940
     ttccgacgcc aagctgaggc gcaagaatct tcttgccgtc ttccttgacg ttcggaatgc      3000
     gttcggaagc gtccggcatg aatgcttgct caaagttctt cggcacttcg atgctcccca      3060
     ttacctggtt gaactcgtga gggatattta caccggtgcg acctgccgtg ttagatcttc      3120
     ggttggtgag accggtgata taccctgtga tcgaggtgtc aggcagggct atcccctgtc      3180
     tggcattctt ttcaacctgg taacggaggt gctaataccg gggctcagtg ccgggaatga      3240
     tggctaccgg atggcttgct taggtggtaa gctcactcaa gtcctggcct acgctgacga      3300
     tctggtggta gtcacggaaa accgtgatca gatgctacgt cagctgggtg tgtgtgagga      3360
     attcggccgt tgggcaggcc ttgcattcaa tcaacggaag tgtggcctga tcggctggag      3420
     gacgttgcgg ggagggagga gggtcgcact ggaggatcct ctgctcctta acggagtaga      3480
     gatccccctg ttgcggcccg gtgaacacta taaatacctt ggcgccatga ctggcgtcat      3540
     gagtgttccc cgcaccggat cccagctgat caaggacttc cgtgcaaggc tccaacgact      3600
     gtttacatcg ttcctcacac cacaccagaa gctgatcgct ctgaaacggt ttctgctgcc      3660
     aagtctcagc tttcatctga gggttcgtcc gattgcgcgg tctgagctga tcgcgctcga      3720
     ccgtcgcgtg cgcgagtgcc ttagggtggc gtttcgcttg accaagccct cgtgtcaggc      3780
     tgtgtttcat acaccgactg acatggatgg tctgggtgtc ccgtcggtat gcagtgagag      3840
     cagcatactg acgatcgccc aggggttcaa ggtgttaacg tcacccgacg gcacagtgtc      3900
     cgcgacggct tcggcgcgcg tgaagctcta cgccgctaaa tttggcggcc tcactgaagc      3960
     aggtccttcg gactgggcgc gttatctatc tggtgatgac gtcaacggga atagcactcg      4020
     caaacccggc gctaacctgc cttctggtct gtggactcgc gtccgctgtg ccagcaggca      4080
     gttaggtgct gtgtggcgcg tttgcccgga aaacggcatc actgtccggg tgcgtaattc      4140
     tgtgattacc tcccgagacc gacggaagct catcagatcc ttccacgatt gctctaatca      4200
     gcagtggaag gagcagtgga tgcagcaccc caaccaggag aagaccgctg cagcgcatat      4260
     ggcttatgcc gatgcgaacc gctgggtgaa gcagccgtcg gttatggaac ctcatacata      4320
     cttttttgca ttgagggcgc gcttgaacct gttacccact agggtttcac gagctattta      4380
     tagcagggac caacacccgg acattttatg ccgacgttgt ggtgcgtcag ttgagtccct      4440
     cccgcatgta ctaaaccatt gtcctcccaa tatgagcata atactcggga ggcataattt      4500
     ggtactgcag gaggttctga acgcggtaga caaaacccag ttcaaagaga tatccgttga      4560
     ccgaacggtc cccgagcaca tgtcggagac aggtgaggcc ttgcggcctg acatagtggc      4620
     acggcggaat gacggttccg tcgtggtcgt cgacgtggct tgcccgttcg atcaaaaggc      4680
     gaactttgat gaggcggcaa aacggaagct cctaaagtac gacaagcttt gttgcaatat      4740
     cgctgcctcc acaggtaaac ctgtggagtg tcattcgata gtcgtgggct ccttggggag      4800
     cctcgcggag ggtctgtcca cctccctccg ggctttggga ataaccgatt ttgctcgctc      4860
     taagcttgtc gcttgccatc aagggtagcc aaaagatttg gtgttcttgg cgagctgcag      4920
     tcccggcaga gtaggcgaga tcgtgagctc tacaccgctt cacgatttga cgagttcttc      4980
     ttgagtcgat ccccaacggc aacgcactcc aaatttaacg accgcatggc gacgccactg      5040
     atctcccagt catccgtgct ccgagggcac ttaaggggaa ccgattcact gatgctgcaa      5100
     gttggcgggg gcgcactcac caatggaaga tgagggagcc caacgatgcc ccgaactacc      5160
     gcaccgtccc cagcaccgtg tccttgtgag taatattt                              5198
//
