ID   Merlin1_CI  repbase; DNA   ; CIN   ; 1791 BP.
XX
AC   .
XX
DT   16-JUN-2003 (Rel. 4.01, Created)
DT   16-JUN-2003 (Rel. 4.01, 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
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-1791
RA   Feschotte C., Wessler R.S.;
RT   "Merlin1_CI, a family of Merlin/IS1016-like DNA transposons from the
RT   sea squirt Ciona intestinalis.";
RL   Repbase Reports 3(5), 93-93 (2003).
XX
CC   [1] (Consensus)
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 previosly in the AF293351 GenBank
CC   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   Putative Merlin1_CIp transposase:
CC   MQKDFEGENSESLPCIRCKSCGTYVSPRKNSFFAFMDNRNRANVKISYKQVMAILINWVQRVPVGTTQQ
CC   NYGFGAHTVTDWYNFCREMCMLGFSKREPMGGPNTIVEIDESLLRGKRKYNRAGIEGPWIFGMCHVTVD
CC   SEGARSTQEVRFFHVLRRDKQTLLPIIQNEVLPSTTIHSDQWAAYTGLDQLGYSHQSVNHSENFIDPQT
CC   GAHTQTIESTWHHMKTTLLRNMRGVEPELLDSYLAELWARKLYRDHAALLEKLFDWIVEAYPIRNI.
XX
SQ   Sequence 1791 BP; 504 A; 380 C; 393 G; 508 T; 6 others;
     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.
XX
AC   .
XX
DT   16-JUN-2003 (Rel. 4.01, Created)
DT   16-JUN-2003 (Rel. 4.01, 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   Merlin1m_CI; Merlin1_CI.
XX
OS   Ciona intestinalis
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-605
RA   Feschotte C., Wessler R.S.;
RT   "Merlin1m_CI, a family of nonautonomous Merlin/IS1016-like DNA
RT   transposons from the sea squirt Ciona intestinalis.";
RL   Repbase Reports 3(5), 96-96 (2003).
XX
CC   [1] (Consensus)
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
SQ   Sequence 605 BP; 170 A; 109 C; 132 G; 184 T; 10 others;
     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
//
