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Table 1 Excision sites of Dart-related TEs identified by transposons-display (TD) (designated as Dart-TDE) in the rice-Zizania introgressants

From: Transpositional reactivation of the Dart transposon family in rice lines derived from introgressive hybridization with Zizania latifolia

Excision sites

Excision position§

Locus-specific primers (5'-3')

Excised from

Excision flanks

Dart-TDE-1

Chr.2

Position:11650578

Non-coding

For: tgcgcacaatcacctctatg

Rev: cttgtggtgcaaccaaccta

RZ1,

RZ2

acaatcacctctatg<Dart>aatgcacacactcat

acaatcacctctatg---------aatgcacacactcat

Dart-TDE-2

Chr.4

Position: 2633169

Non-coding

For: gtgcgcgtaatgctagaaaa

Rev: cagggagggagggattagag

RZ1, RZ2

acaatcacctctatg<Dart>aatgcacacactcat

acaatcacctctatg---------aatgcacacactcat

Dart-TDE-3

Chr.7

Position: 20137929

Non-coding

For: cccccatacttaccgcatta

Rev: cctaggtgttctgccgactc

RZ1,

RZ2,

RZ35

ttgtaaattaactcc<Dart>aaaccatctcctatc

ttgtaaattaactcc---------aaaccatctcctatc

Dart-TDE-5

Chr.11

Position:16475838

Non-coding

For: tgagtgacgtgaagccaaag

Rev: acagatcacggcagggttac

RZ2

aggtcggttaagcct<Dart>aagaaccacgaataa

aggtcggttaagcct------aagaaccacgaataa

Dart-TDE-7

Chr.4

Position:18387453

Non-coding

For: cctctaggcacctccctttt

Rev: caggagcaacaattgcatgt

RZ2

ctcccttttttttta<Dart>gaactaatgactttt

ctccctttttttaa gaactaatgactttt

Dart-TDE-8

Chr.1

Position:18893612

Non-coding

For: tggtttggaggtcggttaag

Rev: cacatgtcagccaaaaccac

RZ2

catcagattaagaaa<Dart>tccggtgaaaccatc

catcagattaagaaa---------tccggtgaaaccatc

Dart-TDE-10

Chr.11

Position:22507932

Non-coding

For: gagaagagcacgggaagttg

Rev: aactggctgttcgctcaagt

RZ2

taccgcattaaccac<Dart>ttaggtaggatacat

taccgcattaaccac---------ttaggtaggatacat

Dart-TDE-11

Chr.8

Position: 15326441

Non-coding

For: tcgtgttcccaaattcacac

Rev: catatatcccgcagaaaagca

RZ1, RZ2

cctccacctctaca<Dart>aaaatttctactgttc

cctccacctctaca--------aaaatttctactgttc

Dart-TDE-15

Chr.3

Position: 20176647

Non-coding

For: aacgagagcaagggagatgaa

Rev: ttaagccagggcaagtacacg

RZ2

tcctacgtcactg<Dart>ttgaggcgagccaaa

tcctacgtcactg---------ttgaggcgagccaaa

Dart-TDE-16

Chr.9

Position: 21368076

Non-coding

For: gtgcatggattttgaccttta

Rev: ctgtgctcacttcgctactacta

RZ1

atattgccatttaa<Dart>gtgtcatcgcctta

atattgccatttaa--------gtgtcatcgcctta

Dart-TDE-19

Chr.10

Position: 7832680

Non-coding

For: ggtgtaacgattgctaaggcg

Rev: agtggggggagagtaagatga

RZ2

tcttttttttacgca<Dart>tgcagaggtgacg

tcttttttttacgca<Dart>tgcagaggtgacg

Dart-TDE-20

Chr.11

Position: 7910449

Os11g0247800 exon

For: agagttcttgccaaccatgc

Rev: ggaagagggaaaaaccaagc

RZ1, RZ2

tctaatacctctag<Dart>gactgctttccacatg

Tctaatacctctag--------gactgctttccacatg

Dart-TDE-21

Chr.7

Position: 16720991

Non-coding

For: cgatcgagaatttccgagac

Rev: tggtctgttcgttgtccaaa

RZ1

tttcaccccctatat<Dart>tggtaccatcaattt

Tttcaccccctatat--------tggtaccatcaattt

Dart-TDE-23

Chr.6

Position: 6273602

Non-coding

For: cttttgggctgtgatggagt

Rev: ttaaggacgatgccaaaacc

RZ2

ttctgtccaccccta<Dart>gctggtatttatat

ttctgtccaccccta--------gctggtatttatat

Dart-TDE-25

Chr.6

Position: 26631010

Non-coding

For: cctcggtttccattagca

Rev: gtacggcctggcaagtga

RZ1, RZ2

ttttgtccaccccta<Dart>tctactcctagttgc

Ttttgtccaccccta--------tctactcctagttgc

  1. §Excisions refer to events occurred in one or more of the three introgressants (RZ1, RZ2 and RZ35). Naturally, the corresponding loci in Matsumae all contain a copy of Dart-related TE, whereas in Nipponbare only some of the loci contain the element, pointing to genotypic polymorphism with regard to presence/absence of the Dart-related TEs for a given genomic locus.
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BMC Plant Biology

ISSN: 1471-2229

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