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Table 4 Characterization of 14 additional sites (isolated from the mPing -specific TD profiles) flanking de novo mPing insertions in the S2 progenies of etoposide-treated plants

From: Changes in DNA methylation and transgenerational mobilization of a transposable element (mPing) by the Topoisomerase II inhibitor, Etoposide, in rice

Insertion site

Insertion positiona

Locus-specific primers

Inserted into

TIRs

TSDs (5’-3’)

  

(5’-3’)

(S2 plant individuals)

(5’-3’)

 

mPing- mPL1

Chr.4; Position:

for: tggtttgctgggacatgtaa

3-15,17,19

ggccagtcacaatgg

TAA

 

35202559-35203218

rev: gctcttgcataagagccaaca

   

mPing- mPL2

Chr.2; Position:

for: gcagccagtacgtagcacag

2,9,10

ggccagtcacaatgg

TAA

 

28002407-28003049

rev: acgaacgtgggctgttttag

   

mPing- mPL3

Chr.5; Position:

for: tttgtcggcgtctactccat

2,9,10

ggccagtcacaatgg

TAA

 

22152251-22152950

rev: tttgcagctggcttatagca

   

mPing- mPL4

Chr.3; Position:

for: gctcgtggctgaagacctta

2,9,10

ggccagtcacaatgg

TTA

 

9219105-9219744

rev: tcgtctctcggtgacacagt

   

mPing- mPL5

Chr.12; Position:

for: atgtgcactgtgcctggtag

2

ggccagtcacaatgg

TTA

 

838497-839154

rev: tctcgctctttcagtgagca

   

mPing- mPL6

Chr.8; Position:

for: cggagcacggagtacttatca

2,9,11-12,15-16

ggccagtcacaatgg

TAA

 

28053221-28053889

rev: gctctaaatcacctagccaacg

   

mPing- mPL10

Chr.1; Position:

for: tggctggtccttaccttttg

10-12,14-17,19

ggccagtcacaatgg

TTA

 

23659253-23659876

rev: gacgtggagaggtggaagag

   

mPing- mPL15

Chr.3; Position:

for: ttgagagcatccacaacgaa

2,9,10

ggccagtcacaatgg

TTA

 

12714414-12715082

rev: atcggcattagcacaaagga

   

mPing- mPL26

Chr.2; Position:

for: caaagccaaaacaaggatgc

9,10

ggccagtcacaatgg

TTA

 

13161847-13162504

rev: aagggcgcatattagcaaaa

   

mPing- mPL29

Chr.4; Position:

for: acaatcaatggcttccttgc

2,10

ggccagtcacaatgg

TTA

 

32802687-32803380

rev: ccaagtgtcatgcctgctta

   

mPing- mPL30

Chr.1; Position:

for: gtgggaagtgatgaggagga

2-4,8-10,18

ggccagtcacaatgg

TTA

 

30258277-30258933

rev: cgcgggggattagaatactt

   

mPing- mPL35

Chr.8; Position:

for: aaagagaaaagcagcggact

2

ggccagtcacaatgg

TAA

 

28053307-28054025

rev: aaatgacggttttgttttgc

   

mPing- mPL36

Chr.11; Position:

for: gccgcgagctaatgatagtt

2,8,10

ggccagtcacaatgg

TTA

 

392454-393170

rev: gtaaccctgccctgactcat

   

mPing- mPL37

Chr.3; Position:

for: tttacgtcaggggaatggac

1,7,8,10,14,16-17

ggccagtcacaatgg

TAA

 

17530417-17531150

rev: tccgcgttcttcagtttcta

   
  1. a Based on BlastN at the NCBI website.