Award #0321460
Award #0604966
Award #0821966

Repeats and Tranposable Elements

Transposons were annotated by the wuBLAST version of RepeatMasker against the dicots section of mipsREdat (REdat_v8.6_Eudico, 91 Mb, 10,561 entries).

This transposon library is connected to a repeat classification scheme (mips_REcat) and contains a collection of transposons from public sources (1,974 entries) as well as de novo detected LTR-retrotransposons (8,587 entries) from At, Gm, Lj, Solanum esculentum, and Mt using LTR-STRUC (McCarthy and McDonald, 2003).

Transposon Classification

#

# perc

bp (Mb)

perc of TE bp

% of genome

Mobile Element (-)

206,112

100

80.1

100

30.5

Class I: Retroelement (RXX)

177,271

86

69.5

86.7

26.5

LTR Retrotransposon (RLX)

163,826

79.5

63.4

79.1

24.2

Ty1/copia (RLC)

14,510

7

10.8

13.5

4.1

Ty3/gypsy (RLG)

11,849

5.8

14.9

18.6

5.7

unclassified LTR (RLX)

137,467

66.7

37.7

47.1

14.4

non-LTR Retrotransposon (RXX)

13,210

6.4

6

7.5

2.3

LINE (RIX)

11,511

5.6

5.8

7.3

2.2

SINE (RSX)

1,699

0.8

0.2

0.2

0.1

unclassified retrotroelement (RXX)

235

0.1

0

0

0

Class II: DNA Transposon (DXX)

26,487

12.9

8.4

11.2

3.4

DNA Transposon Superfamily (DTX)

16,456

8

6.2

7.8

2.4

CACTA superfamily (DTC)

549

0.3

0.4

0.5

0.1

hAT superfamily (DTA)

1,551

0.8

0.6

0.7

0.2

Mutator superfamily (DTM)

10,753

5.2

3.9

4.9

1.5

Tc1/Mariner superfamily (DTT)

158

0.1

0.1

0.1

0

PIF/Harbinger (DTH)

3,445

1.7

1.3

1.6

0.5

MITE (DXX)

3,012

1.5

0.5

0.6

0.2

Helitron (DHH)

1,548

0.8

0.6

0.8

0.2

Unclassified DNA transposon (DXX)

5,471

2.7

1.6

2

0.6

Unclassified Element (XXX)

2,354

1.1

1.7

2.1

0.6

#

# perc

bp (Mb)

perc of TE bp

% of genome

Mobile Element

84,253

100

19.9

100

18.3

Class I: Retroelement (RXX)

75,777

89.9

18.3

92.3

16.9

LTR Retrotransposon (RLX)

67,602

80.2

14.6

73.4

13.5

Ty1/copia (RLC)

7,892

9.4

2.6

13.2

2.4

Ty3/gypsy (RLG)

4,833

5.7

1.5

7.6

1.4

unclassified LTR (RLX)

54,877

65.1

10.4

52.5

9.6

non-LTR Retrotransposon (RXX)

8,064

9.6

3.7

18.8

3.5

LINE (RIX)

7,213

8.6

3.7

18.4

3.4

SINE (RSX)

851

1

0.1

0.5

0.1

unclassified retrotroelement (RXX)

111

0.1

0

0.1

0

Class II: DNA Transposon (DXX)

8,042

10.1

1.4

7.7

1.4

DNA Transposon Superfamily (DTX)

5,683

6.7

1.1

5.3

1

CACTA superfamily (DTC)

239

0.3

0

0.3

0.1

hAT superfamily (DTA)

676

0.8

0.1

0.7

0.1

Mutator superfamily (DTM)

3,539

4.2

0.7

3.4

0.6

Tc1/Mariner superfamily (DTT)

53

0.1

0

0.1

0

PIF/Harbinger (DTH)

1,176

1.4

0.2

0.9

0.2

MITE (DXX)

952

1.1

0.1

0.7

0.1

Helitron (DHH)

434

0.5

0.2

0.9

0.2

unclassified DNA transposon (DXX)

1,407

1.7

0.2

0.9

0.2

For more information on how this data was generated, see the 2011 Nature paper