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Table 1 Copy number, divergence, and age of mouse L1 families

From: Revisiting the evolution of mouse LINE-1 in the genomic era

Familya

Repeat masker classification

Promoter type

LPR structure

Genomic copy numberb

Number of FL elements

Average pairwise divergence (% ± S.E.)c

Age (Myr)d

L1MdA_I

L1MdA

A

66-42

4,249

1,620

0.376 ± 0.073

0.21 (0.17-0.25)

L1MdA_ II

L1MdA

A

66-42-42

5,156

1,240

2.939 ± 0.294

1.62 (1.45-1.78)

L1MdA_ III

L1MdA

A

66-42-42

4,337

606

3.916 ± 0.304

2.15 (1.99-2.32)

L1MdA_IV

L1MdF2

A

66-42-42

1,209

645

4.346 ± 0.414

2.39 (2.16-2.62)

L1MdA_V

L1MdF3

A

66-42-42

945

299

5.167 ± 0.341

2.84 (2.65-3.03)

L1MdA_VI

L1MdF3

A

66-66

5,497

219

8.554 ± 0.434

4.70 (4.47-4.94)

L1MdA_VII

L1MdF2

A

66-66

5,684

759

8.346 ± 0.414

4.59 (4.36-4.82)

Tf_I

L1Md_T

F

66-42-42

5,601

1,593

0.462 ± 0.095

0.25 (0.20-0.31)

Tf_II

L1Md_T

F

66-42-42

 

1,282

0.496 ± 0.087

0.27 (0.22-0.32)

Tf_III

L1Md_T

F

66-42-42

4,678

1,892

2.233 ± 0.196

1.23 (1.12-1.34)

Gf_I

L1Md_F, L1Md_T

F

66-42-42-42

2,177

615

1.356 ± 0.250

0.75 (0.61-0.88)

Gf_II

L1Md_T

F

66-66-66

770

368

3.929 ± 0.421

2.16 (1.93-2.39)

L1MdF_I

L1MdF2

F

66-42-42

5,112

1,209

3.853 ± 0.278

2.12 (1.97-2.27)

L1MdF_II

L1MdF2

F

66-42-42

 

609

4.537 ± 0.271

2.50 (2.35-2.64)

L1MdF_III

L1MdF2

F

66-66

 

548

8.040 ± 0.400

4.42 (4.20-4.64)

L1MdF_IV

L1MdF2

F

66-42-42

6,179

964

11.627 ± 0.503

6.39 (6.12-6.67)

L1MdF_V

L1VL1, L1MdF2

F

66-42

3,936

884

11.683 ± 0.487

6.43 (6.16-6.69)

L1MdFanc_I

L1Md_F, L1_Mus1

Fanc

66-42

4,398

418

12.366 ± 0.610

6.80 (6.47-7.14)

L1MdFanc_II

L1_Mus2

Fanc

66-66-66

16,491

460

16.795 ± 0.821

9.24 (8.79-9.69)

L1MdN_I

L1VL1, L1Md_F, L1Md_F3

N

66-42-42

2,237

367

3.447 ± 0.212

1.90 (1.78-2.01)

L1MdV_I

L1VL1, L1_Mus1

V

45-66

5,777

318

15.257 ± 0.647

8.39 (8.04-8.75)

L1MdV_II

L1_Mus3

V

66

3,848

470

18.318 ± 0.855

10.07 (9.60-10.55)

L1MdV_III

Lx

V

66-66

NA

N/A

17.575 ± 0.968

9.67 (9.13-10.20)

L1MdMus_I

L1_Mus1

Mus

66-66-42-56

4,947

535

12.068 ± 0.590

6.64 (6.31-6.96)

L1MdMus_II

L1_Mus2

Mus

66-66

1,924

304

14.971 ± 0.521

8.23 (7.95-8.52)

L1Lx_I

L1_Mus3

Lx

66-66

1,649

384

19.864 ± 0.846

10.93 (10.46-11.39)

L1Lx_II

L1_Mus4

Lx

66-66

3,546

186

23.907 ± 0.998

13.15 (12.60-13.70)

L1Lx_III

L1_Mus4

Lx

66-66

3,667

193

18.595 ± 0.841

10.23 (9.76-10.69)

L1Lx_IV

Lx

Lx

66-66

NA

N/A

25.642 ± 1.237

14.10 (13.42-14.78)

  1. aFamily names based on Repeat Masker database.
  2. bThe genomic copy number of Tf_I and II and F_I, II, and III were combined due to the small number of diagnostic characters at the 3' end.
  3. cAverage pairwise divergences were calculated using the maximum composite likelihood method (MEGA 4.0 package).
  4. dDates were calculated assuming a substitution rate of 1.1% / Myr.