Table 2 Diversity of TEs in mammalian species.
From: Families of transposable elements, population structure and the origin of species
Species (genome size) | < 1% divergence | < 5% divergence | |||
|---|---|---|---|---|---|
| Â | Repbase ID names (genomic copy number in parentheses) | No. Families | Total Count | No. Families | Total Count |
Human (2.87GB) | AluYa5(2696), AluYb8(1499), AluY(215), AluYc1(433), L1HS(332), AluYg6(242), AluYb9(213), AluYd8(122), AluYa8(40), LTR5_Hs(38), AluYh9(18), HERVK(6). | 12 | 5981 | 48 | 33613 |
Chimpanzee (2.90GB) | AluY(150), AluYc1(1320), PTERV1c_LTR(80), CERV1_LTR(53), L1Pt(24), AluYa5(11), AluYb8(7). | 8 | 1799 | 50 | 23832 |
Rhesus macaque (2.64GB) | AluMacYb2(1122), AluMacYb4(1047), AluMacYa3(364), L1_RS1_5end(69), MacERVK2_LTR1a(52), MacERV1_LTR4a(40), MacERV1_LTR3a(23), MacERV3_LTR2(22), MacERV4_LTR1a(22), MacERV4_LTR4(20), MacERV3_LTR3(14), MacERV2_LTR1(11), MacERVK2_LTR1c(11), MacERV1_LTR4d(9), MacERV2_LTR2a(8). | 15 | 2834 | 67 | 70319 |
Marmoset (2.76GB) | HAL1-1C_Cja(32). | 1 | 32 | 11 | 1299 |
Tarsier (2.77GB) | LTR10_TS(11), LTR13_TS(7). | 2 | 18 | 23 | 7705 |
Mouse lemur (1.85GB) | LTR3_Mim(49), ERV1-Mim_LTR(23), LTR10_Mim(22), LTR1_Mim(22), ERV2N1-Mim_LTR(14), LTR10B_Mim(8), LTR14_Mim(5). | 7 | 143 | 26 | 6066 |
Bushbaby (1.97GB) | GarnAlu1(80), LTR8_OG(21). | 2 | 101 | 12 | 18970 |
Mouse (2.62GB) | L1_MM(1244), RLTRETN_MM(154), IAPLTR1_Mm_LTR(65), MMERGLN_LTR(59), IAPLTR1a_MM(58), RLTR1IAP_MM(54), RLTR6B_Mm(39), B1_Mm(34), B2_Mm1a(30), IAPEY4_LTR(30), LTRIS_Mm(26), B1_Mus2(23), ERVB7_1-I_MM(22), ORR1A0(20), ERVB7_1-LTR_MM(11), IAPLTR1a_I_MM(11), ERVB4_1B-LTR_MM(10), MTA_Mm_LTR(10), MMERVK10C(8), IAPLTR3(6), RLTR13B2(6), L1Md_Gf_5end(5), LTRIS3(5). | 23 | 1930 | 113 | 72236 |
Rat (2.48GB) | ID_Rn1(4510), B2_Rn(349), L1_RN(212), NICER2_Rn(113), ID_Rn2(107), RNLTR12(73), B2_Rn1(61), RNLTR19A(61), RNLTR8C(54), B2_RnY(50), NICER1B_Rn_LTR(37), RNIAP1aLTR(26), RNIAP1bLTR(18), RNLTR8C2(16), RNNICER3_I(15), B2_Rat2(12), RNLTR12-int(11), RNLTR2a(9), NICER3A_Rn(8), B2_Rn2(7), ERVB5_3-LTR_RN(6). | 21 | 5755 | 92 | 67356 |
Kangaroo rat (1.84GB) | DIPODE1(126), BC1_Dor(115), DERV2a_LTR(32), LTR13B_Dor(18), L1-1_Dor(14), ERV2-Dor_LTR(9). | 6 | 314 | 21 | 54065 |
Guinea pig (2.66GB) | CAVID(392), L1-1C_Cpo(377), L1-1D_Cpo(139), HAL1-1H_Cpo(106), HAL1-3D_Cpo(54), HAL1-1G_Cpo(50), HAL1-1E_Cpo(37), ERV1NA-CPo_LTR(36), 5S_CPo(15), ERV1A1-CPo_LTR(9). | 10 | 1215 | 39 | 38173 |
Squirrel (1.91GB) | LTR3_Str(65), ERV2-1_STr-LTR(40), LTR27_Str(19), STRID3(9), LTR8_Str(7). | 5 | 140 | 47 | 13754 |
Rabbit (2.08GB) | LTR26_OC(24), LTR10_OC(23), ERVH_OC_LTR(5). | 3 | 52 | 36 | 47855 |
Pika (1.92GB) | CSINE3_OP(210), ERV2-1N-OP_LTR(48), LTR2B1_Opr(40), ERV2-1-LTR_Opr(31), ERV2-4_Opr-LTR(22), LTR10_Opr(14), LTR30_Opr(10), LTR7_Opr(10), ERV1-1_OPr-LTR(8), ERV2-2_Opr-LTR(8). | 10 | 401 | 54 | 14259 |
Cow (2.73GB) | ERV2-1-LTR_BT(25), BTLTR1B(14), L1-BT(7). | 3 | 46 | 31 | 63422 |
Alpaca (1.92GB) | Â | 0 | 0 | 10 | 420 |
Dog (2.38GB) | L1-Y_CF(354), SINEC2A1_CF(79), CfERVF1_LTR(18), SINEC2A2_CF(11). | 4 | 462 | 14 | 81969 |
Cat (1.64GB) | SINEC_Fc(2312), ERV1-2_FCa-LTR(36), ERV1-3_FCa-LTR(24). | 3 | 2372 | 16 | 59515 |
Horse (2.42GB) | ERE1(532), L1-1_EC(61) | 2 | 593 | 20 | 19683 |
Megabat (1.83GB) | ERV1-1_PVa-LTR(102), ERV2-2_PVa-LTR(21), ERV2-3_PVa-LTR(12), LTR15_PVa(5). | 4 | 140 | 16 | 1924 |
Bat (1.67GB) | nhAT6_ML(1428), nhAT4a_ML(975), nhAT2_ML(823), nhAT1_ML(310), nhAT5b_ML(295), hAT-2N2_ML(227), nhAT3_ML(167), nhAT5a_ML(13), LTR30A_ML(9), ERV1X1-LTR_ML(7), ERV2X1-LTR_ML(7), SPIN_NA_1_Et(6), Ves(6), LTR27D2_ML(5), MARIN1_ML(5). | 15 | 4283 | 55 | 99014 |
Hedgehog (2.13GB) | Vingi-1N3_EE(311), LTR4_EE(54), LTR1C_EE(38), ERV2-4_EE-LTR(28), (13), ERV2-1_EE-LTR(11), LTR26_EE(8), ERV2-3_EE-LTR(7), LTR13_EE(5). | 9 | 475 | 63 | 14890 |
Shrew (1.83GB) | LTR6_Sar(45), LTR1_Sar(22), LTR2_Sar(22), LTR7_Sar(10), LTR8_Sar(8), LTR18C_Sar(5). | 6 | 112 | 25 | 2803 |
Elephant (2.30GB) | Â | 0 | 0 | 7 | 1052 |
Tenrec (2.11GB) | Â | 0 | 0 | 5 | 4783 |
Hyrax (2.41GB) | ERV2-6_Pca-LTR(166), ERV2-3_Pca-LTR(130), ERV2-1-Pca_LTR(56), MLT1Z_Pca(16), ERV1-2_PCa-LTR(8), LTR15B_Pca(7). | 6 | 383 | 40 | 9945 |
Armadillo (2.15GB) | Â | 0 | 0 | 6 | 5950 |
Sloth (2.12GB) | ERV2N1_CHo-LTR(402), LTR3_Cho(142), ERV2N1B_CHo-LTR(6), LTR5A_Cho(6). | 4 | 556 | 23 | 3709 |
Opossum (3.34GB) | L1-1_MD(953), SINE-1_MD(193), ERV2_MD_I(109), ERV2_MD_LTR(70), L1A-2_MD(42), MARINERNA6_MD(10), LTR32_MD(9), ERV1_MD_I(7). | 8 | 1393 | 70 | 46497 |
Wallaby (2.54GB) | MERVK1B_LTR(10), MERVK1D_LTR(5). | 2 | 15 | 7 | 9514 |
Platypus (1.84GB) | Â | 0 | 0 | 10 | 214 |