Table 3 Non-LTR retrotransposons (LINEs, SINEs, and composites)

LINE

L1

L1, L1HS, L1M1B_5, L1M1_5, L1M2A1_5, L1M2A_5, L1M2B_5, L1M2C_5, L1M2_5, L1M3A_5, L1M3B_5, L1M3C_5, L1M3DE_5, L1M3D_5, L1M4B, L1M6B_5end, L1M6_5end, L1M7_5end, L1MA1, L1MA10, L1MA2, L1MA3, L1MA4, L1MA4A, L1MA5, L1MA5A, L1MA6, L1MA7, L1MA8, L1MA9, L1MA9_5, L1 MB1, L1 MB2, L1 MB3, L1MB3_5, L1 MB4, L1MB4_5, L1 MB5, L1MB6_5, L1 MB7, L1 MB8, L1MC1, L1MC2, L1MC3, L1MC4, L1MC4B, L1MC4_5end, L1MC5, L1MCA_5, L1MCB_5, L1MCC_5, L1MD1, L1MD1_5, L1MD2, L1MD3, L1MDA_5, L1MDB_5, L1ME1, L1ME2, L1ME3, L1ME3A, L1ME3C_3end, L1ME3D_3end, L1ME3E_3end, L1ME3F_3end, L1ME4, L1ME4A, L1ME5, L1ME5_3end, L1MEA_5, L1MEB_5, L1MEC_5, L1MED_5, L1MEE_5, L1MEe_5end, L1MEf_5end, L1MEg_5end, L1ME_ORF2, L1P4a_5end, L1P4b_5end, L1P4c_5end, L1P4d_5end, L1P4e_5end, L1PA10, L1PA11, L1PA12, L1PA12_5, L1PA13, L1PA13_5, L1PA14, L1PA14_5, L1PA15, L1PA16, L1PA16_5, L1PA17_5, L1PA2, L1PA3, L1PA4, L1PA5, L1PA6, L1PA7, L1PA7_5, L1PA8, L1 PB1, L1 PB2, L1PB2c, L1 PB3, L1 PB4, L1PBA1_5, L1PBA_5, L1PBB_5, L1PREC1, L1PREC2, L1P_MA2, HAL1, HAL1B (HAL1b), HAL1M8, IN25, MER25, X9_LINE

CR1

CR1L, CR1_HS, CR1_Mam, L3, L3b_3end, X1_LINE, X2_LINE, X5A_LINE, X5B_LINE, X6A_LINE, X6B_LINE, X7A_LINE, X7B_LINE, X7C_LINE, X7D_LINE, X8_LINE, X17_LINE, X18_LINE, X19_LINE, X20_LINE, X21_LINE

L2

L2, L2B, L2C, L2D, X15_LINE, X24_LINE, UCON49, UCON86

Crack

X13_LINE

RTE

X3_LINE, X11_LINE, UCON82

RTEX

L4, L5, ALINE

R4

X4_LINE

Vingi

X12_LINE

Tx1

MARE6

Penelope

UCON13

SINE

SINE1/7SL

(AluY)

ALU, AluY, AluYa1, AluYa4, AluYa5, AluYa8, AluYb10, AluYb11, AluYb3a1, AluYb3a2, AluYb8, AluYb8a1, AluYb9, AluYbc3a, AluYc1, AluYc2, AluYc5, AluYd2, AluYd3, AluYd3a1, AluYd8, AluYe2, AluYe5, AluYf1, AluYf2, AluYf5, AluYg6, AluYh9, AluYi6, AluYk11, AluYk12, AluYk13

(AluS)

AluSc, AluSc5, AluSc8, AluSg, AluSg1, AluSg4, AluSg7, AluSp, AluSq, AluSq10, AluSq2, AluSq4, AluSx, AluSx3, AluSx4, AluSz, AluSz6

(AluJ)

AluJb, AluJo, AluJr, AluJr4

(Monomeric Alu)

FAM, FLAM, FRAM, PB1D11

SINE2/tRNA

MIR, MIR3, MIRb, MIRc, THER1, THER2, MARE3, UCON3, UCON55, LFSINE_Vert, LmeSINE1b, LmeSINE1c, MamSINE1

SINE3/5S rRNA

AmnSINE1_HS, DeuSINE

Unclassified

MER131

Composite

SVA

SVA2, SVA_A, SVA_B, SVA_C, SVA_D, SVA_E, SVA_F