| SINE | | Species | Promoter | LINE tail | | Description of SINE/LINE pair |
| | | Mammals | | | | | MIR (CORE-SINEs: Ther-1, Mon-1) | [97–99] | All mammals | tRNA | L2 | [15] | [100] | CORE-SINEs (MIR3/Ther-2) | [15, 99] | Mammals | tRNA | L3 | [101] | [15, 34, 102] | CORE-SINEs (Mar-1/MAR1_MD) | [15, 99] | Marsupials | tRNA | RTE-3_MD | [15] | [15, 34, 102] | MAR4 (MAR4_MD, WALLSI3) | [15] | Opossum and wallaby, Monodelphis domestica, Macropus eugenii | (5′-end of RTE) | RTE-2 (MD, ME) | [15] | [15, 34] | RTESINE1 | [15] | Opossum, Monodelphis domestica | (5′-end of RTE) | RTE-1_MD | [15] | [34] | Ped-1 | [103] | Springhare, Pedetes capensis (Rodentia) | 5S rRNA | BovB_Pca | [103] | [103] | Ped-2 | [103] | Springhare, Pedetes capensis (Rodentia) | tRNA (ID SINE) | BovB_Pca | [103] | [103] | Bov-tA | [104, 105] | Ruminants | tRNAGlu | Bov-B | [105, 106] | [100, 104] | Bov-A2 | [104, 105] | Ruminants | (5′-end of BovB) | Bov-B | [105, 106] | [104] | SINE2-1_EC | [15] | Horse, Equus caballus | tRNA | RTE-1_EC | [15] | [15, 34] | Afro SINEs (AFRO_LA, PSINE1) | [15, 107] | All Afrotherians | tRNA | RTE1 (LA, Pca) | [15] | [34, 103, 108] | RTE1-N1_LA | [15] | Elephant, Loxodonta africana | (5′-end of RTE) | RTE1_LA | [15] | [15] | SINE2-1_Pca | [15] | Hyrax, Procavia capensis | tRNA | RTE1_Pca | [15] | [15] |
| | | Birds and Reptiles | | | | | TguSINE1 | [15] | Zebra finch, Taeniopygia guttata | tRNAIle | CR1-X | [15] | [15] | Tortoise Pol III/SINE | [31, 109–111] | Tortoises and turtles, Cryptodira | tRNALys | PsCR1 | [112] | [31, 113] | Sauria SINE | [114, 115] | Lizard, Anolis carolinensis | tRNA | Anolis Bov-B | [114] | [114] | Anolis SINE 2 | [115] | Lizard, Anolis carolinensis | (Box A & B) | Anolis LINE 2 | [115] | [115] | SINE2-1B_Acar/ SINE2-1_Acar | [15] | Lizard, Anolis carolinensis | tRNA | Vingi-2_Acar | [116] | [15, 34] |
| | | Amphibians | | | | | V-SINEs (SINE2-1_XT) | [15] | Frog, Xenopus (Silurana) tropicalis | tRNA | L2-4_XT (L2-3, L2-6, L2-2) | [15] | [15, 34] | CORE-SINEs (MIR_Xt) | [15] | Frog, Xenopus (Silurana) tropicalis | tRNA | L2-5_XT | [15] | [34] |
| | | Fish | | | | | Sma I | [117, 118] | Chum and pink salmon, Oncorhynchus | tRNALys | SalL2 | [23] | [23, 31, 32] | Fok I | [118] | Charr, Salvelinus | tRNALys | SalL2 | [23] | [23, 31, 32] | SlmI | [119] | All salmonids, Salmonidae | tRNALeu | RSg-1 | [120] | [119] | CORE-SINEs (Hpa I) | [102, 118] | All salmonids, Salmonidae | tRNA | RSg-1 | [120] | [31] | CORE-SINEs (AFC, SINE2-1_AFC) | [102, 121, 122] | Cichlid fish, Cichlidae | tRNA | CiLINE2 | [121] | [121] | CORE-SINEs (UnaSINE1, UnaSINE2) | [123] | Eel, Anguilla japonica | tRNA | UnaL2 | [36, 123] | [36, 123] | HAmo SINE | [124] | Carp, Cyprinidae | tRNA | HAmoL2 | [124] | [124] | DeuSINEs (AmnSINE1, SINE3) | [21, 125] | Mammals, chicken, zebrafish, catfish | 5S rRNA | CR1-4_DR (CR1-7, CR1-9, CR1-13) | [15] | [21, 34, 125] | DeuSINEs (LmeSINE1, SacSINE1) | [125] | Coelacanth and dogfish shark, Latimeria menadoensis, Squalus acanthias | tRNA | CR1-4_DR-like | [15] | [125] | DeuSINEs (OS-SINE1) | [119, 125] | Salmon and trout, Oncorhynchus, Salmo | 5S rRNA | RSg-1 | [120] | [125] | V-SINEs (HE1) | [126, 127] | Sharks and rays, M. manazo, S. torazame, H. japonicus, T. californica | tRNA | HER1 | [126] | [126] | V-SINEs (DANA) | [127–129] | Zebrafish, Danio rerio | tRNA | CR1-3DR/ZfL3 | [15, 127] | [127] | V-SINEs (Lun1) | [127] | Lungfish, Lepidosiren paradoxa | tRNA | LfR1 | [127] | [127] | SINEX-1_CM/SINE2-1_CM | [130] | Elephant shark, Callorhinchus milii | tRNA | CR1-2_CM | DQ524334 | [34, 130] |
| | | Chordates | | | | | DeuSINEs (BflSINE1) | [125] | Amphioxus, Branchiostoma floridae | tRNA | Crack-16_BF | [15] | [34] |
| | | Deuterostomes | | | | | SURF1/SINE2-4c_SP | [15, 131] | Sea urchin, Strongylocentrotus purpuratus | tRNA | CR1-4_SP | [15] | [34] | DeuSINEs (SINE2-3_SP) | [15, 125] | Sea urchin, Strongylocentrotus purpuratus | tRNA | CR1Y_SP (CR1X_SP) | [15] | [15, 34] | SINE2-8_SP (SINE2-6, SINE2-4b) | [15] | Sea urchin, Strongylocentrotus purpuratus | tRNA | L2-1_SP/CR1-3_SP | [15] | [34] |
| | | Protostomes | | | | | Gecko | [132] | Mosquito, Aedes aegypti | tRNA | I-74_AAe (MosquI, I-58, I-59, I-62, I-64, I_Ele10, 14, 35, 37) | [15, 133] | [34, 132] |
| | | Eumetazoans | | | | | Nve-Nin-DC-SINE-1 (*1) | [134] | Sea anemone, Nematostella vectensis | tRNA | L2-22_NV | [15] | [134] | Nve-Nin-DC-SINE-2 (*1) | [134] | Sea anemone, Nematostella vectensis | tRNA | CR1-5_NV | [15] | [134] | Nve-Nin-DC-SINE-3 (*1) | [134] | Sea anemone, Nematostella vectensis | tRNA | CR1-15_NV | [15] | [134] | SINE2-1_NV | [15] | Sea anemone, Nematostella vectensis | tRNA | CR1-16_NV | [15] | [34] | SINE2-5_NV | [15] | Sea anemone, Nematostella vectensis | tRNA | Rex1-24_NV | [15] | [34] |
| | | Fungi | | | | | Mg-SINE | [135] | Rice blast fungus, Magnaporthe grisea | tRNA | MgL/MGR583 | AF018033 | [32, 34] | SINE2-1_BG | [15] | Powdery mildew fungus, Blumeria graminis | tRNA | Tad1-24_BG (HaTad1-3, 1-5) | [15] | [34] |
| | | Amoebozoa | | | | | EdSINE1 (SINE-lile) | [136] | Amoeba, Entamoeba dispar | Unknown | R4-1_ED | [15] | [34] | R4-N1_ED (SINE-lile) | [15] | Amoeba, Entamoeba dispar | Unknown | R4-1_ED | [15] | [34] | EhLSINE1/ehapt2 (SINE-lile) | [137, 138] | Amoeba, Entamoeba histolytica | Unknown | EhLINE1/EhRLE1 | [30, 137] | [137] | EhLSINE2 (SINE-like) | [137] | Amoeba, Entamoeba histolytica | Unknown | EhLINE2/EhRLE3 | [30, 137] | [137] |
| | | Land plants | | | | | TS | [35] | Tobacco, Nicotiana tabacum | tRNA | RTE-1_Stu | [15] | [34] | ZmSINE2/SINE2_SBi | [66] | Maize, Zea mays; Sorghum, Sorghum bicolor | tRNA | LINE1-1_ZM | [15] | [34, 66] | ZmSINE3 | [66] | Maize, Zea mays | tRNA | LINE1-1_ZM | [15] | [66] |
| | | Green algae | | | | | SINEX-1_CR | [15, 83] | Chlamydomonas reinhardtii | Unknown | RandI-2/ DualenCr3 | [15, 139] | [34, 83] | SINEX-2_CR | [15, 83] | Chlamydomonas reinhardtii | Unknown | RandI-2 (RandI-3) | [15, 139] | [83] | SINEX-3_CR | [15, 83] | Chlamydomonas reinhardtii | tRNA | L1-1_CR | [15] | [15, 83] | SINEX-4_CR | [15, 83] | Chlamydomonas reinhardtii | Unknown | RandI-2 (RandI-3) | [15, 139] | [34, 83] | SINEX-5_CR/SINEX-6_CR | [83] | Chlamydomonas reinhardtii | tRNA | RandI-5 | [15] | [83] |
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