This table lists major phylogenetic subdivisions for eukaryotic transposable elements below that of the superfamily level. Subdivisions below the TE superfamily level have been proposed and named based on phylogenetic groupings since the mid 1990s. This list also includes several more recently proposed superfamilies that have not been incorporated into existing classification schemes.
It is the hope that by compiling these, researchers may consider them when describing TEs in new genomes, or new TEs. Also, some of these named groups are surely synonymous, while others may partially overlap each other in terms of assigned members. I hope this spurs researchers to investigate these synonymies and overlaps in the hope of creating an updated hierarchy with which to classify TEs below superfamilies. Ideally, well supported subdivisions should be used as labels for elements in reference libraries.
This list is maintained by Tyler A. Elliott and a more frequently updated version of this list may be found here. Suggestions, updates and error corrections can be directed to Tyler, or by commenting on this page.
| Superfamily/Clade/Division | Subdivision | Additional References |
|---|---|---|
| Tc1/Mariner | Tc1 | 2, 3 |
| Tc1/Mariner | Mariner | |
| Tc1/Mariner | pogo | |
| Tc1/Mariner | MMTS | |
| Tc1/Mariner | maT | |
| Tc1/Mariner | rosa | |
| Tc1/Mariner | LTIR | |
| Tc1/Mariner | ITmD37D | |
| Tc1/Mariner | ITmD39D/plants | |
| Tc1/Mariner | ITmD37E/mosquito | |
| Tc1/Mariner | Impala | |
| Tc1/Mariner | Incomer | |
| Tc1/Mariner | Lsra/DD41D | |
| Tc1/Mariner | irritans | |
| Tc1/Mariner | mauritiana | 2 |
| Tc1/Mariner | cecropia | 2 |
| Tc1/Mariner | mellifera | 2 |
| Tc1/Mariner | capitata | 2 |
| Tc1/Mariner | mori | |
| Tc1/Mariner | Ludens | |
| Tc1/Mariner | Atlantis | |
| Tc1/Mariner | CRI | |
| Tc1/Mariner | marmoratus | |
| Tc1/Mariner | urt | |
| Tc1/Mariner | lineata | |
| Tc1/Mariner | vertumnana | |
| Tc1/Mariner | elegans | |
| Tc1/Mariner | briggsae | |
| Tc1/Mariner | nosferatis | |
| Tc1/Mariner | Gallus | |
| Tc1/Mariner | TLEWI | |
| Tc1/Mariner | Traveler | |
| Tc1/Mariner | Gambol | |
| Tc1/Mariner | TRT | |
| Tc1/Mariner | Tnp/DD37E | |
| Tc1/Mariner | PlantMar | |
| Tc1/Mariner | Visitor/VS | |
| Tc1/Mariner | Azteca | |
| Tc1/Mariner | mosellana | |
| pogo | pogoR | |
| pogo | Fot/Fot-like | |
| pogo | Passer | |
| pogo | Tigger | |
| pogo | Lemi | |
| pogo | Mover | |
| hAT | hobo | |
| hAT | Ac | |
| hAT | Buster | 2 |
| hAT | Tip | 2 |
| hAT | Rover | 2 |
| hAT | Roamer | |
| hAT | Viridiplantae-group | |
| hAT | Fungi-group | |
| hAT | Mammal-group | |
| hAT | Teleost-group | |
| hAT | Ascidia-group | |
| hAT | Cnidaria-group | |
| hAT | Nematoda-group | |
| hAT | Insect-group | |
| CMC | Caspar | |
| CMC | TAT-1 | |
| CMC | Mandrake | |
| CMC | Isaac | 2 |
| CMC | Balduin | |
| CMC | Jorge | |
| CMC | Enac | |
| CMC | Alpha | |
| CMC | Beta | |
| CMC | Delta | |
| CMC | Gamma | |
| CMC | Epsilon | |
| CMC | Zeta | |
| CMC | Eta | |
| CMC | Theta | |
| CMC | Mirage | |
| CMC | Chapaev | |
| CMC | Chapaev3 | |
| CMC | TEC | |
| CMC | Plavaka | |
| Transib | RAGL | |
| Transib | ProtoRAG | |
| Transib | TransibSU | |
| piggyBac | Teratorn/Albatross | |
| piggyBac | Group 1 | |
| piggyBac | Group 2 | |
| piggyBac | Group 3 | |
| piggyBac | Group 4 | |
| piggyBac | Group 5 | |
| piggyBac | Metazoa 1 | |
| piggyBac | Metazoa 2 | |
| piggyBac | C. intestinalis Group | |
| Merlin | Microsporidean Group 1 | |
| Merlin | Microsporidean Group 2 | |
| Merlin | Microsporidean Group 3 | |
| Merlin | Microsporidean Group 4 | |
| Merlin | Microsporidean Group 5 | |
| Merlin | Microsporidean Group 6 | |
| Merlin | Microsporidean Group 7 | |
| Merlin | Microsporidean Group 8 | |
| PIF/Harbinger | PIF | |
| PIF/Harbinger | Harbinger | |
| PIF/Harbinger | Spy | |
| PIF/Harbinger | Pangu | |
| PIF/Harbinger | Nuwa | |
| PIF/Harbinger | ISL2EU | |
| PIF | A1 | |
| PIF | A2 | |
| PIF | A3 | |
| PIF | A4 | |
| PIF | A5 | |
| PIF | A6 | |
| PIF | B | |
| PIF | C | |
| PIF | D | |
| PIF | E | |
| PIF | M | |
| PIF | P | |
| Pong | O1 | |
| Pong | O2 | |
| Pong | P1 | |
| Pong | P2 | |
| Pong | Q | |
| GingerRoot | ||
| Academ | Academ-3TSD | |
| Academ | Academ-4TSD | |
| Academ | Academ-8-9TSD | |
| Academ | Academ-9-10TSD | |
| P-element | Galileo | |
| P-element | Galileo-V | |
| P-element | Galileo-W | |
| P-element | 1360 | |
| P-element | A | |
| P-element | B | |
| P-element | C | |
| P-element | D | |
| P-element | E | |
| P-element | F | |
| P-element | G | |
| P-element | H | |
| P-element | I | |
| P-element | J | |
| P-element | K | |
| P-element | L | |
| P-element | M | |
| P-element | N | |
| P-element | O | |
| P-element | P | |
| P-element | Group 1 | |
| P-element | Group 2 | |
| P-element | Group 3 | |
| P-element | Group 4 | |
| P-element | Group 5 | |
| P-element | Group 6 | |
| P-element | Group 7 | |
| P-element | Group 8 | |
| P-element | Group 9 | |
| P-element | Group 10 | |
| P-element | Group 11 | |
| MUDR | Rehavkus | |
| MUDR | TvMULE | 2 |
| MUDR | Phantom-Ca | 2 |
| MUDR | Curupira | 2 |
| MUDR | MULE-Ag | |
| MUDR | MULE-Mucorales | |
| MUDR | MULE-Co | |
| MUDR | Ghost sub-group Cnidaria | |
| MUDR | Ghost | |
| MUDR | Spectre | |
| MUDR | MULE-Ov | |
| MUDR | MULE-Pi | |
| MUDR | MULE1_EI | |
| MUDR | MULE-Ei | |
| MUDR | EMULE | |
| MUDR | MuDR-6_HM | |
| MUDR | MULE-Cg | |
| MUDR | MULE-Phytophthora_1 sub-group Sm | |
| MUDR | MULE-Phytophthora_1 | |
| MUDR | MuDRx-Phytophthora | |
| MUDR | MULE-Tv | |
| MUDR | MULE-Mollusca | |
| MUDR | Phantom | 2 |
| MUDR | MULE-Trichinella | |
| MUDR | Hop sub-group MULE-Cglob | |
| MUDR | sub-group Mutyl | 2 |
| MUDR | sub-group plants, Phytophthora, Puccinia and Fungi | |
| MUDR | sub-group Fungi | |
| MUDR | Jittery sub-group MULE-Cc | |
| MUDR | sub-group Dicots and Monocots | |
| MUDR | MULE-Diatoms | |
| MUDR | MULE-Cc | |
| MUDR | MULE-Phytophthora_2 | |
| MUDR | MuDR-4_Sm | |
| MUDR | MULE-Cm | |
| MUDR | MULE-Solanaceae_1 | |
| MUDR | MULE-Capsicum | |
| MUDR | MULE-Solanaceae_2 | |
| MUDR | VANDAL | |
| MUDR | MuDR-9_OS | |
| MUDR | MULE-Monocots | |
| MUDR | MDR | |
| MUDR | MUDRAVI2 | |
| MUDR | MUDR | |
| MUDR | sub-group Phytophthora | |
| MUDR | sub-group MUDRAVI | |
| Helitron | Hel1 | |
| Helitron | FoHeli | |
| Helitron | Helentron | |
| Helitron | HeligloriaA | |
| Helitron | HeligloriaB | |
| Helitron | Heliminu | |
| Helitron | Helisimi | |
| Helitron | Lep1 | |
| Helitron | Helianu | |
| Helitron | Hel1a | |
| Maverick/Polinton | Group 1 | |
| Maverick/Polinton | Group 2 | |
| Crypton | A | |
| Crypton | F | |
| Crypton | I | |
| Crypton | S | |
| Crypton | V | |
| Crypton | Enterprise | |
| Zisupton | Zisupton | |
| Zisupton | Dileera | |
| Zisupton | Kyakuja | |
| Penelope | EN(-) | |
| Penelope | EN(+) | |
| Penelope | Neptune | |
| Penelope | Nematis | |
| Penelope | Perere | |
| Penelope | Athena | |
| Penelope | Poseidon | |
| Penelope | Cercyon | |
| Penelope | Osiris | |
| Penelope | Coprina | |
| Penelope | CA Clade | |
| Penelope | Dryad | |
| Ty3/Gypsy | Chromovirus | |
| Ty3/Gypsy | Non-Chromovirus | |
| Ty3/Gypsy | OTA | |
| Ty3/Gypsy | Chlamyvir | |
| Ty3/Gypsy | Tcn1 | 2 |
| Ty3/Gypsy | Galadriel | |
| Ty3/Gypsy | Tekay | |
| Ty3/Gypsy | Del | |
| Ty3/Gypsy | Reina | |
| Ty3/Gypsy | CRM | |
| CRM | CR1 | |
| CRM | CR2 | |
| CRM | CR3 | |
| CRM | CR4 | |
| CRM | CR5 | |
| CRM | CR6 | |
| CRM | Cereba | |
| Ty3/Gypsy | Hypo | |
| Ty3/Gypsy | Chromo-Unclassified | |
| Ty3/Gypsy | Phygy | |
| Ty3/Gypsy | Selgy | |
| Ty3/Gypsy | REM | |
| Ty3/Gypsy | G-Rhodo | |
| Ty3/Gypsy | TF1-2 | 2 |
| Ty3/Gypsy | Pyggy | 2 |
| Ty3/Gypsy | MGLR3 | 2 |
| Ty3/Gypsy | Maggy | 2 |
| Ty3/Gypsy | MarY1 | 2 |
| Ty3/Gypsy | Pyret | 2 |
| Ty3/Gypsy | V-Clade | 2 |
| Ty3/Gypsy | Ty3 | |
| Ty3/Gypsy | Skipper | |
| Ty3/Gypsy | Tse3 | |
| Ty3/Gypsy | CsRN1 | |
| Ty3/Gypsy | 412/mdg1 | 2, 3 |
| Ty3/Gypsy | Gypsy | |
| Ty3/Gypsy | 17.6 | |
| Ty3/Gypsy | Osvaldo | 2 |
| Ty3/Gypsy | Gmr1 | |
| Ty3/Gypsy | Cer2-3 | |
| Ty3/Gypsy | Cer1 | |
| Ty3/Gypsy | Mag | 2 |
| Ty3/Gypsy | A-Clade | |
| Ty3/Gypsy | B-Clade | |
| Ty3/Gypsy | C-Clade | |
| Ty3/Gypsy | Tor1 | |
| Ty3/Gypsy | Tor2 | |
| Ty3/Gypsy | Tor4 | |
| Ty3/Gypsy | Cigr-1 | |
| Ty3/Gypsy | Micropia/Mdg3 | 2, 3 |
| Ty3/Gypsy | Archon | |
| Ty3/Gypsy | Chronos | |
| Ty3/Gypsy | Ogre | |
| Ty3/Gypsy | Athila | |
| Ty3/Gypsy | TatI | 2 |
| Ty3/Gypsy | TatII | |
| Ty3/Gypsy | TatIII | |
| Ty3/Gypsy | Retand | |
| Ty3/Gypsy | Tat | |
| Ty3/Gypsy | MolGy1 | |
| Ty3/Gypsy | MolGy2 | |
| Ty3/Gypsy | MolGy3 | |
| Ty3/Gypsy | MolGy4 | |
| Ty3/Gypsy | MolGy5 | |
| Ty3/Gypsy | MolGy6 | |
| Ty3/Gypsy | MolGy7 | |
| Ty3/Gypsy | MolGy8 | |
| Ty3/Gypsy | MolGy10 | |
| Ty3/Gypsy | MolGy11 | |
| Ty3/Gypsy | MolGy12 | |
| Ty3/Gypsy | MolGy13 | |
| Ty3/Gypsy | MolGy14 | |
| Ty3/Gypsy | MolGy16 | |
| Ty3/Gypsy | ReTe1 | |
| Ty3/Gypsy | Saci-2 | 2 |
| Ty3/Gypsy | Mlig-specific | |
| Ty3/Gypsy | Osiris | |
| Ty3/Gypsy | Ulysses | 2 |
| Ty3/Gypsy | Isis | 2 |
| Ty3/Gypsy | Isis-like | |
| Ty3/Gypsy | Blastopia | 2 |
| Ty3/Gypsy | Sacco | |
| Ty3/Gypsy | Chimpo | 2 |
| Ty3/Gypsy | Bica | 2 |
| Ty3/Gypsy | Helos1 | |
| Ty3/Gypsy | GyDi1 | |
| Ty3/Gypsy | GyDi2 | |
| Ty3/Gypsy | Tag | |
| Ty3/Gypsy | GEC1 | |
| Ty3/Gypsy | GEC2 | |
| Ty3/Gypsy | GyRex1-like | |
| Ty3/Gypsy | GyPemo2-like | |
| Ty3/Gypsy | Dingle | |
| Ty1/Copia | CoDi-A/CoDi-I | 2 |
| Ty1/Copia | CoDi-B/CoDi-II | 2 |
| Ty1/Copia | CoDi-C | 2 |
| Ty1/Copia | CoDi-D | 2 |
| Ty1/Copia | Bryco | |
| Ty1/Copia | Lyco | |
| Ty1/Copia | Oryco | |
| Ty1/Copia | Retrofit | 2 |
| Ty1/Copia | Osser | 2 |
| Ty1/Copia | PyRE1G1 | 2 |
| Ty1/Copia | Hydra | |
| Ty1/Copia | Ty/Pseudovirus | |
| Ty1/Copia | Copia | |
| Ty1/Copia | 1731 | 2 |
| Ty1/Copia | Tricopia | |
| Ty1/Copia | Mtanga | 2 |
| Ty1/Copia | Humnum | |
| Ty1/Copia | pCretro | 2 |
| Ty1/Copia | Gymco-I | |
| Ty1/Copia | Gymco-II | |
| Ty1/Copia | Gymco-III | |
| Ty1/Copia | Gymco-IV | |
| Ty1/Copia | Ale | |
| Ty1/Copia | Ivana | |
| Ty1/Copia | Ikeros | |
| Ty1/Copia | Tork | |
| Ty1/Copia | Alesia | |
| Ty1/Copia | Angela | |
| Ty1/Copia | Bianca | |
| Ty1/Copia | SIRE | 2 |
| Ty1/Copia | TAR | |
| Ty1/Copia | Maximus | |
| Ty1/Copia | Hopscotch | |
| Ty1/Copia | Tnt1 | |
| Ty1/Copia | Tos17 | |
| Ty1/Copia | Tont1 | |
| Ty1/Copia | GalEA | 2 |
| Ty1/Copia | FunCo1 | |
| Ty1/Copia | FunCo2 | |
| Ty1/Copia | FunCo3 | |
| Ty1/Copia | FunCo4 | |
| Ty1/Copia | FunCo5 | |
| Ty1/Copia | FunCo6 | |
| Ty1/Copia | FunCo7 | |
| Ty1/Copia | FunCo9 | |
| Ty1/Copia | FunCo10 | |
| Ty1/Copia | FunCo11 | |
| Ty1/Copia | FunCo14 | |
| Ty1/Copia | FunCo15 | |
| Ty1/Copia | FunCo16 | |
| Ty1/Copia | FunCo17 | |
| Ty1/Copia | FunCo18 | |
| Ty1/Copia | FunCo19 | |
| Ty1/Copia | FunCo21 | |
| Ty1/Copia | FunCo22 | |
| Ty1/Copia | FunCo23 | |
| Ty1/Copia | FunCo24 | |
| Ty1/Copia | FunCo25 | |
| Ty1/Copia | FunCo26 | |
| Ty1/Copia | FunCo27 | |
| Ty1/Copia | Copia2 | 2 |
| Ty1/Copia | Copiabis | |
| Ty1/Copia | Copia2bis | |
| Ty1/Copia | Xanthias | 2 |
| Ty1/Copia | New Xanthias | |
| Ty1/Copia | CEC1 | |
| Ty1/Copia | CEC2 | |
| Ty1/Copia | CEC3 | |
| Ty1/Copia | CEC4 | |
| Ty1/Copia | CoLesa1-like | |
| DIRS | DIRS | 2 |
| DIRS | Ngaro | |
| DIRS | VIPER | |
| DIRS | TATE | 2 |
| DIRS | PAT | 2, 3 |
| BEL/Pao | Sinbad | 2 |
| BEL/Pao | BEL | |
| BEL/Pao | Pao | |
| BEL/Pao | Tas | 2 |
| BEL/Pao | Suzu | |
| BEL/Pao | Flow | |
| BEL/Pao | Dan | |
| BEL/Pao | Ninja | 2 |
| BEL/Pao | Diver | 2, 3 |
| BEL/Pao | Diver2 | 2, 3 |
| BEL/Pao | Belmondo | |
| BEL/Pao | Belmondo2 | |
| BEL/Pao | Batumi/Max | 2, 3, 4 |
| BEL/Pao | Roo/RooA | 2, 3, 4 |
| BEL/Pao | Sparrow | |
| BEL/Pao | Surcouf | |
| BEL/Pao | BEC1 | |
| BEL/Pao | BEC2 | |
| BEL/Pao | BEC3 | |
| BEL/Pao | BEC4 | |
| BEL/Pao | BEC5 | |
| LINE | Hamp | |
| LINE | LEC1 | |
| LINE | LEC2 | |
| LINE | LEC3 | |
| R2 | R2-A1 | |
| R2 | R2-A2 | |
| R2 | R2-A3 | |
| R2 | R9 | |
| R2 | R2-B1 | |
| R2 | R2-B2 | |
| R2 | R2-C1 | |
| R2 | R2-D1 | |
| R2 | R2-D2 | |
| R2 | R2-D3 | |
| R2 | R2-D4 | |
| R2 | R2-D5 | |
| R2 | R8 | |
| R2? | BLAG | |
| R1 | R6 | |
| R1 | RT | |
| R1 | R7 | |
| R1 | Mino | |
| R1 | Waldo | |
| R1 | SART | |
| R1 | TRAS | |
| NeSL | Utopia | |
| NeSL | R5 | |
| Tx1 | Keno | |
| Tx1 | Mutsu | |
| Tx1 | Kibi | |
| L1 | Vetebrate Group | |
| L1 | Plant Group | |
| L1 | Group A | |
| L1 | Group B | |
| L1 | Group C | |
| L1 | LIb | 2 |
| L1 | LINE-CS | 2 |
| L1 | BNR | |
| L1 | PUR | |
| L1 | nubo | 2 |
| L1 | Karma | 2 |
| L1 | cin4 | 2 |
| L1 | Tal1 | |
| L1 | Algal | 2 |
| L1 | Oomycete | |
| L1 | M | |
| L1 | F | |
| L1 | ME1 | |
| L1 | ME2 | |
| L1 | ME3 | |
| L1 | Mammals | |
| L1 | Lizard clade 1 | |
| L1 | Lizard clade 2 | |
| L1 | Frog clade 1 | |
| L1 | Frog clade 2 | |
| L1 | Fish clade 1 | |
| L1 | Fish clade 2 | |
| RTE | Plant/Animal | 2 |
| RTE | Rex3/RTE | 2 |
| RTE | BovB | 2, 3 |
| RTE | BovB-IA | |
| RTE | BovB-IB | |
| RTE | BovB-II | |
| RTE | C. elegans/Bombyx RTE | 2 |
| RTE | I | |
| RTE | II | |
| RTE | II | |
| RTE | IV | |
| RTE | V | |
| RTE | VI | |
| RTE | VII | |
| Jockey | Lin1 | |
| Jockey | Lin2 | |
| Jockey | Lin3 | |
| Jockey | Lin4 | |
| Jockey | Lin5 | |
| Jockey | Lin6 | |
| Jockey | Lin7 | |
| Jockey | Syrinx | |
| CR1 | CR1A | |
| CR1 | CR1B | |
| CR1 | Group A | |
| CR1 | Group B | |
| CR1 | Group C | |
| CR1 | Group D | |
| CR1 | Group E | |
| CR1 | Group F | |
| CR1 | Group G | |
| Rex1 | 1 | |
| Rex1 | 2 | |
| Rex1 | 3 | |
| Rex1 | 4 | |
| Rex1 | Babar |