full_name title description hyperlink count repeatmasker_type repeatmasker_subtype repbase_equiv wicker_equiv curcio_derbyshire_equiv piegu_equiv Accidental Accidental/spontaneous integration events. Accidental;Normally_Non-integrating_Virus Virus families that are more likely the result of spontaneous integration rather than Retrotranposition. 25 Other DNA_virus Artifact Elements often found in cloning vectors that may contaminate sequencing projects. 43 ARTEFACT Interspersed_Repeat A repetitive sequence with copies interspersed throughout an organisms genome. Interspersed_Repeat;Pseudogene Duplications of existing genes in an organism. Interspersed_Repeat;Pseudogene;RNA Non-translated, small RNA genes often found in high copy number. Related genes are included 17 RNA Interspersed_Repeat;Pseudogene;RNA;rRNA Copies of a ribosomal RNA (rRNA) gene or pseudogene. 4969 rRNA Interspersed_Repeat;Pseudogene;RNA;scRNA 75 scRNA Interspersed_Repeat;Pseudogene;RNA;snRNA Copies of a small nuclear RNA (snRNA) gene or pseudogene. Small nuclear RNAs include 7SK RNA and the U1 to U13. They are dependent on external promoters and are theferore much less frequently involved in the creation of a SINE 2369 snRNA Interspersed_Repeat;Pseudogene;RNA;tRNA Copies of a transfer RNA (tRNA) gene or pseudogene. In mammals, tRNAs copies can occur in relatively large numbers (up to a thousand copies) The boundary between a large number of accidentally retroposed or otherwise duplicated (pseudo)genes and a low copy number SINE (selected on its ability to propagate) is nebulous 8301 tRNA Interspersed_Repeat;Transposable_Element Families that are the direct result of transposition events. Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition Elements that do not require an RNA intermediate in their transposition lifecycle. Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;DNA_Polymerase Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;DNA_Polymerase;Casposon Archaeal and bacterial mobile elements at the origin of CRISPR-Cas immunity. PMID 24884953, 26764427 https://www.ncbi.nlm.nih.gov/pubmed/?term=24884953 DNA Casposons Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;DNA_Polymerase;Maverick 17459 DNA Maverick DNA/Polinton D/M (Maverick)/M (Maverick) Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;DNA_Polymerase;Maverick;Maverick-Mavirus Maverick-Mavirus DNA Maverick-Mavirus DNA/Polinton D/M (Maverick)/M (Maverick) Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Helicase Circular ssDNA Intermediate. Circular ssDNA Intermediate RC DNA D/H/H Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Helicase;Helentron 1 RC Helentron DNA/Helentron Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Helicase;Helitron-1 115883 RC Helitron DNA/Helitron D/H/H (Helitron) Y2-transposons Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Helicase;Helitron-2 83 RC Helitron-2 DNA/Helitron D/H/H (Helitron) Y2-transposons Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase DNA transposons with terminal inverted repeats ranging from 6 bp to many kb. Autonomous elements have a DD(E/D) transposase. Most DNA transposons fall in this class. Some non-autonomous elements, hairpin 68854 DNA DNA D Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Academ Academ superfamily of DNA transposons. Found in metazoans and fungi, autonomous Academ elements encode a ca 1.5 kb protein containing an XPG exonuclease domain, a Cys8 zinc finger, and a DDE transposase domain unlike those of others. Termini tend to be TAGÉCTA and a 3 bp target site is duplicated. Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Academ;Academ-1 First described family of Academ DNA transposon. 10566 DNA Academ-1 DNA/Academ D/T (TIR) DDE-transposons DDE-transposons/CutOPasI/Academ Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Academ;Academ-2 Second described family of Academ DNA transposon. 290 DNA Academ-2 DNA/Academ D/T (TIR) DDE-transposons DDE-transposons/CutOPasI/Academ Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Academ;Academ-H Family of Academ transposons described in rust fungi. 105 DNA Academ-H DNA/Academ D/T (TIR) DDE-transposons DDE-transposons/CutOPasI/Academ Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;CACTA A group of DNA transposons with characteristic CACTA…TAGTG termini. Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;CACTA;CMC CACTA (EnSpm), Mirage, Chapaev group with related DNA transposons. 48 DNA CMC Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;CACTA;CMC;Chapaev_group Superfamily including Chapaev and Chapaev-3 elements. Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;CACTA;CMC;Chapaev_group;Chapaev So-far animal-specific elements with a specific DDE transposase. 619 DNA CMC-Chapaev DNA/Enspm/Cacta D/T (TIR)/C (CACTA) DDE-transposons DDE-transposons/CutOPasI/CMC Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;CACTA;CMC;Chapaev_group;Chapaev-3 So-far animal-specific elements with a specific DDE transposase. 6921 DNA CMC-Chapaev-3 DNA/Enspm/Cacta D/T (TIR)/C (CACTA) DDE-transposons DDE-transposons/CutOPasI/CMC Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;CACTA;CMC;EnSpm 34370 DNA CMC-EnSpm DNA/Enspm/Cacta D/T (TIR)/C (CACTA) DDE-transposons DDE-transposons/CutOPasI/CMC Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;CACTA;CMC;Mirage 13 DNA CMC-Mirage DNA/Enspm/Cacta D/T (TIR)/C (CACTA) DDE-transposons DDE-transposons/CutOPasI/CMC Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;CACTA;Transib Group of DNA transposons at the basis of our adaptive immune system. 8163 DNA CMC-Transib DNA/Enspm/Cacta D/T (TIR)/R (Transib) DDE-transposons DDE-transposons/CutOPasI/CMC Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Dada 759 DNA Dada DNA/Dada D/T (TIR) DDE-transposons DDE-transposons/CutOPasI/Dada Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Ginger 24 DNA Ginger DNA/Ginger1 D/T (TIR) DDE-transposons DDE-transposons Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Ginger;Ginger-1 Ginger-1 233 DNA Ginger-1 DNA/Ginger1 D/T (TIR) DDE-transposons DDE-transposons Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Ginger;Ginger-2 Ginger-2 1000 DNA Ginger-2 DNA/Ginger2 D/T (TIR) DDE-transposons DDE-transposons Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;IS3EU 5137 DNA IS3EU DNA/IS3EU D DDE-transposons/CopOPasI/IS3 Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Kolobok 2599 DNA Kolobok Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Kolobok;Hydra-specific_Branch 4978 DNA Kolobok-Hydra DNA/Kolobok D/T (TIR) DDE-transposons DDE-transposons/CutOPasI/Kolobok Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Kolobok;Kolobok-E 1131 DNA Kolobok-E DNA/KolobokE D/T (TIR) DDE-transposons DDE-transposons/CutOPasI/Kolobok Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Kolobok;Kolobok-H 94 DNA Kolobok-H DNA/ D/T (TIR) DDE-transposons DDE-transposons/CutOPasI/Kolobok Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Kolobok;T2 12037 DNA Kolobok-T2 DNA/Kolobok D/T (TIR) DDE-transposons DDE-transposons/CutOPasI/Kolobok Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Merlin 6970 DNA Merlin DNA/Merlin D/T (TIR)/E (Merlin) DDE-transposons DDE-transposons/CutOPasI/IS1595-Merlin Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Mutator-like Mutator-like Element aka MULE. Mutator-like Element aka MULE 58 DNA MULE DNA/MuDR D/T (TIR)/M (Mutator) DDE-transposons DDE-transposons/CutOPasI/IS256/MuDR/Mutator/Rehavkus Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Mutator-like;F 20 DNA MULE-F DNA/MuDRF D/T (TIR)/M (Mutator) DDE-transposons DDE-transposons/CutOPasI/IS256/MuDR/Mutator/Rehavkus Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Mutator-like;MuDR 22656 DNA MULE-MuDR DNA/MuDR D/T (TIR)/M (Mutator) DDE-transposons DDE-transposons/CutOPasI/IS256/MuDR/Mutator/Rehavkus Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Mutator-like;NOF 2217 DNA MULE-NOF DNA/MuDR D/T (TIR)/M (Mutator) DDE-transposons DDE-transposons/CutOPasI/IS256/MuDR/Mutator/Rehavkus Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Mutator-like;Ricksha Ricksha subclass 25 DNA MULE-Ricksha DNA/MuDR D/T (TIR)/M (Mutator) DDE-transposons DDE-transposons/CutOPasI/IS256/MuDR/Mutator/Rehavkus Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Novosib 74 DNA Novosib DNA/Novosib D Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;PIF-Harbinger 66 DNA PIF Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;PIF-Harbinger;HarbS 51 DNA PIF-HarbS DNA/HarbS D/T (TIR)/H (PIF-Harbinger) DDE-transposons DDE-transposons/CutOPasI/IS5/PIF/Harbinger Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;PIF-Harbinger;Harbinger 64355 DNA PIF-Harbinger DNA/Harbinger D/T (TIR)/H (PIF-Harbinger) DDE-transposons DDE-transposons/CutOPasI/IS5/PIF/Harbinger Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;PIF-Harbinger;ISL2EU 3921 DNA PIF-ISL2EU DNA/ISL2EU D/T (TIR)/H (PIF-Harbinger) DDE-transposons DDE-transposons/CutOPasI/IS5/PIF/Harbinger Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;PIF-Harbinger;Spy 2740 DNA PIF-Spy DNA/Harbinger D/T (TIR)/H (PIF-Harbinger) DDE-transposons DDE-transposons/CutOPasI/IS5/PIF/Harbinger Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;P_Element 10941 DNA P DNA/P D/T (TIR)/P DDE-transposons DDE-transposons/CutOPasI/P (?) Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;P_Element;Fungi-specific_Branch 40 DNA P-Fungi DNA/P D/T (TIR)/P DDE-transposons DDE-transposons/CutOPasI/P (?) Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;PiggyBac_Group Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;PiggyBac_Group;PiggyBac 21819 DNA PiggyBac DNA/piggyBac D/T (TIR)/B (PiggyBac) DDE-transposons DDE-transposons/CutOPasI/ISI380/PiggyBac Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;PiggyBac_Group;PiggyBac-A 5 DNA PiggyBac-A DNA/piggyBacA D/T (TIR)/B (PiggyBac) DDE-transposons DDE-transposons/CutOPasI/ISI380/PiggyBac Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;PiggyBac_Group;PiggyBac-X 82 DNA PiggyBac-X DNA/piggyBacX D/T (TIR)/B (PiggyBac) DDE-transposons DDE-transposons/CutOPasI/ISI380/PiggyBac Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Sola Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Sola;Sola-1 5110 DNA Sola-1 DNA/Sola1 D/T (TIR) DDE-transposons DDE-transposons/CutOPasI/Sola Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Sola;Sola-2 5009 DNA Sola-2 DNA/Sola2 D/T (TIR) DDE-transposons DDE-transposons/CutOPasI/Sola Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Sola;Sola-3 396 DNA Sola-3 DNA/Sola3 D/T (TIR) DDE-transposons DDE-transposons/CutOPasI/Sola Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Tc1-Mariner 2417 DNA TcMar DNA/Mariner D/T (TIR)/T (Tc1-Mariner) DDE-transposons DDE-transposons/CutOPasI/ITM (IS630/Tc1/Mariner)/Zator Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Tc1-Mariner;Ant1 A group of DNA transposons so far limited to fungi. 143 DNA TcMar-Ant1 DNA/Mariner D/T (TIR)/T (Tc1-Mariner) DDE-transposons DDE-transposons/CutOPasI/ITM (IS630/Tc1/Mariner)/Zator Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Tc1-Mariner;Cweed 20 DNA TcMar-Cweed DNA/Mariner D/T (TIR)/T (Tc1-Mariner) DDE-transposons DDE-transposons/CutOPasI/ITM (IS630/Tc1/Mariner)/Zator Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Tc1-Mariner;Gizmo 16 DNA TcMar-Gizmo DNA/Mariner D/T (TIR)/T (Tc1-Mariner) DDE-transposons DDE-transposons/CutOPasI/ITM (IS630/Tc1/Mariner)/Zator Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Tc1-Mariner;IS885 TcMar-IS885 2 DNA TcMar-IS885 DNA/Mariner D/T (TIR)/T (Tc1-Mariner) DDE-transposons DDE-transposons/CutOPasI/ITM (IS630/Tc1/Mariner)/Zator Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Tc1-Mariner;ISRm11 5954 DNA TcMar-ISRm11 DNA/Mariner D/T (TIR)/T (Tc1-Mariner) DDE-transposons DDE-transposons/CutOPasI/ITM (IS630/Tc1/Mariner)/Zator Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Tc1-Mariner;Mariner 38452 DNA TcMar-Mariner DNA/Mariner D/T (TIR)/T (Tc1-Mariner) DDE-transposons DDE-transposons/CutOPasI/ITM (IS630/Tc1/Mariner)/Zator Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Tc1-Mariner;Mogwai 2 DNA TcMar-Mogwai DNA/Mariner D/T (TIR)/T (Tc1-Mariner) DDE-transposons DDE-transposons/CutOPasI/ITM (IS630/Tc1/Mariner)/Zator Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Tc1-Mariner;Sagan 90 DNA TcMar-Sagan DNA/Mariner D/T (TIR)/T (Tc1-Mariner) DDE-transposons DDE-transposons/CutOPasI/ITM (IS630/Tc1/Mariner)/Zator Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Tc1-Mariner;Stowaway 1929 DNA TcMar-Stowaway DNA/Mariner D/T (TIR)/T (Tc1-Mariner) DDE-transposons DDE-transposons/CutOPasI/ITM (IS630/Tc1/Mariner)/Zator Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Tc1-Mariner;Tc1 117526 DNA TcMar-Tc1 DNA/Mariner D/T (TIR)/T (Tc1-Mariner) DDE-transposons DDE-transposons/CutOPasI/ITM (IS630/Tc1/Mariner)/Zator Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Tc1-Mariner;Tc2-group Containing the sister clades of Tc2, Pogo, Fot1, and Tigger DNA transposons. Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Tc1-Mariner;Tc2-group;Fot1 7070 DNA TcMar-Fot1 DNA/Mariner D/T (TIR)/T (Tc1-Mariner) DDE-transposons DDE-transposons/CutOPasI/ITM (IS630/Tc1/Mariner)/Zator Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Tc1-Mariner;Tc2-group;Pogo 4167 DNA TcMar-Pogo DNA/Mariner D/T (TIR)/T (Tc1-Mariner) DDE-transposons DDE-transposons/CutOPasI/ITM (IS630/Tc1/Mariner)/Zator Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Tc1-Mariner;Tc2-group;Tc2 9272 DNA TcMar-Tc2 DNA/Mariner D/T (TIR)/T (Tc1-Mariner) DDE-transposons DDE-transposons/CutOPasI/ITM (IS630/Tc1/Mariner)/Zator Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Tc1-Mariner;Tc2-group;Tigger So far animal-specific mariner-like elements with the mammalian Tigger1 as type specimen. 27401 DNA TcMar-Tigger DNA/Mariner D/T (TIR)/T (Tc1-Mariner) DDE-transposons DDE-transposons/CutOPasI/ITM (IS630/Tc1/Mariner)/Zator Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Tc1-Mariner;Tc4 4582 DNA TcMar-Tc4 DNA/Mariner D/T (TIR)/T (Tc1-Mariner) DDE-transposons DDE-transposons/CutOPasI/ITM (IS630/Tc1/Mariner)/Zator Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Tc1-Mariner;m44 3419 DNA TcMar-m44 DNA/Mariner D/T (TIR)/T (Tc1-Mariner) DDE-transposons DDE-transposons/CutOPasI/ITM (IS630/Tc1/Mariner)/Zator Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Zator 4561 DNA Zator DNA/Zator D DDE-transposons/CutOPasI/ITM (IS630/Tc1/Mariner)/Zator Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;Zisupton 4418 DNA Zisupton DNA/Zisupton D Zisupton Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;hAT hobo Activator Tam3 Elements. hobo Activator Tam3 Elements 17820 DNA hAT DNA/hAT D/T (TIR)/A (hAT) DDE-transposons DDE-transposons/CutOPasI/hAT Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;hAT;Activator A large class in plants and animals named after the maize element. 96648 DNA hAT-Ac DNA/hAT D/T (TIR)/A (hAT) DDE-transposons DDE-transposons/CutOPasI/hAT Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;hAT;Blackjack A group of hAT transposons possibly closest to Charlie elements. 15667 DNA hAT-Blackjack DNA/hAT D/T (TIR)/A (hAT) DDE-transposons DDE-transposons/CutOPasI/hAT Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;hAT;Charlie Mostly animal-specific hAT transposons with the mammalian Charlie1 as type specimen. 73912 DNA hAT-Charlie DNA/hAT D/T (TIR)/A (hAT) DDE-transposons DDE-transposons/CutOPasI/hAT Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;hAT;Pegasus 479 DNA hAT-Pegasus DNA/hAT D/T (TIR)/A (hAT) DDE-transposons DDE-transposons/CutOPasI/hAT Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;hAT;Restless 215 DNA hAT-Restless DNA/hAT D/T (TIR)/A (hAT) DDE-transposons DDE-transposons/CutOPasI/hAT Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;hAT;Tag1 6408 DNA hAT-Tag1 DNA/hAT D/T (TIR)/A (hAT) DDE-transposons DDE-transposons/CutOPasI/hAT Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;hAT;Tip100 Widespread class of hAT elements, including the Arthur and Zaphod elements in ancient mammals. 61196 DNA hAT-Tip100 DNA/hAT D/T (TIR)/A (hAT) DDE-transposons DDE-transposons/CutOPasI/hAT Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;hAT;hAT1 36 DNA hAT-hAT1 DNA/hAT1 D/T (TIR)/A (hAT) DDE-transposons DDE-transposons/CutOPasI/hAT Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;hAT;hAT19 4897 DNA hAT-hAT19 DNA/hAT19 D/T (TIR)/A (hAT) DDE-transposons DDE-transposons/CutOPasI/hAT Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;hAT;hAT5 4971 DNA hAT-hAT5 DNA/hAT5 D/T (TIR)/A (hAT) DDE-transposons DDE-transposons/CutOPasI/hAT Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;hAT;hAT6 1233 DNA hAT-hAT6 DNA/hATa D/T (TIR)/A (hAT) DDE-transposons DDE-transposons/CutOPasI/hAT Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;hAT;hATm 4604 DNA hAT-hATm DNA/hATm D/T (TIR)/A (hAT) DDE-transposons DDE-transposons/CutOPasI/hAT Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;hAT;hATw 83 DNA hAT-hATw DNA/hATw D/T (TIR)/A (hAT) DDE-transposons DDE-transposons/CutOPasI/hAT Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;hAT;hATx 2321 DNA hAT-hATx DNA/hATx D/T (TIR)/A (hAT) DDE-transposons DDE-transposons/CutOPasI/hAT Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Transposase;hAT;hobo 1539 DNA hAT-hobo DNA/hAT D/T (TIR)/A (hAT) DDE-transposons DDE-transposons/CutOPasI/hAT Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Tyrosine_Recombinase Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Tyrosine_Recombinase;Crypton 898 DNA Crypton DNA/Crypton D/Y (Crypton)/C (Crypton) Y1-transposons Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Tyrosine_Recombinase;Crypton;Crypton-A 4172 DNA Crypton-A DNA/CryptonA D/Y (Crypton)/C (Crypton) Y1-transposons Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Tyrosine_Recombinase;Crypton;Crypton-C 86 DNA Crypton-C DNA/CryptonC D/Y (Crypton)/C (Crypton) Y1-transposons Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Tyrosine_Recombinase;Crypton;Crypton-F 66 DNA Crypton-F DNA/CryptonF D/Y (Crypton)/C (Crypton) Y1-transposons Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Tyrosine_Recombinase;Crypton;Crypton-H 413 DNA Crypton-H DNA/CryptonH D/Y (Crypton)/C (Crypton) Y1-transposons Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Tyrosine_Recombinase;Crypton;Crypton-I 4001 DNA Crypton-I DNA/CryptonI D/Y (Crypton)/C (Crypton) Y1-transposons Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Tyrosine_Recombinase;Crypton;Crypton-R 5 DNA Crypton-R DNA/CryptonR D/Y (Crypton)/C (Crypton) Y1-transposons Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Tyrosine_Recombinase;Crypton;Crypton-S 177 DNA Crypton-S DNA/CryptonS D/Y (Crypton)/C (Crypton) Y1-transposons Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Tyrosine_Recombinase;Crypton;Crypton-V 2649 DNA Crypton-V DNA/CryptonV D/Y (Crypton)/C (Crypton) Y1-transposons Interspersed_Repeat;Transposable_Element;Class_II_DNA_Transposition;Tyrosine_Recombinase;Crypton;Crypton-X 5 DNA Crypton-X DNA/CryptonX D/Y (Crypton)/C (Crypton) Y1-transposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition Elements that require an RNA intermediate in their transposition lifecycle. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE Long Interspersed Nuclear Element. https://en.wikipedia.org/wiki/Long_interspersed_nuclear_element 4180 LINE non-LTR/ R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-I Based on reverse transcriptase phylogeny, an outlier group containing the Ambal, CRE and Odin LINE elements. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-I;Ambal A group of LINE so far specific to Diatoms. 37 LINE CRE-Ambal non-LTR/Ambal R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-I;CRE 5310 LINE CRE non-LTR/CRE R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-I;CRE;CRE-1 LINE CRE-1 non-LTR/CRE R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-I;CRE;CRE-2 LINE CRE-2 non-LTR/CRE R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-I;Odin 18 LINE CRE-Odin non-LTR/- R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II The bulk of the LINE elements. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Genie 1 LINE Genie non-LTR/- R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-1 Containing the sister classes of Proto-1, L1-like, R2-like, and R4-like LINE elements. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-1;L1-like Containing the sister classes of DRE, L1, Tx1, and Zorro LINE elements. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-1;L1-like;DRE 45 LINE L1-DRE non-LTR/ R/I (LINE)/L (L1) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-1;L1-like;L1-group Containing the closely related L1 and Tx1 LINE elements. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-1;L1-like;L1-group;L1 A large group of LINE elements with mammalian LINE-1 (L1) as type specimen. 97732 LINE L1 non-LTR/L1 R/I (LINE)/L (L1) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-1;L1-like;L1-group;Tx1 10139 LINE L1-Tx1 non-LTR/Tx1 R/I (LINE)/L (L1) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-1;L1-like;Zorro 12 LINE L1-Zorro non-LTR/ R/I (LINE)/L (L1) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-1;Proto-1 8 LINE Proto1 non-LTR/Proto1 R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-1;R2-like Containing the sister clades of R2, Hero and NeSL LINEs. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-1;R2-like;Hero 2122 LINE R2-Hero non-LTR/Hero R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-1;R2-like;NeSL 928 LINE R2-NeSL non-LTR/NeSL R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-1;R2-like;R2 1384 LINE R2 non-LTR/R2 R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-1;R4-like Containing the sister clades of Deceiver, Dong-R4, and Dualen LINE elements. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-1;R4-like;Deceiver 11 LINE Deceiver non-LTR/- R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-1;R4-like;Dong-R4 7869 LINE Dong-R4 non-LTR/R4 R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-1;R4-like;Dualen 133 LINE Dualen non-LTR/RandI/Dualen R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2 Containing the sister classes of Proto-2, R1-like, and RTE-like LINE elements. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;Proto-2 7674 LINE Proto2 non-LTR/Proto2 R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;R1-like Containing Tad1, CR1-related and R1-related LINEs. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;R1-like;CR1-group Containing the sister classes of CR1, L2 and Rex-Babar LINEs. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;R1-like;CR1-group;CR1 A large group of LINE elements with Chicken Repeat 1 (CR1) as type specimen. 114119 LINE CR1 non-LTR/CR1 R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;R1-like;CR1-group;CR1;Zenon 13089 LINE CR1-Zenon non-LTR/CR1 R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;R1-like;CR1-group;L2-group A large group of L2-like elements that can still need to be subclassified. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;R1-like;CR1-group;L2-group;L2 A large group of LINE elements with mammalian LINE-2 (L2) as type specimen. 155258 LINE L2 non-LTR/L2 R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;R1-like;CR1-group;Rex-Babar 30893 LINE Rex-Babar non-LTR/Rex1 R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;R1-like;R1-group Containing the I, Jockey, LOA and R1 LINEs. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;R1-like;R1-group;I-group Containing the sister classes of I and Jockey LINE elements. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;R1-like;R1-group;I-group;I 21800 LINE I non-LTR/I + Nimb R/I (LINE)/I TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;R1-like;R1-group;I-group;Jockey 30026 LINE I-Jockey non-LTR/Jockey R/I (LINE)/J (Jockey) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;R1-like;R1-group;R1-subgroup Containing the closely related LOA and R1 LINEs. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;R1-like;R1-group;R1-subgroup;LOA 21899 LINE R1-LOA non-LTR/Loa R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;R1-like;R1-group;R1-subgroup;R1 29574 LINE R1 non-LTR/R1 R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;R1-like;Tad1 1126 LINE Tad1 non-LTR/Tad1 R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;RTE-like 3071 LINE RTE non-LTR/RTE R/I (LINE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;RTE-like;ORTE 236 LINE RTE-ORTE non-LTR/RTE R/I (LINE)/T (RTE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;RTE-like;RTE-group Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;RTE-like;RTE-group;BovB A subgoup of RTE elements with the bovine BovB as the type specimen. 63421 LINE RTE-BovB non-LTR/RTE (and 1 RTETP) R/I (LINE)/T (RTE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;RTE-like;RTE-group;RTE 22346 LINE RTE-RTE non-LTR/RTE R/I (LINE)/T (RTE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE;Group-II;Group-2;RTE-like;RTE-group;RTE-X 14082 LINE RTE-X non-LTR/RTEX R/I (LINE)/T (RTE) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;Lacking_Small_RNA_pol_III_Promoter 2053 Retroposon non-LTR R Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;Lacking_Small_RNA_pol_III_Promoter;I-derived Nonautonomous retroposons derived from I-type LINEs. Retroposon I-derived SINE R/S (SINE) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;Lacking_Small_RNA_pol_III_Promoter;L1-dependent A retroposon mobilized by an L1-type LINE. 635 Retroposon L1-dep non-LTR R Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;Lacking_Small_RNA_pol_III_Promoter;L1-dependent;SVA 72 Retroposon SVA non-LTR R Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;Lacking_Small_RNA_pol_III_Promoter;L1-derived Nonautonomous retroposons derived from L1-type LINEs. 81 Retroposon L1-derived SINE R/S (SINE) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;Lacking_Small_RNA_pol_III_Promoter;L2-derived Nonautonomous retroposons derived from L2-type LINEs. 32 Retroposon L2-derived SINE R/S (SINE) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;Lacking_Small_RNA_pol_III_Promoter;R4-derived Nonautonomous retroposons derived from R4-type LINEs. Retroposon R4-derived SINE R/S (SINE) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;Lacking_Small_RNA_pol_III_Promoter;RTE-derived Nonautonomous retroposons derived from RTE-type LINEs. 76 Retroposon RTE-derived non-LTR R Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE Short LINE-dependent retroposons with an internal (usually pol III) promoter. The median length of described SINEs is ca. 250 bp ±130 bp SD. The canonical SINE has a tRNA 5' end with the internal promoter, a core of unknown function shared with multiple other SINE families, a 3' end identical to that of the LINE responsible for its mobility, and a simple repeat tail. A few SINEs have a LINE-derived internal pol II promoter, and many lack either or both the core and LINE-derived regions. https://en.wikipedia.org/wiki/Retrotransposon#SINEs 7990 SINE SINE R/S (SINE) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;5S-RNA_Promoter SINEs with an internal promoter derived from 5S RNA. 874 SINE 5S SINE/SINE3 R/S (SINE)/S (5S) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;5S-RNA_Promoter;Deu-core Animal-wide conserved SINE central region, with the core of the ancient AmnSINE1 as type specimen. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;5S-RNA_Promoter;Deu-core;L2-end SINE with a 3' end derived from a L2-type LINE. 2568 SINE 5S-Deu-L2 SINE/SINE3 R/S (SINE)/S (5S) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;5S-RNA_Promoter;Deu-core;Unknown_LINE-dependent 2377 SINE 5S-Deu SINE/SINE3 R/S (SINE)/S (5S) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;5S-RNA_Promoter;MIR-core SINE with a conserved central core region originally described for MIR. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;5S-RNA_Promoter;MIR-core;RTE-end SINE with a 3' end derived from an RTE-type LINE. 50 SINE 5S-Core-RTE SINE/SINE3 R/S (SINE)/S (5S) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;5S-RNA_Promoter;No_or_Unknown_Core SINEs lacking a central region or with central region yet unrelated to that of other SINEs. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;5S-RNA_Promoter;No_or_Unknown_Core;RTE-end SINE with a 3' end derived from an RTE-type LINE. 46 SINE 5S-RTE Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;5S-RNA_Promoter;Sauria-core Conserved central region so far limited to squamate SINEs. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;5S-RNA_Promoter;Sauria-core;RTE-end SINE with a 3' end derived from an RTE-type LINE. 5 SINE 5S-Sauria-RTE SINE/SINE3 R/S (SINE)/S (5S) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;7SL-RNA_Promoter SINEs with an internal promoter derived from 7SL RNA. 78 SINE 7SL SINE/SINE1 R/S (SINE)/L (7SL) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;7SL-RNA_Promoter;No-core SINEs lacking a central region. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;7SL-RNA_Promoter;No-core;L1-dependent A retroposon mobilized by an L1-type LINE. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;7SL-RNA_Promoter;No-core;L1-dependent;Alu A SINE family specific to primates and rodents. 6901 SINE Alu SINE/SINE1 R/S (SINE)/L (7SL) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;U-RNA_Promoter SINEs with an internal promoter derived from a spliceosomal U-RNA. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;U-RNA_Promoter;No_or_Unknown_Core SINEs lacking a central region or with central region yet unrelated to that of other SINEs. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;U-RNA_Promoter;No_or_Unknown_Core;L1-dependent 5 SINE U-L1 Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;U-RNA_Promoter;No_or_Unknown_Core;Unknown_LINE-dependent 694 SINE U SINE/SINEU R/S (SINE) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;Unknown_Promoter Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;Unknown_Promoter;Ceph-core Containing a SINE core originally discovered in Cephalopod SINEs. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;Unknown_Promoter;Ceph-core;RTE-end SINE with a 3' end derived from an RTE-type LINE. 2 SINE Ceph SINE R/S (SINE) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;Unknown_Promoter;MIR-core SINE with a conserved central core region originally described for MIR. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;Unknown_Promoter;MIR-core;RTE-end SINE with a 3' end derived from an RTE-type LINE. SINE Core-RTE SINE R/S (SINE) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;Unknown_Promoter;MIR-core;Unknown_LINE-dependent SINE Core SINE R/S (SINE) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter SINEs with an internal promoter derived from a tRNA. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;Ceph-core Containing a SINE core originally discovered in Cephalopod SINEs. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;Ceph-core;RTE-end SINE with a 3' end derived from an RTE-type LINE. 15 SINE tRNA-Ceph-RTE SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;Ceph-core;Unknown_LINE-dependent 2 SINE tRNA-Ceph SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;Deu-core Animal-wide conserved SINE central region, with the core of the ancient AmnSINE1 as type specimen. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;Deu-core;CR1-end SINE with a 3' end derived from a CR1-type LINE. 107 SINE tRNA-Deu-CR1 SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;Deu-core;I-end SINE with a 3' end derived from a I-type LINE. 142 SINE tRNA-Deu-I Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;Deu-core;L2-end SINE with a 3' end derived from a L2-type LINE. 688 SINE tRNA-Deu-L2 SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;Deu-core;RTE-end SINE with a 3' end derived from an RTE-type LINE. 445 SINE tRNA-Deu-RTE Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;Deu-core;Unknown_LINE-dependent 1500 SINE tRNA-Deu SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;MIR-core SINE with a conserved central core region originally described for MIR. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;MIR-core;L2-end SINE with a 3' end derived from a L2-type LINE. 18211 SINE MIR SINE/SINE2 R/S (SINE) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;MIR-core;Mermaid SINE tRNA-Mermaid SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;MIR-core;RTE-end SINE with a 3' end derived from an RTE-type LINE. 751 SINE tRNA-Core-RTE SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;MIR-core;Unknown_LINE-dependent 1258 SINE tRNA-Core SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;Meta-core Animal-wide conserved SINE central region. https://www.ncbi.nlm.nih.gov/pubmed/?term=26872770 Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;Meta-core;Unknown_LINE-dependent 1312 SINE tRNA-Meta SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;No-core SINEs lacking a central region. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;No-core;L1-dependent A retroposon mobilized by an L1-type LINE. 3239 SINE ID SINE R/S (SINE) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;No-core;L1-dependent;B2 A rodent specific SINE family. 1172 SINE B2 SINE/SINE1 R/S (SINE)/L (7SL) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;No_or_Unknown_Core SINEs lacking a central region or with central region yet unrelated to that of other SINEs. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;No_or_Unknown_Core;BovB-end SINE with a 3' end derived from a BovB-type LINE. 66 SINE RTE-BovB SINE R/S (SINE) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;No_or_Unknown_Core;CR1-end SINE with a 3' end derived from a CR1-type LINE. 747 SINE tRNA-CR1 SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;No_or_Unknown_Core;I-end SINE with a 3' end derived from a I-type LINE. 165 SINE tRNA-I SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;No_or_Unknown_Core;Jockey-end 4 SINE tRNA-Jockey SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;No_or_Unknown_Core;L1-dependent A retroposon mobilized by an L1-type LINE. 694 SINE tRNA-L1 SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;No_or_Unknown_Core;L2-end SINE with a 3' end derived from a L2-type LINE. 1094 SINE tRNA-L2 SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;No_or_Unknown_Core;R1-end SINE with a 3' end derived from an R1-type LINE. 5 SINE R1 SINE R/S (SINE) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;No_or_Unknown_Core;R2-end SINE with a 3' end derived from an R2-type LINE. 13 SINE tRNA-R2 SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;No_or_Unknown_Core;RTE-end SINE with a 3' end derived from an RTE-type LINE. 5241 SINE tRNA-RTE SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;No_or_Unknown_Core;Rex-end SINE with a 3' end derived from an Rex-type LINE. 15 SINE tRNA-Rex SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;No_or_Unknown_Core;Tad1_End SINE with a 3' end derived from a Tad1-type LINE. SINE tRNA-Tad1 SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;No_or_Unknown_Core;Unknown_LINE-dependent 19463 SINE tRNA SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;Sauria-core Conserved central region so far limited to squamate SINEs. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;Sauria-core;L2-end SINE with a 3' end derived from a L2-type LINE. 140 SINE tRNA-Sauria-L2 SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;Sauria-core;RTE-end SINE with a 3' end derived from an RTE-type LINE. 414 SINE tRNA-Sauria-RTE SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;Sauria-core;Unknown_LINE-dependent 80 SINE tRNA-Sauria SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;V-core Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;V-core;CR1-end SINE with a 3' end derived from a CR1-type LINE. 181 SINE tRNA-V-CR1 SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;V-core;L2-end 11 SINE tRNA-V-L2 SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;V-core;RTE-end RTE-end 83 SINE tRNA-V-RTE SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;V-core;Unknown_LINE-dependent 569 SINE tRNA-V SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;V_and_MIR-core Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_Promoter;V_and_MIR-core;L2-end SINE with a 3' end derived from a L2-type LINE. 28 SINE tRNA-V-Core-L2 SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_and_5S_RNA SINEs retaining fragment of both a tRNA and 5S RNA; promoter can come from either. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_and_5S_RNA;No_or_Unknown_Core SINEs lacking a central region or with central region yet unrelated to that of other SINEs. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_and_5S_RNA;No_or_Unknown_Core;Unknown_LINE-dependent SINE tRNA-5S Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_and_7SL_RNA SINEs retaining fragment of both a tRNA and 7SL RNA; promoter can come from either. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_and_7SL_RNA;No-core SINEs lacking a central region. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_and_7SL_RNA;No-core;L1-dependent A retroposon mobilized by an L1-type LINE. 742 SINE B4 SINE/SINE1 R/S (SINE)/L (7SL)? Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_and_7SL_RNA;No_or_Unknown_Core SINEs lacking a central region or with central region yet unrelated to that of other SINEs. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;SINE;tRNA_and_7SL_RNA;No_or_Unknown_Core;Unknown_LINE-dependent SINE tRNA-7SL SINE/SINE2 R/S (SINE)/T (tRNA) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;snoRNA 14 Retroposon sno Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;LINE-dependent_Retroposon;snoRNA;L1-derived 5 Retroposon sno-L1 Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Long_Terminal_Repeat_Element 9357 LTR LTR R/L (LTR) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Long_Terminal_Repeat_Element;Bel-Pao The third large group of LTR elements besides Gypsy/ERV and Copia. 39757 LTR Pao LTR/BEL R/L (LTR)/B (Bel-Pao) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Long_Terminal_Repeat_Element;Gypsy-ERV Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Long_Terminal_Repeat_Element;Gypsy-ERV;Gypsy 182249 LTR Gypsy LTR R/L (LTR)/G (Gypsy) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Long_Terminal_Repeat_Element;Gypsy-ERV;Pararetroviridae Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Long_Terminal_Repeat_Element;Gypsy-ERV;Pararetroviridae;Caulimoviridae Plant and insect DNA reverse-transcribing viruses lacking a provirus state in their cycle. 1904 LTR Caulimovirus LTR R/L (LTR)/R (Retrovirus) ?? Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Long_Terminal_Repeat_Element;Gypsy-ERV;Retroviridae 254 LTR Cassandra LTR R/L (LTR) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Long_Terminal_Repeat_Element;Gypsy-ERV;Retroviridae;Orthoretrovirinae 1494 LTR ERV LTR R/L (LTR)/E (ERV) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Long_Terminal_Repeat_Element;Gypsy-ERV;Retroviridae;Orthoretrovirinae;ERV1 Exogenous representatives are called Gamma- and Epsilonretroviruses. 69873 LTR ERV1 LTR/ERV1 R/L (LTR)/E (ERV) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Long_Terminal_Repeat_Element;Gypsy-ERV;Retroviridae;Orthoretrovirinae;ERV1;SINE-like 4 SINE ERV1 Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Long_Terminal_Repeat_Element;Gypsy-ERV;Retroviridae;Orthoretrovirinae;ERV2-group Most endogenous retroviruses not incldued in class I. Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Long_Terminal_Repeat_Element;Gypsy-ERV;Retroviridae;Orthoretrovirinae;ERV2-group;ERV2 Exogenous representatives are called Alpha-, Beta- and Delta-viruses. 29360 LTR ERVK LTR/ERV2 R/L (LTR)/E (ERV) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Long_Terminal_Repeat_Element;Gypsy-ERV;Retroviridae;Orthoretrovirinae;ERV2-group;ERV3 Class 3 endogenous retroviruses with HERVL as type specimen. 50609 LTR ERVL Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Long_Terminal_Repeat_Element;Gypsy-ERV;Retroviridae;Orthoretrovirinae;ERV2-group;ERV3;MaLR Mammalian-specific non-autonomous LTR elements dependent on class 3 (ERVL) ERVs . 18810 LTR ERVL-MaLR LTR/ERV3 R/L (LTR)/E (ERV) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Long_Terminal_Repeat_Element;Gypsy-ERV;Retroviridae;Orthoretrovirinae;ERV2-group;ERV4 A so far non-avian reptile specific class of ERVs. https://www.ncbi.nlm.nih.gov/pubmed/?term=25499090 1554 LTR ERV4 LTR/ERV4 R/L (LTR)/E (ERV) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Long_Terminal_Repeat_Element;Gypsy-ERV;Retroviridae;Orthoretrovirinae;ERV2-group;Lenti 3 LTR ERV-Lenti LTR/Lentivirus R/L (LTR)/E (ERV) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Long_Terminal_Repeat_Element;Gypsy-ERV;Retroviridae;Spumaretrovirinae 84 LTR ERV-Foamy LTR R/L (LTR)/E (ERV) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Long_Terminal_Repeat_Element;TRIM A placeholder for not-yet-classified non-autonomous LTR elements with short internal sequences. 4 LTR TRIM LTR R/L (LTR) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Long_Terminal_Repeat_Element;Ty1-Copia 53512 LTR Copia LTR/Copia R/L (LTR)/C (Copia) Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Penelope-like_Elements 33285 PLE non-LTR/Penelope R/P (PLE)/P (Penelope) TP-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Penelope-like_Elements;Athena PLE Athena Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Penelope-like_Elements;Chlamys 1113 PLE Chlamys Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Penelope-like_Elements;Coprina PLE Coprina Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Penelope-like_Elements;Hydra 94 PLE Hydra Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Penelope-like_Elements;Naiad 186 PLE Naiad Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Penelope-like_Elements;Nematis PLE Nematis Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Penelope-like_Elements;Neptune PLE Neptune Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Penelope-like_Elements;Poseidon PLE Poseidon Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Tyrosine_Recombinase_Elements Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Tyrosine_Recombinase_Elements;DIRS 16089 LTR DIRS LTR/DIRS R/Y (DIRS)/D (DIRS) Y-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Tyrosine_Recombinase_Elements;DIRS;Q DIRS-Q subclass 3 LTR DIRS-Q LTR/DIRS R/Y (DIRS)/D (DIRS) Y-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Tyrosine_Recombinase_Elements;Ngaro 9510 LTR Ngaro non-LTR R/Y (DIRS)/N (Ngaro) Y-retrotransposons Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Tyrosine_Recombinase_Elements;Viper-group Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Tyrosine_Recombinase_Elements;Viper-group;TATE 14 Unknown TATE Interspersed_Repeat;Transposable_Element;Class_I_Retrotransposition;Retrotransposon;Tyrosine_Recombinase_Elements;Viper-group;Viper 81 LTR Viper LTR/DIRS R/Y (DIRS)/V (Viper) Y-retrotransposons Interspersed_Repeat;Unknown A placeholder for unknown classes of interspersed repeats. 1847884 Unknown Interspersed_Repeat;Unknown;Centromeric Primarily or only found in centromeric regions. Unknown centromeric Low_Complexity Stretches of sequence with unusually simple composition. I.e. AT rich sequence. Low_complexity Other A placeholder for unknown classes of repetitive sequence. 14 Other Segmental_Duplication Long segments of DNA with near-identical sequence. 12 Segmental Tandem_Repeat Repeated stretches of one or more nucleotides directly adjacent to each other. https://en.wikipedia.org/wiki/Tandem_repeat Tandem_Repeat;Satellite Medium to long pattern tandem repeats found in long runs. https://en.wikipedia.org/wiki/Satellite_DNA 13192 Satellite Tandem_Repeat;Satellite;Acromeric Satellites occurring specifically in the short arm of acromeric chromosomes. 9 Satellite acromeric Tandem_Repeat;Satellite;Centromeric Primarily or only found in centromeric regions. 313 Satellite centromeric Tandem_Repeat;Satellite;Macro 14 Satellite macro Tandem_Repeat;Satellite;Subtelomeric 35 Satellite subtelomeric Tandem_Repeat;Satellite;W-chromosomal 70 Satellite W-chromosome Tandem_Repeat;Satellite;Y-chromosomal 41 Satellite Y-chromosome Tandem_Repeat;Simple Short pattern tandem repeats found in short runs. 9249 Simple_repeat