TE Classification Cheat Sheet

1. Wicker et al. 2007 TE Classification Cheat Sheet Class I (RNA intermediate; Retrotransposons LTR Flanking LTRs – start 5’-TG-3’ end 5’-CA-3’ 4-6 bp TSD GAG and POL: AP, INT, RH, and RT Gypsy, Copia, Retrovirus, ERV. Bel-Pao DIRS No TSD Termini contain SDR or inverted repeats SINE Non-autonomous 5’: usually tRNA derived 3’: can be LINE derivative 3’ end: poly(T) tail, A- or AT- rich, or 3-5 bp tandem repeat Small <500 bp LINE Several kb long Encode RT and nuclease Weak RT causes many truncated members 3’ end: poly(A) tail, tandem repeat, A-rich region PLE Functional Intron LTR-like flanking sequences Classified by: Class II (DNA transposons) • Class -- divided by presence of RNA intermediate • Subclass -- distinguish between ‘copy and paste’ and ‘cut and paste’ • Order -- differences in insertion mechanisms and organization • Superfamily -- differences in protein structure and non-coding domains and TSDs • Family -- DNA sequence similarity • Subfamily -- phylogenetic; autonomous and non-autonomous derivatives • Insertion -- individual copy after insertion event TIR Cut and paste Flanked by inverted repeats Encodes transposase Different superfamilies distinguished by TIR and TSD size Helitron Copy and paste Short hairpin structure at 3’ end 3’ end: TC or CTRR motif Encodes tyrosine recombinase Maverick Copy and paste 10-20 kb Long TIRs border Encode DNAPB and INT • Bioinformatics Steps to Classify: • BLASTN 2. BLASTX 3. Search for shared motifs • (if none are found to be part of superfamily/order, it is classified unknown)