MITEs were de novo identified from 41 sequenced plant genomes using MITE-hunter and RSPB (Han and Wessler, 2010; Lu et al., 2012; Yang, 2013). All identified MITE sequences were classified into superfamilies and families based on structure and sequence characteristics. One or a few full-length MITE sequences (called seed sequence) from each family were used as query sequences to search for related sequences from a genome using RepeatMask. All retrieved sequences, including partial ones, were listed in the MITEdb. Another database (MITErepdb), which contains only one or a few full-length elements (seed elements) from each MITE family, was also constructed. All elements in the MITErepdb were checked manually, and their TSD sequences are included and shown in red.
To check if a sequence has similarity with MITE elements, put the sequence of interest in the box provided on the BLAST web page, and choose one of the two MITE databases for BLASTN search. Please be noted that false positives, caused by RepeatMask, may occur when MITEdb is used. However, if the MITErepdb is chosen, the chance to have false positive will decrease considerably.
You may download sequences of one single MITE element, one MITE family from a species, or all MITE elements from a genome, etc. The title of each sequence in the MITEdb includes its species name, chromosome position/scaffold name, MITE family name, and full/partial status. The name of a MITE family is composed of species name (three-letter-code), followed by superfamily name (superfamilies are represented using different letters including DTT for Tc1/Mariner, DTM for Mutator, DTA for hAT, DTC for CACTA, DTH for PIF/Harbinger,DTP for P element, DTN for Novosib, DTx for unknown, DTx_Mim for Mim group), and a distinct number.
References
1. Han Y, Wessler SR. MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Nucleic Acids Res, 2010, 38:e199
2. Lu C, Chen J, Zhang Y, Hu Q, Su W, Kuang H. Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa. Mol Biol Evol, 2012, 29:1005-1017.
3. Yang G. MITE Digger, an efficient and accurate algorithm for genome wide discovery of miniature inverted repeat transposable elements. BMC bioinformatics, 2013, 14:186