REXdb: a reference database of transposable element protein domains
Database is described in the article: Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification, Mobile DNA 2019, 10:1 https://doi.org/10.1186/s13100-018-0144-1
REXdb is utilized in repeat analysis tools RepeatExplorer2 and DANTE which are available on our Galaxy server
Latest release – Viridiplantae v4.0
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The database contains two files – protein sequences and classification table. Protein sequences are provided in fasta format. Sequence IDs have the following syntax:
>Protein-domain-name__REXdb_IDnumber aa sequence
For example:
>Ty1-RT__REXdb_ID1442 WRQAMVDEMAALHSNGSWDLVVLPSGKSTVGCRWVYAVKVGPDGQVDRLKARLVAKGYTQ VYGSDYGDTFSPVAKIASVRLLLSMAAMCSWPLYQLDIKNAFLHGDLAEEVYMEQPPGFV AQGESGLVCRLRRSLYGLKQSPRAWFSRFSSVVQEFGMLRSTADHSVFYHHNSLGQCIYL VVYVDDIVITGSDQDGIQKLKQHLFTHFQTKDLGKLKYFLGIEIAQSSSGVVLSQRKYAL DILEETGMLDCKPVDTP
Classification of mobile elements is provided in tab-delimited classification table which is linked to protein sequences via their REXdb_IDnumbers :
REXdbIDNumber ClassLevel1 ClassLevel2 ClassLevel3 ...
Numbers of classification levels are different for different types of mobile elements. Below are examples of records from the classification table:
REXdb_ID1 Class_I LTR Ty1/copia Ale REXdb_ID2256 Class_I LTR Ty1/copia Angela REXdb_ID6786 Class_I LTR Ty3/gypsy non-chromovirus OTA Tat TatII
Alternativelly, REXdb can be downloaded in format compatible with REPET annotation tool.