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 v3.0
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The database archive 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.
Classification levels of mobile elements included in the database:
--mobile_element
¦--Class_I
¦ ¦--SINE
¦ ¦--LTR
¦ ¦ ¦--Ty1/copia
¦ ¦ ¦ ¦--Ale
¦ ¦ ¦ ¦--Alesia
¦ ¦ ¦ ¦--Angela
¦ ¦ ¦ ¦--Bianca
¦ ¦ ¦ ¦--Bryco
¦ ¦ ¦ ¦--Lyco
¦ ¦ ¦ ¦--Gymco-III
¦ ¦ ¦ ¦--Gymco-I
¦ ¦ ¦ ¦--Gymco-II
¦ ¦ ¦ ¦--Ikeros
¦ ¦ ¦ ¦--Ivana
¦ ¦ ¦ ¦--Gymco-IV
¦ ¦ ¦ ¦--Osser
¦ ¦ ¦ ¦--SIRE
¦ ¦ ¦ ¦--TAR
¦ ¦ ¦ ¦--Tork
¦ ¦ ¦ °--Ty1-outgroup
¦ ¦ °--Ty3/gypsy
¦ ¦ ¦--non-chromovirus
¦ ¦ ¦ ¦--non-chromo-outgroup
¦ ¦ ¦ ¦--Phygy
¦ ¦ ¦ ¦--Selgy
¦ ¦ ¦ °--OTA
¦ ¦ ¦ ¦--Athila
¦ ¦ ¦ °--Tat
¦ ¦ ¦ ¦--TatI
¦ ¦ ¦ ¦--TatII
¦ ¦ ¦ ¦--TatIII
¦ ¦ ¦ ¦--Ogre
¦ ¦ ¦ °--Retand
¦ ¦ °--chromovirus
¦ ¦ ¦--Chlamyvir
¦ ¦ ¦--Tcn1
¦ ¦ ¦--chromo-outgroup
¦ ¦ ¦--CRM
¦ ¦ ¦--Galadriel
¦ ¦ ¦--Tekay
¦ ¦ ¦--Reina
¦ ¦ °--chromo-unclass
¦ ¦--pararetrovirus
¦ ¦--DIRS
¦ ¦--Penelope
¦ °--LINE
°--Class_II
¦--Subclass_1
¦ °--TIR
¦ ¦--MITE
¦ ¦--EnSpm/CACTA
¦ ¦--hAT
¦ ¦--Kolobok
¦ ¦--Merlin
¦ ¦--MuDR/Mutator
¦ ¦--Novosib
¦ ¦--P
¦ ¦--PIF/Harbinger
¦ ¦--PiggyBac
¦ ¦--Sola1
¦ ¦--Sola2
¦ °--Tc1
¦ °--Mariner
°--Subclass_2
°--Helitron
Past releases
Viridiplantae V2.2
under construction