REXdb is a comprehensive reference database specifically designed for the study of transposable element protein domains. It plays a crucial role in the analysis of repetitive sequences in genomic data.
Key Publication The database is detailed 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 integrated with several repeat analysis tools: RepeatExplorer2, DANTE and DANTE_LTR which are available on Galaxy server: https://repeatexplorer-elixir.cerit-sc.cz/galaxy
REXdb consists of two primary databases:
- Viridiplantae Database (current version: 4.0)
- Metazoa Database (current version: 3.1)
Each database contains:
- A FASTA file with protein sequences.
- A classification table for sequence categorization.
Sequences in REXdb follow this syntax:
>Protein-domain-name__REXdb_IDnumber
AA sequenceExample:
>Ty1-RT__REXdb_ID1442
WRQAMVDEMAALHSNGSWDLVVLPSGKSTVGCRWVYAVKVGPDGQVDRLKARLVAKGYTQ
VYGSDYGDTFSPVAKIASVRLLLSMAAMCSWPLYQLDIKNAFLHGDLAEEVYMEQPPGFV
AQGESGLVCRLRRSLYGLKQSPRAWFSRFSSVVQEFGMLRSTADHSVFYHHNSLGQCIYL
VVYVDDIVITGSDQDGIQClassification of mobile elements is provided in tab-delimited classification table which is referencing 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 TatIIThe classification of mobile elements is based the following hierarchical classification scheme:
Viridiplantae v4.0
This version include additional sequences of non-angiosperm element and non-angiosperm lineages. In the classification tree, new lineages are labeled with asterix
--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
¦ ¦ ¦ ¦--Alexandra *
¦ ¦ ¦ ¦--Ferco *
¦ ¦ ¦ ¦--Bryana *
¦ ¦ ¦ °--Ty1-outgroup
¦ ¦ °--Ty3/gypsy
¦ ¦ ¦--non-chromovirus
¦ ¦ ¦ ¦--non-chromo-outgroup
¦ ¦ ¦ ¦--Phygy
¦ ¦ ¦ ¦--Selgy
¦ ¦ ¦ °--OTA
¦ ¦ ¦ ¦--Athila
¦ ¦ ¦ ¦--Tatius *
¦ ¦ ¦ °--Tat
¦ ¦ ¦ ¦--TatI
¦ ¦ ¦ ¦--TatII
¦ ¦ ¦ ¦--TatIII
¦ ¦ ¦ ¦--Ogre
¦ ¦ ¦ °--Retand
¦ ¦ °--chromovirus
¦ ¦ ¦--Chlamyvir
¦ ¦ ¦--Tcn1
¦ ¦ ¦--chromo-outgroup
¦ ¦ ¦--CRM
¦ ¦ ¦--Galadriel
¦ ¦ ¦--Tekay
¦ ¦ ¦--Reina
¦ ¦ ¦--Ferney *
¦ ¦ °--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
°--HelitronViridiplante v3.0
--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