REXdb

REXdb: a reference database of transposable element protein domains

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

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

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