RetrogeneDB is a database of retrocopy annotations in sequenced eukaryotic genomes. It currently stores information about 62 animal and 37 plant genomes from Ensembl. Updated RetrogeneDB database allows users to search for retrocopies and their parental genes using numerous criteria. For selected organisms retrocopy expression estimation from RNA-Seq, ChIP-Seq, EST, CAGE and experimental studies are provided.

As this site is under maintenance now, please visit this mirror instead: RetrogeneDB 2.0

You may view the older version of the RetrogeneDB at

What is new in RetrogeneDB2 in comparison to RetrogeneDB?


RetrogeneDB 2

How many species were analyzed? 62 species
(all animals)
99 species
(62 animal + 37 plant species)
Number of identified retrocopies 84808 retrocopies 86458 retrocopies
Number of identified parental genes 34286 genes 35975 genes
RNA-Seq expression validation 14 species
(97 RNA-Seq libraries)
23 species
(195 RNA-Seq libraries)
ChIP-Seq expression validation ---- 223 Human and 140 Mouse retrocopies,
based on 53 and 4 ChIP-Seq libraries respectively
EST expression validation ---- 557 retrocopies, 31 species
TSS expression validation ---- 799 Human and 796 Mouse retrocopies,
based on 1829 and 1072 FANTOM5 libraries respectively
Experimental validation ---- 51 Human and 11 Mouse retrocopies
Orthological relationships between retrogenes ---- 4240 orthological groups, within three subgroups:
eytheria (13 species)
teleost (5 species)
neognath (3 species)
Association of retrocopies with large genomic indels ---- for human, based on 1000 genomes project data
+ improved website layout, search options and used BLAST algorithm version. Numerous improvements were based on the opinion of the users of the previous version of RetrogeneDB, as well as Beta version of RetrogeneDB 2 .