Welcome to RetrogeneDB 2
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.
You may view the older version of the RetrogeneDB at retrogenedb.amu.edu.pl/
What is new in RetrogeneDB2 in comparison to RetrogeneDB?
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 |