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. 2017 Jan 1;2017:bax038.
doi: 10.1093/database/bax038.

RetrogeneDB-a Database of Plant and Animal Retrocopies

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Free PMC article

RetrogeneDB-a Database of Plant and Animal Retrocopies

Wojciech Rosikiewicz et al. Database (Oxford). .
Free PMC article

Abstract

Database url: http://yeti.amu.edu.pl/retrogenedb.

Secondary database url: http://rhesus.amu.edu.pl/retrogenedb.

Figures

Figure 1.
Figure 1.
Phylogenetic tree of 99 species used within the updated RetrogeneDB database. The same tree is embedded into the database ‘browse’ web-page and interactively used to select a species of interest. Animal and plant species are colored in light red and green, respectively. Four chosen species, Homo sapiens, Mus musculus, Drosophila melanogaster and Arabidopsis thaliana, were highlighted for easier navigation. The web-based phylogenetic tree is drawn using the jsPhyloSVG library (37).
Figure 2.
Figure 2.
RetrogeneDB data access strategies.
Figure 3.
Figure 3.
Selected species summary. This page provides a list of all retrocopies and parental genes together with access to the data download section. It also displays, whenever applicable, an overall view of the expression data. The page contains the following sections: (A) Basic information; (B) Summary, which lists the number of retrocopies supported by the additional data indicated by badge; and (C) Browse retrocopies, parental genes and download tabs.
Figure 4.
Figure 4.
Search form that allows the user to search for either retrocopies (A) or parental genes (B), using Retrocopy ID or Ensembl accession number (C), or specifying various search parameters (D). The results are displayed at the bottom of the page (E).
Figure 5.
Figure 5.
Retrocopy detailed view page comprising two basic sections: retrocopy summary (A), and the detailed information (B) contained within the following tabs: genome context; sequence of the retrocopy; retrocopy–parental gene protein alignment used for retrocopy identification; expression validation of the retrocopy; retrocopy and/or parental gene homology information; and in the case of humans, a population studies tab, which inform of retroduplication variation (RDV) evidence and retrocopy expression levels in 50 human libraries from 5 populations.

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