RetrogeneDB–a database of plant and animal retrocopies
| Autor: | Michal Kabza, Izabela Makalowska, Magdalena Regina Kubiak, Jan Grzegorz Kosiński, Joanna Ciomborowska-Basheer, Wojciech Rosikiewicz |
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| Rok vydání: | 2017 |
| Předmět: |
Expressed Sequence Tags
0301 basic medicine Expressed sequence tag Genome Sequence Analysis RNA business.industry Sequence analysis MEDLINE Eukaryota Computational biology Plants Biology General Biochemistry Genetics and Molecular Biology User-Computer Interface 03 medical and health sciences 030104 developmental biology Text mining Database Update Databases Genetic Animals RNA General Agricultural and Biological Sciences business Phylogeny Information Systems |
| Zdroj: | Database: The Journal of Biological Databases and Curation |
| ISSN: | 1758-0463 |
| Popis: | For a long time, retrocopies were considered ‘junk DNA’, but numerous studies have shown that retrocopies may gain functionality and become so-called retrogenes. Retrogenes may code fully functional proteins that coexist with parental gene products or may even replace them. Retrocopies may also function as regulatory RNAs and, for example, become a source of small interfering RNAs, act as trans natural antisense transcripts or as alternative targets for miRNAs. Numerous researchers have emphasized that retrogenes play a crucial role in various organisms’ developmental stages and diseases. Despite the ever-growing evidence of the importance of retrocopies, resources dedicated to retroposition are very limited. Here, we report an update of the RetrogeneDB, which, to the best of our knowledge, is the largest database dedicated to retrocopies. It provides annotations of 86 458 retrocopies in 62 animal and 37 plant species. The database contains information about the retrocopies’ localization, open reading frame conservation, expression, RNA Polymerase II activity and the alternative transcription start site studies. Orthologous relationships between retrogenes were also determined, which made retrocopy conservation studies much more valuable. Additionally, based on the RNA-Seq data from the Geuvadis project, the expression levels of retrocopies were estimated in a total of 50 individuals from 5 human populations. The information is now presented in a new, more user-friendly web interface, with easy access to the source data, which may be used for the downstream analysis. RetrogeneDB is freely available at http://yeti.amu.edu.pl/retrogenedb. Database URL: http://yeti.amu.edu.pl/retrogenedb Secondary database URL: http://rhesus.amu.edu.pl/retrogenedb |
| Databáze: | OpenAIRE |
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