Transposable elements (TEs) are DNA sequences able to jump throughout the genome. TEs can be classified into two major classes, depending on the mechanism used to transpose. Many reviews are available if you want to know a bit more about TEs:
Since TEs are able to insert into the host genome, they act as important mutagen agents. Furthermore, TEs carry within their sequences, all the motifs necessary to be transcribed : promoters, transcription factor binding sites, polyadenylation signals and etc. All these signals, along with entire TE open reading frames, can be co-opted/domesticated, by the host genome. Therefore, many copies are known to influence host gene expression. For a recent review in this subject we suggest to you, our recent publication on Mobile DNA, in which we present C-GATE. A previous catalogue on this topic was published by Juergen Brosius, a pioneer in this field and also Makalowski. Another website that may be helpful when looking for in silico TE exaptations can be found here.
C-GATE (catalogue of genes affected by transposable elements) is a catalogue of TE exaptation events, including information on the TE copy but also on the affected gene. C-GATE was conceived not only for the TE community but also to the non-TE researchers. If you are interested in finding information on specific TE exaptation events or if you found a TE copy near a gene and want to know if the TE has been reported before to act as a regulatory sequence, this is the place to look. Furthermore, we hope to stimulate the curiosity of non-TE researchers and increase collaboration between scientific communities.
With time, we hope C-GATE will be a complete catalogue on exapted TEs but also on any information related to the repeats. We welcome new ideas to improve this catalogue. It is important to note that C-GATE does not hold cases where TEs cause diseases in single individuals, since this cannot be considered as an exaptation event. In inbred strains, if a copy is known to cause harmful effects, but the strain is kept by human breeding, the case will not be present in C-GATE because it does not reflect natural exaptation of the TE copy. A putative C-GATE (pC-GATE) is also available and shows only examples where the biological significance of the exaptation is unknown.
What are transposable elements (TEs)?
Impact of TEs on host genes
Why use C-GATE?
Image from Biemont and Vieira, Nature, 2006
C-GATE was introduced as a short article in Mobile DNA in 2012.
You are invited to use C-GATE, to correct it when necessary and specially to add new data when available. The catalogue is interactive and therefore dependent on the users. Of course we are open to suggestions and improvements. Have fun!
C-GATE entries : 225
pC-GATE entries : 10133
17 species are present in C-GATE and 21 in pC-GATE.