About DBTGR[help]

Tunicates, which include the sedentary ascidians, or sea squirts, Ciona intestinalis and Ciona savignyi, are lower chordates and share basic gene repertoires and many characteristics, both developmental and physiological, with vertebrates. Although the adult animal shows no resemblance to vertebrate animals, the fertilized egg from an ascidian tunicate develops within a day into a tadpole-like larva (consisting of about 2'600 cells) which shares a basic body plan with vertebrates. Therefore, decoding regulatory systems of tunicates will contribute toward elucidating the genetic regulatory systems underlying the developmental and physiological processes of vertebrates.

DBTGR provides information on tunicate gene regulation, including the location of expression, the identified regulatory elements present in the promoter sequence and the transcription factors involved.

The information provided was essentially obtained from published experimental work and includes the description of 12 transcription factors and 140 promoters. Furthermore, the location of 81 reported transcription factor binding sites and identified conserved motifs are available.

In addition to the published information, 71 putative promoter sequences for Ciona savignyi are given, as well as 2236 predicted bindings sites, based on the reported consensus sequences.

Currently, 37 papers are cited in the database.



More about DBTGR

Using DBTGR[help]

Searching the database with an empty query will result in the listing of all entries.

When searching the database, the following terms can be used to modify the query:
+	will return only rows where the modified term is present (e.g. +muscle)
-	will return only rows where the modified term is absent (e.g. -muscle)
*	will return matches where words starting by the modified term are present (e.g. neur* will match both neuron and neural)
"..."	will return only matches containing the enclosed sentence (e.g. "central nervous system")

In the result page, the arrowheads above and below a field name allow to reorder the results based on the data of that field.

Contributors

Nicolas Sierro	Human Genome Center, Institute of Medical Science, University of Tokyo
Riu Yamashita	Human Genome Center, Institute of Medical Science, University of Tokyo
Keun-Joon Park	Human Genome Center, Institute of Medical Science, University of Tokyo
Takehiro Kusakabe	Department of Life Science, Graduate School of Life Science, University of Hyogo
Kengo Kinoshita	Human Genome Center, Institute of Medical Science, University of Tokyo
Kenta Nakai	Human Genome Center, Institute of Medical Science, University of Tokyo

Reference

Please cite the following reference when you publish your research results using this database:
Sierro, N., Kusakabe, T., Park, K.J., Yamashita, R., Kinoshita, K., Nakai, K.
DBTGR: a database of tunicate promoters and their regulatory elements. Nucleic Acids Res. (2006) 34:D552-D555.
(NAR Online)


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