About DBTGR

Content

The database currently contains:

81 gene expression reporter vectors.
247 gene activity entries.
226 promoters.
456 promoter sequences.
110 reported binding sites.
12 transcrition factors.
48 publications.

A list of all the publication included in DBTGR can be seen here.

JASPAR binding site predictions

Genome-wide binding site predictions for the JASPAR core matrices are available in the genome browser.
These predictions were obtained by evaluating the matrix score of each position in the genome and calculating the probability of reaching by chance an equal or higher matrix score from a third-order Markov model of the C. intestinalis genome. In other words, for a genome position with a probability of 1e-6, only one site in a million is expected to have a matrix score at least as high. Only genome positions for which this probability, known as p-value, was lower than 1e-5 are visible in the genome browser.

Colors

Gene models: The gene models from JGI and Ensembl are shown in the genome browser. Light red is used for the JGI models, and light blue for the Ensembl models.
Reported cis-elements: Black is used for sites that have been experimentally verified. Gray indicate a published prediction for which no experimental validation was given.
Genome alignments: Conserved positions are given in black, and aligned positions that are not conserved in white. Grey is used to indicate positions for which no alignment is available.

Tips and tricks

Searching the database is case-insensitive and will return all the records containing the entered query as a substring. There is no need to use a wildcard character such as *. In fact, this will result in the server returning a 'page not found' error, as it cannot be used in the unique URL associated with each page of the database.
The order of the columns of any table can be rearranged by drag and drop. The order of the columns is however not preserved when you reload the page.
The rows of any table can be sorted according to the values in a given column by clicking on its header. Successive clicking on the same header will switch the sort order between ascending and descending. The order of the rows is not preserved when you reload the page.
In the genome browser, each track can be hidden or revealed by clicking on its label. If possible, the state of each track is preserved between sessions using cookies.
The order of the genome browser tracks can be rearranged by dragging and dropping the track images. If possible, the order of the tracks is preserved between sessions using cookies.

Citing DBTGR

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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