Databases of Orthologous Promoters
How to cite this record FAIRsharing.org: DoOP; Databases of Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.1bnhyh; Last edited: Nov. 23, 2018, 11:26 a.m.; Last accessed: Dec 19 2018 4:40 p.m.
Record updated: Sept. 27, 2016, noon by The FAIRsharing Team.
Edits to 'https://fairsharing.org/FAIRsharing.1bnhyh' by 'The FAIRsharing Team' at 21:12, 26 Sep 2016 (approved): 'description' has been modified: Before: DoOP is a database of eukaryotic promoter sequences (upstream regions) aiming to facilitate the recognition of regulatory sites conserved between species. The annotated first exons of human and Arabidopsis thaliana genes were used as queries in BLAST searches to collect the most closely related orthologous first exon sequences from Chordata and Viridiplantae species. Up to 3000 bp DNA segments upstream from these first exons constitute the clusters in the chordate and plant sections of the Database of Orthologous Promoters. Release 1.0 of DoOP contains 21,061 chordate clusters from 284 different species and 7548 plant clusters from 269 different species. The database can be used to find and retrieve promoter sequences of a given gene from various species and it is also suitable to see the most trivial conserved sequence blocks in the orthologous upstream regions. Users can search DoOP with either sequence or text (annotation) to find promoter clusters of various genes. In addition to the sequence data, the positions of the conserved sequence blocks derived from multiple alignments, the positions of repetitive elements and the positions of transcription start sites known from the Eukaryotic Promoter Database (EPD) can be viewed graphically After: DoOP is a database of eukaryotic promoter sequences (upstream regions), aiming to facilitate the recognition of regulatory sites conserved between species. Based on the Arabidopsis thaliana and Homo sapiens genome annotation, this resource is also a collection of the orthologous promoter sequences from Viridiplantae and Chordata species. The database can be used to find promoter clusters of different genes as well as positions of the conserved regions and transcription start sites, which can be viewed graphically.
Conditions of UseApplies to: Data use
DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants.
Barta E., Sebestyén E., Pálfy TB., Tóth G., Ortutay CP., Patthy L.,
Nucleic Acids Res. 2005
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NK60352 (Hungarian Scientific Research Fund, Hungary)
NK72730 (Hungarian Scientific Research Fund, Hungary)