Databases of Orthologous Promoters
Names
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Databases of Orthologous Promoters
metasource: Fairsharing.org
version: FAIRsharing.org: DoOP; Databases of Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.1bnhyh; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
DoOP
metasource: Fairsharing.org
version: FAIRsharing.org: DoOP; Databases of Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.1bnhyh; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
DoOP - Databases of Orthologous Promoters
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Names
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Databases of Orthologous Promoters
metasource: Fairsharing.orgversion: FAIRsharing.org: DoOP; Databases of Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.1bnhyh; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
DoOP
metasource: Fairsharing.orgversion: FAIRsharing.org: DoOP; Databases of Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.1bnhyh; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
DoOP - Databases of Orthologous Promoters
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Other names: DoOP, DoOP - Databases of Orthologous Promoters
Names
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Databases of Orthologous Promoters
metasource: Fairsharing.orgversion: FAIRsharing.org: DoOP; Databases of Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.1bnhyh; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
DoOP
metasource: Fairsharing.orgversion: FAIRsharing.org: DoOP; Databases of Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.1bnhyh; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
DoOP - Databases of Orthologous Promoters
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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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.
Description
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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.
metasource: Fairsharing.orgversion: FAIRsharing.org: DoOP; Databases of Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.1bnhyh; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
DoOP (http://doop.abc.hu/) 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 21061 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. This work was supported by Biotechnology 2001 grant BIO-0117/01 from the Central Technical Development Target Funds (Hungary). B.E. and G.T. were recipients of 'Bolyai Fellowship’ awarded by the Hungarian Academy of Sciences.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://doop.abc.hu/Webpage
More detailed information about this field from each metasource.
http://doop.abc.hu/
metasource: Fairsharing.orgversion: FAIRsharing.org: DoOP; Databases of Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.1bnhyh; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Licence:
Name: Creative Commons Attribution 4.0 International (CC BY 4.0)Licence name
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Creative Commons Attribution 4.0 International (CC BY 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: DoOP; Databases of Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.1bnhyh; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Licence URL
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https://creativecommons.org/licenses/by/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: DoOP; Databases of Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.1bnhyh; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications:
Publications
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DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants
PMID: 15608291
metasource: Fairsharing.org
version: FAIRsharing.org: DoOP; Databases of Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.1bnhyh; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes
PMID: 19534755
metasource: Fairsharing.org
version: FAIRsharing.org: DoOP; Databases of Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.1bnhyh; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications
More detailed information about this field from each metasource.
DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants
PMID: 15608291
metasource: Fairsharing.org
version: FAIRsharing.org: DoOP; Databases of Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.1bnhyh; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes
PMID: 19534755
metasource: Fairsharing.org
version: FAIRsharing.org: DoOP; Databases of Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.1bnhyh; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
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DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants
PubMed citations: 10.
10 articles citing: DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants
HRGFish: A database of hypoxia responsive genes in fishes. PMID:28205556
A mutation degree model for the identification of transcriptional regulatory elements. PMID:21708002
Evolutionarily conserved, growth plate zone-specific regulation of the matrilin-1 promoter: L-Sox5/Sox6 and Nfi factors bound near TATA finely tune activation by Sox9. PMID:21173167
Antler development and coupled osteoporosis in the skeleton of red deer Cervus elaphus: expression dynamics for regulatory and effector genes. PMID:20697743
DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes. PMID:19534755
CYP86B1 is required for very long chain omega-hydroxyacid and alpha, omega -dicarboxylic acid synthesis in root and seed suberin polyester. PMID:19525321
Natural variation in CBF gene sequence, gene expression and freezing tolerance in the Versailles core collection of Arabidopsis thaliana. PMID:18922165
EPD in its twentieth year: towards complete promoter coverage of selected model organisms. PMID:16381980
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters. PMID:16381947
The Molecular Biology Database Collection: 2005 update. PMID:15608247 -
DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes
PubMed citations: 4.
4 articles citing: DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes
Abscisic-acid-dependent basic leucine zipper (bZIP) transcription factors in plant abiotic stress. PMID:26669319
CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes. PMID:23228284
ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites. PMID:22253291
The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community. PMID:19534734
Tags:
Tags
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orthologous
metasource: Fairsharing.org
version: FAIRsharing.org: DoOP; Databases of Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.1bnhyh; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
promoter
metasource: Fairsharing.org
version: FAIRsharing.org: DoOP; Databases of Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.1bnhyh; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
transcriptional regulator sites and transcription factors
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
orthologous
metasource: Fairsharing.orgversion: FAIRsharing.org: DoOP; Databases of Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.1bnhyh; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
promoter
metasource: Fairsharing.orgversion: FAIRsharing.org: DoOP; Databases of Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.1bnhyh; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
transcriptional regulator sites and transcription factors
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
orthology promoter nucleic acid sequence transcription
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