RESOURCESRESOURCES

Transcriptional Elements

Tools and resources for the analysis, characterization and comparison of sequence elements that influence transcription in Arabidopsis and other plants.

AGRIS- The Arabidopsis Gene Regulatory Information Server

http://arabidopsis.med.ohio-state.edu/

Arabidopsis Gene Regulatory Information Server. An information resource of Arabidopsis cis regulatory elements and transcription factors.

From the abstract: Three interlinked databases, AtTFDB, AtcisDB and AtRegNet, furnish comprehensive and updated information on transcription factors (TFs), predicted and experimentally verified cis-regulatory elements (CREs) and their interactions, respectively. Tools recently incorporated into AGRIS include the integration of AtRegNet with visualization tools, such as the recently developed ReIN application. All the information in AGRIS is publicly available and downloadable upon registration.

Database of Arabidopsis Transcription Factors (DATF)

http://datf.cbi.pku.edu.cn/

The Database of Arabidopsis Transcription Factors (DATF) collects all Arabidopsis transcription factors (total 1922 Loci; 2290 Gene Models) and classifies them into 64 families.

From the abstract: The DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals.

Database of Orthologous Promoters

http://doop.abc.hu/

DoOP is a database of eukaryotic promoter sequences (upstream regions), aiming to facilitate the recognition of regulatory sites conserved between species. You can search the database with sequences or text (annotation) to find promoter clusters of different genes. In addition to the sequence and annotation data, the positions of the conserved regions and transcription start sites can be viewed graphically. A number of plant species are supported. 

From the abstract: 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.

EARS

http://wsbc.warwick.ac.uk/ears/

Comparative genomics tool used to search for alignment conserved regions in orthologous regulatory regions from plants.

From the abstract: Here, we demonstrate a robust and highly sensitive, in silico method to identify evolutionarily conserved regions within non-coding DNA. Sequence conservation within these regions is taken as evidence for evolutionary pressure against mutations, which is suggestive of functional importance.

Plant cis-Acting Regulatory Elements (Plant CARE)

http://bioinformatics.psb.ugent.be/webtools/plantcare/html/

A referential database with 435 different names of plant transcription sites describing more than 159 plant promoters and the possibility to store all plant transcription sites, consensus and matrices described in the literature into the database. Use Plant CARE to run sophisticated queries on the data, like looking for sites linked to a specific function, and submit a sequence to a program which will look for transcription sites known by PlantCARE.

From the abstract: PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequences and individual sites on particular promoter sequences. Data about the transcription sites are extracted mainly from the literature, supplemented with an increasing number of in silico predicted data. 

Plant Transcription Factor Database (PTFB)

http://plntfdb.bio.uni-potsdam.de/v3.0/

PTFDB is an integrative plant transcription factor database that provides a web interface to access  close to complete sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana, Populus trichocarpa, and Oryza sativa.

From the abstract: The Plant Transcription Factor Database (PlnTFDB) is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species (sensu lato) whose genomes have been completely sequenced and annotated. For each gene family, a basic description is provided that is complemented by literature references, and multiple sequence alignments of protein domains. TF or TR gene entries include information of expressed sequence tags, 3D protein structures of homologous proteins, domain architecture and cross-links to other computational resources online.

PlantNATsDB

http://bis.zju.edu.cn/pnatdb/?species=ath

A comprehensive database of plant natural antisense transcripts, a type of regulatory RNA. It has a user-friendly interface, including a simple 'viewer' as well as a search option. 

From the abstract: PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. The PlantNATsDB is freely available at http://bis.zju.edu.cn/pnatdb/

PlantProm DB

http://linux1.softberry.com/berry.phtml?topic=plantprom&group=data&subgroup=plantprom

The new release of PlantProm DB contains 578 unrelated entries including 151, 396 and 31 promoters with experimentally verified TSS from monocot, dicot and other plants, respectively.

From the abstract: PlantProm DB, a plant promoter database, is an annotated, non-redundant collection of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s), TSS, from various plant species.

plantpromoterDB

http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/index.cgi

A plant promoter database that provides promoter annotation of Arabidopsis and rice. Contains information on promoter structures, transcription start sites (TSSs) that have been identified from full-length cDNA clones and also a vast amount of TSS tag data.