PlantCARE

PlantCARE catalogs cis-acting regulatory elements in plant promoters and provides annotated sequence representations and evidence to support studies of transcriptional regulation.

Key Features:

• Comprehensive Data Representation: Regulatory elements are represented as positional matrices, consensus sequences, and individual site sequences specific to particular genes.
• Integration with External Databases: Entries include direct links to EMBL for full gene sequences, TRANSFAC for transcription factor data, and MEDLINE for literature references.
• Experimental Evidence and Functional Information: Each regulatory element is annotated with a general description, levels of confidence regarding experimental evidence, functional insights, and positional information on promoters.
• In Silico Prediction and Literature Data: The database combines manually curated literature-derived data with in silico predicted regulatory elements.
• Sequence-based Element Search: The resource supports searching for cis-acting regulatory elements within query sequences.
• Clustering and Motif Search Methods: PlantCARE provides links to clustering and motif search methods for investigation of co-expressed gene clusters.
• Contribution and Curation Process: Newly identified regulatory elements can be submitted and undergo a curation process before inclusion in the database.

Scientific Applications:

• Gene Regulation Analysis: Enables analysis of regulatory elements to decipher mechanisms of gene regulation under different environmental conditions.
• Transcription Factor Research: Facilitates studies of transcription factor binding sites and their roles and interactions in plant development and stress responses.
• Promoter Sequence Analysis: Supports analysis of promoter sequences to investigate transcriptional control of genes.

Methodology:

Regulatory elements are represented as positional matrices, consensus sequences, and individual site sequences; in silico prediction is used alongside literature-derived entries; sequence-based searches for cis-acting regulatory elements are supported and links are provided to clustering and motif search methods.