GreenCircRNA

GreenCircRNA catalogs plant circular RNAs (circRNAs) and predicts their roles as microRNA (miRNA) decoys to support analysis of circRNA-mediated regulatory networks.

Key Features:

• Dataset scope: Data derived from over 4,100 RNA-seq datasets covering 69 plant species and encompassing more than 210,000 circRNAs, sourced from NCBI, EMBL-EBI, and Phytozome.
• miRNA decoy (ceRNA) predictions: Predictions of circRNAs acting as competitive endogenous RNAs (ceRNAs) are provided for 38 plant species.
• Genomic and host-gene annotation: Genomic locations and host gene details are recorded for each circRNA.
• Expression quantification: Expression levels are quantified from RNA-seq datasets.
• Full-length sequences: Full-length circRNA sequences are included.
• Gene Ontology annotations: GO numbers associated with host genes are provided.
• circRNA–miRNA–mRNA interaction data: Predicted interaction networks linking circRNAs, miRNAs, and mRNAs are reported.
• Visualizations: Visual representations of circRNAs are included.

Scientific Applications:

• Regulatory network analysis: Analysis of predicted circRNA–miRNA–mRNA interactions to study post-transcriptional regulation in plants.
• Identification of candidate ceRNAs: Prioritization of circRNAs that may act as miRNA decoys for experimental validation.
• Comparative analysis across species: Cross-species comparison of circRNA repertoires across 69 plant species.
• Study of development, metabolism, and stress responses: Investigation of potential roles of circRNAs in plant development, metabolism, and biotic or abiotic stress responses.

Methodology:

circRNAs were identified from >4,100 RNA-seq datasets obtained from NCBI, EMBL-EBI, and Phytozome; predictions of circRNAs acting as miRNA decoys (ceRNAs) were performed for 38 species, and annotations include genomic location, host gene details, expression levels, full-length sequences, Gene Ontology (GO) numbers, and visual representations.