RiceLncPedia

RiceLncPedia provides a comprehensive database of rice long non-coding RNAs (lncRNAs), integrating annotations, expression profiles from 2313 publicly available RNA-seq libraries, genomic SNPs, transposon overlaps, and lncRNA–miRNA interactions to support functional and comparative analyses.

Key Features:

• Extensive lncRNA repository: Contains 6,978 annotated rice lncRNAs with associated sequence and genomic coordinates.
• Expression profiles: Quantified expression data for lncRNAs across 2,313 publicly available rice RNA-seq libraries.
• Genomic SNPs in lncRNA transcripts: Catalogues single nucleotide polymorphisms mapped to lncRNA transcripts for analyses of genetic variation.
• LncRNA–phenotype associations: Includes associations between lncRNAs and phenotypic traits to facilitate functional genomics studies.
• Transposon overlap analysis: Reports overlaps between lncRNAs and transposable elements to assess genomic context and evolutionary relationships.
• LncRNA–miRNA interactions and precursors: Documents predicted interactions between lncRNAs and microRNAs and instances where lncRNAs serve as miRNA precursors.
• Multi-omics data integration: Integrates multiple omics data types with lncRNA annotations to enable comprehensive analyses.

Scientific Applications:

• Gene expression regulation: Enables investigation of lncRNA roles in transcriptional and post-transcriptional regulation in rice.
• Genetic diversity and variation analysis: Supports studies of SNP impacts on lncRNA sequences and potential functional consequences.
• Phenotype association studies: Facilitates linking lncRNAs to observable traits and dissecting molecular bases of phenotypic variation.
• Evolutionary and transposon studies: Allows analysis of lncRNA overlap with transposable elements to explore genomic evolution and stability.
• Post-transcriptional regulation via miRNAs: Supports studies of lncRNA–miRNA interactions and lncRNA-derived miRNA precursors in regulatory networks.
• Integrative multi-omics analyses: Enables combined analyses across omics layers to study lncRNA functions in development and environmental responses.

Methodology:

Identification and characterization of lncRNAs were performed from 2,313 publicly available rice RNA-seq libraries with integration of multi-omics data into the database.