MicroRNA: RiceNCexp integrated rice microRNA sequences from miRBase and PmiREN. If the sequence only exists in the miRBase, the suffix of the microRNA name is "_miRbase". If the sequence only exists in PmiREN, the suffix of the microRNA name is "_PmiREN". If the sequence exists in both miRBase and PmiREN, the suffix of the microRNA name is "_Both". In addition, novel miRNAs also were predicted by RiceNCexp and suffixed with "_RiceNCexp".
Long non-coding RNA: RiceNCexp extracted the lncRNAs information from NCBI rice annotation file(GCF_001433935.1_IRGSP-1.0) and obtained its sequences.
PhasiRNA and PHAS Gene: RiceNCexp used the phased siRNA analysis tool PhasiRNAnalyzer to predict the phased siRNA from 307 rice sRNA-seq datasets (including different tissues and treatments), and integrated the prediction results to obtain the mature phased siRNAs(phasiRNAs) and the PHAS gene.
RiceNCexp provides the expression matrix of Non-coding RNAs and protein-coding gene in all samples (lncRNA, PHAS Gene and protein-coding gene: RNA-Seq, 491; microRNA and phasiRNA: sRNA-Seq, 274)
RiceNCexp provides the expression matrix of Non-coding RNAs and protein-coding gene in co-expression samples which are both RNA-Seq sequencing data and sRNA-Seq sequencing data (116) in same experiments.
RiceNCexp identifies 7898 novel lncRNAs and 71 novel miRNAs.Users can download FASTA-formatted sequences and genomic location information of all novel lncRNAs and miRNAs.