Endogenous small non-coding RNAs (sRNAs), including microRNAs, PIWI-interacting RNAs and small interfering RNAs, play important gene regulatory roles in animals and plants by pairing to the protein-coding and non-coding transcripts. However, computationally assigning these various sRNAs to their regulatory target genes remains technically challenging.
Recently, a novel tool, StarScan (sRNA target Scan) was developed for discovering potential sRNA-mediated RNA cleavage events from degradome sequencing data in plants and animals (20 species). StarScan searches sRNA (miRNA, siRNA, piRNA, etc.) targets in annotated (lncRNAs, circRNAs, pseudogenes, 5' UTR, CDS, 3' UTR and introns) and unannotated genomic regions. StarScan web server performs an ultrafast and exhaustive search for potential sRNA–target interactions in various genomic regions.
Long non-coding RNAs (lncRNAs) are emerging as important regulatory molecules in developmental, physiological, and pathological processes. However, the precise mechanism and functions of most of lncRNAs remain largely unknown.
protein-lncRNA interaction resources: RBP-lncRNA Base, that analyzing millions of RNA-binding protein (RBP) binding sites from 117 CLIP-Seq datasets generated by 50 independent studies, we identified 22,735 RBPlncRNA regulatory relationships.