NapRNAdb is the first dedicated database for comprehensive integration of public napRNA resources and systematic prediction of potential napRNAs across species. Specifically, it has curated over 30,000 napRNAs from orphan studies in humans and mice, with expression profiles delineated across diverse cell types and physiological conditions. Given that most napRNAs derive from evolutionarily conserved repetitive elements, it identifies 197,439 candidate napRNAs in 38 species through sequence conservation principles. Importantly, it provides a "Predict" tool that enables assessment of napRNA gene amplification potential for any target sequence via blastn, megablast, and dc-megablast modes. Conveniently, users can query gene names to determine their involvement in de novo napRNA origination. Moreover, systematic analysis of interactions between napRNAs and regulatory factors, including RNA modifications, RNA-binding proteins, disease-related single-nucleotide polymorphisms (SNPs), and single-nucleotide variations (SNVs), illuminates their roles in gene expression and cell proliferation. In summary, NapRNAdb serves as a dynamic resource platform propelling the exploration of napRNA regulatory landscapes and functions across species.