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zflncRNApedia is a comprehensive resource for the systematic study of long non-coding RNAs in zebrafish. The resource provides a unified view of the zebrafish lncrnome giving an insight to the genomic context, expression and regulation of each of the lncRNAs. It currently contains 2,267 lncRNAs derived from three recently published datasets on lncRNAs discovered in zebrafish. Depending on their genomic location, they have been classified into 4 categories: Intronic (86), Overlapping (485), Promoter associated (309) and linc RNAs (1386). Expression levels across 15 distinct data-sets encompassing developmental stages and adult tissues has been reported along with the mapping of genomic variations and retroviral insertion lines to lncRNA loci.