IncSLdb: a resource for long non-coding RNA subcellular localization

While long non-coding RNAs (IncRNAs) may play important roles in cellular function and biological process, we still know little about them. Growing evidences indicate that subcellular localization of IncRNAs may provide clues to their functionality. To facilitate researchers functionally characterize thousands of IncRNAs, we developed a database-driven application, IncSLdb, which stores and manages user-collected qualitative and quantitative subcellular localization information of IncRNAs from literature mining. The current release contains >11 000 transcripts from three species. Based on the accumulated region of IncRNAs, we classify transcripts into three basic localization types (nucleus, cytoplasm and nucleus/cytoplasm). In some conditions, the nucleus and cytoplasm types can be divided into three more accurate subtypes (chromosome, nucleoplasm and ribosome). Besides browsing and downloading data in IncSLdb, our system provides a set of comprehensive tools to search by gene symbols, genome coordinates or sequence similarity. We hope that IncSLdb will provide a convenient platform for researchers to investigate the functions and the molecular mechanisms of IncRNAs in the view of subcellular localization.