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. 2018 Jan 1:2018:1-6.
doi: 10.1093/database/bay085.

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

Xiao Wen  1 , Lin Gao  1 , Xingli Guo  1 , Xing Li  1 , Xiaotai Huang  1 , Ying Wang  1 , Haifu Xu  1 , Ruijie He  1 , Chenglong Jia  1 , Feixiang Liang  1
Affiliations

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

Xiao Wen et al. Database (Oxford). .

Abstract

While long non-coding RNAs (lncRNAs) may play important roles in cellular function and biological process, we still know little about them. Growing evidences indicate that subcellular localization of lncRNAs may provide clues to their functionality. To facilitate researchers functionally characterize thousands of lncRNAs, we developed a database-driven application, lncSLdb, which stores and manages user-collected qualitative and quantitative subcellular localization information of lncRNAs from literature mining. The current release contains >11 000 transcripts from three species. Based on the accumulated region of lncRNAs, 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 lncSLdb, our system provides a set of comprehensive tools to search by gene symbols, genome coordinates or sequence similarity. We hope that lncSLdb will provide a convenient platform for researchers to investigate the functions and the molecular mechanisms of lncRNAs in the view of subcellular localization.

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Figures

Figure 1
Figure 1
Workflow and construction process of lncSLdb.
Figure 2
Figure 2
Statistics of species and types in lncSLdb. (A) The number of lncRNA transcript of different species in lncSLdb. lncSLdb collects more than 11 000 lncRNAs, mainly from three species (human,mouse and fruit fly). (B) The distribution of subcellular localization types in lncSLdb. lncSLdb collects >14 000 subcellular localization items, classified into three basic types and three subtypes.
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