Long non-coding RNA databases | Non-coding transcript data analysis
Long non-coding RNAs (lncRNAs) form the largest class of non-protein coding genes in the human genome. While a small subset of well-characterized lncRNAs has demonstrated their significant role in diverse biological functions like chromatin modifications, post-transcriptional regulation, imprinting etc., the functional significance of a vast majority of them still remains an enigma. Increasing evidence of the implications of lncRNAs in various diseases including cancer and major developmental processes has further enhanced the need to gain mechanistic insights into the lncRNA functions.
A comprehensive searchable biologically oriented knowledgebase for long noncoding RNAs in Humans. lncRNome hosts information on over 17,000 long noncoding RNAs in Human. The resource provides information on the types, chromosomal locations, description on the biological functions and disease associations of long noncoding RNAs.
Contains more than 37 700 manually curated RNA subcellular localization in multiple biological processes. RNALocate integrates all types of RNA symbols, mainly including microRNA symbols from the miRBase database, long noncoding RNA (lncRNA) and mRNA symbols from NCBI Gene and Ensemble genome database. The database concerns 65 species, mainly including Homo sapiens, Mus musculus, and Saccharomyces cerevisiae. It is searchable by localization, organism or RNA category.
A manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDNA database documents 24713 associations between 142 NSDs and 8593 ncRNAs in 11 species, curated from more than 1300 articles. This database provides a user-friendly interface for browsing and searching and allows for data downloading flexibility. In addition, NSDNA offers a submission page for researchers to submit novel NSD-ncRNA associations. It represents a useful and valuable resource for researchers who seek to understand the functions and molecular mechanisms of ncRNA involved in NSDs.
A comprehensive database for long noncoding RNA (lncRNA) in Human and Mouse. LncRBase hosts information on basic lncRNA transcript features, with additional details on genomic location, overlapping small noncoding RNAs, associated Repeat Elements, associated imprinted genes, and lncRNA promoter information. Users can also search for microarray probes mapped to specific lncRNAs and associated disease information as well as search for lncRNA expression in a wide range of tissues.
Provides regulatory information about lncRNAs, such as targets, regulatory mechanisms, and experimental evidences for regulation and key molecules participating in regulation. LncReg is developed by collecting 1081 validated lncRNA-associated regulatory entries, including 258 non-redundant lncRNAs and 571 non-redundant genes. With regulatory relationships information, LncReg can provide overall perspectives of regulatory networks of lncRNAs and comprehensive data for bioinformatics research, which is useful for understanding the functional roles of lncRNAs.
A searchable database of lncRNA sequences and annotation in plants. PlncRNADB includes about 5100 lncRNAs from A. thaliana, A. lyrata, P. trichocarpa and Z. mays. The sequences were obtained either from the literature or by annotation based on reference-guided transcriptome assembly.
Localizes lncRNA in human cells based on RNA-sequencing datasets. LncATLAS enables non-expert users to rapidly access a rich variety of easily-interpreted data on their 39 lncRNA of interest. It is based on standard GENCODE annotations, the de facto official annotation for both protein-coding and lncRNA genes and it is quantitative.