Table 2

Online lncRNA resources

DatabaseNomenclaturesizeDescription of key featuresProvenance of lncRNAsReference
lncRBasehsaLB_AN_74656133 361Comprehensive database categorising lncRNA according to genomic context. Integrates, coding potential, expression data, associated genomic elements and publicationslncRNAdb, Broad Institute, Ensembl, NONCODE, H-InvDB13
lncipedialnc-SMUG1-7113 513Grouping of isoforms that share at least one exon. Integrates prediction of secondary structure, locus conservation and coding potentiallncRNAdb, Ensembl, Gencode, RefSeq, NONCODE, Broad Institute and two further RNA Seq publications19
NONCODEn343067/NONHSAT02851095 135ncRNA database with detailed information regarding provenance and expressionRefSeq, literature mining and specialised databases17
lncRNASNPlnc-SMUG1-732 108Lists overlapping miRNA binding sites and SNPs, predicting the influence of SNPs on secondary structure and miRNA binding and providing corresponding miRNA expression datalncipedia, dbSNP and stringency filtering27
EnsemblENSG0000022863023 498Integrative database of genome annotation with detailed information regarding provenanceComputational prediction from ESTs and chromatin marks28
GencodeENSG0000022863015 877Integrative database including information on DNA methylation, occupancy and chromatin state, along with RNA expression and bindingHAVANA manual annotation and Ensembl annotation pipeline, mostly validated29
HavanaOTTHUMT 0000032866214 396Manual genomic annotation supported by transcriptional evidenceManual annotation29
Broad InstituteTCONS_0007905414 353Expression levels in 24 tissues and cell types, stringent set of 4662 lincRNARNA Seq in 24 tissues and cell types16
ChIPBaselncRNA2314-110 559Integrates chromatin immunoprecipitation sequencing data with lncRNA occupancyEnsembl, refseq, UCSC, lncRNAdb and various publications30
RefSeqNR_047517.16917Non-redundant database of annotated sequencesData submitted to the International Nucleotide Sequencing Database31
lincPolyXLOC_000000*4662Similar to lncRNASNP, with SNPs categorised according to phenotype and conservation data integrated in the place of miRNAsStringent set from Broad Institute32
lncRNAdbHOTAIR166Manually curated database ofexperimentally validated, functional lncRNAsLiterature mining33
  • This selection of resources is not exhaustive, but presents a broad spectrum of available and up to date tools. Included is an example of the nomenclature preferred by each database, with all entries referring to the lncRNA HOTAIR.

  • *HOTAIR is not found in lincPoly.