Home LiteratureArticle Details
PMID: 21112873 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

lncRNAdb: a reference database for long noncoding RNAs.

Nucleic acids research ·Vol. 39 ·No. Database issue ·2011-01-00 ·Pages D146-51

Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS

Abstract

Large numbers of long RNAs with little or no protein-coding potential [long noncoding RNAs (lncRNAs)] are being identified in eukaryotes. In parallel, increasing data describing the expression profiles, molecular features and functions of individual lncRNAs in a variety of systems are accumulating. To enable the systematic compilation and updating of this information, we have developed a database (lncRNAdb) containing a comprehensive list of lncRNAs that have been shown to have, or to be associated with, biological functions in eukaryotes, as well as messenger RNAs that have regulatory roles. Each entry contains referenced information about the RNA, including sequences, structural information, genomic context, expression, subcellular localization, conservation, functional evidence and other relevant information. lncRNAdb can be searched by querying published RNA names and aliases, sequences, species and associated protein-coding genes, as well as terms contained in the annotations, such as the tissues in which the transcripts are expressed and associated diseases. In addition, lncRNAdb is linked to the UCSC Genome Browser for visualization and Noncoding RNA Expression Database (NRED) for expression information from a variety of sources. lncRNAdb provides a platform for the ongoing collation of the literature pertaining to lncRNAs and their association with other genomic elements. lncRNAdb can be accessed at: http://www.lncrnadb.org/.

MeSH Terms
Databases, Nucleic Acid Disease/genetics Host-Pathogen Interactions Humans RNA, Untranslated/chemistry,metabolism,physiology
Chemicals
RNA, Untranslated
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Amaral Paulo P
Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
Clark Michael B
Gascoigne Dennis K
Dinger Marcel E
Mattick John S
References (65)
65 references, click to expand
  1. Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription.
    Genome Biol. 2007;8(3):R43 PMID: 17386095
  2. Subtractive hybridization identifies novel differentially expressed ncRNA species in EBV-infected human B cells.
    Nucleic Acids Res. 2007;35(10):e73 PMID: 17478510
  3. The bereft gene, a potential target of the neural selector gene cut, contributes to bristle morphogenesis.
    Genetics. 2002 May;161(1):231-47 PMID: 12019237
  4. RNAdb 2.0--an expanded database of mammalian non-coding RNAs.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D178-82 PMID: 17145715
  5. A liver X receptor (LXR)-beta alternative splicing variant (LXRBSV) acts as an RNA co-activator of LXR-beta.
    Biochem Biophys Res Commun. 2009 Dec 25;390(4):1260-5 PMID: 19878653
  6. A starvation-induced noncoding RNA modulates expression of Dicer-regulated genes.
    Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):12897-902 PMID: 18723671
  7. Potential structural role of non-coding and coding RNAs in the organization of the cytoskeleton at the vegetal cortex of Xenopus oocytes.
    Development. 2005 Aug;132(15):3445-57 PMID: 16000384
  8. S. pombe mei2+ encodes an RNA-binding protein essential for premeiotic DNA synthesis and meiosis I, which cooperates with a novel RNA species meiRNA.
    Cell. 1994 Aug 12;78(3):487-98 PMID: 7520368
  9. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation.
    Genome Res. 2008 Sep;18(9):1433-45 PMID: 18562676
  10. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a.
    Mol Cell. 2010 Jun 11;38(5):662-74 PMID: 20541999
  11. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA.
    Nature. 2008 Jan 10;451(7175):202-6 PMID: 18185590
  12. ANRIL expression is associated with atherosclerosis risk at chromosome 9p21.
    Arterioscler Thromb Vasc Biol. 2010 Mar;30(3):620-7 PMID: 20056914
  13. Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase.
    Nat Med. 2008 Jul;14(7):723-30 PMID: 18587408
  14. Identification and characterization of a virus-inducible non-coding RNA in mouse brain.
    J Gen Virol. 2006 Jul;87(Pt 7):1991-1995 PMID: 16760401
  15. Antisense transcription in the mammalian transcriptome.
    Science. 2005 Sep 2;309(5740):1564-6 PMID: 16141073
  16. Research resource: expression profiling reveals unexpected targets and functions of the human steroid receptor RNA activator (SRA) gene.
    Mol Endocrinol. 2010 May;24(5):1090-105 PMID: 20219889
  17. The genetic signatures of noncoding RNAs.
    PLoS Genet. 2009 Apr;5(4):e1000459 PMID: 19390609
  18. A susceptibility locus for papillary thyroid carcinoma on chromosome 8q24.
    Cancer Res. 2009 Jan 15;69(2):625-31 PMID: 19147577
  19. The non-coding Air RNA is required for silencing autosomal imprinted genes.
    Nature. 2002 Feb 14;415(6873):810-3 PMID: 11845212
  20. Role for antisense RNA in regulating circadian clock function in Neurospora crassa.
    Nature. 2003 Feb 27;421(6926):948-52 PMID: 12607002
  21. Specific expression of long noncoding RNAs in the mouse brain.
    Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):716-21 PMID: 18184812
  22. The eukaryotic genome as an RNA machine.
    Science. 2008 Mar 28;319(5871):1787-9 PMID: 18369136
  23. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D61-5 PMID: 17130148
  24. Genome-wide atlas of gene expression in the adult mouse brain.
    Nature. 2007 Jan 11;445(7124):168-76 PMID: 17151600
  25. Genomic analysis of mouse retinal development.
    PLoS Biol. 2004 Sep;2(9):E247 PMID: 15226823
  26. RNA maps reveal new RNA classes and a possible function for pervasive transcription.
    Science. 2007 Jun 8;316(5830):1484-8 PMID: 17510325
  27. Long non-coding RNAs: insights into functions.
    Nat Rev Genet. 2009 Mar;10(3):155-9 PMID: 19188922
  28. The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons.
    J Cell Sci. 2007 Aug 1;120(Pt 15):2498-506 PMID: 17623775
  29. Characterization of a germ-line deletion, including the entire INK4/ARF locus, in a melanoma-neural system tumor family: identification of ANRIL, an antisense noncoding RNA whose expression coclusters with ARF.
    Cancer Res. 2007 Apr 15;67(8):3963-9 PMID: 17440112
  30. Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D183-7 PMID: 17099227
  31. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation.
    Mol Cell. 2008 Oct 24;32(2):232-46 PMID: 18951091
  32. Collection of mRNA-like non-coding RNAs.
    Nucleic Acids Res. 1999 Jan 1;27(1):192-5 PMID: 9847177
  33. The steroid receptor RNA activator protein is recruited to promoter regions and acts as a transcriptional repressor.
    FEBS Lett. 2010 Jun 3;584(11):2218-24 PMID: 20398657
  34. piRNABank: a web resource on classified and clustered Piwi-interacting RNAs.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D173-7 PMID: 17881367
  35. A gene atlas of the mouse and human protein-encoding transcriptomes.
    Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6062-7 PMID: 15075390
  36. An Alu-like RNA promotes cell differentiation and reduces malignancy of human neuroblastoma cells.
    FASEB J. 2010 Oct;24(10):4033-46 PMID: 20581224
  37. The H19 locus acts in vivo as a tumor suppressor.
    Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12417-22 PMID: 18719115
  38. Maternally expressed gene 3, an imprinted noncoding RNA gene, is associated with meningioma pathogenesis and progression.
    Cancer Res. 2010 Mar 15;70(6):2350-8 PMID: 20179190
  39. Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction.
    J Hum Genet. 2006;51(12):1087-1099 PMID: 17066261
  40. miRBase: tools for microRNA genomics.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8 PMID: 17991681
  41. The transcriptional landscape of the mammalian genome.
    Science. 2005 Sep 2;309(5740):1559-63 PMID: 16141072
  42. P53 mRNA controls p53 activity by managing Mdm2 functions.
    Nat Cell Biol. 2008 Sep;10(9):1098-105 PMID: 19160491
  43. Human U19 intron-encoded snoRNA is processed from a long primary transcript that possesses little potential for protein coding.
    RNA. 1998 Apr;4(4):445-54 PMID: 9630250
  44. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis.
    Nature. 2010 Apr 15;464(7291):1071-6 PMID: 20393566
  45. Target mimicry provides a new mechanism for regulation of microRNA activity.
    Nat Genet. 2007 Aug;39(8):1033-7 PMID: 17643101
  46. Complex I binding by a virally encoded RNA regulates mitochondria-induced cell death.
    Science. 2007 Jun 1;316(5829):1345-8 PMID: 17540903
  47. The UCSC Genome Browser database: update 2010.
    Nucleic Acids Res. 2010 Jan;38(Database issue):D613-9 PMID: 19906737
  48. ncRNAimprint: a comprehensive database of mammalian imprinted noncoding RNAs.
    RNA. 2010 Oct;16(10):1889-901 PMID: 20801769
  49. Noncoding RNA in development.
    Mamm Genome. 2008 Aug;19(7-8):454-92 PMID: 18839252
  50. Database resources of the National Center for Biotechnology Information.
    Nucleic Acids Res. 2010 Jan;38(Database issue):D5-16 PMID: 19910364
  51. Recurrent focal copy-number changes and loss of heterozygosity implicate two noncoding RNAs and one tumor suppressor gene at chromosome 3q13.31 in osteosarcoma.
    Cancer Res. 2010 Jan 1;70(1):160-71 PMID: 20048075
  52. tRNADB-CE: tRNA gene database curated manually by experts.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D163-8 PMID: 18842632
  53. Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications.
    Brief Funct Genomic Proteomic. 2009 Nov;8(6):407-23 PMID: 19770204
  54. Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation.
    BMC Neurosci. 2010 Feb 05;11:14 PMID: 20137068
  55. Experimental approaches to identify non-coding RNAs.
    Nucleic Acids Res. 2006 Jan 25;34(2):635-46 PMID: 16436800
  56. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
    Genome Res. 2004 Oct;14(10B):2121-7 PMID: 15489334
  57. Altered expressions of the noncoding hsromega gene enhances poly-Q-induced neurotoxicity in Drosophila.
    RNA Biol. 2006 Jan-Mar;3(1):28-35 PMID: 17114940
  58. Bsr, a nuclear-retained RNA with monoallelic expression.
    Mol Biol Cell. 2007 Aug;18(8):2817-27 PMID: 17507654
  59. A role for noncoding transcription in activation of the yeast PHO5 gene.
    Proc Natl Acad Sci U S A. 2007 May 8;104(19):8011-6 PMID: 17470801
  60. Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor.
    Sci Signal. 2010 Feb 02;3(107):ra8 PMID: 20124551
  61. Noncoding RNAs produced by oncogenic human herpesviruses.
    J Cell Physiol. 2008 Aug;216(2):321-6 PMID: 18484093
  62. A mammalian gene with introns instead of exons generating stable RNA products.
    Nature. 1996 Feb 1;379(6564):464-6 PMID: 8559254
  63. A novel non-protein-coding infection-specific gene family is clustered throughout the genome of Phytophthora infestans.
    Microbiology (Reading). 2007 Mar;153(Pt 3):747-59 PMID: 17322195
  64. NRED: a database of long noncoding RNA expression.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D122-6 PMID: 18829717
  65. The H19 non-coding RNA is essential for human tumor growth.
    PLoS One. 2007 Sep 05;2(9):e845 PMID: 17786216
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkq1138
Published
2011-01-00
Epub
2010-00-25
Pages
D146-51
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3013714
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkq1138 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2