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NONCODE specifications


Unique identifier OMICS_02785
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 5.0
Maintained Yes


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Mammals
    • Bos taurus
  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Gallus gallus


  • person_outline Yi Zhao
  • person_outline Runsheng Chen

Publications for NONCODE

NONCODE citations


Long noncoding RNAs are associated with metabolic and cellular processes in the jejunum mucosa of pre weaning calves in response to different diets

PMCID: 5940403
PMID: 29765519
DOI: 10.18632/oncotarget.24898

[…] iltering. For our lncRNA analysis with PLEK we developed a bovine-specific model as suggested by the authors of PLEK. This model was calculated based on Bos taurus lncRNA sequences extracted from the NONCODE 2016 database ( and Bos taurus protein-coding mRNA sequences extracted from the NCBI Bos taurus UMD3.1.1 genome assembly ( […]


The use of long non coding RNAs as prognostic biomarkers and therapeutic targets in prostate cancer

PMCID: 5945524
PMID: 29755696
DOI: 10.18632/oncotarget.25038

[…] hat are designed specifically for lncRNAs. There are several databases that are dedicated to the curation of novel reported lncRNAs, including LncRNABase [], LNCipedia [], lncRNAdb [], LncRNAWiki [], NONCODE [], TANRIC [] and the ncRNA expression database []. Sequencing technology has evolved rapidly enough to allow lncRNA profiling at a single-cell resolution [], which averts future complications […]


Macrophage Derived Extracellular Vesicles Induce Long Lasting Immunity Against Hepatitis C Virus Which Is Blunted by Polyunsaturated Fatty Acids

Front Immunol
PMCID: 5906748
PMID: 29706960
DOI: 10.3389/fimmu.2018.00723
call_split See protocol

[…] ttp:// The sequencing results were subsequently analyzed for Gene Ontology (GO) Term enrichment by DAVID (Database for Annotation, Visualization and Integrated Discovery v6.8) or for NONCODE GO terms by Blast2GO. Selected transcripts were confirmed by quantitative RT-PCR. […]


Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells

PLoS One
PMCID: 5892903
PMID: 29634734
DOI: 10.1371/journal.pone.0195468

[…] overlap with a reference transcript”, “Unknown, intergenic transcript”, and “Exonic overlap with reference on the opposite strand”. We also compared the residual transcripts with known lncRNAs in the NONCODE2016 database and filter out the same or similar transcripts []. The remaining unknown transcripts were filtered by length 200 nt, exon number 1, ORF 300 nt. CPC (Coding Potential Calculator), […]


Differential Expression Profiling of Long Noncoding RNA and mRNA during Osteoblast Differentiation in Mouse

Int J Genomics
PMCID: 5885395
PMID: 29765976
DOI: 10.1155/2018/7691794

[…] All sequencing reads were aligned to the mouse genome reference (mm10) using the GSNAP alignment tool []. Ensembl release 74 annotations were used to measure gene expression. In the case of lncRNAs, NONCODE v4 ( annotations were used. Since NONCODE v4 annotations were based on mm9 mouse genome assembly, the positions of lncRNAs of NONCODE were converted from mm9 to mm10 usi […]


Integration of lncRNA and mRNA Transcriptome Analyses Reveals Genes and Pathways Potentially Involved in Calf Intestinal Growth and Development during the Early Weeks of Life

PMCID: 5867863
PMID: 29510583
DOI: 10.3390/genes9030142

[…] also transcripts that possessed an open reading frame with the ability to code for a peptide of 100 or more amino acids.The retained transcripts were compared with known bovine lncRNA annotation from NONCODE2016 database [] using Cuffcompare. Transcripts with class codes “=” (predicted transcript has exactly the same introns as the reference transcript), “c” (predicted transcript is contained with […]


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NONCODE institution(s)
Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China; CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China; School of Medicine, MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing, China; Chinese Academy of Sciences, LuoYang Branch of Institute of Computing Technology, Luoyang, China
NONCODE funding source(s)
Supported by National Natural Science Foundation of China [31371320, 31401119, 31501066]; National Science Foundation for Young Scholars [31701141, 31701149].

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