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FlyBase Genome Annotators, (2014). Analysis of candidate long non-coding RNA loci identified by Young et al., 2012. 
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FlyBase analysis
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Research paper

Identification and Properties of 1,119 Candidate LincRNA Loci in the Drosophila melanogaster Genome.
Young et al., 2012, Genome Biol. Evol. 4(4): 427--442 [FBrf0217966]

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Each of the 1119 regions identified by Young et al. was viewed in FlyBase GBrowse with tracks containing existing gene models and RNA-Seq coverage and junction data visible. 70 of the 1119 regions corresponded to UTR sequences of coding genes; 56 corresponded to genes annotated in FlyBase as encoding small polypeptides; 417 corresponded to existing (124) or supported new lncRNAs; 2 corresponded to pseudogenes. An identified region may have been annotated with more than one new lncRNA gene model, if the RNA-Seq data supported genes with different expression patterns or encoded on opposite strands. There were several reasons why a proposed region was not annotated as a new non-coding gene: (1) insufficient evidence, meaning the RNA-Seq signal was either too low or to diffuse to allow annotation of a discrete transcript; (2) no stranded data, meaning that RNA-Seq signal of sufficient quality was observed only in the non-stranded RNA-Seq samples, so a transcript could not be annotated; (3) TE region, meaning transcription was likely to be within or initiate within a transposable element. Details may be found in associated file (link below) on the FlyBase ftp site; note that the spreadsheet has 2 sheets, with the same data sorted differently.

Associated Files
File date: 2014.10.16 ; File size: 96535 ; File format: xlsx ; File name: lincRNA.Young_et_al_2012.141016.xlsx
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    Genes (596)
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