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Chunk #9 — Analyzing long noncoding transcript annotation

Source
GENCODE: the reference human genome annotation for The ENCODE Project.
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yes

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not subject to NMD), and no high conservation, confirmed by PhyloCSF (see later section), through the majority of exons. The transcripts are not required to be polyadenylated but 16.8% are, and chromatin marks have been identified for 13.9% (Derrien et al. 2012). These lncRNAs can be further reclassified into the following locus biotypes based on their location with respect to protein-coding genes:Antisense RNAs: Locus that has at least one transcript that intersects any exon of a protein-coding locus on the opposite strand, or published evidence of antisense regulation of a coding gene.LincRNA: Locus is intergenic noncoding RNA.Sense overlapping: Locus contains a coding gene within an intron on the same strand.Sense intronic: Locus resides within intron of a coding gene but does not intersect any exons on the same strand.Processed transcript: Locus where none of its transcripts contain an ORF and cannot be placed in any of the other categories because of complexity in their structure.