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Yup - in a lot of cases the transcription of non-coding RNAs is from introns. Some of them are within genes (intragenic) and others are intergenic (between genes). In humans, a large number of both have been documented http://www.nature.com/ng/journal/v47/n3/full/ng.3192.html Coming to your question about why they are not transcribed - it again comes down ...

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