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Are Long Noncoding Rna (Lncrna) Included In The Ucsc Or Ensembl Genome Assemblies?

Are lncRNA's present in the UCSC or ENSEMBL genome assemblies. My understanding is that the subset of poly-adenylated lncRNA's should be present in a TruSeq prep, and I am interested in aligning my reads to these.

rna-seq

2 answers

Assuming human, yes. Ensembl include them in the annotation file "Homo_sapiens.GRCh37.68.gtf". UCSC has a special track for them called "lincRNAsTranscripts".

so is this not true for mouse?

Mouse Ensembl models include lincRNAs, UCSC I'm no sure if a track exists.

ENCODE annotated new data-set of lncRNA's (locus & transcripts) http://big.crg.cat/

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