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

Question

[Dave Bridges]

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.

Answer 1

[JC]

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

[Dave Bridges]

so is this not true for mouse?

[JC]

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

Answer 2

[PoGibas]

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