noncoding RNA list of mouse mm9

Question

[kanwarjag]

I am trying to get list of ncRNA of mm9 from any database I tried UCSC browser and followed the protocol 'NR'' but it is stated that it will not give all the ncRNA. Any pointers please

Thanks

Answer 1

[jhb80]

Long, small or both types of ncRNA?

I'd suggest GENCODE (http://www.gencodegenes.org/mouse_releases). Version M1 is based on mm9, but the more up-to-date versions (currently M9) are based on mm10.

NONCODE (http://www.noncode.org/) is another good source / reference collection.

[kanwarjag]

Interested in all including lincRNA as well as small IN Genode I found linRNA but not other

Long non-coding RNA gene annotation CHR It contains the comprehensive gene annotation of lncRNA genes on the reference chromosomes This is a subset of the main annotation file GTF GFF3

[jhb80]

You can use the standard (=comprehensive) gtf file. The GENCODE gtf contains Ensemble-based transcript- and gene-biotype information. You can then pull out the transcript- (or gene-) identifiers for all different types of non-coding RNA you're interested. Check out http://www.gencodegenes.org/mouse_stats/current.html for all the contained biotypes. LincRNA is only a subset, others include 'processed transcript', pseudogenes, miRNA, snoRNA, etc etc etc.

[Charles Warden]

That stats link is really helpful - I've heard that GENCODE has a lot of predicted gene annotations, but it is still much more conservative than NONCODE (although NONCODE is available for species other than human and mouse):

http://www.noncode.org/analysis.php

[kanwarjag]

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