I am having a hard time finding the sequences of small nucleolar RNAs in Wormbase.
I came so far that U6 seems to be called rsn-7 in C. elegans but I can not find the sequence anywhere.
Hi,
WormBase packages together all known ncRNA genes into one file called ‘wormrnaXXX.tar.gz’ (where XXX is the current release number of WormBase) which is available with each release. This will contain the snRNA genes:
ftp://ftp.wormbase.org/pub/wormbase/genomes/elegans/sequences/ncrna
Alternatively, go here: http://www.wormbase.org/db/searches/wb_query
and perform the query ‘Find Transcript; snRNA’ and you will see links to 87 snRNA genes in WormBase. I imagine that you might be able to do the same thing using the WormMart interface.
Regards,
Keith