Fruitfly zip codes, regulatory elements and RNA genes
Zipcodes and regulatory elements
UTR-located Drosophila zipcodes & cis-reg elements in Rfam:
|Nanos||Rfam:RF00161||FBgn:0002962||Nanos Biology (lots of links)|
|Hsp90||Rfam:RF00433||FBgn:0001233||heat shock, not zipcode. In 5'UTR|
|Bicoid||Rfam:RF00551||FBgn:0000166||Irion & St Johnston: bicoid RNA localization requires specific binding of an endosomal sorting complex. Nature 2007;445:554-8.|
We have sucked out alignments of these from the MAVID whole-genome alignments (see Mercator Perl for detailed methodology).
All of these elements also appear to have Rfam hits across multiple species (see below) though possibly not all the species... the MAVID alignments may be useful for expanding coverage.
Rfam hits in Drosophila
We have (up to) 12-species alignments of these, built using Infernal, located here (on our cluster NFS):
See also AAA:Noncoding_RNA
Links to relevant Rfam families:
- Rfam:RF00161 (see also Nanos Biology)
- Rfam:RF00168 (looks completely bogus)
- Nanos (see Nanos Biology): (predictably) Infernal alignment is better than MAVID, but misses gappier species. xfold seems to pick up main two stems in MAVID alignment. varspeed picks up two main protein-binding sites (stem & loop) in MAVID and Rfam seed alignment, but only stem in Infernal alignment (even though loop CUGGC binding site is 100% conserved) - Ian Holmes - 23 Feb 2007 21:31:08
-- Ian Holmes - 23 Feb 2007