Fly Zipcodes

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Fruitfly zip codes, regulatory elements and RNA genes

Zipcodes and regulatory elements

UTR-located Drosophila zipcodes & cis-reg elements in Rfam:

Gene Rfam Flybase Notes
Nanos Rfam:RF00161 FBgn:0002962 Nanos Biology (lots of links)
Fushi tarazu Rfam:RF00227 FBgn:0001077
Hairy Rfam:RF00437 FBgn:0001168
K10 Rfam:RF00207 FBgn:0000810
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.
orb FBgn:0004882
oskar FBgn:0003015
Exuperantia FBgn:0000615  ?
gurken Rfam:RF00626

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):

/mnt/nfs/projects/12fly-ncRNA/cm-align/ncRNA-cmalign-tidy_stock/

See also AAA:Noncoding_RNA

Links to relevant Rfam families:

Notes

  • 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