Fruitfly zip codes, regulatory elements and RNA genes

Zipcodes and regulatory elements

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

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 Noncoding RNA (AAA wiki)

Links to relevant Rfam families:

• 5S ribosomal RNA
• 5.8S ribosomal RNA
• U1 spliceosomal RNA
• U2 spliceosomal RNA
• Nuclear RNase P
• U4 spliceosomal RNA
• Eukaryotic type signal recognition particle RNA
• U5 spliceosomal RNA
• U6 spliceosomal RNA
• Group I catalytic intron
• Selenocysteine insertion sequence
• Histone 3' UTR stem-loop
• Nanos 3' UTR translation control element (see also Nanos Biology)
• Lysine riboswitch (looks completely bogus)
• K10 transport/localisation element (TLS)
• FIE3 (ftz instability element 3') element
• Hsp90 cis-regulatory element
• Hairy RNA localisation element (HLE)
• Potassium channel RNA editing signal
• Simian virus 40 late polyadenylation signal (SVLPA)

Notes

%COMMENT%

• 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) - IanHolmes - 23 Feb 2007 21:31:08

-- IanHolmes - 23 Feb 2007