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Index of /EvidentialGene/arthropods/honeybee/evg3hbee/lola

      Name                         Last modified       Size  

[DIR] Parent Directory 30-Jun-2015 22:42 - [TXT] amel_OGSv32_lola1.gff 06-Jun-2014 16:02 2k [TXT] evg3hbee_lola66.introns 07-Jun-2014 19:04 3k [TXT] evg3hbee_lola_in1489888.gff 07-Jun-2014 19:04 7k [TXT] evg3hbee_lola_in1489888.list 07-Jun-2014 19:04 2k [   ] lola-altintrons-bee-wasp.pdf 06-Jun-2014 23:29 24k [IMG] lola-altintrons-bee-wasp.png 06-Jun-2014 23:29 53k [TXT] lola-altintrons-bee-wasp.txt 08-Jun-2014 21:19 2k

Gene lola* is notable: it has the most alternate-introns found in any
gene, just as for Nasonia jewel wasp, with 55 found alt introns spread
over 200Kb in 1kb steps (more expected, Nasonia has 180+).  If you
study bee/wasp/ant social behavior, lola alts guide brain axon growth,
remember that name:   
  El-oh-el-aye Lola, lo lo lo lo Lola

Nasonia Jewel Wasp, the gene with most abundant alternate intron splicing is lola, 
sharing 1 common splice point. All are 3' alternates, sharing common 5' exons.
  eg.    xxxxx ... yyy
         xxxxx ........ zzz
         xxxxx .............. aaa
               ^ common hub exon/intron splice point
These are found with RNA-seq mapping to genome.

Location SCAFFOLD2:4430867:-   n=180  = lola, or Longitudinals lacking protein,
Gene id Nasvi2EG036900, alt t1 .. t86 , n=86 annotated alternates,
with 180 alternate introns found in RNA-seq mapping to same splice point.

Separation of lola hub-3' introns:
  median distance = 1048 bases, max=5083, min=511
  hub intron minimum, maximum span: 10457 .. 301261
  This fairly regular spacing over 300 Kb span is suggestive of more unfound 
  splice variants at each 1kb step, up to ~300 splice variants.

Apis mellifera honey bee has similar lola alternate introns from hub intron splice point,
Location Group9_12:148988:+, Gene id amel45:GB53441, matches nasonia OGSv2.0:Nasvi2EG036900

In evg3hbee EvidentialGene mRNA assembly, 55 such hub-alternate introns are found.
More probably exists in un-assembled reads.  These span about 180 Kb in Apis, 
versus 300 Kb in Nasonia.   Note also the recent 2014 NCBI Gnomon/Eukpipe gene annotation 
for honey bee finds the same lola hub intron with ~55 alternates. However about 20 have
a bit different 3' splice than Evigene's gene assembly, again suggesting unfound alts.

Developed at the Genome Informatics Lab of Indiana University Biology Department