Index of /EvidentialGene/arthropods/honeybee/evg3hbee/lola
Name Last modified Size
Parent Directory 30-Jun-2015 22:42 -
amel_OGSv32_lola1.gff 06-Jun-2014 16:02 2k
evg3hbee_lola66.introns 07-Jun-2014 19:04 3k
evg3hbee_lola_in1489888.gff 07-Jun-2014 19:04 7k
evg3hbee_lola_in1489888.list 07-Jun-2014 19:04 2k
lola-altintrons-bee-wasp.pdf 06-Jun-2014 23:29 24k
lola-altintrons-bee-wasp.png 06-Jun-2014 23:29 53k
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.