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Index of /EvidentialGene/nasonia/genes/lola

      Name                         Last modified       Size  

[DIR] Parent Directory 08-Feb-2012 15:20 - [   ] 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.huball180.longint 10-Feb-2014 21:22 10k [TXT] lola.longint 19-Nov-2011 14:40 4k [TXT] lola.shortint 19-Nov-2011 15:17 3k [TXT] lola86.aa 27-Jan-2012 17:29 44k [   ] lola86.mus 27-Jan-2012 17:30 99k [TXT] nasv4-altmany-loci.txt 08-Jun-2014 13:36 4k

Nasonia genes with most abundant alternate intron splicing, sharing 1 common splice point.
Probably all are 3' alternates, sharing common 5' exons.
	eg.    xxxxx ... yyy
	       xxxxx ........ zzz
	       xxxxx .............. aaa
	             ^ common exon/intron splice point

Common splice point and number of alternate end points

SCAFFOLD2:4430867:-   n=180  = lola, Longitudinals lacking protein
    Nasvi2EG036900t1 .. t86 , n=86 annotated alternates, up to 180 alternate introns with same splice point
    lola.huball.longint = 180 hub intron locations from common hub to 3' found in RNA/EST
    lola.longint = 89 hub introns annotated as alternate transcripts
    lola.shortint = short introns in 5' and 3' exons
    hub intron minimum, maximum size: 10457 .. 301261

Separation of lola hub-3' introns:
   n=180; ave distance=1624; (max,75,med,25,min)=11415 1718 1048 728 3
   median +/- 25% quantile distance: 1048 bases, 728 .. 1718
   This fairly regular spacing over 300 Kb span is suggestive of more unfound splice variants at
   each 1kb step, up to 275 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.

Other alt-intron genes in Nasonia
SCAFFOLD22:1828030:-  n=77, all rare introns?
	Nasvi2EG010865t1, Rap guanine nucleotide exchange factor 2
SCAFFOLD28:596277:+		n=23 , 17 frequent, cds introns; needs fixing as 1 locus
	Nasvi2EG037173t1 .. Nasvi2EG037176t2   SCAFFOLD28:591000-653000  Zinc finger protein 426 
	.. looks like lola, 4 common 5' exons > 17-23 longint staggered from 1 splice, some shortint
	.. now is ~18 loci composed of the alternate exons, needs reconstruction as 1 locus + alternates
		Nasvi2EG037173t1 625 aa, longest span
		Nasvi2EG037173t2 944 aa, Nasvi2EG037175t1 993 aa, Nasvi2EG037176t1 644 aa  cluster in ARP9_G7769
	** lola proteins cluster with ZFN-629 : 
				ARP9_G4677=ZFN 629 or 569,Nasvi2EG001760t1 ARP9_G6346=lola ARP9_G4676=lola ARP9_G236=x1,Nasvi2EG001747t1,Nasvi2EG001748t1;  
	   this locus clusters with ARP9_G7769, ZFN-426
  -- similarity probably due to transcription factor components, eg
       Transcription factor GAGA is found in insect genes: lola, zinc fingers
	.. vel2,vel4 have most of 3' longint parts, to 1 short mid exon needs pasting to 5' end
	  nvit1v4aSallLoc28689t2.. nvit1v4aSallLoc28702t1 nvit1v4aSallLoc28691t1
SCAFFOLD14:1429329:-  n=19, 13 frequent,cds introns
  Nasvi2EG007817t1 Antichymotrypsin/Serine Protease inhibitor
  >> aphid: acyp2eg0007429t1, Alaserpin/serpin/serine protease inhibitor 4, nalt=14
SCAFFOLD58:498255:+  n=16,  all rare introns?
	Nasvi2EG016140t1 Sentrin-specific Protease 

SCAFFOLD2:1828459:-  n=12, 5 frequent, utr introns
	Nasvi2EG001444t1   ARP9_G3045,1/12/9

SCAFFOLD102:30443:-      n=11 
	Nasvi2EG037282t1 DSCAM, well known alt spliced gene
  >  aphid also ..
SCAFFOLD13:462085:-      n=11, 3 frequent introns
	Nasvi2EG007389t1	gonadal protein gdl   SCAFFOLD13:460946-461987 .. 466620+
  ** BAD alts of Nasvi2EG007388t1 using intron + direction; bad velvasm; ESTs have <- int dir
		nvit1v4aSallLoc9114t12 nvit1v4aSallLoc9114t18   nvit1v2Svelmid4Loc126t12 ..

SCAFFOLD28:1360326:-     n=11 < 7 frequent, utr introns
SCAFFOLD31:1264195:-     n=11 < 7 frequent utr introns
	Nasvi2EG012714t1  Rab-protein 5; Ras-related protein Rab-5C
 >> cacao multiplex alt gene: Thecc1EG020064t1, Ras-related protein RABA5e (maybe.. messy ints)
SCAFFOLD1:1005395:-      n=10	< 4 frequent, cds protein
	Nasvi2EG000107t1	Cytospin-A

Developed at the Genome Informatics Lab of Indiana University Biology Department