#VEGA or Encode pseudogene
(I.pseudoVegaProcessed>0.5 || I.pseudoVegaUnprocessed>0.5 || 
I.pseudoEncode>0.5)
#not known, spliced, or in intron on the same strand
and I.mgcKnown=0 and I.otherKnown=0 and intronsKnown=0
and splicedEST=0 and submitted=0
#not olfactory
###and I.horde=0
#longer
###and I.length>=300
#has a protein match
and (D.scorePfam>0 or D.scoreBlastP>0)
#at least slight synteny
and (I.netSyntenyMm8>0.1 or I.netSyntenyRn4>0.1 or I.netSyntenyCanFam2>0.1)
#remove simple repeat and duplicated regions
and simpleRepeat<0.01
and duplicated<0.01
and length(I.name)<18 #filter out random chr
and not(I.name like "orfchrY%") #filter out chr Y