We would value any lab work that takes a closer look at the abnormal splicing shown by the alignment of yk1541b03.3 to the two genes Y39B6A.14 and Y39B6A.16.
There is good evidence that these are two separate genes.
yk1541b03.3 aligns to two exons in the middle of Y39B6A.14 and then jumps to the last two exons of Y39B6A.16.
This sort of thing is often dismissed as a chimaeric transcript, but here the two ends are too close for this to be a random event.
The two genes from part of the same operon.
This splice would probably form non-functional products for the genes affected.
The C. briggsae contigs in this region are incomplete and so the entire orthologous C. briggsae operon is not in one contiguous sequence (in the cb25 assembly). Maybe you could look in the new C. briggsae assembly to see how the C. briggsae ortholog looks?
Do you trust the BLAT alignment?
Keith
P.S. I assume that this data is only in the Sanger database at the moment as I don’t see this EST alignment on the live or dev sites.
No weird trans-splicing has to have occurred to create this chimera. In operons, polycistronic cDNAs has been observed many times. To make this one, a dicistronic pre-mRNA was probably just spliced strangely to splice out the 3’ end of .14 and the 5’ end of .16. This kind of thing probably happens more frequently when a rare polycistronic pre-mRNA that contains splice sites that are not supposed to see each other is formed.