I have just created a large pseudogene opposite the perfectly good coding gene R10E8.3 (this will be available in release WS184).
I do not, in general, like having more than UTR regions overlapping, but in this case the EST evidence for the pseudogene is overwhelming.
The coding gene is also well supported by EST and protein homology evidence and by a trans-spliced leader sequence site.
What is going on here? ???
The pseudogene R10E8.7 is now extended by adding 4 exons to the 3’ end, which makes it overlap with the gene R10E8.3 on the opposite strand. This is classed as a pseudogene because there is a lot of EST evidence for it being transcribed and spliced but no reasonable CDS can be made.
The 5’ end has a transposon-like pattern of inverted repeats around a repeat region. It is possible that this is not a copy of a coding gene, but is an accidental construct made by a transposon moving a promoter region here. The transcription of this pseudogene may have some regulatory effect on the gene on the opposite strand (R10E8.3)
Only one of several possible non-coding isoforms of this pseudogene has been made.
The EST alignments for the pseudogene are definitely on the correct strand, as shown by the strong splice sites that they use.