I just thought you might enjoy this one…
The 3’ splice site of the penultimate intron (intron 5) does not have a strongly scoring splice site and the EST alignments show that splicing occurs at several sites within a region of about 50 bases. This results in a family of transcripts all differing slightly as they splice into different positions around the end of this intron.
There is mass-spectroscopy evidence that this gene produces a protein product.
There is some RNAi evidence of a phenotype (embryonic lethal, maternal sterile).
It looks as if there has been an integration of a transposon-like element in this intron which has distrupted the original 3’ splice site and now the transcription mechanism is producing a family of transcripts splicing to several different sites over a region of about 50 bases. Some of these transcripts are then viable enough to avoid being destroyed by NMD and to make a protein detectable by mass-spec.
I would expect to see strong selection at this locus for variants with any sort of in-frame splice site motif.
Gary