Up until WS247 rpa-3 and rpa-4 existed a 2 distinct genes in the WormBase annotation. This was recently revised as it appears that rpa-3 is a partial duplication
of rpa-4 but it lacks it’s 5’ end and probably the promoter and regulatory regions.
Transcription still appears to be very active and actually covers the whole locus (rpa-3/4). It would seem that based on both EST and RNASeq sequence data
that transcription starts on rpa-4 and continues to include the duplicated exons of what was rpa-3.
The question is…do all of the 5 coding Isoforms of the new rpa-4 annotation give rise to valid mRNAs and protein products?
The duplication appears to be so recent that the following Isoform structures are identical.
1 CDS F59A3.6e has the same structure as F59A3.6c
2 CDS F59A3.6f has the same structure as F59A3.6d
This loci appears to be unique* in the genome of C. elegans as this has not been seen before in the course of WormBase curation.
The only way of resolving this loci is for someone that has access to wet lab access to work on it.
- there might be other example that we just haven’t come across.