A stop codon killed my ORF!

[Emilie]

Hello all,

After performing multiple RACE PCR experiments in order to obtain the
5'end of my gene, I finally succeded in obtaining the entire gene.
Everything seemed to be ok, the predicted peptide showed good
alignement to other related proteins with plenty of conserved regions,
but... there is a stop. About 600 bp downstream the ATG [total length
= 2.8 Kb] . There are conserved regions before and after the stop.
I checked the sequence several times, reamplifying with a
proof-reading polymerase as well as my usual one.
I am looking for a plausible explanation. Why the stop? Could it be a
pseudogene? why would it be transcribed?
Could it be a defect in splicing a small intron, resulting in the
stop?
I don't really know how to justify that result, can you help?
Any advice is grately appreciated!

-------
Emilie
Department of Biological Sciences, Warwick University
c.emilie at gmail.com