alternatively spliced form? - (Sep/21/2005 )

I used RT-PCR to amplify a sequence from a rat cell line. The primers were designed using the information of reported human gene sequence and a predicted rat sequence (~1kb). The PCR product was cloned into pcDNA3.1 and sequenced. Surprisingly, compared with the human sequence and the predicted rat sequence, the cloned sequence has a deletion of ~40 amino acids in the middle (closer to the N-terminus). Otherwise the clone sequence has very high homology with those sequence. Is this an alternatively spliced form? can it be an RT-PCR artifact? how can i pursue this further ?

hi
you can do a northern blot and see if the related band appear. By a western, do you reveal two different proteins in a high resolutive gel (40aa drive a little heavier protein...)
are homologues known in these organisms? in the DNA seq, can you predict an alternative splicing?
fred