Interrupted reading frame, help!

[gc]

In article <1994Apr13.134355.1 at wehi.edu.au>, chai_z at wehi.edu.au wrote:

> Hello there,
> 
> I'm cloning an insulin or insulin-realated genes from a mollusc. I pulled out
> a cDNA using oligo probe of a reference sequences. My sequence showed 87%
> homology with the reference sequence, but by taking away 4 bases in the middle.
> The extra bases interrupted the reading frame. Furthermore, the whole cDNA 
> (1488 bases) contained many stop codons, which resulted in very short reading 
> frames (the biggest one is about 70 aa). 

> Any comments are appreciated.
> 
> Zhonglin Chai
> Melbourne
> (chai_z at wehi.edu.au)


Two possibilities come to mind.  The insertion may be a cDNA arifact.
Reverse transcriptase has been known to make mistakes.  A more likely
possiblity, considering the abundance of stops is that you've cloned a
pseudogene.  There are examples of pseudogenes that can still be transcibed
but not translated.  I would advise using this cDNA to do a Southern to
see if there are multiple related genes.  Also, I'd take this clone and
use it to screen a genomic library.  The genomic library wouldn't be
affected by the cloning artifacts that can screw up cDNA libraries.


-- 
--gc