RACE vs. cDNA screening

[Ricky Boernke]

Dear all,

using degenerate primers I was able to PCR an internal portion of
my gene of interest. Since I am also interested in the 5' and 3'
regions, respectively, I was thinking about the appropriate method
to identify these parts of the cDNA too. I could easily use my PCR 
fragment as a probe to screen a respective cDNA library, however, 
this is quite time and labour consuming. Thus, I was also 
considering to run a RACE PCR. But what you here from other 
people is that doing RACE is often problematic.
Moreover, I expect my gene to be represented
by several isoforms which I think could become a problem when 
assembling the RACE fragments into a contigous cDNA. You can never
be sure whether you glue the proper 3 and 5' ends together and thus
might end up with a chimeric clone. Or wouldn't you regard this as
a problem. I don't now yet how different the isoforms will be.
Any input welcome

Cheers
Ricky