Transcription start of STM?

Hi all,

My grad student is trying to map the transcription start site of our
leafy spurge STM gene so we can be sure how much promoter sequence we
have. All of his 5' Race products end 21 bp 5' from the ATG which would
suggest that the TATATAG that is about 25 bp 5' from the putative
transcription start site is the likely functional TATA box. In fact,
that particular sequence is also present in the arabidopsis STM gene at
the same place relative to the ATG. All would seem well and good except
that we have one cDNA clone pulled from our library that clearly has a
different transcription start site 5' to most of our cDNA and 5' RACE
products.

So my question is, has anyone here mapped the transcription start site
of STM in Arabidopsis? Is there evidence of multiple start sites for
STM?

One other oddity we are running across is there seems to be some
differences in our cDNA and genomic clones at those simple sequence
repeats near the 5' end of the STM coding sequence (found in both
arabidopsis and leafy spurge STM). I was wondering if they are real or
if they are cloning artifacts. As it is pretty clear that there is
only one copy of STM in Arabidopsis, has anyone noticed any slippage in
their clones at these repeat sequences? Any info will be greatly
appreciated.

Dave Horvath
USDA/ARS
Fargo ND