I'm looking at this gene that has interesting
transcription properties. I have
the genomic sequence near the 5' end of
the transcriptional strat site.
A promoter finder found this sequence which
has CCATC and TATAAAA and a GC box--real pretty canonical promoter
but it's an "MLT1" repeat about 200 nucs upstream
of my transcr start site and same orientation 5' to 3'.
Another (predicted)promoter lies closer to the transcr start site,
maybe the "real" prmoter, but less typical-looking.
Might this promoter-like seq play a role in the transcription of
my gene? If it's such a canonical looking promoter,
might it interfere? The chimp ortholog doesn't have this retroviral
promoter in its sequence but only human does.