BCB 444/544X
Lab 9 Answer Key
Promoter Prediction
1.) How many genes were submitted? How many were returned?
35 genes submitted, 56 returned
2.) What is one likely explanation for this?
Also alternative splice sites result in different proteins.
3.) How many motifs did the server find?
3, by default this was the max the server returned.
4.) Did this search find any more genes with similar conserved upstream
regions?
Yes, quite a few.
5) Do you think these are genuine conserved motifs? Why or why not?
Answers may vary
6.) What are the results of this search?
1462 sites were predicted but only returned the top 750.
7.) Are the motifs discovered in our previous search identified as known
binding motifs? If so describe which one(s)? Include motif length in your
description discussion. (Hint: Sort the TESS results sequence order by
clicking the “Beg” column title to numerically order the items. Search for the
meme motifs by the looking within / near TESS regions for which meme
identified conserved motifs. )
Motif 3 is identified as several smaller regions by TESS. However,
TESS identifies motifs across most of the entire region.
8.) What difficulties do you see with predicting conserved promoter
regions?
Promoter regions by definition are degenerate, consist of only four
bases (ACTG), and are not often extremely long. This makes if very
difficult to clearly identify conserved promoter regions.