[Genome] Where are the promoters and PlyA in Genescan (BED)

[Ricardo Godinez Moreno]

Hi,

I would like to know how introns are localized and re-formated as bed or gtf
files in the UCSC genome browser.

The reason of this is because I am doing statistics of intron length using
Genescan gene predictions with the original genescan format wich includes
Promoters, PlyA signals. I am comparing this results to intron lengths using
reformated genescan genesets (GTF BED) in genome browser which only include
exons and introns but not Promoters or plyA signals.

My concern about how intron length is calculated, is because I think that since
bed and gtf formats only have exons and introns but not promoters or poly A
signals. I suppose that plyA and promoters may be included as introns in the
genescan genesets.

In summary. I need to compare genome browser intron length using genescan
genesets and compare them to my own genescan results. But I wonder if introns
have been confused with poly A or promoter elements. If so, how can I fix that.

Ricardo.




--
RICARDO GODINEZ MORENO
PhD Student
HARVARD UNIVERSITY
26th OXFORD ST.
Dept of Organismic Evoutionary Biology
Cambrdige MA. 02138
Lab:   (617)4962401
Office:(617)4968387
http://www.oeb.harvard.edu/faculty/edwards/people/RicardoGodinez.htm