ga-rich repeats and function - ga-rich repeats and function (Dec/26/2001 )

Does anyone know how to predict whether a ga-rich repeat region in the 5' flanking region of a gene (eg promoter) has functional significance? Also is there any computer software designed for this purpose?

-Ruth-

Some software can predict if the GC rich sequence in the 5 flanking region to be a CpG island or not. Many gene especially housekeeping genes have CpG island in their 5' flanking region. In terms of functional significance, I only know that CpG island may be involved in hypermathylation which may lead to gene inactivation. This is frequently found with some tumor supressive gene such as E-cadherin, p53, p16 and others.

Hope it helps.

-pcrsequence-

Have you tried any of the promoter databases such as Eukaryotic Promoter database?
If you blast against this database with your sequence, it possible that there
may be similar regions. Have you also checked this region against repeat
databases?

-darryl-

where would one find access to the "eukaryotic promoter database"

Thanks

-Peter Terry-

Her is the EPD
http://www.epd.isb-sib.ch/

(Edited by long at 4:19 am on Feb. 26, 2001)

(Edited by long at 4:20 am on Feb. 26, 2001)

-long-