Eukaryotic Promoter Database

The Eukaryotic Promoter Database

The Eukaryotic Promoter Database contains information on eukaryotic promoters of RNA polymerase II with an indication of the transcription start location. Only those promoters are included in this data base in which the transcription start has been revealed experimentally.

Here is an example of some entries in the EPD database.

XX
ID   PV_U1     standard; single; PLN.
XX
AC   EP17001;
XX
DT   ??-NOV-1988 (Rel. 17, created)
DT   23-JUN-1997 (Rel. 50, Last annotation update).
XX
DE   U1 small nuclear RNA
OS   Phaseolus vulgaris (kidney bean)
XX
HG   Homology group 98; Leguminous snRNA 1
AP   none.
XX
DR   EMBL; J03563.1; PVUG1; [-351, 254].
XX
RN   [1]
RX   MEDLINE; 88097434.
RA   Van Santen V.L., Spritz R.A.;
RT   "Nucleotide sequence of a bean (Phaseolus vulgaris) U1 small
RT   nuclear RNA gene: Implications for plant pre-mRNA splicing";
RL   Proc. Natl. Acad. Sci. U.S.A. 84:9094-9098(1987).
XX
ME   Nuclease protection [1].
XX
SE   gagtcatgcaaaatagactacaaatataagatttgtcaccctgagttccATACTTACCTG
XX

This is in EMBL format, which GCG needs to reformat into a different format for searching with it's pattern matching programs. For example, the restriction enzyme and prosite files are in this format. This means that you can use programs like Map and Motifs and Findpatterns to search this database.

There isn't much annotation in this database. If you need to find out more about these sites, you have to look up the original literature reference. You can also go to the main EPD web site and search for the name of the factor. Then you can get a bit more info.

Searching the EPD

You can use programs like Map, MapSort, Motifs and Findpatterns to search this database.

The TFD database is stored in the genrundata subdirectory on PMGM. When the program asks what database to use. Type in.

Program

What to type in

Map

map -data=genrundata:tfd.dat

Motifs

motifs -data=genrundata:tfd.dat

FindPatterns

findpatterns -data=genrundata:tfd.dat

You can copy this file to your own directory using Fetch, and modify the database. You could also use Findpatterns to search for a specific sequence pattern.

Other Sites with EPD information

Searching for Regulatory Elements with GCG

GCG's TFD Site

EPD Home Page

Pattern Searching Techniques

Program	What to type in
Map	`map -data=genrundata:tfd.dat`
Motifs	`motifs -data=genrundata:tfd.dat`
FindPatterns	`findpatterns -data=genrundata:tfd.dat`