Extract multiple Genes' Promoter Sequence

How to extract promoter sequence

Step 1. Use keyword to query the database

MmPD supports to search promoter location based on keyword search. keywords include the NCBI mRNA Accession number, NCBI Unigene cluster ID, NCBI LocusLink ID, and others (some gene name, like Cdc2a).

Step 2. Give the 5'- and 3'- flanking region length

For each promoter, you can choose the lengths of the upstream region and downstream region of known/predicted transcript start sites by giving the lengths (in base pairs). The default lengths of 5'- and 3'- flank regions are 700 bps and 300 bps seperately. You can change them to any length less than 100000 bps. 3'- flank region length should be always a positive integer or zero while the 5'- flank region length can either be positive or negative ( the results are same) but zero.

Step 3. Get your promoter regions

After choosing a type of keyword, and giving a keyword in blank after "ID:", you will query result after clicking the "submit" button.

The result will report how many sequences are found based on keyword query and the location of the sequences. If you use Promoter ID to query the database, only this promoter's information will be displayed. Otherwise, all the promoters' information of the found gene will be listed. The table includes the genome location of each promoter and their related Gene ID.Click on Promoter ID and Gene ID in this table will go to Gbrowser to display the related regions.

The number of extracted promoter sequences are also reported above the extracted sequences. All the promoter sequences are displayed in FASTA format, which the definition line includes the pomoter ID, genome locaion of the extracted regions, your query ID. The base pairs in the upstream region of transcript start site are in lower cases while those in the downstream are in capital cases.

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Created by Zhenyu Xuan. All rights are reserved
Please contact xuan@cshl.edu if you have any problem about this database.