Frequently Asked Questions

What is SwitchDB?
SwitchDB is a freely available database and online product catalog of human gene regulatory sequences. It allows users to identify promoters and 3’UTRs corresponding to a single gene or a large collection of genes, and it allows users to order cloned elements in a luciferase reporter vector.

How does SwitchGear identify all of the promoters in the genome?
This technical note provides a detailed description of how SwitchGear defines human gene models and predicts transcription start sites for them.

Why does my gene have alternative promoters?
It has been estimated that greater than 25% of all human genes have more than one transcription start site. A given transcript may initiate from different start sites in different cell types or under different cellular conditions or stimuli. Additionally, several transcription start sites may be utilized in a single cell type. SwitchDB catalogs many potential alternative transcription start sites for genes and ranks them based on experimental evidence.

Which promoter should I choose when there are alternatives?
Choosing the correct transcription start site is important to obtaining relevant results from a promoter assay. The search results in SwitchDB display the coordinate of each clone, and the primary promoter for each gene is the promoter that has the strongest experimental evidence for containing a transcription start site for that gene. In the absence of any other information, you are best off going with the primary promoter displayed in the search results for a given gene.

When alternative promoters for a gene exist, you can view these in the search result table by clicking on the “view alternatives” link. Clicking on the coordinates in the search result table opens a window in the UCSC genome browser of the exact sequence that is cloned in the vector.  This allows you to see the cloned fragment in the context of other genomic features.  Using this information, you can decide which of the alternative promoters to choose if you are looking for a promoter that corresponds to certain genomic features of interest.

Where can I find more information on the vector and reporter gene?
SwitchGear uses a destabilized form of luciferase called luc2P developed by Promega for it's reporter gene. This optimized luciferase protein has a half-life of ~1 hour enabling detailed analysis of kinetic responses yet still provides a very robust signal.  Vector maps for all of SwitchGear's reporter vectors can be found here.