More promoter sequences with 1 gene ID with Ensembl

Question

[martinosuperman]

When I search through a promoter sequence database, like Gene2Promoter and Eukaryotic Promoter Database (EPD), sometimes, I get more sequences with 1 gene ID. How can that be?

It has the fact that each gene ID corresponds to 1 promoter sequence? Or am I wrong? How can it be that 1 gene ID gives more promoter sequences as result? Are those promoter sequences allele sequences of that specific gene ID?

Answer 1

[Devon Ryan]

Genes can have multiple transcripts, each possibly with different start positions. Consequently, a gene can also have multiple promoter sequences.

[pld]

To expand on this, eukaryotic transcription regulation can require multiple different factors binding at different locations. In general, eukaryotic regulation is more complex, you can have different activators, different repressors, etc. Compared to prokaryotes, eukaryotic promoters tend to be more degenerate as well.

It was a fun moment when I ran MEME on eukaryotic promoters after being used to seeing bacteria TF motifs for four years!