Understanding why a promoter is annotated for a distant gene

11 views

Skip to first unread message

Robert Calef

unread,

Feb 14, 2025, 11:52:38 AMFeb 14

to Ask EPD

Hi there,

I was looking into sourcing validated promoter sequences for human genes, and was using EPD to pull transcription start sites. When looking into genes that didn't seem to have a TSS in EPD, I noticed this example:

https://epd.expasy.org/cgi-bin/epd/get_doc?db=hgEpdNew&format=genome&entry=SEPT8_1

This promoter is located at chr5:132,830,647 and seems to be annotated with the SEPT8 gene, which is about 60kb away (chr5:132,750,819-132,777,239). However, this promoter does sit right next to the SHROOM1 gene (chr5:132,822,141-132,830,647).

I'm new to this dataset, so was curious, why is the promoter assigned to SEPT8 and not SHROOM1? Thank you!

Best,

Robert

CCG EPFL

unread,

Mar 2, 2025, 10:45:27 AMMar 2

to Ask EPD

Dear Robert,

I have looked into this issue and am embarrassed to say that this is clearly an error in our database. SEPT8_1 is, as you write, the promoter of SHROOM1. SEPT8_2 is the major promoter of the gene formerly called SEPT8 and now renamed to SEPTIN8.

We are sorry for the confusion this may have caused to you and others and are investigating how it was possible that this error has occurred. Thank you very much for having brought this issue to our attention.