Is the promoter part of whole of gene in the UCSC database?

Question

[Zahra]

Hi all,

The UCSC has an optional section to choose the interest position of a gene for BED file creation. I want to survey if the mutations are in the promoter region of my genes. Are they included in the whole gene sequence or I should survey the upstream of the gene?

Thanks for any help.

Answer 1

[i.sudbery]

You need to survey upstream of the gene. Generally the promoter is not included in the defination of the gene, which usually runs from the transcription start site of the most upstream transcript to the polyA site of the most downstream transcript.