can i take promoter upstream 2kb from tss ?

Question

[isha.lily20]

Hello

I am beginner in computational field, got no help from any one in lab, can any one tell me about it, whether can i take promoter 2kb from tss ?

Thank you

[dthorbur]

Depending on which model system you are using it may also be worthwhile to check if any orthologs in better annotated species have promoters annotated. Otherwise, if you have the time, you can also look into the new tools being developed to predict promoters using genomic data like ReFeaFi.

[isha.lily20]

i am working on rice

[dthorbur]

I don't work on plants so I don't know what the regulatory landscape is like, but you can find orthologs and some regulatory annotations on databases like Ensembl Plants. Alternatively, check the literature for regulation of the orthologs - A. thaliana orthologs might be good start.

[dthorbur]

Just a quick update since I was looking for D. melanogaster core promoters today, I came across the Eukaryotic Promoter Database which has curated and annotated promoters in a bunch of models including A. thaliana and Z. mays. Thought it would be worth sharing since this may provide a little more information on the core promoters of orthologous genes.

Answer 1

[jared.andrews07]

Yes, that is a fairly common cutoff for defining a promoter region.