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aspiring bioinformatician here, I'd like to ask you for help with an university assignment. First let me post the entire question:

Design primers for bisulfite sequencing of the promoter of the ACE2 gene in microbat Myotis lucifugus (based on the annotation of the Broad Institute Myoluc2.0/myoLuc2). The gene is localized on the contig GL429816. As a transcription start, use the start of the ACE2 transcript variant XM_023753670.1; once you find ACE2 in the UCSC genome browser .You will find it in NCBI RefSeq track

I don't want anyone to solve it for me but I do have a problem with one aspect. I am not clear on how to determine what is a valid promotor for this gene in microbat. I do know it is the upstream sequence however I am not clear on how to tell the number of upstream bases that are the actual promotor. I did find some sources for the actual promotor sequence determined by much smarter people than myself however those are for ACE in humans so I am afraid that it is not applicable in my case.

Any help will be appreciated, even just pointing me in the right direction where I could find my answer would be enough. (And yes I tried contacting my teacher about this, but unfortunately he is not answering and the deadline is approaching rather quickly).

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  • $\begingroup$ Thank you I decided to use 900bp, just because that is the legnth the teacher used in of his lectures. I would like to select you comment as an answer, but it's not possible it seems. $\endgroup$ Feb 13 at 17:49
  • $\begingroup$ Posted it as answer, not sure if a moving function exists, maybe if you are a moderator. $\endgroup$
    – ATpoint
    Feb 14 at 13:41
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I think there is no fixed size. Ideally you would have something like histone ChIP-seq or ATAC-seq data to approximate the relevant upstream interval. Since this is not always possible most people go with -500bp. Others might have different suggestions though. Maybe matching known motifs of transcription factors that regulate that promoter to the upstream region can help approximating a better window. But as Sanger sequencing usually gives about 1kb of sequence I'd just take a 500bp to 1kb window and sequence that, fwd and rev primers for sequencing to have double confirmation.

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