Body: <p>Could you tell me how to find the promoter position of a gene in the chromosome?
  Recently I did ATAC-seq expriment and got the result, showing that the peaks related to some genes is assigned to &quot;promoter&quot;. The result gives the chromosome position of the peak but I am curious about whether the promoters of these genes really overlap the peak position. For example, a peak in chromosome 1 (ref genome: mm39; position: 149975557~149975957) is assigned to the gene &quot;Ptgs2&quot;, and the annotation is &quot;Promoter (&lt;=1kb)&quot;. So where can I get the precise coordination of the promoter for &quot;Ptgs2&quot;? I tried UCSC, Ensembl, or NCBI's Genome Data Viewer but cannot find the promoter information of the gene.</p>
  <p>Thank you！</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-06-06T15:53:07.097Z
Comments.Text: Does this help? https://epd.expasy.org/epd/cgi-bin/get_doc?db=mmEpdNew&format=genome&entry=Ptgs2_1 Also, how exactly are you defining the "start" and "end" positions of a promoter? I admit I haven't worked on this sort of thing much, but I believe they're kind of "fuzzy", promoters.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-06-06T18:18:55.407Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Tags: <atac-seq>
Title: How to know protomter position in the chromosome?
ThreadText: # How to know protomter position in the chromosome?
  
  (Asked by: username_0 on 2024-06-06)
  
  Could you tell me how to find the promoter position of a gene in the chromosome?
  Recently I did ATAC-seq expriment and got the result, showing that the peaks related to some genes is assigned to "promoter". The result gives the chromosome position of the peak but I am curious about whether the promoters of these genes really overlap the peak position. For example, a peak in chromosome 1 (ref genome: mm39; position: 149975557~149975957) is assigned to the gene "Ptgs2", and the annotation is "Promoter (<=1kb)". So where can I get the precise coordination of the promoter for "Ptgs2"? I tried UCSC, Ensembl, or NCBI's Genome Data Viewer but cannot find the promoter information of the gene.
  
  Thank you！
  
  **Tags:** atac-seq
  
  > **Comments:**
  > **username_1**: Does this help? https://epd.expasy.org/epd/cgi-bin/get_doc?db=mmEpdNew&format=genome&entry=Ptgs2_1 Also, how exactly are you defining the "start" and "end" positions of a promoter? I admit I haven't worked on this sort of thing much, but I believe they're kind of "fuzzy", promoters.  
  > **username_2**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  
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  ## 0 answers
  
  