which positions of upstream or downstream sequences would be considered for motif discovery?

Question

[Calangoa]

Hi there, For discovery of motifs associated with regulatory region of set of genes in mouse, which positions of upstream or downstream sequences would be considered? Forexample from 2000 sequence upstream of genes to 0( strat codon ) or 400 sequence upstream of gened to 0 for transcription activators and 400 seq. Upstream of genes to 50 seq. Downstream of genes for transcription repressor?

[natasha.sernova]

In mouse (and human) RNA-regulation is preferred.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6249886/

“With the advent of transcriptomic studies, it was revealed that only 2% of the genome has protein-coding capacity [1, 2], and the vast majority of transcripts that do not have protein coding capacity are called non-coding RNAs (ncRNAs)”.

Since according to the following post:

Gem: Genome Wide Event Finding And Motif Discovery

"A typical application of motif discovery is to identify short words (or patterns) of DNA sequence that indicate, e.g. where a DNA binding protein binds the genome."

I am not sure that your question has any relation to RNA-regulation.

Refs 1 and 2: 1. Consortium EP. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57–74. doi: 10.1038/nature11247. [PMC free article] [PubMed] [CrossRef] [Google Scholar] 2. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, et al. Landscape of transcription in human cells. Nature. 2012;489(7414):101–108. doi: 10.1038/nature11233. [PMC free article] [PubMed] [CrossRef] [Google Scholar]

The second article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684276/