Identification of conserved transcription factor binding sites across species?

23 May 2019 1 1K Report

Hi all,

I'm trying to use PWMs for a transcription factor of interest to identify conserved binding sites in upstream promoters (up to 5 kb from TSS), across several vertebrate species. My model organism is X. laevis. Are there any good tools available for such a comparison, especially when laevis will be my reference genome?

Kyle

Frederic Lepretre

Hi Kyle

hard question since xenopus is poorly documented compared to human and mouse....but you can go to the UCSC website (http://genome-euro.ucsc.edu/cgi-bin/hgGateway?hgsid=232356951_cvH7Ujq0RnJ05n2imG82FbMf9imk) and have a look for your gene of interest. there are comparative genomics tracks if it helps.

fred

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