I'm trying to identify conserved regions in a gene region across species. I want to show the bp location, the sequence and % of conservation. I came across Vista Browser but it hasn't been updated since 2012-2013. I have tried the UCSC genome browser and Ensembl but haven't been able to generate the figure I want. Could somebody help me on this? I really appreciate it!
UCSC have an option for tracking Evolutionary conserved non-protein-coding regions of few vertebrates.
If your aim is to annotate the conserved regions of a gene to functional domains or gene product or protein then you may try Conserved Domain Database of NCBI
https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi
https://www.ncbi.nlm.nih.gov/Structure/cdd/docs/cdd_how_to.html
In addition to Anuraj Nayarisseri 's good advice, UCSC (http://genome.ucsc.edu) has several options as genome browser or table browser and some interesting tools, and you can visualize your own data as a track in the genome browser.
all the best
fred
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