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#182137 Multiple sequence alignment of only the promoter regions of a gene

Posted by pcrman on 05 March 2020 - 07:54 PM in Molecular Biology

This can be achieved in many ways.


To generate publication quality alignment graphs of sequences, the best way is to download the actual sequences for each species, and use some programs such as VectorNTI to make the alignment.


To retrieve promoter sequences, you can use UCSC genome browser. Promoter sequence for a gene can be defined as the sequence upstream of the TSS of the gene (as shown in the screenshot below). So once you have identified the gene in UCSC, you can ask the browser to  give you the DNA sequence upstream of the gene.


Human hg38 chr12 6532594 6536448 UCSC Genome Browser v394.png

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