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Multiple sequence alignment of only the promoter regions of a gene

Sequencing alignment

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#1 Natalia KM

Natalia KM


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Posted 05 March 2020 - 06:22 PM

Hi everyone,


Can someone help me do a multiple sequence alignment of the promoter regions of PPARGC1A gene to generate a publication quality figure to include a number of different species in comparison to human? I have tried multiple software but don't know how to look at the promoter region only or how to work out where the promoter sequences start?


Any help would be greatly appreciated along with how to use the software.


Thanks so much

#2 pcrman



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Posted 05 March 2020 - 07:54 PM

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

#3 Natalia KM

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Posted 06 March 2020 - 01:14 AM

Thank you pcrman!


I went onto this website but got rather confused as I dont have much experience of analyzing genes. I know there are 2 promoters in my gene of interest PPARGC1A. I would like to do a sequence alignment of both promoters comparing human to other species. Could you possibly give me an example of how to find the TSS and the upstream section using the example of PPARGC1A?


I have attached a screenshot of what came up but I cant work out where the TSS is or where the promoter is located? How much further upstream do I need to go to locate the 2 promoters in my gene and how do I find these promoter sequences?


If you can give me a step by step for PPARGC1A in human, I should be able to get the other species myself following your instructions. 


After alignment, the next step is to find a specific motif in the two promoters that a specific transcription factor binds to which is: GTCACGTG.


Really appreciate the help.



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