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I am reading a paper which talks about promoter/enhancer regions of certain protein coding genes. These genes are for which evidence points to having strong MEF2 transcription factor binding sites.

The paper says

Sequence data were taken mainly from the international nucleotide sequence database. Accession numbers and approximate locations of the MEF2 site centers are as follows: human adolase A, X06351 and 1985/1986, rat adolase A, X04260 and 450/451...

Now, I looked up accession number X06351 but I find no evidence of a enhancer region on that page.

Can someone explain to me how I should be looking for these sites?

The paper is available for free and can be found here: Link to paper My interest is in the first and third paragraphs of Materials and Methods where the first paragraphs gives a general description of the MEF2 sites and the third paragraphs gives specific accession numbers.

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  • $\begingroup$ Can you provide a link to that paper? $\endgroup$
    – WYSIWYG
    Feb 28, 2015 at 20:45
  • $\begingroup$ The NCBI nucleotide page will not have information on regulatory regions. Check out UCSC browser for that gene and allow the display of tracks for regulatory regions. If the annotations are there in the records then it will display that region. The paper mentions the center of the enhancer site, look for the 1895th position in the sequence. $\endgroup$
    – WYSIWYG
    Feb 28, 2015 at 20:47
  • $\begingroup$ I've added the paper in question. I'll check out the UCSC browser and see what I can find there. $\endgroup$
    – masfenix
    Feb 28, 2015 at 20:48
  • $\begingroup$ So what information are you looking for exactly? $\endgroup$
    – WYSIWYG
    Feb 28, 2015 at 20:53
  • $\begingroup$ Well basically like you said, the annotation. I want to look at the specific bases at site 1985/1986 and some sort of validation that this is indeed a MEF2 binding site. But I don't know how to use that accession number and put it in the genome browser. $\endgroup$
    – masfenix
    Feb 28, 2015 at 20:54

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The NCBI nucleotide page does not have information on regulatory regions.

UCSC browser also displays regulatory regions mostly based on the ENCODE ChIP-Seq data. ENCODE project has MEF2 ChIP-Seq experiment for human cell lines. You can have a look at that. There is a MEF2 ChIP-seq experiment for mouse too.

You can analyse these data for a more detailed information.

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  • $\begingroup$ I am relatively new to this. So basically, if I look at the peaks of MEF2 Chip-Seq data from ENCODE I should see a peak where my original paper is saying there exists a binding site? $\endgroup$
    – masfenix
    Feb 28, 2015 at 21:13
  • $\begingroup$ @masfenix Yes you would see a peak there. You can also get the sequence of MEF2 binding site. $\endgroup$
    – WYSIWYG
    Feb 28, 2015 at 21:16

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