primer design for a gene - (Oct/27/2014 )

Hello,

I want to design some primer pairs for a gene to obtain whole exons and introns, so I looked into ensembl.org. In this web page after I entered my gene name, I see 9 transcripts. Regarding which transcript can I design primer pairs?

Well, first you must answer yourself a simple question, "what is a gene?", Then goes questions "what I need it for?" and "why I needed then this way" and then you'll become closer to chosing the right one.

Gene is MTHFR and this gene has 9 transcripts. I want to sequence all exons and introns. So I don' t know to choose which transcript...

Thanks for your help

The point is, unless you know exactly what are you planning to achieve with that, you can't choose the right one.

(you already did anyway, but for future purposes..)

You last answer wasn't any much closer to the point.

There may be reason why to sequence an exon sequences of a gene..  because you are looking for mutations in coding sequence of a protein that has a certain function. There may be many transcripts, but not all of them make a protein, some make the same protein even when the transcripts are different.  There may be different proteins isoforms and you are interested in all of them or just some of them.
For that reason, to see if a DNA mutation affects the protein, you do usually sequence the exon-intron boundaries too (and/or known mutation sites), to find out potencial splicing affecting mutations, but not all of the intron sequence, usually, as introns may span several dozens Kbps.

Also, you may be aware of a promoter of enhancer in some of the introns, and you may want to sequence them too (or only them). In that case you don't usually care more about a genomic coordinate that position relative to transcript, but in some cases it may be transcript specific, so you will know which transcript you want to see.

In any case sequencing all exons and introns is not usual as there is no point in that I can think of now. 

If you don't have a clue why do you want exactly is the reason you want to sequence it all, you are starting with a wrong foot.

Just by a quick peek on human MTHFR on Ensembl, I can see nine transcripts coding ORF, but only two of them are actually coding a validated protein, both of them the same one.

So if you wanted to check for mutations in the protein, you would sequence either one. But not complete introns, for that I still don't know why you wanted those. The last exon of the reference transcript is however 5kb long, unless you have any reasons to do

Also all the transcripts are actually identical in most of the exons anyway, so sequencing the longest would cover the others too.

The whole gene spans 20 kbp, if you really want to sequence all exons and introns, for some weird reason, there actually is no point in caring about transcripts, the DNA region is those 20 kbp, just sequence it from start to end, possibly with some NGS. But it's very unlikely you actually want that.