[Genome] one question

[Kayla Smith]

Alex,

I'm not sure I quite understand what you're asking but I'll see if I can 
answer your question anyway.

It's great that you found the Sequence Retrieval Region Options menu. 
There are two boxes which you may find useful.  The "Promoter/Upstream 
by XXXX bases" and also the "Downstream by XXXX" bases.  You can put 
which ever value you like in those boxes.  Just backspace over where it 
says "1000" and type in how much upstream and downstream sequence you want.

One thing to note is that Nkx2.5 is on the negative strand.  There are 
two ways to get sequence and they will give you different results.

1.  Using the blue "DNA" button on the top of the page when you have 
Nkx2.5 in view.   This will give you genome sequence in the 5' to 3' 
direction.

2.  Clicking into the Known Gene details page for Nkx2.5 and requesting 
sequence from there.   Once you've clicked on Nkx2.5 in the Known Genes 
track in the browser, you're taken to a details page.  Scroll down on 
this page until you get to the "Sequence" link.  This sequence will be 
given to you in the direction of transcription of the gene, which in the 
case of Nkx2.5 will be in the 3' to 5' direction.

If you were asking whether there is some official promoter sequence to 
Nkx2.5 I can't answer that for you.  That's more of a scientific 
question than a Genome Browser related question.

I hope this information is helpful to you for extracting sequence. 
Please don't hesitate to contact us again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group


Kang (Alex) Chen wrote:
> Hi,
> This is Alex from MMCRI(Maine Medical center Research Institute).I want
> to establish a plasmid with Nkx2.5 promoter and i search it on your
> website.Sequence Retrieval Region Options:  Promoter/Upstream by XXXX
> bases. How could i get the correct information about the exact promoter
> sequence since there are too much or too less sequence according to my
> choose.
> Thanks
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