[Genome] genomic sequence marker

Tue Oct 24 15:57:42 PDT 2006

Baojin Fu,

I am sorry that I did not fully answer your question previously.
We have an STS markers track for human which is in the Mapping and 
Sequencing tracks section. If you go to your region of interest on the 
human Genome Browser and then turn the visibility of this track to full then
you will see the position of STS markers. If you click on the markers in 
the track on the Genome Browser image, then you will see a details page 
which provides primers for that marker.

Alternately, you can get information for STS markers in a region using the 
Table Browser. To do this, click on the Tables link on the top menu bar 
and then select the Human genome and assembly of interest. Then select 
the Mapping and Sequencing Tracks group and the STS Markers for the track. 
Then choose position as the region and you can add your region of interest 
to the position box.
Using the stsMap table will give you positional information for STS 
markers. However,  doing a join on the stsInfo2 table with provide
additional information such as the primer sequences. This can be done 
by using the output format "selected fields from primary and related tables".

I found a paper referring to Loc220032. I don't know if this is the paper 
that you are looking at. It mentions a region from the Loc220032 locus to 
FLJ23441 locus. Loc220032 locus is the gene, GDPD4, and the 220032 is the 
Gene ID in NCBI's Entrez Gene. FLJ23441 is a gene called NARS2. So perhaps 
you need to use the Known Genes and/or the RefSeq track to identify genes 
in your region of interest and then use the genomic sequence from these 
gene loci as templates for the design of primers.

If you use the STS marker primers or other primers, you could use the
isPcr tool as I suggested before (accessed by clicking on PCR on the blue
menu bar) to find the location of the primers. By turning on the
Conservation track, you could also see the uniqueness of the primer
sequences compared to other species. Zooming in to a short region of the
genome allows you to see the actual bases in the multiple alignment in the
Conservation track.

I hope that this helps you. Please let us know if you have further questions.

Rachel

On Tue, 24 Oct 2006, Baojin Fu wrote:

> Hello Rachel:
> Thank you very much for your prompt reply.
>
> Probably I did not make my question quite clear in my first email. My
> goal is find a unique human genomic DNA sequence for my primer design.
> Ideally this genomic sequence is part of a kind of "genomic marker" or a
> locus, something that have been mapped previously, or people can find.
> For example, in one paper in my hand they use genomic sequence of
> "Loc220032" as template for their primer design. I want to do the
> exactly same kind of primer design, but I just do not know how I can
> also get or find this kind of "marker" or "locus" on the internet.If I
> use this kind of genomic sequence as my primer design template, I can
> simply, for example when writing a paper, I can say that "the primers
> paire was designed using sequence of "name of the sequende", Not just
> say using a random genomic sequence even though the sequence is unique
> and human specific.
>
> I hope I make it clear this time.
> You previous reply is also very helpful.
>
> Thanks again.
>
> Baojin
>
>
>>>> Rachel Harte <hartera at soe.ucsc.edu> 10/24/06 12:17 PM >>>
> Baojin Fu,
>
> There are a number of primer design tools that are available and you
> can
> find these by searching for them using Google. One such program
> available
> on the internet is Primer3:
>
> http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi
>
> Also, if you are interested in designing intronic primers then
> ExonPrimer
> is a useful tool that works for specific genes and is accessible via
> the
> UCSC Known Genes tracks e.g.
>
> http://ihg.gsf.de/cgi-bin/primer/ExonPrimerUCSC.pl?db=hg18&acc=BC100027
>
>
> You can get to this through the Known Genes details page. If you click
> on
> an alignment to a gene in the Known Genes track of the Browser, then
> select
> the ExonPrimer link in the Quick Links section then it will take you to
>
> the ExonPrimer program and it will design primers for that gene that
> you
> selected.
>
> Typically, the criteria for designing primers are:
>
> About 18-30 bp in length
> Melting temperature of 50-60C
> GC content of 45-55%
> The primers should not form a stable hairpin.
> Primers should not self dimerize or dimerize with other primes used in
> a
> PCR reaction.
>
> We have a tool called isPcr that you can access by clicking on the PCR
> on
> the top blue menu bar of the Genome Browser pages or you can go there
> directly using this link:
>
> http://genome.ucsc.edu/cgi-bin/hgPcr?command=start
>
> This program is tuned to find short sequences in the genome.
> This will help you to check the genomic location of a pair of primers
> and
> the region that would be amplified by them. You should check the
> primer sequences in the genome using the Genome Browser with the
> Repeats
> tracks (RepeatMasker and Simple Repeats) turned on - it is desirable to
>
> avoid designing primers to repeat regions. Also, if you turn on the
> Conservation track, this will help you to determine whether primers
> are
> unique to human. Another track that would be useful to use is the SNP
> track
> to see if there are known variations in the primer sequences.
>
> I hope that this helps you. Please let us know if you have further
> questions.
>
> Rachel
>
>  On Tue, 24 Oct 2006, Baojin Fu wrote:
>
>> We've identified a amplified region on one human chromosome using
>> microarray technique. Next we'd like to confirm this amplified
> region
>> using quantitive real-time pcr. Therefore I need to design at least
>> three set of primer pairs: one locacted within , one up- and one
>> downstream of the amplified region. Then using a normal diploid cell
> as
>> control I should be able to quantify the copy number of the target
>> region.
>> Now my question is: I have to use genomic sequence as template to
>> design PCR primer. The sequence must be human specific and unique
> (no
>> redundant, for example). What kind of sequence I should use? Can I
>> randomly choose a fragment of the sequence within my interested
> region
>> and then do a BLAST to make sure it's both human specific and unique?
> Is
>> this a valid way to do this? Or there is some known genomic
> "markers"
>> (not genes) on the chromosome, which is unique in sequence and
> suitable
>> for PCR primer design? If this is true, how can I search/locate
> them?
>>
>> Thanks a lot.
>>
>>
>>
>> Baojin Fu  M.D.
>> Research Assoicate
>> Division of GI/Liver Pathology
>> Johns Hopkins University School of Medicine
>> CRB-II, Ste 316
>> 1550 Orleans St
>> Baltimore, MD 21231
>> Tel: 410-955-3511
>> Fax: 410-614-0671
>> _______________________________________________
>> Genome maillist  -  Genome at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>>
>
>

-- 
Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu