I am struggling to use the maizeGDB (genome database) effectively. There's a loci I am looking for to check whether it was sequenced. I am trying to look at around the loci to first identify tightly linked markers then zoom into the gene(s) to identify SNPs. I need help to obtain the sequences so I can develop those markers.
I think that it will depend of what data do you have about your loci.
1) If you have a loci name, you can search in the Gene Model page (http://www.maizegdb.org/gene_model.php). If you have a result, the best way to look in the elements surrounding the loci is to use the Gbrowse link in the result loci page.
2) If you have the sequence of a homologous loci you can try a Blast (http://blast.maizegdb.org/home.php?a=BLAST_UI). Again once you have the results you can go to GBrowse to analyze the region.
3) If you have coordinates, you can use GBrowse (http://gbrowse.maizegdb.org/gb2/gbrowse/maize_v2) specifying the region as ChrX:start..end, for example, Chr9:11,774,733..11,776,491. You can play with these numbers, so if you want to get 5,000 bp downstream the example you can write in the GBrowe Landmark or Region box Chr9:11,769,733..11,774,733.
To see the surrounding markers you need to check the box Genetic Map All on (Select Track tab in GBrowse)
If you want to download the sequences, you can use File > Export as ... > ... Fasta sequence in the upper left link in GBrowse.
I hope this helps,
it's a normal loci which has not been characterised, as in there are no primers for it. The Ht1 locus is mapped to chromosome 2 bin 2.07. The ht1 locus is flanked by 349bp of mmp84 and 1245bp of IDP7244. The locus coordinates are 206,643,048 to 207,194,203 which translates to 551,155bp. This is all I have so far. There are RFLP probes closely linked with the locus; umc122 is 1.2cM while umc22 is 4.3cM. I don't have sequnce information of these probes or the areas flanking the ht1 locus. How do I get to the sequence?
What i have understood that you are interested in Ht1 locus which is mapped to chromosome 2 bin 2.07, and want to retrieve the sequence for marker development.
For homologous loci you can try BLAST as said by Aureliano. You can try with NCBI all databases search with keywords as Maize. You will get complete CD as Zea mays clone 243437 HT1 protein kinase mRNA, complete cds. it may help you.
Also you can try with phytozome.
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