I have SALK sequence no of a T-DNA mutant of a gene. now i want to make a genomic diagram with the position of insertion. How could I find the position of insertion. I check the SALK homepage but little hard for me to understand from there. please help.
Hi,
In the sequence viewer of any particular salk line (from arabidopsis.org), you can see the position of insertion. The other way is by locating the flanking sequence of insertion line. For details you may check this one http://signal.salk.edu/isects.html.
At the SALK homepage or TAIR you will find the link for your gene informations. Then, you can find the link with the T-DNA sequencing and also the indicated flanking primers for validation. The T-DNA sequencing provided by SALK is not very accurate (since it was a whole-sequencing analysis). I suggest you to perform a PCR (3 primers: Left board T-DNA + flanking primers) and sequence the mutant band on the agarose gel, thus you can get the exact position of the T-DNA insertion. Good luck!
Thanks all for your kind replies.
I want to draw a genomic diagram for the T-DNA insertion line, for that I want to know the position of insertion. I can't enter the Arabidopsis.org and SALK web page is confusing for me. So need to know step by step procedure to find T-DNa insertion in SALK website.
Thanks
Regards,
Pratima
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