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[Arabidopsis] T-DNA insertion site

Michelle Tjahjadi via arab-gen%40net.bio.net (by mtjahjadi from ucdavis.edu)
Fri May 18 18:24:58 EST 2012


Hi all,

Is there a way to find the specific site of a T-DNA insertion? I'm looking
at several SALK, SAIL, and GABI lines. TAIR, T-DNA Express, and the
respective company websites only seem to provide the flanking sequences.
Using the SALK T-DNA primer website, SALK can provide LP and RP primers to
confirm the insertion. When I search for these primers, I get the sequence
of each primer, and there is a segment that states, ex: "Insertion chr1
8999832". At first, I thought the number corresponds to the exact gene
number at the insertion site, but now I'm thinking it's the flanking
sequence. SALK also states that the insertion can be up to 300 bp away from
the flanking sequence, so I really think the gene number is site of
flanking sequence. Does anybody know for sure? Besides ordering the stock
and doing the actual PCR myself, is there another way to find the exact
location of a T-DNA insertion online?

Thanks,
Michelle


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