Flanking Sequences for Insertion Mutants

We have updated the presentation of flanking sequence information for all Syngenta, Salk, and INRA/Genoplante mutants analyzed through the SeedGenes project. With this update, you can retrieve the original border sequences, view predicted insertion sites in relation to the TAIR Sequence Viewer, and see BLAST results used to assign each border to a region of the genome. You can also print a PDF of each original document.

We recommend that you read the instructions provided to make maximal use of this feature.

In the following example, flanking sequences from both sides of the T-DNA insert in Syngenta line 12727 matched genomic sequences in the first exon of At1g01040. Nucleotides between the two borders were likely deleted upon T-DNA insertion. BLAST alignment with Border #2 (downstream) begins with a 15 bp perfect match (highlighted) and continues to the right, past the final "AATG" in the highlighted sequence. The predicted insertion site is indicated with a red triangle. Alignment with Border #1 (upstream) begins with two bases before the 15 bp perfect match and continues to the left, past the final "TAGC" in the highlighted sequence. Two different predictions of the insertion site, based on BLAST alignment and 15 bp perfect match, are indicated with two red triangles pointing in the same direction. Green triangles included with Salk mutants indicate predicted insertion sites based on sequences generated at OSU. The choice of a 15 bp perfect match as the start of the predicted insertion site was based on experience with variable alignments involving large numbers of flanking sequences.

Sequence Files for Syngenta T-DNA Vectors: pCSA104 pCSA110 pDAP101