SimpleSearch - GK primer tool

5 T-DNA insertion predictions/alleles that hit this region of BAC YUP8H12 are displayed.
Natural antisense transcript overlaps with AT1G05200 Natural antisense transcript overlaps with AT1G05205 Natural antisense transcript overlaps with AT1G05230 glutamate receptor 3.4 hexokinase-1 protein Transmembrane protein 97, Putative Transmembrane protein 97, Putative homeodomain GLABROUS 2 295A04 448C06 546E07 385G05 973G12

Jump to position where primers should be designed: Position:
Jump to gene code:

Primer design

Please cite our paper when using GABI-Kat primer design: [Huep et. al. 2014]

TM: MIN distance: MAX distance:

Hints to use the primer design tool in SimpleSearch:
- primers are designed between MIN and MAX distance (in bp) to the specified position on the pseudochromosome;
- the tool attemps to offer the best primer with respect to genome-wide uniqueness and selective power for paralogs;
- selection of a larger area may allow design of better primers;
- you can design additional primers after you have designed a first primer pair.

Please cite the following publication if the primer design tool was useful for you:
Huep G, Kleinboelting N and Weisshaar B. An easy-to-use primer design tool to address paralogous loci and T-DNA insertion sites in the genome of Arabidopsis thaliana. Plant Methods. 2014 10:28 [PubMed]

The primer design went public on 20140327 (see the News & history page, news entry 20140327). Please report bugs to the Email address mentioned in the footer!

Further hints to use the visualisation tool in SimpleSearch:
- many items have tooltip information. Example: the BAC ID of the genome region is displayed upon mouse-over the black line;
- click on the "triangles" (insertion position flags) to reach the data we have about the respective line;
- click on the "multi triangle" (the larger ones) to get a list of lines that contain insertions close to the indicated genome position;
- use the zoom in / zoom out buttons to get a display of a larger or smaller genome region;
- a click on the arrow heads at the left and right end of the black line will move the displayed region.