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NASC

The European Arabidopsis Stock Centre

IMA Lines

Donated by

  • V. Sundaresan Department of Plant Biology, College of Biological Sciences, University of California, Davis

Click here to view all 508 of these lines.

Description

The IMA Ds Insertion lines were generated by Prof. Sundaresan and colleagues from the National University of Singapore (The Plant Cell, 11: 2263-2270). The full text of this paper is available from the Plant Cell e-journal site and is Copyright (c) by the American Society of Plant Physiologists.

Ds insertion lines with sequenced positions of the Ds elements

These Arabidopsis thaliana (ecotype Landsberg) lines contain mostly single copy insertions of modified maize transposable Dissociation (Ds) elements inserted into different positions within the genome.

Each Ds element carries a NPTII gene, and therefore plants with Ds insertions are resistant to kanamycin. The Ds elements in these lines are stable, but capable of remobilization if the Ac transposase is provided, e.g., by crossing with one of the Ac starter lines (N8043, N8049). Ds elements also carry the GUS reporter gene designed to act as gene trap (SGT or GT) or enhancer trap (SET). For gene trap lines GUS expression requires that the orientation of the GUS reporter gene lie in the same direction as the disrupted gene. For details of the Ds elements and the transposon mutagenesis system please see Sundaresan, V. et al. (1995).

Sequences flanking the Ds insertions in the following transposant lines were amplified using TAIL-PCR (Liu et al., 1995). Sequences were analyzed by BLAST searches in two public databases: NCBI GenBank and Arabidopsis GenBank in Stanford.

How to find your gene in the database:

  • Search for your gene using atensembl
  • If your gene has a Ds insertion it will be visible on the contig view or gene report page
  • You can then follow the link to order the appropriate germplasm line.
  • If you know the SGT number, gi number, embl accession or BAC clone name you could try and search the germplasm database

IMPORTANT NOTE

We detected up to 7% cross-contamination in the sequencing data in our lines, that result mainly from PCR-contamination, but also occasionally from seed contamination. Since the flanking sequence data was obtained from single runs, each line has to be independently confirmed. This confirmation is accomplished most simply by performing PCR amplification of DNA from the line, using gene specific primers and Ds-specific primers. The presence of PCR products of the correct size on a gel is usually sufficient confirmation, although sequencing of the products can be performed if necessary.

Primers info

The following primers complimentary to the ends of Ds element can be used for PCR amplification. Distance from the 5'-end of each primer to the corresponding end of transposon is indicated.

For 3'-end of Ds:

  • Ds3'-1 ggTTCCCgTCCgATTTCgACT 179bp
  • Ds3'-2 CgATTACCgTATTTATCCCgTTC 131bp
  • Ds3'-3 TCgTTTCCgTCCCgCAAgT 82bp

For 5'-end of Ds:

  • Ds5'-1 ACggTCgggAAACTAgCTCTAC 173bp
  • Ds5'-2 TCCgTTCCgTTTTCgTTTTTTAC 114bp
  • Ds5'-3 CggTCggTACgggATTTTCC 39bp