Ac/Ds Tagging: Frequently Asked Questions

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1. Using the Website

You can search by gene ID, description, or region to find the closest Ds insertion from the Ac/Ds home page, under Quick Search.

  • Gene ID ->(type e.g. GRMZM2G087804_T01)
  • Gene Description ->(type e.g. GLK)
  • Region: Ac/Ds left menu -> Genes -> Search ->chr:from..to ->(type e.g. 1:200000..400000) -> Go

You can also search or browse directly on the Ds Insertions page, or the Genes page.

From the Ac/Ds home page (http://plantgdb.org/prj/AcDsTagging/, find the search box under Find a Ds insertion line: Search by Barcode ID or GenBank GI and enter the GenBank gi (usually a 9 digit number). Press "Show Ds Record" to view the Record page for the barcode accession line associated with that fDs sequence.

  • Not all fDs sequences are placed; the Record page may indicate that the sequence has matches in the B73 genome but no placement location has been determined
  • Not all fDs sequences have a match to the B73 genome. In such cases there will be no Placement data on the Record page.

Note that you can search for additional barcodes by entering a GenBank gi or barcode in Jump to Record on the Records page.

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You can download fDs fasta files and data tables from our ftp site. The path is:

Ac/Ds left menu -> Download (ftp);  Link: ftp://ftp.plantgdb.org/download/MaizeData/AcDs/)

There is a README file describing what's available

You can also download a .csv (comma separated values) file of your search results any of the AcDs Web page tables (e.g. Insertion Sites or Genes in the left menu).

Yes! There is a barcode record for each Ds regardless of placement. You can browse the list or search by ID:

Browse insertions: Ac/Ds left menu -> Insertion Sites -> Non-Placed Ds ->Search-> Barcode (type e.g. B.S07.1597) -> Go

Search by Ds ID: Ac/Ds left menu -> Home -> Quick Search ->Find a Ds insertion line ->(type e.g. B.S07.1597) -> Go

From this page you can view all information including the BLAST data used to determine placement status (click on Quality Score)

  • The AcDs placement data will be updated at approximately six month intervals
  • Between updates we will be filling in confirmation data as it becomes available
  • Note that once the maize RefGen assembly is updated, we will generate a new set of placement coordinates and publish them according to the version

PlantGDB has been optimized for use with Firefox 3, Safari, or Internet Explorer 7 / 8. Many advanced features require that Javascript be enabled. If you encounter problems viewing any page at PlantGDB.org, please contact us using our feedback page. Please include a description of what didn't work as expected, and what web browser/operating system you were using. We will do our best to address the problem.

2. Ds Placement

Location in the genome is based on cloned flanking sequence (fDs), matched to the latest version of the B73 reference genome. Complicating this analysis are a number of factors including sequence divergence between B73 and W22, possible missing regions, presence of near-identical gene sequences, and the high level of repeated DNA in maize. As a result, not all sequences can be placed with confidence. We display those that have passed our heuristic matching methodology, described in the Ds Help pages.

As of 3/2011 a total of 1,933 Ds insertions have been placed in the B73 RefGen_v2 genome, distributed on all 10 chromosomes as well as unmapped assemblies (i.e. chromosome "0" or "11"). After accounting for duplicate insertion sites a total of 1,704 distict Ds insertions are found.

We have computed the distance from the nearest gene of each "placed" Ds insertion site, and we estimate that 50% of gene loci are within 500 kb of a Ds insertion (data for the maizesequence.org 5a.59 working gene set).

A paper describing the distribution of Ds elements with respect the the RefGen_v1 maize assembly is available (E. Vollbrecht, J. et al. Genome-Wide Distribution of Transposed Dissociation Elements in Maize. Plant Cell, First published on June 25, 2010; 10.1105/tpc.109.073452 Abstract; pdf)

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