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 ~ AGR Insert Sequence Page

Many Arabidopsis lines have been mutated by inducing transposition of marked elements. Sequencing the DNA adjacent to a randomly inserted transposon produces an insert sequence, which can be matched to the genome sequence to identify its possible genomic location. Therefore, a researcher can find genes of interest that might be disrupted by insertions and then order (from NASC) the corresponding lines.

To see if there is an insert located in your sequence of interest please try our BLAST server or register a sequence with our InsertWatch facility. InsertWatch allows you to store your sequences of interest in a private database held by NASC. As soon as NASC obtain new insert sequences, they will be searched against your submitted sequences (using BLAST). If there are any matches NASC will email you with full details of the match along with web links to the NASC stock catalogue so that you can order the corresponding insert lines.

Additionally NASC allow you to perform a keyword search of pre-computed insert sequence blast analysis. This allows the researcher to ask general questions such as 'show all kinases that may contain an insert'.

You can also retrieve insert sequence information directly from AGR by selecting an option from the following drop-down menu, or by exploring one of the links below.

Browse AGR insert information:

Types of insert information stored in AGR:

  • SALK inserts - T-DNA Sequenced INsert sites, generated by Dr. Joseph Ecker at the SIGnAL lab - Salk Institute. Inserts derived from the SALK lines

  • GABI-KAT inserts -generation of Flanking Sequence Tags (FSTs) from T-DNA-mutagenised A. thaliana plants (accession Columbia) at the GABI-KAT. Sequences available. NASC has no seeds for these lines. For more information contact GABI-KAT directly.

  • IMA inserts - generated by Professor Sundaresan at the Institute of Molecular Agrobiology. Created using Ds elements. Insertion locations taken from Plant Cell, 1999. Lines available.

  • Pereira ITS inserts - Inhibitor Tagged Sites, generated by Dr. Andy Pereira. Created using En-I (Spm) elements. Sequences available.

  • CSHL inserts - Flanking sequences from gene trap and enhancer trap lines generated in Rob Martienssen's lab. See the GeneTrap webpage for sequences, expression patterns and information about seed. Seed corresponding to Genbank sequences have been deposited at NASC.

    JIC INSERTS

  • Activates The activate collection are a population of Ds activation tagged lines generated at the John Innes Centre. Flanking sequence has been obtained to po stulate the insertion position within the genome. See the Activates collection

  • Gene Traps The Gene Trap(FGT) collection was produced at the JIC. The collection was generated by the mobilization of a gene-Trap Ds transposable element. The population provides a resource of loss-of-function mutations gene expression patterns via translational fusions with the reporter gene, GUS. See the Pub Med Abstract

  • SM lines The SM lines were produced at the JIC. See the Plant Cell, 1999

  • SINS inserts - Sequenced INsert sites, generated by Prof. Jonathan Jones at the Sainsbury Laboratory. Inserts derived from the SLAT lines. Lines & sequences available,

  • Launchpad inserts - Generated by Dr. Paul Muskett at the John Innes Centre. Created using Ds elements.

Quick search AGR... 
Type in a relevant keyword or phrase, e.g. 'auxin', 'trna', 'lax2', 'SINS'


NEWS update: April 2003

Our InsertWatch facility (launched late December, 2000) has now registered (April 2003) over 12,000 sequences. The majority of researchers have taken the opportunity to simultaneously register multiple sequences with InsertWatch.

There are now well over 100,000 insert sequences in AGR, 95,000 of these from the Salk Institute. All currently held Salk sequences have now been blasted against researchers submitted sequences.

Remember, please email us if you have any problems in using any of our insert facilities. Thank you for using us!

The InsertWatch team.


 ~ Links

NASC
Nottingham Arabidopsis Stock Centre

NASC BLAST server
For blasting against insert sequences

InsertWatch
Let NASC watch out for inserts in your gene of interest!

IMA info
Detailed information about IMA lines

SLAT lines
Information on how SLAT lines were generated

AGR
Arabidopsis Genome Resource

ATIS
Arabidopsis Transposon Insertion Service at the JIC

TAIR
The Arabidopsis Information Resource

Other Arabidopsis sites
Arabidopsis links at the Google search directory


Contact us
Please email us if you have any questions.



Page last modified: Thursday, 15-Jul-2004 16:11:58 BST
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