What is a gene trap?

Gene trapping creates random insertional mutations in the genome that are immediately accessible to molecular characterization. Gene trap vectors contain a promoterless reporter gene and/or selectable marker which is activated upon insertion within an endogenous gene, hence, "gene trapping".

The gene trap vector itself provides a DNA tag for the rapid identification of the disrupted locus. When carried out in mouse embryonic stem (ES) cells, gene trap insertions can be transmitted to the germline of mice to examine the function of the trapped gene in vivo. In contrast to other mutagenesis methods such as the use of ENU, gene traps generally induce null mutations.

Gene trapping is a rapid and cost-efficient method that is ideally suited for large-scale mutagenesis of the mammalian genome. Mutations are relatively inexpensive to create and mutant cell lines are easily stored and distributed. The IGTC is committed to creating a large public resource of gene trap insertions that can be used to analyse gene function in mice. This resource is intended to provide all investigators equal access to knock-out mice and thereby accelerate the rate by which new mutant strains of mice can be generated for research purposes.

For more information, see the Gene Trap Tutorial.

How much does a gene trap cell line cost?

Gene trap cell lines are generally available for a nominal handling fee, although each IGTC member has different distribution policies.

What is the best way to search the IGTC for a match to my gene?

The IGTC offers multiple entry points to the database: BLAST, Browse, Search, Expression Search and Biological Patchways. If you have the full cDNA sequence of your gene of interest, the best way to query the database for traps in the relevant locus is by using BLAST to search either the cell line tags directly or to search the transcripts of the gene identified by the IGTC pipeline.

If you are looking for specific identifiers or a genomic region, use the Browse feature to search the IGTC annotated database. You can also browse through gene traps in different biological pathways or by GO Term association from the sidebar links.

See the Finding a gene/locus tutorial for more information.

Why do I get a strong BLAST homology to a cell line tag using my cDNA sequence, but the cell line is not annotated with my gene?

Annotation at the IGTC is done using UCSC BLAT, a high-confidence matching tool that searches against the NCBI reference genome, and AutoIdent, a program that uses BLAST to search against the GenBank database and applies heuristics to filter out low confidence matches. See the pipeline description for more details. The IGTC recommends you investigate the tag sequence yourself to confirm the match or annotation before requesting the line.

How do I request a cell line I am interested in?

Each IGTC member lab has its own policy regarding cell line distribution. Follow the link from the cell line information page. You will be directed to the correct site to request the particular cell line. Consortium members will provide you with further information about ordering and handling the cells.

Where can I find out more about gene trapping and the IGTC?

Check out the Tutorials for general overviews or Relevant Publications page for papers and publications about gene trap and related subjects, or email with questions.

What does it mean to say "this sequence is oriented +/+ to the genome"?

Depending on the vector design, a gene trap may interrupt transcription in one direction only. Depending on the techniques used to isolate and amplify the insertion locus, the sequence tag will reflect either that same orientation or its opposite. dbGSS does not provide sequence orientation information; however, the IGTC pipeline assigns an orientation based on information supplied by IGTC members.