MTID: a database of Sleeping Beauty transposon insertions in mice

Abstract

The Sleeping Beauty (SB) transposon system provides the first random insertional mutagen available for germline genetic screens in mice. In preparation for a large scale project to create, map and manage up to 5000 SB insertions, we have developed the Mouse Transposon Insertion Database (MTID; http://mouse.ccgb.umn.edu/transposon/). Each insertion's genomic position, as well as the distance between the insertion and the nearest annotated gene, are determined by a sequence analysis pipeline. Users can search the database using a specified nucleotide or genetic map position to identify the nearest insertion. Mouse reports describe insertions carried, strain, genotype and dates of birth and death. Insertion reports describes chromosome, nucleotide and genetic map positions, as well as nearest gene data from Ensembl, NCBI and Celera. The flanking sequence used to map the insertion is also provided. Researchers will be able to identify insertions of interest and request mice or frozen sperm that carry the insertion.

Figure 1

A Mouse Report from MTID. Insertion identifiers are linked to the corresponding insertion report. The Genotype field describes the components of the Sleeping Beauty system carried by the given mouse.

Figure 2

Detail of an MTID Insertion Report. Genomic position data are derived for both the public and Celera versions of the genome. Nearest gene data are determined for annotation information from Ensembl, NCBI and Celera. Predicted genes from Ensembl are currently divided into two classes: those confirmed based on similarity to EST sequences (Estgene) and those confirmed based on similarity to other sequences (Core). The distance between the insertion and the nearest gene is provided in parenthesis in the Relative Position field. When an insertion is identified within a gene this number represents the distance between the insertion and the nearest terminus of the gene.