Gene Trap Track Settings

International Gene Trap Consortium Sequence Tag Alignments (All Genes and Gene Predictions tracks)

Display mode: Duplicate track

Alignment Gap/Insertion Display Options Help on display options
	Draw double horizontal lines when both genome and query have an insertion
	Draw a vertical purple line for an insertion at the beginning or end of the query, orange for insertion in the middle of the query

Display data as a density graph:

Display data as a rearrangement graph:

Data schema/format description and download

Assembly: Mouse July 2007 (NCBI37/mm9)
Data last updated at UCSC: 2009-07-01

Description

This track shows alignments of International Gene Trap Consortium sequence tags to the mouse genome. Items are labeled by cell line and colored by source:

BG:	BayGenomics (USA)
CMHD:	Centre for Modeling Human Disease (Toronto, Canada)
EGTC:	Exchangeable Gene Trap Clones (Kumamoto University, Japan)
ESDB:	Embryonic Stem Cell Database (University of Manitoba, Canada)
FHCRC:	Soriano Lab Gene Trap Database (originally at Fred Hutchinson Cancer Research Center, Seattle, USA; now at Mount Sinai School of Medicine, Manhattan, NY)
GGTC:	German Gene Trap Consortium (Germany)
SIGTR:	Sanger Institute Gene Trap Resource (Cambridge, UK)
TIGEM:	TIGEM-IRBM Gene Trap (Naples, Italy)
TIGM:	Texas Institute for Genomic Medicine (Houston, Texas)

Methods

The IGTC pipeline uses BLAT to align sequence tags from dbGSS to the mouse genome and BLAST to match sequence tags to genes. The pipeline filters and reconciles the two sets of alignments to associate cell lines with trapped genes.

Credits

Thanks to the International Gene Trap Consortium for providing this track.