Description

This track shows alignments between $organism Radiation Hybrid (RH) map sequences (consisting of ESTs and other genetic markers) and the genome. Many of thse markers are not genetically polymorphic and so can not be placed on genetic maps. These markers with RH map positions are useful for locating genes that are in genomic regions where there are mutations and are useful in the positional cloning of zebrafish genetic mutants which exhibit interesting phenotypes. 8707 sequences were aligned and they consist of:

The majority of these sequences are single-read sequences (in the range of about 40 - 1300 bp). The ESTs usually represent fragments of transcribed genes. Aligning regions (usually exons) are shown as black boxes connected by lines for gaps (usually spliced out introns). In full display mode, arrows on the introns indicate the direction of transcription. This direction is taken by looking at the splice sites.

Strand information provided for the sequences (+/-) indicates the direction of the match between the sequence and the matching genomic sequence. It bears no relationship to the direction of transcription of the RNA with which it might be associated.

To generate this track, $organism RH map sequences were aligned against the genome using the blat program. Only alignments with a base identity level within 0.1% of the best are kept. Alignments must also have at least 80% base identity to be kept (pslReps parameters used were -nearTop=0.0001 -minAli=0.8 -noIntrons).

Credits

The $Organism RH map track is produced at UCSC from sequence data from the following sources:

The track was produced in collaboration with the Zebrafish Genome Initiative at Childrens Hospital, Boston.