## Description

This track shows alignments between $organism T51 radiation hybrid (RH) map sequences, consisting of ESTs and other genetic markers, and the genome. Many of these markers are not genetically polymorphic and therefore cannot be placed on genetic maps. The markers with RH map positions are useful for locating genes lying in genomic regions with mutations and in the positional cloning of zebrafish genetic mutants that exhibit interesting phenotypes.

This track shows alignments for 11514 RH map sequences (October 3, 2006 update) that consist of:

- 5265 markers mapped by Dr. Robert Geisler at the Max Planck Institute (MPI) for Developmental Biology, Germany (Max-Planck-Institut fur Entwicklungsbiologie or MPIEB).
- 6249 markers mapped by Dr. Yi Zhou and Dr. Leonard I. Zon (Zon Lab) at the Zebrafish Genome Project Initiative at Childrens Hospital, Boston (CHBG).

The linkage group number is equivalent to the chromosome number for zebrafish. Position, which is relative to the top of the linkage group, is the marker number used by the SAMapper software. Marker types can be BAC_END, EST, GENE, SSLP or STS. The markers are from the following sources:

- BACENDS - end sequences of fingerprinted BAC clones.
- CUSTOM - various markers and genes sent from outside labs to CHBG for mapping.
- INSERTMUT - genomic sites where retroviral insertions occurred in insertional mutants.
- MGH - SSLP markers from the lab of Dr. Mark Fishman at Massachusetts General Hospital.
- NCBI - marker primer or parent sequences retrieved from the NCBI databases.
- OTHER_ZFEST - zebrafish ESTs generated elsewhere other than the Washington University Genome Center at St. Louis.
- SEQPROJ - contig or scaffold from the zebrafish genome sequencing project at The Wellcome Trust Sanger Institute.
- SHOTGUN - random shotgun sequences from The Wellcome Trust Sanger Institute.
- THISSE - cDNAs that have specific expression patterns found by in situ hybridization and provided from the lab of Drs. Bernard and Christine Thisse at the Institute of Genetics and Molecular and Cellular Biology.
- WU_ZFEST - individual ESTs and EST assemblies from the Washington University Genome Center at St. Louis.
- WZ - EST assemblies from the Washington University Genome Center at St. Louis.

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.

## Display Conventions and Configuration

This track follows the display conventions for PSL alignment tracks. The strand information (+/-) indicates the direction of the match between the EST and the matching genomic sequence. It bears no relationship to the direction of transcription of the RNA with which it might be associated.

## Methods

To generate this track, $organism RH map sequences were aligned against the genome using blat. Only alignments with a base identity level within 0.1% of the best and at least 80% base identity with the genomic sequence were kept. The following pslReps parameters were used: -nearTop=0.0001 -minAli=0.80 -minCover=0.20.

## Credits

The $Organism RH Map track was produced by UCSC in collaboration with the Zebrafish Genome Project Initiative at Childrens Hospital, Boston, from sequence data obtained from the individuals and institutions mentioned in the Description section.