PubMed Nucleotide Protein Genome Structure Taxonomy

Danio rerio genome data and search tips Revised May 5, 2004

The Map Viewer help document describes how to use the Map Viewer software. This page describes the data available for Danio rerio (zebrafish), and the search tips specific to that organism. You can also return to the Danio rerio genome view search page. The Map Viewer home page allows you to search the genome data of any organism represented in MapViewer.

  1. Scope of Data
  2. Available Maps
  3. Types of mapped objects, and maps on which they can be found
  4. Searchable Terms
  5. Interpretation of Display
  6. Constructing URLs

Scope of Data back to top

The Entrez Map Viewer integrates zebrafish sequence and map data from a variety of sources, described below. The maps are integrated with each other as described in the Show Connections section of the general Map Viewer help document. The current Zebrafish Map Viewer reflects the state of data as of January 2001. An update is in progress.

Additional resources are accessible from the Zebrafish Genome Resources page. LocusLink, a curated resource, provides a searchable interface for locus-specific data; searches can be limited to zebrafish by using the organism pop-up menu. GenBank sequence data for Danio rerio can be retrieved through the Taxonomy Browser. Whole genome shotgun (WGS) sequence data for the rat are accessible in the Trace Archive, which can be searched using MegaBLAST. EST and mRNA sequences are grouped into gene-oriented clusters in UniGene, and orthologous clusters in other organisms are identified through the HomoloGene project.

Available Maps back to top

The available maps for Danio rerio include:

Map Name Description

Genetic Linkage (Meiotic) Maps back to top

Gates et al. (GAT) A Haploid Panel containing 389 markers is described by Gates et al. (1999) in "A genetic linkage map for zebrafish: comparative analysis and localization of genes and expressed sequences" (Genome Research 9:334-47).   More: http://zebrafish.stanford.edu/genome/Gates99_GR/, Will Talbot (Stanford)

Heat Shock (HS) A diploid panel produced by heat shock treatment of haploid embryos (one-cell stage) was described by Kelly et al. (2000) in "Genetic linkage mapping of zebrafish genes and ESTs" (Genome Research 10:558-567).  More: http://zebrafish.stanford.edu/genome/HeatShock99, Will Talbot (Stanford)

Boston MGH Cross (MGH) A microsatellite map covering 2350 cM of the zebrafish genome, with an average resolution of 3.3 cM, is described by Knapik et al. (1998) in "A microsatellite genetic linkage map for zebrafish" (Nature Genetics 18:338-343), and Shimoda et al. (1999) in "Zebrafish genetic map with 2000 microsatellite markers" (Genomics 58:219-232).   More: http://zebrafish.mgh.harvard.edu/, Marc Fishman (Harvard)

Mother of Pearl (MOP) A haploid panel constructed from a single female heterozygous for the mother-of-pearl (mop) coloration mutation. This panel contains 556 markers with a framework of 211 RAPD (random amplified polymorphic DNA) markers and 122 SSLP (simple sequence-length polymorphism) microsatellite markers. It is described by Postlethwait et al. (1998) in "Vertebrate genome evolution and the zebrafish gene map" (Nature Genetics 18:345-349).   More: http://www.neuro.uoregon.edu/ionmain/htdocs/faculty/postleth.html, John Postlethwait (University of Oregon)

SNP (variation) Single nucleotide polymorphism (SNPs) available in dbSNP that were mapped to the Heat Shock (HS) panel.  Submitted by Will Talbot (Stanford).  More: http://zebrafish.stanford.edu/genome/

Zebrafish Genome Integrated Map (ZMAP) A composite genetic map of coding sequence markers from the T51 and LN54 RH maps, the HS map, and the MGH map. ZMAP was constructed by insertion of previously mapped T51, LN54, and HS markers into framework of the MGH map. The ZMAP was created by Allen Day, Tom Conlin, and John H. Postlethwait at the University of Oregon. As of May 2004, the map has 30,012 markers and is continuing to be updated. ZMAP has links to ZFIN, Entrez Gene (gene), UniGene (ug) and UniSTS (sts), where available.  More information about ZMAP is available at ZFIN: http://zfin.org/cgi-bin/webdriver?
MIval=aa-crossview.apg&OID;=ZDB-REFCROSS-010114-1.

Radiation Hybrid Maps back to top

Loeb/NIH/5000/4000 (LN54) A radiation hybrid panel of 93 cell lines, constructed via fusion of zebrafish and mouse cells irradiated with 4000 rads (81 lines) or 5000 rads (12 lines). This panel is described by Hukriede et al. (1999) in "Radiation hybrid mapping of the zebrafish genome" (PNAS 96:9745-9750). The data are updated at http://mgchd1.nichd.nih.gov:8000/zfrh/rharchive/ZFIN.txt on a monthly basis, and will also be updated in NCBI's Map Viewer at approximately that interval.   More: http://dir.nichd.nih.gov/lmg/lmgdev.htm, Neil Hukriede, Jonathan Epstein (NIH).  Additional LN54 mapping data was provided by the WashU-Zebrafish Genome Resources Project http://zfish.wustl.edu/.

Goodfellow T51 (T51) A whole-genome radiation hybrid panel of 94 cell lines, constructed by fusion of zebrafish and hamster cells irradiated with 3000 rads. The panel covers a total genetic distance of 27729 cR3000 with a resolution of 1cR = 61kb, and is described by Geisler et al. (1999) in "A radiation hybrid map of the zebrafish genome" (Nature Genetics 23:86-89).   More: http://wwwmap.tuebingen.mpg.de/, Robert Geisler (Tuebingen).  Additional T51 mapping data was provided by the Children's Hospital Zebrafish Genome Initiative, http://134.174.23.167/zonrhmapper/.

Types of objects and maps on which they can be found back to top

Genes back to top

Polymorphisms back to top

STSs back to top

Searchable Terms back to top

Text Terms back to top

The Danio rerio data are searchable with the following types of terms:

  • gene symbol
  • marker name
  • marker alias
    Sometimes two or more marker names refer to the same primer pair, and are therefore considered synonyms or "aliases." In such cases, any one of the terms will retrieve the marker.

Truncation and Wildcards back to top

Search terms can also be truncated or include wild cards, as explained in the truncation section of the general Map Viewer Help document.

Map Positions back to top

As noted in the Search By Position section of the Entrez Map Viewer general help document, there are three main ways to search by map position from the Map View of a chromosome:
  1. enter a range of interest in the Region text boxes in side bar
  2. click on the region of interest in the chromosome thumbnail graphic in the sidebar
  3. click on a region of interest in the enlarged Map View of the chromosome

For Danio rerio, the following types of map positions can be entered in option 1:
  • symbols - you can enter marker names or alternate marker names (aliases) to display a region of the chromosome between those mapped elements. Note that both mapped elements must be present on the maps that share the same coordinate system in order for the range search to work properly.

  • numerical positions - It is not necessary to specify units. The Map Viewer will interpret the range in the units of the master map. For example:
    • cM - if the master map is a genetic linkage map, the search program interprets the region number as a centiMorgan (cM) unit (e.g., 1 or 12 or 12.5)
    • cR - if the master map is a radiation hybrid map, the program interprets the region number as a centiRay (cR) unit (e.g., 10 or 10.5 or 234).

Interpretation of Display back to top

Verbose Mode back to top

By default, the master map at the right side of the display is shown in verbose mode, which provides descriptive information (as available) for each object on the master map.

Colored dots indicate uniqueness of STS positions back to top

The righmost edge of the verbose display includes columns of colored dots that indicate which maps have data for each marker. The color of the dots indicates whether an STS has been mapped to a unique position on that map:

green dot marker has been mapped to only one location in the linkage group being displayed
green dot with black slash marker has been mapped to multiple locations in the linkage group being displayed
green and yellow dot marker has been mapped to the linkage group being displayed, and also to another linkage group
yellow dot marker has been mapped to one location, but in a different linkage group from the one being displayed
yellow dot with black slash marker has been mapped to multiple locations in a different linkage group from the one being displayed

For example, if you are viewing linkage group 2, a yellow dot indicates that the map named in the column header has placed that marker in a single location on another linkage group.

Polymorphism Column back to top

The polymorphism column indicates whether the marker has been used to detect a polymorphism, with Y for yes and N for no.

Detailed Marker Information back to top

To see detailed mapping information about a marker, follow the link for that marker to its UniSTS record.

Constructing URLs that link to Map Viewer back to top

If you would like to create WWW links to the Map Viewer, the instructions for constructing URLs are given in the general Map Viewer Help document. You can construct URLs that either perform a search or display a specific mapped object or chromosomal region.

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