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Marker Search Help

This page gives information about how to find your marker of interest in RGD.  Click the links below for information about specific search tools:

Using the General/Keyword Search
Using the Marker Search Tool
Using RGD’s “Classic” Marker Search Form

Finding SSLP information

1.  Using the General/Keyword Search

Keyword search at the top of any RGD page

The general RGD search available at the top of each page is a quick route to finding SSLPs. Use this box to search by marker symbol, alias, position, UniSTS ID and more.  Click here for more information about how the Keyword Search works.

2.  Using the Marker Search Tool

RGD’s current marker search tool is a simplified version of the “classic” marker search (see below).  It incorporates the most commonly used search capabilities without the complexity of the original tool.
Current Marker Search
  1. Enter a search term in the Keyword search box.  This can be a specific marker symbol or part of a symbol with an asterisk (*) as a wildcard.
  2. You can limit the results obtianed from the keyword search by specifying a location or you can use the position entry boxes to search by position without using a keyword.  To include position information in your search, enter a chromosome number and, if desired, a base pair start and stop position.  You can enter just the chromosome number if you wish.  Choose the assembly/map to which you would like to limit your position information, for example the rat reference assembly RGSC Genome Assembly v3.4.  RGD has information for a number of different genomic, genetic and RH maps.
  3. RGD stores data for markers in rat, mouse and human for comparative purposes.  Choose any one species, or perform your search across species.
  4. For any given map/assembly ther will be some RGD markers which do not have position data.  You can choose to include or exclude these unmapped markers.
  5. For those users who are familiar with RGD’s former marker search tool, or who want to be able to limit their search using more criteria than are available in the current search tool, the classic marker search is still available by clicking on this link.  For more information about how searches work on the RGD website click the “View all search features” link.
Click here to access the Marker Search Tool.

3.  Using RGD’s “Classic” Marker Search Form

RGD's Classic Search

Quick Guide

1. To find a particular SSLP(s), enter the SSLP symbol or alias symbol (wildcard searches can be performed using the contains option)

2. Searches can be limited to any of several criteria

  • find SSLPs at a particular chromosome, map, and map positions
  • find SSLPs associated or not associated with a particular gene
  • find SSLPs having allele data related to a specific rat strain

3. The output format section allows the user to customize the reporting of the search results to sort alphabetically based on symbol, to sort in ascending order based on chromosome, and to sort based on position. The sorting based on position requires selecting a map and chromosome in the limits section.


Below is a more detailed explanation of each element of the search form which will allow the user greater flexibility to refine your searches.

SSLP Symbol or alias
Enter a SSLP symbol or alias to search for. Various options are available to refine the search. The options are Equals, Contains, Begins with, Ends with.

Limit to map position
Restrict the returned SSLPs to ones mapped to particular map positions. These parameters allow a user to search for SSLPs using many possible combinations of parameters.

  • Find all SSLPs on a particular chromosome
  • Find all SSLPs on a particular chromosome between a position range for a particular map
  • Find all SSLPs on a particular chromosome for a particular map

Limit to SSLPs associated with a gene
Restrict the returned SSLPs to ones associated with genes in RGD. These SSLPs typically are used as genetic markers for tightly linked genes. The user can select an option from the drop down list.

  • “not selected” option – means this parameter will not be used to limit the search results
  • “any” option – means limit the results to all SSLPs that are associated with genes in RGD
  • List of genes option – means limit the results to any SSLP associated with the selected gene

Limit to strains with alleles size data
Restrict the returned SSLPs to ones associated with strains with allele data in RGD. The user can select an option from the drop down list.

  • “not selected” option means this parameter will not be used to limit the search results

Results ordered by

  • Symbol – sorts returned results alphabetically by SSLP symbol
  • Chromosome – sorts returned results by chromosome
  • Position – sorts returned results based on position on a chromosome for a selected map

Records per page
Defines the number of found SSLPs that are returned on each results page, the more results displayed, the longer the page and the longer it will take to download.

Click here to try out the Classic Marker Search.

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