• What is a SSLP?
• How do I find information about an SSLP?
• What information do you have on each SSLP?
• What other information can I get to via an SSLP?
• Can I download all your SSLP data?
• Let me start searching...

"SSLP stands for Simple Sequence Length Polymorphisms, also known as microsatellite DNA. SSLPs are 1-6 simple nucleotide repeat sequences, highly polymorphic in length of repeat among strains and are often used as genetic markers for genotyping."

Most of the SSLP markers available in RGD have been generated for use in genetic mapping experiments and many of these are placed on the various maps stored within RGD.

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1. Using the General Search

The general RGD search available at the top of each page is a quick route to finding SSLPs. This will search SSLP symbols and aliases only. (See General RGD Search help for more information).

2. Using the SSLP Search Form

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.

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The SSLP Result report has several sub-report pages and also has batch download capability.

There are several functions provided on the results page that allow the user to easily navigate through detailed information about the records that match the search criteria.

• Select/unselect all results on current page by clicking on the check box on the header line
• Select the wanted items by checking the checkbox at the beginning of each record
• Navigate records by clicking on a page number at the top or the bottom of the results page
• View all checked items in one page only by clicking on the "View Selected" button at the bottom of the results page
• View all checked items in excel format by clicking on the "Download Selected" button at the bottom of the results page
• View all items in excel format by clicking on the "Download All" button at the bottom of the results page
• View all map data for selected SSLPs by clicking on the "View Selected Map Data" button
• View all map data for all SSLPs in the results by clicking on the "Download All Map Data" button
• Go back to result summary page by clicking on "Go Back" button at the bottom of the results page

The Maps to mutiple chromosomes pop-up box looks like the following example.

The Selected Items Report looks like the following example.

The Download Report looks like the following report. The file can be saved as an Excel file by clicking on the File button in the upper left corner of the web browser window and saved by selecting Save as type: Microsoft Excel Workbook.

The Selected Map Data Report looks like the following report.  The report shows all map data in RGD for the selected SSLPs. The map data includes the genomic map data including chromosome and start-end base positions on the Rat Genome Sequencing Consortium's (RGSC)assembly, other maps have their name and position units displayed in the header.

The View Selected Download Map Report and the Download All Map Data Report look like the following. The file can be saved as an Excel file by clicking on the File button in the upper left corner of the web browser window and saved by selecting Save as type: Microsoft Excel Workbook.

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The SSLP report also contains information on objects related to this SSLP within RGD. This includes links to Strain, QTL, Map and Gene reports. There are also a variety of tools available that contain SSLP data:

• VCMAP - comparative map tool based on rat radiation hybrid map which contains many SSLPs
• Genome Scanner - enables the selection of polymorphic markers between two sets of strains

The FTP site contains two files related to the SSLP data contained within the database:

1. SSLPS file - All fundamental SSLP data contained in RGD
2. SSLPS_ALLELES - Allele sizes for over 4500 SSLPs in 48 rat strains

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Below is a description of each of the information sections available on the SSLP report. Not all information will be available for every SSLP.

The report is divided into several sections each containing different categories of data.

The report also has summary icons at the top of the report. The icons are displayed, if data is available in the icon's section of the report. The icons hyperlink to their sections on the report allowing easier navigation on large reports.

Name Section:

Symbol
The official SSLP symbol.

Alias Symbols
A previous symbols used for the SSLP.

Sequence Section:

Expected Size
The expected size of the PCR product produced by using the primer pair listed with a genomic template containing this microsatellite marker. The expected size was calculated during the original characterization of this microsatellite marker in one particular inbred rat strain and is highly strain dependent, i.e. in a different rat strain the product size may be slightly different or perhaps very different from the expected size reported here.

View Strain Variations
A hyperlink to the Strain Variations report. The report is displayed below. The homozygotes hyperlink at the top of the page hyperlinks to the list of strains that are homozygous for the allele size of the SSLP.  The heterozygotes hyperlink at the top of the page hyperlinks to the list of strains that are heterozygous for the allele size of the SSLP. 

Primer pairs
The primers used to amplify the SSLP region. The report label is hyperlinked to the sequence report for the primer pair.

Template
The genomic sequence that the primer pair will amplify.  The primer pairs are highlighted in the sequence with an underline and blue text. The report label is hyperlinked to the sequence report for the template sequence.

Genome Section:

Genome View
Displays an image of the SSLP with the genome locations displayed above the image. The assembly used to determine the coordinates are also displayed.

Browsers
A drop down box provides hyperlinks to various genome viewing tools. The hyperlink will enter the tool with the chromosome and coordinates using values of +/- 2,000,000 or +/- 500,000 bases from the actual SSLP's coordinates depending on which tool is selected.  This adding to the start and end positions of the SSLP was done to allow the user to work with a larger viewing perspective of the genome than what the SSLP's coordinates can offer. See the drop-down box's choice of links below.

Mapping Data
Mapping information contained in RGD is shown for the gene itself if it has been mapped directly onto one of the standard maps or has been located on the cytogenic map by FISH or similar techniques. The mapping information is linked to further information as shown below:

• Symbol - links to the main report for that object (an SSLP report)
• Map Name - links to the Map report for that map
• Chr. (Chromosome) - links to the map for that particular chromosome
• Position - links to the map for that chromosome with the location of the particular marker highlighted in the text listing of the markers.

Related Objects Section:

Candidate Genes
Genes known to be closely linked to this SSLP marker, or genes that contain this SSLP within their open reading frames.

Other Database Links Section:

The labels hyperlink to a report that lists all available external databases and links to their reports.  Some labels hyperlink to external databases directly, if their is a unique ID for that database.

References Section:

Links to a Reference summary report. The report contains a list of the reference's RGD ID, title, citation, and hyperlinks to the RGD reference report and the Pubmed reference report.

Database Information Section:

Database Information
This section lists the RGD ID of the SSLP and also has a hyperlink to the Nomenclature and Modification History report.

The SSLP's Nomenclature and Modification History report looks like the report below.

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