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Marker Report Page Help

A user may navigate to a marker report page by using the Marker Search Tool, or by entering the marker symbol into the General Search bar at the top of any RGD page. Clicking on the marker symbol on any of the search result pages will navigate to the Marker Report page.

Use these links to jump to information about the corresponding sections of the Marker Report pages:

General Section
Strains and Sequence Section
Region Section
QTL Section
Additional Information Section

Jump To…

General Section

1. The Marker Report page will indicate the species for that marker and the left side of the screen shows an outline of the information available in the report. Users can jump to any section by clicking on the title in the left sidebar.

2. General information includes the marker symbol, alias, RGDID and the expected PCR product size.
There is a table of chromosome and position locations, with sources given.

3. Clicking on the assembly in the JBrowse column will open a JBrowse interactive page for that marker location.

4. Also listed are strains, QTLs, and genes with which the marker is associated. Each is a clickable link to a further report page.

5. RGD does not manually assign ontology annotations to Markers, but references are given for the marker information displayed. These include any curated references associated with that marker, sources of imported data, and published papers of mapping data.

Click here to access the Marker Search Tool.

 

Strains and Sequence Section

6. A marker which is a simple sequence length polymorphism (SSLP) is defined by the PCR primer pair used to amplify and visualize the segment of DNA containing the polymorphism.  Data is also stored at RGD for ESTs, SNPs and other types of markers, which may or may not have associated primer pairs.

7. Many SSLPs are polymorphic in size among rat strains due to differing numbers of short nucleotide repeats within the SSLP sequence.  Where RGD has information about strain-specific sizes of an SSLP’s PCR product, these nucleotide sizes are listed with the corresponding strain/substrain symbol in the Strain Variation section of the report. Strain names are clickable and will take the user to the strain report page.

 

 

Region Section

8. The Region section of the report page contains information about genes or other data objects in the SSLP’s immediate genomic neighborhood as well as links to the GenBank nucleotide sequence of the SSLP.

 

 

QTL Section

The QTLs in region section provides a table of QTLs and genes which overlap the position of the SSLP. 

9. The menu at the top of the page provides links for:
Full Report  which links to the interactive QTL search page.
CSV and TAB which allow the user to download the list in either comma separated values (CSV) format or tab delimited (TAB) format.
Printer opens a dialog to send the list to your default printer.
GViewer sends the list to the GViewer genome-wide viewer tool to view the results in the context of the entire genome.

10. The QTL table provides columns of information about each QTL as noted in the column names. For more about QTLs and the data in this table, click here to access information about the RGD QTL report pages.

 

 

Additional Information Section

11. RGD imported marker data from UniSTS until NCBI discontinued the database. In addition, marker information is curated from the literature and received directly from researcher submissions.  Whether automatically imported or manually entered into the database, they are displayed in the External Database Links section.  These can include links to NCBI Gene for more information about the genes and QTLs. Clicking the accession ID takes the user to the corresponding record at the external database. 

 

 

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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.