Marker Report Page Help

 

Marker Summary Section:

1. General tab:  shows most of the information which RGD has on the marker
2. Genes in Region tab:  links to GBrowse where you can explore the region of the genome where your marker of interest is located.  Follow this link to view the genomic neighborhood including genes models from RGD, Entrez Gene and Ensembl, QTLs, congenic strains, SNPs from dbSNP and Ensembl, strain specific variants, disease-related genes, QTLs and strains, and links to the syntenic region(s) in human.  For more on how to use the RGD GBrowse Genome Browser, click here to access the GBrowse help pages (LINK).

Summary Section Data:

3.  Nomenclature and expected size:
  • Symbol:  The current symbol for the marker;  this is considered the name by UniSTS
  • Also known as:  Any previous symbols for the marker, or symbols or other identifiers for the marker in use by other databases
  • Expected size:  The size in base pairs of the marker PCR product.  RGD imports most of these values from NCBI's UniSTS.  Imported values refer to the size in the current reference assembly of the rat genomic sequence (RGSC 3.4 at time of writing).  If UniSTS does not have a value for expected size, this would be the size of the PCR product reported by the submitting researcher where available.
4.  Position:
The position section of the marker report gives map positions for any or all of the maps for which RGD has data, including:

  1. Map:  the name of the map or genome assembly to which this data refers
  2. Chr:  chromosome
  3. Position:  for genome assembly maps this is the base pair position on the corresponding chromosome in that assembly;  for genetic maps this is the centimorgan (cM) position; for RH maps it is the centiray (cR) position.
  4. Strand:  RGD does not usually assign a strand to marker positions
  5. Source:  the source of this position data;  for data downloaded to RGD via the UniSTS pipeline, this is UniSTS.  When the position was either calculated by RGD curators or submitted to RGD by a researcher the source is RGD.

In many cases, RGD displays positions on the RGSC 3.4 reference assembly from both UniSTS and RGD.  For historical and comparison purposes, the original position submitted by a researcher or determined by RGD curators when the marker itself was first submitted have been retained in the RGD database and are displayed on the marker report page.  In the example here the only difference between this position and the one imported from UniSTS is that the start position is off by one nucleotide.  However, in some cases these differences will be substantial.

5.  Model:  The Model section provides a link to the marker in GBrowse.  If the marker has a single position on the current reference assembly, an image of the marker in GBrowse will appear in the marker section as in this example from the marker D1Mco122:

For many markers the image of the marker in GBrowse will appear in the Model section of the page.

Regardless of whether an image appears in this section, a link is provided to the GBrowse tool.

6.  More on D3Mgh21:  Links to more information about the marker, such as GBrowse (listed as Genes in Region), Ensembl and NCBI.

7.  RGD Object Information:  This box contains RGD metadata about the marker, such as the RGD ID, the date the record was created in the database, the species, the date the record was last modified and the status of the record in RGD.

Marker Annotation Section:

Since RGD does not currently assign ontology annotations to Markers, for Markers the "Annotation" section includes any curated references associated with that marker.  Some of these will be "internal" references, i.e. ones which RGD curators have entered into the database to give information about where data came from and/or how it was loaded into the RGD database.  In this example, the reference "Data downloaded from Wellcome Trust, University of Oxford" is this type of reference.  Other references, such as " Kwitek AE, et al., Genome Res. 2004 Apr;14(4):750-7", are abstracts for published papers which have been downloaded from NCBI's PubMed database.

Marker Strains and Sequence Section:

Sequence:


A marker which is a simple sequence length polymorphism or SSLP is generally defined by the PCR primer pair used to amplify and visualize the segment of DNA containing the polymorphism.  For this reason, most if not all RGD SSLP marker reports will include information about their primer pair in the Strains and Sequence section.  As is customary for DNA sequences, primers are always listed in the 5' to 3' direction.

RGD also stores data for other types of makers, such as ESTs, which may or may not have associated primer pairs.

In some cases the sequence section will also contain a "template" sequence.  This is the genomic sequence which includes the primer pair and usually a small region on either side.  You can locate the primers in the template sequence by using your browser's search/find function to locate the forward primer and the "reverse complement" of the reverse primer in the template sequence.

Click here to access a Web tool to produce the reverse complement of a DNA sequence.

Strain Variation:

Many SSLPs are polymorphic in size between different 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 page.


If you have information about an SSLP product size which is not included in that SSLP's report page, we would encourage you to contact us with that information.  Your help and support in ensuring the comprehensiveness of RGD's data would be greatly appreciated by both us and your fellow researchers.

Marker Region Section:

The Region section of the report page contains information about other data objects in the SSLP's immediate genomic neighborhood as well as links to the GenBank nucleotide sequence of the SSLP.
The QTLs in region and Genes in Region sections contain tables of QTLs and genes which overlap the position of the SSLP.  Each table contains the following helpful links at the top:
  1. Full Report links to the interactive RGD search result page for the objects in the list.  The search results page in turn links to each of those objects providing easy access to additional information about that object.  For more about the search results page, click here to access the search results help pages.
  2. CSV and TAB allow you to download the list in either comma separated values (CSV) format or tab delimited (TAB) format.  The list can then be saved and/or used in other tools such as RatMine for further analysis.
  3. Printer sends the list to your default printer so you can print and save a copy of the list without needing to print the rest of the page.
  4. GViewer sends the list to the GViewer genome-wide viewer tool so you can view the results in the context of the entire genome.  For more on using the GViewer tool, click here to access the GViewer tool help pages.

QTLs in Region:

The QTLs in Region table includes the following columns of information where that information is available:
  1. RGD ID:  the unique RGD ID of that QTL
  2. Symbol:  the official symbol of the QTL
  3. Name:  the official name of the QTL
  4. LOD/P-Value:  statistical values assigned to the QTL by the researcher who defined the QTL
  5. Trait:  the phenotypic trait which was measured to define the QTL
  6. Subtrait:  a more specific phenotypic trait which further defines what was measured to define the QTL
  7. Chr/Start/Stop:  The genomic position of the QTL, i.e. the identity of the chromosome, the nucleotide start position and the nucleotide stop position on the current reference assembly (e.g. RGSC 3.4).  The position of a QTL is defined by its flanking and/or peak markers.
  8. Species:  the species of the QTL.  RGD stores information on rat, mouse and human QTLs and curates data for rat and human QTLs.

For more about QTLs and the data in this table, click here to access information about the RGD QTL report pages.

Genes in Region:


The Genes in Region table includes the following columns of information where it is available:
  1. RGD ID:  the unique RGD ID of that gene
  2. Symbol:  the current symbol of the gene
  3. Name:  the current name of the gene
  4. Description:  RGD's gene description.  For human this comes from the human Entez Gene record, for rat they were written by RGD curators based on the literature about that gene.
  5. Chr/Start/Stop:  The genomic position of the gene, i.e. the identity of the chromosome, the nucleotide start position and the nucleotide stop position on the current reference assembly (e.g. RGSC 3.4).
  6. Species:  the species of the QTL.  RGD stores information on rat, mouse and human genes.

For more about genes and the data in this table, click here to access information about the RGD gene report pages.

Nucleotide Sequence:

The Nucleotide Sequences section of the page contains links to GenBank nucleotide sequences which contain this marker. 
The accession ID of the sequence, e.g. "U43332" links to the NCBI nucleotide report for that sequence.
The "Get FASTA" link connects to the NCBI nucleotide sequence in the simpler FASTA format
The "Search GEO for Microarray Profiles" link sends the corresponding nucleotide accession ID to NCBI's Gene Expression Omnibus database to search for related GEO profiles.  If that ID appears in GEO the search will return links to all the corresponding GEO records which you can examine and/or download for information on the expression of that nucleotide sequence.  In the above example, none of the nucleotide IDs are in GEO, but searching for the RefSeq nucleotide ID for the gene listed in the "Genes in Region" section, NM_012736, brings back a number of GEO profiles:

Marker Additional Information Section:

External Database Links:

RGD imports marker data from NCBI's UniSTS database in addition to curating markers from the literature and receiving marker submissions directly from researchers.  Any external database links which are automatically imported or manually entered into the database are displayed in the External Database Links section.  These can include links to UniSTS for more information about the marker itself, and to Entrez Gene for loci such as genes and QTLs which are associated with that marker.
Clicking the accession ID in the right-hand column takes you to the corresponding record at the external database.  In this case, the ID "25062" links to the Entrez Gene record for the Gpd2 gene which overlaps the D3Mgh21 marker.

Curation notes:

Some SSLP records contain curation notes which may contain valuable information about the SSLP.  For instance D1Mco122, RGD: 2315138 contains information about mapping anomalies for that marker.