RGD > Help > Genes

Genes Help
Help Index
Definition
Finding info
Related info/link
Report

 
RGD Definition

"the DNA sequence necessary and sufficient to express the complete complement of functional products derived from a unit of transcription"

Splice variants for each gene are also listed in the gene report and specific information about these can be found in the associated splice variant report.

Does not include:

  • variations such as mutations, pseudogenes
  • Protein products which are derived from the modification of precursor proteins (eg. Agt produces the product angiotensinogen which is cleaved by Ren (renin) to produce angiotensin. Both Agt and Ren are gene objects whereas Angiotensin, being a product of the cleavage and not have its own coding sequence, is not included.

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Finding Gene information

1. Using the General Search

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

2. Using the Gene Search Form

Quick Guide

  1. Enter search term in the keyword box
  2. Change the 'Equals' option to 'Contains' for the broadest search possible
  3. Hit 'Find Gene' to run the search.

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

RGD: Gene Query Form Help Gene Symbol/Alias/Keyword

Enter a gene symbol, alias or keyword to search for. The asterisk '*' is an accepted wildcard, in addition various other options are available to refine the search:

Option Description
Example search
 Finds Excludes
Equals Performs an exact match (case insensitive)
Abc1
 Abc1 Abc1a, Abc
Contains Searches for the occurence of the text anywhere within the fields searched (see Search parameter below)
Bc
 Abc1, Abc1a, Bcd2, Abcess  
Begins with Searches for the occurence of the text at the start of the search fields
Ab
 Abc1, Abc1a Dab1, Gab
Ends with Searches for the occurence of the text at the end of the search fields
Ab
 Dab, Bgab Dab1, Abc1

 

Chromosome

Restrict the returned genes to ones mapped to a particular chromosome. Excludes genes that are unmapped or mapped to a different chromosome

Search

This option allows the restriction of the fields to be searched and hence the scope of the returned results. The options are:

  • current symbol (narrow search)
  • current symbol and name
  • current and withdrawn symbols and names
  • current and withdrawn symbols, names and aliases (broadest search).

Limit to genes with associated SSLPs

Restrict the returned genes to ones that have SSLPs (microsatellite markers) associated with them. Associated SSLPs are believed to be in linkage disequilibria with the gene itself and hence are markers for the gene on genetic and RH maps.

Limit to genes with known Homologs

Restrict the returned genes to ones which have a known homolog listed in RGD (from any organism) .

Limit to genes annotated to ontology term

Restricts the returned genes to ones that have been annotated to ontology concepts containing the entry term.

Results ordered by

  • Symbol - sorts returned results alphabetically by gene symbol
  • Name - sorts returned results alphabetically by gene name
  • Chromosome - sorts returned results by chromosome and then alphabetically by gene symbol

Results per page

Defines the number of hits 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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Related Information/Links

  The report also contains information on objects related to this gene, including QTLs, SSLPs, homologs, mapping, GO annotation, and external database IDs. Links to these objects will provide additional information.

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The Gene Report

Below is a description of each of the information sections available on the gene report which is generated when viewing data available for a particular gene. Not all information will be available for every gene.

RGD: Gene Report Help

Symbol

The official gene symbol

Full Name

The official full text name for the gene

Previous Symbol/alias

Symbols that have been used to refer to this gene in the past.

Previous Name

Names that have been used to refer to this gene in the past

Candidate gene for

QTLs for which this gene has been reported to be a potential candidate gene.

Associated STS

STS markers known to be closely linked to this gene

View Homologs

Links a report of known mouse or human homologs of this gene

Annotations

Summary of known information about this gene including:

  • Product - brief information on the gene product (protein size, etc)
  • Function - brief summary of the gene's function in the cell
  • Description - Other pertinent information about the gene gleaned from the literature curated by RGD.
  • Gene Ontology - Listing of GO terms annotated to this gene, see GO Help for more information

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. Also listed are any associated SSLP map locations which are microsatellite markers that are closely linked to the gene and hence have been used as markers for the gene location on other maps. The mapping information is linked to further information as shown below:

  • Symbol - links to the main report for that object (either a gene or 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.

External Database Links

Links to other databases which have information about this gene. The links are grouped by parent database and each link has a user-friendly text (e.g. PubMed citation, LocusLink gene symbol, etc.) followed in parentheses by the actual accession number used in the parent database (PubMed ID, LocusLink number).

Curated References

References curated by the RGD curation team that contain information pertaining to this gene.

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