05/11 - RGD now includes genes for the 13-lined ground squirrel!

You may have never heard of the 13-lined ground squirrel but due to the similarity between the squirrel retina and that of human it is an established model for retinal function and disfunction1.  In addition, during hibernation squirrels experience repeated cycles of long periods of hypometabolic torpor interspersed with brief periods of euthermic arousal2.  The ability of the animal to survive and even thrive in these conditions makes it an excellent model for metabolism, hypoxia/reperfusion, longevity and more.

At the request of researchers in the squirrel research community, RGD has incorporated the 13-lined ground squirrel (Ictidomys tridecemlineatus) into our database.  Now when you search for genes at RGD, in addition to results for rat, human and mouse, you can access squirrel genes as well.

Once you have one or more squirrel genes, you can use RGD's Analysis and Visualization tools to explore your gene set. 

  • Use the Squirrel JBrowse genome browser to view the genomic neighborhood for your gene or genes of interest. 

  • Perform complex queries for squirrel genes using the OLGA advanced search tool

  • The Gene Annotator (GA) Tool gives you access to all of the functional annotations for your gene list and their orthologs.  (As an example, click here to explore the annotations for the list of squirrel genes annotated to the disease term "Glucose Metabolism Disorders" and its children.) 

A limited set of functional annotations are assigned to squirrel genes at present, but stay tuned.  Additional annotations will be added for squirrel in the near future!

 

For more information about the thirteen-lined ground squirrel:

1Noninvasive imaging of the thirteen-lined ground squirrel photoreceptor mosaic. Sajdak B, et al.  Vis Neurosci. 2016;33:e003. doi: 10.1017/S0952523815000346.  PMID: 26923645

2Thirteen-lined ground squirrel information page in the Storey Lab website
Out cold: biochemical regulation of mammalian hibernation - a mini-review.  Storey KB.  Gerontology. 2010;56(2):220-30. doi: 10.1159/000228829. Epub 2009 Jul 14.  PMID: 19602865