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Map positions, functions and more
Gene Ontology, Phenotype, Pathway info
Search Strains
Genes, QTL & Strains related to Disease
Data mining, analysis and visualization
Phenotypes & Traits linked to the genome
Phenotype data, Assays, Husbandry and more
Pathway reports and diagrams
Featured RGD Video Tutorials

PhenoGen Informatics Genome/Transcriptome Data and Browser

RGD has been providing links from our gene pages to the PhenoGen Informatics Genome/Transcriptome Data Browser, but there's a good chance you don't know all there is to know about the tool. Want more information about how to use it so you can get the most out of its data and functionality? This informative hands-on workshop video is just the tutorial to help you with that!

Introduction to the Variant Visualizer

The examination of SNPs has undergone a recent change, and in response to this change, RGD has released the new Variant Visualizer tool (VarVis), taking the place of the old SNPlotyper tool. VarVis is a visualization and analysis tool for sequence variation. The data currently contains 22 rat strains sequenced by 4 independent labs.

The Gene Annotator

The Gene Annotator takes a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, and/or a chromosomal region, and retrieves annotation data from RGD. This tool will retrieve annotations from any or all ontologies used at RGD for genes and their orthologs, as well as links to additional information at other databases.

Click here to access RGD's Rat Community Videos page.  This page includes all of the tutorial videos that RGD has produced, plus other videos of interest to rat researchers.
 Conference Watch
The Biology of Genomes, Cold Spring Harbor, NY, USA - May 5-9, 2015; Abstract Deadline: February 13, 2015
Great Lakes Bioinformatics Conference, Purdue University, West Lafayette, IN, USA - May 18-20, 2015; Abstract Deadline: March 25, 2015
21st Century Genetics: Genes at Work, Cold Spring Harbor, NY, USA - May 26-31, 2015; Abstract Deadline: March 6, 2015
The 2015 American Statistical Asociation Wisconsin Chapter Annual Meeting: Big data and statistics, Raynor Library Conference Center, Marquette University, Milwaukee, WI, USA - June 5, 2015; Registration Deadline: May 15, 2015
Complex Trait Community 14th Annual Meeting, Oregon Health & Science University Auditorium, Portland, OR, USA - June 8-11, 2015; Abstract and Registration Deadline: April 15, 2015
Rat Genetics and Genomics for Psychiatric Disorders and Addiction Workshop, University of Chicago, Chicago, IL, USA - June 29, 2015; Abstract/Registration Deadline: May 15, 2015
23rd Annual International Conference on Intelligent Systems for Molecular Biology, Convention Centre Dublin, Dublin, Ireland - July 10-14, 2015; Abstract Deadline: February 27, 2015
6th International Conference on Biomedical Ontology, Lisbon, Portugal - July 27-30, 2015; Conference Paper Deadline: March 2, 2015
Gordon Research Conference - Epigenetics, Bentley University, Waltham, MA, USA - August 2-7, 2015; Application Deadline: July 5, 2015
Metabolic Signaling & Disease: From Cell to Organism, Cold Spring Harbor, NY, USA - August 11-15, 2015; Abstract Deadline: May 22, 2015
9th Annual Genomics of Common Diseases Conference, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK - September 2-5, 2015; Abstract and Bursary Deadline: July 7, 2015
EMBO/EMBL Symposium: The Mobile Genome: Genetic and Physiological Impacts of Transposable Elements, EMBL Heidelberg, Germany - September 16-19, 2015; Abstract Deadline: June 24, 2015
Mouse Molecular Genetics Conference, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK - September 16-19, 2015; Abstract Deadline: July 17, 2015
EMBO/EMBL Symposium: The Non-Coding Genome, EMBL Heidelberg, Germany - October 18-21, 2015; Abstract Deadline: July 16, 2015
Genome Informatics, Cold Spring Harbor, NY, USA - October 28-31, 2015; Abstract Deadline: August 14, 2015
AMIA Annual Symposium, Hilton San Francisco Union Square, San Francisco, CA, USA - November 14-18, 2015; Submission Deadline: March 12, 2015
Rat Genomics & Models Conference, Cold Spring Harbor, NY, USA - December 9-12, 2015; Abstract Deadline: September 25, 2015
The 2015 ASCB Annual Meeting, San Diego Convention Center, San Diego, CA, USA - December 12-16, 2015; Abstract Deadline: August 5, 2015
                   
Rat Genetics & Genomics
for Psychiatric Disorders
& Addiction Workshop
Registration is now open. Click here for more information.
Ribosome Biogenesis
Pathway
RGD releases the ribosome biogenesis pathway. Click here to explore the details of this superbly complex system.
Analysis of variants
in 40 rat strains
An article describing the analysis of variation data for 40+ strains has been published in BMC Genomics. The data is available in RGD. Click here to learn more.
microRNA
Pathway
RGD publishes an updated version of the microRNA pathway. Click here to explore the details.
Sensory Organ
Disease Portal
RGD’s Sensory Organ Disease Portal is a cross-species resource that integrates genes, QTL and strains linked to diseases such as diabetic retinopathy, sensorineural hearing loss and more, as well as associated phenotypes, biological processes and pathways. Click here for details.
Translation
Pathway
RGD publishes the translation pathway. Click here to explore the details of this intricate system.
RGD's JBrowse
Genome Browser
RGD announces the official release of JBrowse genome browsers for rat, mouse and human. Click here to learn more, and to try out the faster and more dynamic JBrowse.
Gene Expression & Regulation
Pathway Suite Network
RGD releases an update for this pathway suite network. Click here to explore its aspects.
New Assembly Gene
Comparisons Available
RGD announces new quarterly-updated downloadable files of gene comparisons between genome assemblies. Click here for details.
 Latest News
    06/15 - RGD releases an updated pathway suite network for gene expression and regulation
    06/11 - RGD provides new files comparing genes between genome assemblies rn3.4, rn5 and rn6
    06/09 - RGD releases an interactive diagram page for the translation pathway
    05/06 - Paper describing analysis of variation data for 40+ rat strains published in BMC Genomics
    04/27 - RGD publishes an interactive diagram page for the ribosome biogenesis pathway
    04/08 - Registration is now open for the Rat Genetics and Genomics for Psychiatric Disorders and Addiction Workshop
    03/30 - RGD releases an updated version of the microRNA pathway interactive diagram
    03/09 - RGD announces the publication of a new pathway suite network for gene expression and regulation
    03/02 - RGD publishes an interactive diagram page for the mRNA nuclear export pathway
    02/24 - RGD announces the official release of the JBrowse genome browser
    02/09 - RGD releases an interactive diagram page for the spliceosomal pathway
    01/21 - RGD's latest update paper published in Nucleic Acids Research
    01/05 - RGD publishes a new interactive diagram for the RNA polymerase III transcription pathway
    12/15 - RGD releases a new interactive diagram for the RNA polymerase II transcription pathway
    12/10 - A high resolution PDF of RGD's 2015 Rat Calendar is now available
    10/27 - RGD publishes the interactive pathway diagram page for RNA polymerase I transcription
    09/25 - RGD releases an interactive diagram page for the chromatin remodeling pathway
    09/23 - RGD announces the release of the new Sensory Organ Disease Portal
    09/08 - RGD releases interactive diagram pages for DNA and histone modification pathways
    09/03 - Production for RGD's 2015 Rat Calendar is underway
    07/29 - RGD gene report pages now display disease annotations divided into manual and imported annotations from ClinVar, OMIM and GAD
    07/28 - RGD announces the release of an updated interactive diagram page for the pancreatic cancer pathway
    07/22 - RGD publishes updated interactive diagram pages for the prostate cancer pathway and the altered androgen signaling pathway
    07/07 - RGD releases interactive diagram pages for a comprehensive p53 signaling pathway update and the new altered p53 signaling pathway
    06/23 - RGD releases three interactive diagram pages for ataxia telangiectasia-mutated (ATM) signaling and the two pathways of double-strand DNA break repair it promotes