The laboratory rat is an indispensable tool in experimental medicine and drug development due to an extensive knowledge of rat physiology and availability of many disease models. Rat is used extensively as a model organism for studying human normal and disease processes and for testing drug efficacy and toxicity prior to human clinical trials.

This site brings together information about rat data available at NCBI and other related resources from the research community, including sequence, mapping, and clone information. We welcome your suggestions.

NCBI Rat Resources
Global Query. Query all NCBI databases.
BLAST. Basic Local Alignment Search Tool.
Clone Registry. Information about specific BAC clones.
dbSNP. SNPs and other genetic variation.
 e-PCR. Identify potential sequence tagged sites.
Full-Length cDNAs. Full-length sequencing projects and clones.
Gene. The focal point for genes and associated information.
GEO. A gene expression and molecular abundance repository.
Genome Project. Sequencing, assembly, and annotation projects.
HomoloGene. Eukaryotic homology groups.
Homology Map. Syntenic blocks between rat, mouse, and human.
Map Viewer. Interactive viewer for genome maps, sequence, and genes.
Popset. Sequence data from population studies.
Probe. Nucleic acid reagents for biomedical applications.
RefSeq. The non-redundant Reference Sequence collection.
SAGEmap. A Serial Analysis of Gene Expression data repository.
Splign. A tool for aligning mRNAs to genomic sequence.
Statistics. Numbers of Genes, RefSeqs, and other data types.
Taxonomy. Lineage and organism names.
Trace Archive. Raw sequence data from various sequencing projects.
UniGene. Gene-oriented clusters of transcribed sequences.
UniSTS. Mapping and marker data.

FTP Sites
dbSNP
Gene
Genomes
Map Viewer
RefSeq
UniGene
UniSTS
Find genes or markers in Map Viewer
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Map Viewer
View displays of two annotated rat genome assemblies (RGSCv3.4 and Celera) in addition to radiation hybrid and genetic linkage maps. Take a moment to BLAST your favorite gene sequence against the rat genome sequence and explore the maps available for viewing. Learn more about the Gnomon gene prediction program and the resulting models available in Map Viewer.


Just In...

Statistics. Reports on the number of Genes, RefSeqs, and other data types currently available.

Tips on Finding cDNA Clones: NCBI offers hints on clone searching from the NIH Mammalian Gene Collection (MGC), including clones for rat.


The published rat genome
(April 2004)

Rattus norvegicus

(Photo courtesy of Martin Krzywinski)

Additional Resources
New This Month In:
   CoreNucleotide
   Gene
   Protein
   PubMed
   PubMed Central

Nomenclature Authority:
  RGNC

Genetics, Genomics, & Maps:
  Rat Genome Database
  Ratmap
  VCMAP
  Whitehead/MIT Genetic Maps

Sequence Resources:
  BAC ends at TIGR
  BAC fingerprint database   
  Genome Project at BCM
  MGC clones

Strain and Animal Resources:
  Charles River
  Harlan
  Natl. Bio Resource Project
  PhsyGen Strain Profiles
  RGD Strain Locator
  RRRC
  Taconic

Other Resources:
  ARB Genetic Database
  NIH Rat Genomics and Genetics
  OLETF Project
  Rat Atlas Viewer
  Rat Embyro Development
  TIGR Rat Gene Index
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