Ensembl Rat

Karyotype

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About the Rat genome

Assembly

The latest build provides a preliminary data set based on the version 3.4 "November 2004 Update" of the rat genome assembly. In this update a 15 bp overhang was removed at the join between AABR03100354-AC117058 and the order was reversed for BACs AC133000 and AC136926.

The Rat Genome project is an international collaboration to sequence the genome of the brown rat (Rattus norvegicus). The DNA sequence is generated by Baylor College of Medicine, Celera Genomics, Genome Therapeutics, The Institute for Genome Research, and The University of British Columbia.

The rat data used on this site can be downloaded directly from Baylor College of Medicine.

Annotation

Ensembl is working with the broader rat genomics community (RGD) to provide annotation of the rat genome. We have also participated in the STAR consortium to help identify and map single nucleotide polymorphisms in the rat.

The latest release (August 2006) uses a new rat-specific repeat library, and takes advantage of additional cDNAs and ESTs which have been published since the original RGSC 3.4 genebuild, with the result that around 1800 new gene predictions have been added.

What's New in Ensembl 48

Rattus norvegicus News

• Updated Rat variation data
  Ensembl Rat variation has been updated with an import of the new dbSNP build 126. We have also updated the STAR genotype data, and called SNP/genotypes on Japanese rat strain RNB1.

General News

• Change to SliceAdaptor
  The method fetch_by_region() in Bio::EnsEMBL::DBSQL::SliceAdaptor has an additional optional argument $no_fuzz which, if set to a true value, will ensure that the fuzzy matching is not performed when no exact match for the given $seq_region_name is found.
  Read more...
• Variation API
  AlignStrainSlice has been extended to handle insertions/deletions in the particular individual/strain.
• miRNA updates
  All chordate species have been brought up-to-date with version 10.0 of miRBase.
• GO term projections
  

  For this release we have further increased the number of inter-species GO-term projections.
  Read more...

More news...

Statistics

Assembly:	RGSC 3.4, Dec 2004
Genebuild:	Ensembl, Feb 2006
Database version:	48.34r
Known protein-coding genes:	18,311
Projected protein-coding genes:	1,841
Novel protein-coding genes:	2,841
Pseudogenes:	1,756
RNA genes:	2,924
Genscan gene predictions:	100,863
Gene exons:	246,736
Gene transcripts:	35,194
SNPs:	2,852,757
Base Pairs*:	2,507,066,654
Golden Path Length**:	2,718,897,321
Most common InterPro domains:	Top 40 Top 500

* Total number of base pairs = sum of lengths of DNA table

** Reference assembly (Golden path) length = sum of non-redundant top level seq regions