Rat assembly and gene annotation


This site displays annotation on version 5.0 (March 2012) of the rat (strain BN/SsNHsdMCW) genome assembly, known as 'Rnor_5.0' submitted from the Rat Genome Sequencing Consortium.

This assembly is based on a 6X WGS sequence approach, as used for the mouse genome, and the hierarchical (BAC clone) approach used for the human genome. It is composed of 2738 toplevel sequences, of which 21 are chromosomes, 1278 are unlocalized scaffolds and 1439 are unplaced scaffolds. There are 112,652 contigs with an N50 length of 59.5kb, and 10,848 scaffolds with an N50 length of 2.18Mb.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000001895.3

Gene annotation

The Rat Rnor_5.0 assembly was annotated using the standard Ensembl gene annotation system. To improve the gene set, we have incorporated new data resources which have become available since the last RGSC 3.4 genebuild (December 2004), including an updated rat-specific repeat library, additional RefSeq and UniProt protein sequence data for predicting the coding regions of protein-coding genes, as well as new cDNAs for annotating untranslated regions (UTRs) of protein-coding genes.

More information

General information about this species can be found in Wikipedia.



AssemblyRnor_5.0, INSDC Assembly GCA_000001895.3, Mar 2012
Database version76.5
Base Pairs2,573,362,844
Golden Path Length2,909,698,938
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedApr 2012
Genebuild releasedJan 2013
Genebuild last updated/patchedFeb 2014

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

Small non coding genes

Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, tRNA, scRNA, snlRNA, snoRNA, snRNA, tRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline.


A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.29,188


Genscan gene predictions58,074
Short Variants5,669,486