Rat assembly and gene annotation

Assembly

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

Other assemblies

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.

Statistics

Summary

AssemblyRnor_5.0, INSDC Assembly GCA_000001895.3, Mar 2012
Base Pairs2,573,362,844
Golden Path Length2,909,698,938
Annotation methodFull genebuild
Genebuild startedApr 2012
Genebuild releasedJan 2013
Genebuild last updated/patchedFeb 2014
Database version95.5

Gene counts

Coding genes22,940
Pseudogenes1,751
Gene transcripts29,188

Other

Genscan gene predictions58,074
Short Variants5,669,486

About this species