Rat assembly and gene annotation

Assembly

This site displays annotation on version 6.0 (July 2014) of the rat (mixed female BN/SsNHsdMCW and male SHR) genome assembly, known as 'Rnor_6.0', submitted from the Rat Genome Sequencing Consortium.

This assembly is based on a 6X WGS sequence approach (as used for the mouse genome), 10X PacBio data set and the hierarchical (BAC clone) approach used for the human genome. It is composed of 2738 toplevel sequences, of which 22 are chromosomes, 354 are unlocalized scaffolds and 578 are unplaced scaffolds. There are 75,697 contigs with an N50 length of 100.5kb, and 1,395 scaffolds with an N50 length of 14.99Mb. The Y chromosome is now present in the assembly.

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

Other assemblies

Gene annotation

The Rat Rnor_6.0 assembly was annotated using a mixed approach, with the standard Ensembl gene annotation system and the Ensembl RNASeq pipeline. The RNASeq data set contains 12 samples: liver, muscle, brain, heart, thymus, blood, testis, ovary, kidney, skin, spleen and lung. The HAVANA manual annotation team at the Sanger Institute provided a high quality gene set on gene clusters which are hard to annotate in an automated pipeline.

RNAseq dataset

In addition to the main set, we have predicted gene models for each tissue type using the RNASeq pipeline. We did a BLASTp of these models against UniProt proteins of protein existence level 1 and 2, in order to confirm the open reading frame (ORF). The best BLAST hit is displayed as a transcript supporting evidence.

The tissue-specific sets of transcript models built using our RNAseq pipeline are as follows:

TissueNumber of gene models
Blood9146
Brain12736
Heart9047
Kidney11612
Liver9227
Lung13374
Muscle9255
Ovary12866
Skin12123
Spleen11799
Testis14653
Thymus10865
Merged22338

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 version92.5

Gene counts

Coding genes22,940
Pseudogenes1,751
Gene transcripts29,188

Other

Genscan gene predictions58,074
Short Variants5,669,486

About this species