Rat assembly and gene annotation

Assembly

This site displays annotation on version 6.0 (July 2014) of the rat (strain BN/SsNHsdMCW) 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), 10,2X 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_000001895.4

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_6.0, INSDC Assembly GCA_000001895.4, Jul 2014
Database version81.6
Base Pairs3,042,335,753
Golden Path Length2,870,184,193
Genebuild byEnsembl
Genebuild methodMixed strategy build
Genebuild startedSep 2014
Genebuild releasedJun 2015
Genebuild last updated/patchedJun 2015

Gene counts

Coding genes22,293 (incl 9 readthrough)
Non coding genes8,792
Small non coding genes5,122
Long non coding genes3,146 (incl 2 readthrough)
Misc non coding genes524
Pseudogenes1,447
Gene transcripts39,595

Other

Genscan gene predictions59,821
Short Variants4,979,965