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 version80.6
Base Pairs3,042,335,753
Golden Path Length

The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).

2,870,184,193
Genebuild byEnsembl
Genebuild methodMixed strategy build
Genebuild startedSep 2014
Genebuild releasedJun 2015
Genebuild last updated/patchedJun 2015

Gene counts

Coding genes

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

22,293 (incl 9 readthrough

Readthrough transcripts are tagged by HAVANA and defined as transcripts connecting two independent loci ie. transcript connecting two independent loci. A readthrough transcript has exons that overlap exons from transcripts belonging to two or more different loci (in addition to the locus to which the readthrough transcript itself belongs).

Readthrough transcripts are also annotated by RefSeq.

)
Non coding genes8,792
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, scRNA, snlRNA, snoRNA, snRNA, 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. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.

5,122
Long non coding genes

Long non coding genes are usually greater than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as long non coding genes: 3prime_overlapping_ncrna, ambiguous_orf, antisense, antisense_RNA, lincRNA, ncrna_host, non_coding, non_stop_decay, processed_transcript, retained_intron, sense_intronic, sense_overlapping. The majority of the long non coding genes in Ensembl are annotated manually by HAVANA.

3,146 (incl 2 readthrough

Readthrough transcripts are tagged by HAVANA and defined as transcripts connecting two independent loci ie. transcript connecting two independent loci. A readthrough transcript has exons that overlap exons from transcripts belonging to two or more different loci (in addition to the locus to which the readthrough transcript itself belongs).

Readthrough transcripts are also annotated by RefSeq.

)
Misc non coding genes524
Pseudogenes

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.

1,447
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.39,595

Other

Genscan gene predictions59,821
Short Variants4,979,965