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

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
Database version78.5
Base Pairs2,573,362,844
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).

2,909,698,938
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedApr 2012
Genebuild releasedJan 2013
Genebuild last updated/patchedJul 2014

Gene counts

Coding genes

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

22,777 (incl. 6 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.

)
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.

1,713
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.

144 (incl. 1 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.

)
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.

2,055
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.30,404

Other

Genscan gene predictions58,074
Short Variants5,669,486