Kangaroo rat assembly and gene annotation

Assembly

The Dord_2.0 assembly was submitted by Baylor College of Medicine on 2014/12/12 . The assembly is on the Scaffold level, consisting of 148,226 assembled into 65,193 scaffolds. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for the contigs is 48,087 while the scaffold N50 is 11,931,245 The genome assembly represented here corresponds to GenBank Assembly ID: GCA_000151885.2

Other assemblies

Gene annotation

Ord's kangaroo rat (Dipodomys ordii) is a kangaroo rat native to western North America, specifically the Great Plains and the Great Basin, with its range extending from extreme southern Canada to central Mexico.

The gene annotation process was carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). For each candidate gene region, a selection process was applied to choose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments. Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold. Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of >10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome. lincRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

In accordance with the Fort Lauderdale Agreement , please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblydipOrd1, Jul 2008
Base Pairs1,844,961,421
Golden Path Length2,165,294,802
Annotation methodProjection build
Genebuild startedNov 2008
Genebuild releasedFeb 2009
Genebuild last updated/patchedMay 2010
Database version92.1

Gene counts

Coding genes15,798
Pseudogenes1,010
Gene transcripts19,899

Other

Genscan gene predictions143,756

About this species