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

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

AssemblyDord_2.0, INSDC Assembly GCA_000151885.2, Dec 2014
Base Pairs2,065,314,047
Golden Path Length2,236,368,823
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2016
Genebuild releasedJul 2017
Genebuild last updated/patchedJul 2017
Database version90.2

Gene counts

Coding genes16,911
Non coding genes3,317
Small non coding genes2,750
Long non coding genes9
Misc non coding genes558
Pseudogenes314
Gene transcripts27,593

Other

Genscan gene predictions105,282

About this species