Northern American deer mouse assembly and gene annotation

Assembly

The Pman_1.0 assembly was submitted by Baylor College of Medicine on 2013/12/03 . The assembly is on the Scaffold level, consisting of 212,962 assembled into 30,921 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 36,367 while the scaffold N50 is 3,760,915 The genome assembly represented here corresponds to GenBank Assembly ID: GCA_000500345.1

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000500345.1

Gene annotation

Peromyscus maniculatus is a rodent native to North America. It is most commonly called the deer mouse, although that name is common to most species of Peromyscus, and thus is often called the North American deermouse and is fairly widespread across the continent, with the major exception being the southeast United States and the far north.

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

AssemblyPman_1.0, INSDC Assembly GCA_000500345.1, Dec 2013
Base Pairs2,473,536,444
Golden Path Length2,630,541,020
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedOct 2016
Genebuild releasedFeb 2017
Genebuild last updated/patchedFeb 2017
Database version90.10

Gene counts

Coding genes19,854
Non coding genes3,962
Small non coding genes3,250
Long non coding genes28
Misc non coding genes684
Pseudogenes465
Gene transcripts33,293

Other

Genscan gene predictions59,948

About this species