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Algerian mouse assembly and gene annotation

Assembly

The SPRET_EiJ_v1 assembly was submitted by Wellcome Trust Sanger Institute on 2016/04/26 . The assembly is on the Chromosome level, consisting of 280,393 assembled into 5,404 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 17,887 while the scaffold N50 is 131,945,496.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_001624865.1

Gene annotation

The Algerian mouse, or western Mediterranean mouse, (Mus spretus) is a wild species of mouse closely related to the house mouse, native to open habitats around the western Mediterranean.

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

AssemblySPRET_EiJ_v1, INSDC Assembly GCA_001624865.1, Jul 2016
Base Pairs2,593,170,291
Golden Path Length2,625,571,169
Annotation providerUCSC computational genomics laboratory
Annotation methodExternal annotation import
Genebuild startedJul 2016
Genebuild releasedSep 2016
Genebuild last updated/patchedJan 2018
Database version94.1

Gene counts

Coding genes20,234
Non coding genes10,598
Small non coding genes4,298
Long non coding genes5,762
Misc non coding genes538
Pseudogenes5,684
Gene transcripts100,839

Other

Genscan gene predictions49,996

About this species