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Steppe mouse assembly and gene annotation

Assembly

The MUSP714 assembly was submitted by Oklahoma State Universtiy on July 2018. The assembly is on scaffold level, consisting of 161,217 contigs assembled into 37,536 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 30,918 while the scaffold N50 is 2,198,966.

Gene annotation

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

AssemblyMUSP714, INSDC Assembly GCA_003336285.1, Jul 2018
Base Pairs2,496,083,520
Golden Path Length2,496,083,520
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedDec 2018
Genebuild releasedApr 2019
Genebuild last updated/patchedDec 2018
Database version100.714

Gene counts

Coding genes22,924
Non coding genes7,203
Small non coding genes3,500
Long non coding genes3,174
Misc non coding genes529
Pseudogenes745
Gene transcripts47,114

Other

Genscan gene predictions54,820

About this species

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