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Prairie vole assembly and gene annotation

Assembly

The MicOch1.0 assembly was submitted by Broad Institute on 2012/12/07 . The assembly is on the Chromosome level, consisting of 187,012 assembled into 6,450 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 21,250 while the scaffold N50 is 17,270,019.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000317375.1

Gene annotation

The prairie vole (Microtus ochrogaster) is a small vole found in central North America.

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

AssemblyMicOch1.0, INSDC Assembly GCA_000317375.1, Dec 2012
Base Pairs2,104,337,967
Golden Path Length2,287,357,235
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedOct 2016
Genebuild releasedFeb 2017
Genebuild last updated/patchedFeb 2017
Database version94.10

Gene counts

Coding genes19,130
Non coding genes3,379
Small non coding genes2,811
Long non coding genes10
Misc non coding genes558
Pseudogenes529
Gene transcripts31,519

Other

Genscan gene predictions51,657

About this species