Prairie vole

Microtus ochrogaster

Genome assembly: MicOch1.0 (GCA 000317375.1)

This release features the first assembly of the prairie vole (Microtus ochrogaster) genome, MicOch1.0, provided by The Broad Institute in October 2012. The assembly is composed of 17 autosomal chromosomes, 10 linkage groups and a sex chromosome labelled X. The assembly contains a total sequence length of 2.29Gb with 183Mb of gaps. There are 6450 scaffolds comprised of 187012 contigs with a scaffold N50 of 61.8Mb and a contig N50 of 21.2kb. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer.

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Gene annotation

What can I find? Protein-coding and non-coding genes, splice variants, cDNA and protein sequences, non-coding RNAs.

Preliminary gene annotation in the prairie vole has been generated by a combination of alignments of nucleotide and protein sequences from a number of different sources. We aligned 20764 human and 23042 mouse translations from Ensembl release 71 to provide 13159 and 16901 gene models (with cut-offs of 80% identity and 50% coverage), respectively. In addition to these, we also made 11 models by aligning prairie vole proteins from Uniprot.

Variation

This species currently has no variation database. However you can process your own variants using the Variant Effect Predictor:

Variant Effect Predictor

Summary

Other

Assembly: MicOch1.0, Nov 2012
Database version: 71
Base Pairs: 2,104,321,675
Golden Path Length: 2,287,340,943
Genscan gene predictions: 58,887