Pika

Ochotona princeps

Genome assembly: OchPri3 (GCA 000292845.1)

This release features the second assembly of the America pika (Ochotona princeps, GCA_000292845.1) which became available in August 2012. The assembly comprises 10421 toplevel sequences, all of which are unplaced scaffolds (from 132963 contigs). The N50 of the contigs is 42 kb and the N50 of the scaffolds is 24 Mb. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer.

Download Pika data via FTP

Display your data in Pre

Gene annotation

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

This preview site includes alignments of 3 pika cDNAs. Preliminary gene annotation in American pika has been generated by alignments of Ensembl human and mouse proteins from Ensembl release 73 (September 2013). Of 20721 Ensembl human proteins, 17058 aligned with a percent identity > 50% and coverage > 50%. Of 23025 mouse proteins, 17868 aligned with a percent identity > 50% and coverage > 50%. Ab initio gene predictions and alignments of sequences from UniProt, UniGene and the ENA vertebrate RNA collection are also provided.

Genome statistics

Assembly: OchPri3, May 2012
Database version: 75
Base Pairs: 1,943,976,257
Golden Path Length: 2,229,824,103
Genscan gene predictions: 49,557