Pika assembly and gene annotation

Assembly

This is the first release of the low-coverage 1.93X assembly of the American pika (Ochotona princeps). The genome sequencing and assembly is provided by the Broad Institute.

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 supercontigs is 53.58 kb and is 3.27 kb for contigs. The total number of bases in supercontigs is 3.43 Gb and in contigs is 1.92 Gb.

Gene annotation

Owing to the fragmentary nature of this preliminary assembly, it was necessary to arrange some scaffolds into "gene-scaffold" super-structures,in order to present complete genes. There are 5501 such gene scaffolds, with identifiers of the form "GeneScaffold_1".

Mammalian Genome Project

Ochotona princeps is one of 24 mammals that will be sequenced as part of the Mammalian Genome Project, funded by the National Institutes of Health (NIH). A group of species were chosen to maximise the branch length of the evolutionary tree while representing the diversity of mammalian species. Low-coverage 2X assemblies will be produced for these mammals and used in alignments for cross-species comparison. The aim is to increase our understanding of functional elements, especially in the human genome.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyOchPri2.0, Jun 2007
Database version76.1
Base Pairs1,923,640,532
Golden Path Length4,294,967,295
Genebuild byEnsembl
Genebuild methodProjection build
Genebuild startedJan 2008
Genebuild releasedJul 2008
Genebuild last updated/patchedApr 2013

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

16,006
Small non coding genes

Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, tRNA, scRNA, snlRNA, snoRNA, snRNA, tRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline.

5,732
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

1,327
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.23,065

Other

Genscan gene predictions134,260