Squirrel assembly and gene annotation


Spetri2 is a high coverage assembly for thirteen-lined ground squirrel (Ictidomys tridecemlineatus). It was produced by the Broad Institute of MIT and Harvard.

The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 size of scaffolds is 8.2Mb. The total of all scaffolds is 2.48Gb.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000236235.1

Other assemblies

Gene annotation

The gene set for ground squirrel was built using the Ensembl pipeline. Gene models are based on genewise alignments of squirrel and mammal proteins as well as genetically distant proteins from other species, including most vertebrate proteins from Uniprot. Additionally, mouse and human ensembl translations were aligned using exonerate and genewise. The protein based gene models were then extended using mouse cDNA. In addition to the coding transcript models, non-coding RNAs and pseudogenes were annotated.

Mammalian Genome Project

Ictidomys tridecemlineatus 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.



Assemblyspetri2, INSDC Assembly GCA_000236235.1, Nov 2011
Database version80.2
Base Pairs2,311,060,300
Golden Path Length

The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).

Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedDec 2011
Genebuild releasedMay 2012
Genebuild last updated/patchedMay 2012

Gene counts

Coding genes

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

Non coding genes3,166
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, scRNA, snlRNA, snoRNA, snRNA, 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. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.

Misc non coding genes303

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.

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.23,572


Genscan gene predictions43,697