Squirrel assembly and gene annotation

Assembly

The SpeTri2.0 assembly was submitted by Broad Institute on 2011/11/29 . The assembly is on the Scaffold level, consisting of 153,488 assembled into 12,483 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 44,137 while the scaffold N50 is 8,192,786 The genome assembly represented here corresponds to GenBank Assembly ID: GCA_000236235.1

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

Other assemblies

Gene annotation

The thirteen-lined ground squirrel (Ictidomys tridecemlineatus), also known as the striped gopher or leopard ground squirrel. It is widely distributed over grasslands and prairies of 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

AssemblySpeTri2.0, INSDC Assembly GCA_000236235.1, Nov 2011
Base Pairs2,311,076,758
Golden Path Length2,478,410,228
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2016
Genebuild releasedJul 2017
Genebuild last updated/patchedJul 2017
Database version90.3

Gene counts

Coding genes18,474
Non coding genes6,418
Small non coding genes2,456
Long non coding genes3,428
Misc non coding genes534
Pseudogenes309
Gene transcripts33,373

Other

Genscan gene predictions48,348

About this species