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Arctic ground squirrel assembly and gene annotation

Assembly

The ASM342692v1 assembly was submitted by UAF on August 2018. The assembly is on scaffold level, consisting of 79,883 contigs assembled into 15,884 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 91,013 while the scaffold N50 is 3,964,291.

Gene annotation

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

AssemblyASM342692v1, INSDC Assembly GCA_003426925.1, Aug 2018
Base Pairs2,520,505,282
Golden Path Length2,520,505,282
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2018
Genebuild releasedApr 2019
Genebuild last updated/patchedMar 2020
Database version100.1

Gene counts

Coding genes19,674
Non coding genes3,408
Small non coding genes2,111
Long non coding genes785
Misc non coding genes512
Pseudogenes433
Gene transcripts34,173

Other

Genscan gene predictions45,091

About this species

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