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Eurasian red squirrel assembly and gene annotation

Assembly

The mSciVul1.1 assembly was submitted by SC on December 2019. The assembly is on chromosome level, consisting of 1,807 contigs assembled into 638 scaffolds. From these sequences, 21 chromosomes have been built. 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 16,333,633 while the scaffold N50 is 153,872,958.

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

AssemblymSciVul1.1, INSDC Assembly GCA_902686455.1, Nov 2019
Base Pairs2,878,591,032
Golden Path Length2,878,591,032
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJan 2020
Genebuild releasedMay 2020
Genebuild last updated/patchedJan 2020
Database version101.1

Gene counts

Coding genes22,420
Non coding genes2,410
Small non coding genes2,341
Long non coding genes40
Misc non coding genes29
Pseudogenes1,187
Gene transcripts36,836

Other

Genscan gene predictions66,184

About this species

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