Chinese hamster CriGri assembly and gene annotation

Assembly

The CriGri_1.0 assembly was submitted by Beijing Genomics Institute on 2011/08/23 . The assembly is on the Scaffold level, consisting of 265,787 assembled into 109,152 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 39,361 while the scaffold N50 is 1,147,233 The genome assembly represented here corresponds to GenBank Assembly ID: GCA_000223135.1

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000223135.1

Gene annotation

The Chinese hamster (Cricetulus griseus), is a species of hamster originating from the deserts of northern China and Mongolia.

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

AssemblyCriGri_1.0, INSDC Assembly GCA_000223135.1, Aug 2011
Base Pairs2,318,132,242
Golden Path Length2,399,786,748
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2016
Genebuild releasedJul 2017
Genebuild last updated/patchedJul 2017
Database version90.1

Gene counts

Coding genes19,617
Non coding genes6,605
Small non coding genes3,273
Long non coding genes2,563
Misc non coding genes769
Pseudogenes446
Gene transcripts34,472

Other

Genscan gene predictions53,597

About this species