Chinese hamster PICR (CriGri-PICRH-1.0)

Chinese hamster PICR assembly and gene annotation

Assembly

The CriGri-PICRH-1.0 assembly was submitted by CHO Genome Community on June 2020. The assembly is on chromosome level, consisting of 4,014 contigs assembled into 647 scaffolds. From these sequences, 11 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 2,711,962 while the scaffold N50 is 274,391,693.

Other assemblies

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

AssemblyCriGri-PICRH-1.0, INSDC Assembly GCA_003668045.2, Jun 2020
Base Pairs2,366,634,374
Golden Path Length2,366,634,374
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedAug 2022
Genebuild released
Genebuild last updated/patchedJan 2023
Database version111.2

Gene counts

Coding genes24,185
Non coding genes8,383
Small non coding genes2,277
Long non coding genes6,038
Misc non coding genes68
Pseudogenes1,133
Gene transcripts68,196