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Yarkand deer assembly and gene annotation

Assembly

The CEY_v1 assembly was submitted by Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences on February 2020. The assembly is on chromosome level, consisting of 39,708 contigs assembled into 17,927 scaffolds. From these sequences, 34 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 268,660 while the scaffold N50 is 77,688,133.

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

AssemblyCEY_v1, INSDC Assembly GCA_010411085.1, Feb 2020
Base Pairs2,594,114,534
Golden Path Length2,594,114,534
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedFeb 2020
Genebuild releasedMay 2020
Genebuild last updated/patchedFeb 2020
Database version101.1

Gene counts

Coding genes22,020
Non coding genes4,545
Small non coding genes3,830
Long non coding genes679
Misc non coding genes36
Pseudogenes663
Gene transcripts46,855

Other

Genscan gene predictions53,583

About this species

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