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Rabbit assembly and gene annotation

Assembly

The OryCun2.0 assembly was submitted by The Genome Sequencing Platform, The Assembly Computation and Development Core Team on October 2009. The assembly is on chromosome level, consisting of 84,024 contigs assembled into 3,318 scaffolds. From these sequences, 22 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 64,648 while the scaffold N50 is 35,972,871.

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

AssemblyOryCun2.0, INSDC Assembly GCA_000003625.1, Nov 2009
Base Pairs2,604,023,284
Golden Path Length2,737,490,501
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2009
Genebuild releasedMar 2010
Genebuild last updated/patchedMay 2019
Database version100.2

Gene counts

Coding genes20,612
Non coding genes8,319
Small non coding genes2,520
Long non coding genes5,736
Misc non coding genes63
Pseudogenes656
Gene transcripts51,853

Other

Genscan gene predictions55,138

About this species

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