OryCun2 (GCA_000003625.1) is an assembly of rabbit (Oryctolagus cuniculus). It was sequenced to a 7X. The genome sequencing and assembly are provided by the Broad Institute within the mammalian genome project.
Of the 2.74 Gb genome, approximately 82% has been anchored to chromosomes, which include autosomes 1-21 and sex chromosome X. The remaining unanchored contigs have been concatenated into virtual chromosomes "Un".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 supercontigs is 35348.54kb and is 64.65kb for contigs. The total number of bases in supercontigs is 2.66 Gb and in contigs is 2.60 Gb.
The genome assembly represented here corresponds to GenBank Assembly ID GCA_000003625.1
The gene set for rabbit was built using the Ensembl genebuild pipeline. Gene models are based on genewise alignments of glire proteins as well as genetically distant proteins from other species, including most mammal proteins from Uniprot. To improve the accuracy of models generated from distant species, the Genewise alignments were made to stretches of genomic sequence rather than to 'miniseqs'. Additionnaly, human and mouse one-to-one orthologues were aligned using exonerate, combined with rabbit-specific proteins. The protein based gene models were then extended using rabbit cDNA and EST alignments. The resulting gene models were then assessed by generating sets of potential orthologs to genes from other vertebrate species. Potentially missing predictions and partial gene predictions were identified by examining the orthologs, which were then used to build new gene models.
Mammalian Genome Project
Oryctolagus cuniculus is one of 24 mammals that will be sequenced as part of the Mammalian Genome Project, funded by the National Institutes of Health (NIH). The species were chosen to maximise the branch length of the evolutionary tree while representing the diversity of mammalian species. Low-coverage 2X assemblies will be produced for these mammals and used in alignments for cross-species comparison. The aim is to increase our understanding of functional elements, especially in the human genome.
RNASeq data set
In addition to the main set, we have predicted gene models for each tissue type using the RNA-Seq pipeline. We did a BLASTp of these models against UniProt vertebrate proteins of protein existence level 1 and 2 in order to confirm the open reading frame (ORF). The best BLAST hit is displayed as a transcript supporting evidence.
The tissue-specific sets of transcript models built using our RNAseq pipeline are as follows:
|Tissue||Number of gene models|
General information about this species can be found in Wikipedia.
|Assembly||OryCun2.0, INSDC Assembly GCA_000003625.1, Nov 2009|
|Golden Path Length|
The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).
|Genebuild method||Full genebuild|
|Genebuild started||Nov 2009|
|Genebuild released||Mar 2010|
|Genebuild last updated/patched||Jun 2013|
Genes and/or transcript that contains an open reading frame (ORF).
|Small non coding genes|
Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, scRNA, snlRNA, snoRNA, snRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.
A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.
|Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.||24,964|
|Genscan gene predictions||55,138|