OtoGar3 is a high coverage assembly for bushbaby (Otolemur garnettii). The combined WGS and BAC-end sequence reads were assembled This whole genome shotgun assembly was produced from Illumina short-read sequence data using ALLPATHS-LG assembly software developed by the Broad Institute.
The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 size of scaffolds is 13.852kb. The total of all scaffolds is 2.519Gb.
The genome assembly represented here corresponds to GenBank Assembly ID GCA_000181295.3
The gene set for bushbaby was built using the Ensembl pipeline.
Gene models are based on genewise alignments of bushbaby and primate proteins as well as genetically distant proteins from other species, including most vertebrate proteins from Uniprot. Additionally, human ensembl translations were aligned using exonerate and genewise. The protein based gene models were then extended using human cDNA. In addition to the coding transcript models, non-coding RNAs and pseudogenes were annotated.
General information about this species can be found in Wikipedia.
|Assembly||OtoGar3, INSDC Assembly GCA_000181295.3, Mar 2011|
|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||Jun 2011|
|Genebuild released||Dec 2011|
|Genebuild last updated/patched||Dec 2011|
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.||28,565|
|Genscan gene predictions||45,360|