Bushbaby assembly and gene annotation

Assembly

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

Gene annotation

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.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyOtoGar3, INSDC Assembly GCA_000181295.3, Mar 2011
Database version75.3
Base Pairs2,359,210,396
Golden Path Length2,519,404,493
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedJun 2011
Genebuild releasedDec 2011
Genebuild last updated/patchedDec 2011

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

19,506
Short non coding genes

Short 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 short non coding genes: miRNA, miscRNA, rRNA, tRNA, ncRNA, scRNA, snlRNA, snoRNA, snRNA, tRNA, and also the pseudogenic form of these biotypes. The majority of the short non coding genes in Ensembl are annotated automatically by our ncRNA pipeline.

7,276
Pseudogenes

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.

1,303
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

Other

Genscan gene predictions45,360

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