Brazilian guinea pig assembly and gene annotation

Assembly

The CavAp1.0 assembly was submitted by Leibniz Institute for Zoo and Wildlife research on 2014/01/21 . The assembly is on the Scaffold level, consisting of 2,319,938 assembled into 3,131 scaffolds. 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 1,039 while the scaffold N50 is 27,928,671 The genome assembly represented here corresponds to GenBank Assembly ID: GCA_000688575.1

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000688575.1

Gene annotation

The Brazilian guinea pig (Cavia aperea) (preĆ” in Portuguese) is a guinea pig species found in Argentina, Brazil, Bolivia, Colombia, Ecuador, Guyana, Paraguay, Uruguay and Venezuela.

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

AssemblyCavAp1.0, INSDC Assembly GCA_000688575.1, Jan 2014
Base Pairs2,716,396,567
Golden Path Length2,716,396,567
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedSep 2016
Genebuild releasedFeb 2017
Genebuild last updated/patchedFeb 2017
Database version90.10

Gene counts

Coding genes14,218
Non coding genes3,614
Small non coding genes2,585
Long non coding genes16
Misc non coding genes1,013
Pseudogenes198
Gene transcripts22,510

Other

Genscan gene predictions39,214

About this species