Guinea Pig assembly and gene annotation

Assembly

The Cavpor3.0 assembly was submitted by The Genome Sequencing Platform, The Genome Assembly Team on 2008/03/03 . The assembly is on the Scaffold level, consisting of 61,604 assembled into 3,144 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 80,583 while the scaffold N50 is 27,942,054 The genome assembly represented here corresponds to GenBank Assembly ID: GCA_000151735.1

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000151735.1

Other assemblies

Gene annotation

The domestic guinea pig (Cavia porcellus), or simply guinea pig, also known as cavy or cuy for livestock term, is a species of rodent belonging to the family Caviidae and the genus Cavia. Despite their common name, these animals are not in the pig family Suidae, nor do they come from Guinea. They originated in the Andes, and earlier studies based on biochemistry and hybridization suggest they are domestic descendants of a closely related species of cavy such as C. aperea, C. fulgida, or C. tschudii and, therefore, do not exist naturally in the wild. Recent studies applying molecular markers, in addition to studying the skull and skeletal morphology of current and mummified animals, revealed that the ancestor is most likely Cavia tschudii.

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

AssemblyCavpor3.0, INSDC Assembly GCA_000151735.1, Mar 2008
Base Pairs2,663,369,733
Golden Path Length2,723,219,641
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedDec 2016
Genebuild releasedJul 2017
Genebuild last updated/patchedJul 2017
Database version90.4

Gene counts

Coding genes18,095
Non coding genes8,518
Small non coding genes4,078
Long non coding genes2,654
Misc non coding genes1,786
Pseudogenes242
Gene transcripts34,846

Other

Genscan gene predictions59,277

About this species