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Marmoset assembly and gene annotation

The common marmoset (Callithrix jacchus) is a New World monkey. It originally lived on the northeastern coast of Brazil, but has spread southwards, becoming an invasive species in its non-native regions. It is used as model organisms in areas of research such as teratology, periodontal disease, reproduction, immunology, endocrinology, obesity and aging, and was the first New World monkey to have its genome sequenced.


The ASM275486v1 assembly was submitted by Broad Institute on November 2017. The assembly is on scaffold level, consisting of 88,439 contigs assembled into 39,944 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 155,284 while the scaffold N50 is 129,239,660.

Gene annotation

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.



AssemblyASM275486v1, INSDC Assembly GCA_002754865.1, Nov 2017
Base Pairs2,845,375,248
Golden Path Length2,845,375,248
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedDec 2018
Genebuild releasedJan 2018
Genebuild last updated/patchedMay 2019
Database version104.1

Gene counts

Coding genes22,615
Non coding genes17,353
Small non coding genes6,384
Long non coding genes6,709
Misc non coding genes4,260
Gene transcripts66,095


Genscan gene predictions53,285

About this species