Marmoset assembly and gene annotation


Callithrix jacchus-3.2.1 (GCA_000004665.1) is a draft assembly of the common marmoset genome. This assembly is used by UCSC to create their calJac3 database. It was sequenced to 6X coverage using a female marmoset (animal id #186/17066) DNA source kindly provided by Dr. Suzette Tardif, of the Southwestern National Primate Research Center (San Antonio, Texas). The DNA source for the CHORI-259 BAC library was male and the full brother of the female used for whole genome shotgun sequencing (#186/17066). The combined sequence reads were assembled using the PCAP software (Genome Res. 13(9):2164-70 2003) and filtered for all known non-marmoset sequence contaminants.

The new Callithrix jacchus-3.2.1 assembly spans 2.75Gb with 2.62Gb ordered and oriented along 24 chromosomes. Chromosomes were not available in Callithrix jacchus-3.2 (released in Ensembl 56 and Ensembl 57), which was composed of scaffolds and contigs only.

The N50 length is defined as the scaffold (or contig) length N for which 50% of the genome lies in scaffolds (or contigs) of the N50 size or longer. The Callithrix jacchus-3.2.1 assembly is made up of a total of 73,756 scaffolds with an N50 scaffold length of over 6.4Mb. Scaffolds placed on chromosomes have been annotated as described below.

The sequence assembly was provided by The Genome Center, Washington University School of Medicineand the Human Genome Center, Baylor College of Medicine.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000004665.1

Gene annotation

The gene set for marmoset was built using the Ensembl gene annotation pipeline. Species-specific resources for marmoset are relatively limited and therefore sequences from other primates, especially human, were also used as supporting evidence for coding transcript models. In addition to the coding transcript models, non-coding RNAs and pseudogenes were annotated. Marmoset cDNAs and ESTs and human cDNAs were mapped to the genome using Exonerate.

More information

General information about this species can be found in Wikipedia.



AssemblyC_jacchus3.2.1, INSDC Assembly GCA_000004665.1, Jan 2010
Database version79.321
Base Pairs2,759,289,125
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 byEnsembl
Genebuild methodFull genebuild
Genebuild startedFeb 2010
Genebuild releasedMay 2010
Genebuild last updated/patchedFeb 2014

Gene counts

Coding genes

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

Non coding genes9,000
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.

Misc non coding genes2,575

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.55,116


Genscan gene predictions53,363