Xenopus assembly and gene annotation


The Xenopus tropicalis genome assembly version 4.2 (GCA_000004195.1, November 2009] is the fifth in a series of preliminary assembly releases by the JGI that are planned as part of the ongoing X. tropicalis genome project. This Ensembl website presents the sequence data provided by the JGI.

The reads were assembled using JAZZ, the JGI assembler, producing a genome of approximately 1.51 Gb in scaffolds and 1.36Gb in contigs. The assembly contains 19,549 scaffolds with an average coverage of 7.65X. The N50 length for scaffolds is 1.57 Mb and is 17.04 kb for contigs. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000004195.1

Other assemblies

Gene annotation

The gene set was built using the Ensembl pipeline. 19249 cDNAs were used to add the untranslated regions (UTRs). 31465 Xenopus tropicalis proteins were used to predict the transcript structures. Finally, gene predictions based on UniProt vertebrate proteins were used to fill gaps in the annotation. The gene set contains 18429 protein coding genes, 121 pseudogenes, 52 retrotransposed genes and 1552 non coding RNA.

More information

General information about this species can be found in Wikipedia.



AssemblyJGI 4.2, INSDC Assembly GCA_000004195.1, Nov 2009
Database version80.42
Base Pairs1,358,346,944
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 startedSep 2010
Genebuild releasedFeb 2011
Genebuild last updated/patchedApr 2013

Gene counts

Coding genes

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

Non coding genes1,306
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 genes47

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.24,197


Genscan gene predictions43,859