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Tropical clawed frog assembly and gene annotation


The Xenopus_tropicalis_v9.1 assembly was submitted by DOE Joint Genome Institute on July 2016. The assembly is on chromosome level, consisting of 61,330 contigs assembled into 6,822 scaffolds. From these sequences, 10 chromosomes have been built. 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 71,041 while the scaffold N50 is 135,134,832.

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.



AssemblyXenopus_tropicalis_v9.1, INSDC Assembly GCA_000004195.3, Jul 2016
Base Pairs1,440,398,454
Golden Path Length1,440,398,454
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedApr 2019
Genebuild releasedJun 2019
Genebuild last updated/patchedDec 2019
Database version100.91

Gene counts

Coding genes19,987
Non coding genes1,390
Small non coding genes1,343
Long non coding genes21
Misc non coding genes26
Gene transcripts56,323


Genscan gene predictions35,535

About this species