Tropical clawed frog (UCB_Xtro_10.0)

Tropical clawed frog assembly and gene annotation

Assembly

The UCB_Xtro_10.0 assembly was submitted by University of California, Berkeley on November 2019. The assembly is on chromosome level, consisting of 851 contigs assembled into 167 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 14,634,335 while the scaffold N50 is 153,961,319.

Other assemblies

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.

Statistics

Summary

AssemblyUCB_Xtro_10.0, INSDC Assembly GCA_000004195.4, Nov 2019
Base Pairs1,451,301,209
Golden Path Length1,451,301,209
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedSep 2020
Genebuild released
Genebuild last updated/patchedFeb 2021
Database version111.10

Gene counts

Coding genes22,107
Non coding genes2,023
Small non coding genes1,979
Long non coding genes20
Misc non coding genes24
Pseudogenes484
Gene transcripts52,299

Other

Genscan gene predictions86,324