The Chinese softshell turtle (Pelodiscus sinensis) genome was produced by the RIKEN institute. The genome is 2.1Gb in length; composed of 205,379 contigs with an N50 value of 22kb and 19,903 scaffolds with an N50 value of 3.37Mb.
The genome assembly represented here corresponds to GenBank Assembly ID GCA_000230535.1
The gene set was built using a mixed approach. Due to the lack of species specific sequences and the availability of RNASeq data for Chinese softshell turtle from RIKEN and BGI Institutes, the final gene set comprises of models based orthologous proteins from the vertebrate division of UniProtKB in addition to models from RNASeq data. The RNASeq data contained samples from TK7, TK9, TK11, TK13, TK15, TK17, TK23, gastrula and neurula developmental stages, together with pooled data set and combined data from all nine stages. 8,070 gene models were made exclusively from RNASeq data. The data was also used to add UTR to gene models.
RNASeq data set
In addition to the main set, we have predicted gene models for each tissue type using the RNASeq pipeline. We did a BLASTp of these models against UniProt proteins with protein existence level 1 and 2 in order to confirm the open reading frame (ORF). The best BLAST hit is displayed as a transcript supporting evidence.
The tissue-specific sets of transcript models built using our RNAseq pipeline are as follows:
|Developmental stage||Number of gene models|
|All nine stages||29847|
General information about this species can be found in Wikipedia.
|Assembly||PelSin_1.0, INSDC Assembly GCA_000230535.1, Oct 2011|
|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 method||Mixed strategy build|
|Genebuild started||Nov 2011|
|Genebuild released||Jul 2012|
|Genebuild last updated/patched||Feb 2014|
Genes and/or transcript that contains an open reading frame (ORF).
|Non coding genes||1,042|
|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 genes||36|
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.||21,808|
|Genscan gene predictions||48,910|