PMC:4502367 / 22149-23518 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/4502367","sourcedb":"PMC","sourceid":"4502367","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4502367","text":"The final gene annotation of IPO323 consists of 11,839 gene models (Table 1). Distributions of the number of gene models along the chromosomes of the annotation presented here and the previous JGI annotation are shown in Figure S1. In our new annotation, only 44 gene models were incomplete (i.e., without start and/or stop codon) compared to 1555 incomplete genes in the previous annotation (Table 1). To identify shared and unique gene models, we used a BLAST search (e-value cut-off of 1e-10). We found 4707 identical gene models between the two annotations. Furthermore, we found 442 gene models uniquely predicted by the JGI pipeline and 1200 models uniquely predicted by the pipeline used here. Gene models of our annotation have an average length of 1621 bp and exhibit longer exons (mean exon length 575 vs. 505 bp) and encode longer proteins (488 vs. 437 amino acids) when compared to the annotation generated by the JGI pipeline (Table 1). A BLAST comparison at the nucleotide level of our final gene models against the reconstructed transcripts showed that 10,048 out of the 11,839 predicted genes have support based on the RNA sequencing. In the previous annotation, 9423 predicted genes had support compared to the transcripts reconstructed in this study, which underlines the efficiency of this new annotation to predict biologically relevant gene models.","tracks":[]}